CHA KUIN TAITEIT VAN T ON CEL CARE A MULTILIN US009815864B2

( 12 ) United States Patent Beigelman et al .

( 10 ) Patent No . : ( 45 ) Date of Patent :

US 9 , 815 , 864 B2 Nov . 14 , 2017

( 54 ) SUBSTITUTED NUCLEOSIDES , NUCLEOTIDES AND ANALOGS THEREOF

@ ( 71 ) Applicant : Alios BioPharma , Inc . , South San Francisco , CA ( US )

@ ( 72 ) Inventors : Leonid Beigelman , San Mateo , CA ( US ) ; Jerome Deval , Pacifica , CA ( US ) ; Zhinan Jin , Mountain View , CA ( US )

2012 / 0165286 A1 2013 / 0164261 A1 2013 / 0165400 A1 2013 / 0252920 A1 2013 / 0253181 Al 2013 / 0281687 Al 2014 / 0179627 A1 2014 / 0179910 Al 2014 / 0303108 A1 2014 / 0303113 A 2015 / 0011497 Al 2015 / 0038451 A1 2015 / 0051167 Al 2015 / 0105341 A1 2015 / 0141363 A1 2015 / 0175647 A1

6 / 2012 Beigelman et al . 6 / 2013 Wang et al . 6 / 2013 Beigelman et al . 9 / 2013 Blatt et al . 9 / 2013 Serebryany et al .

10 / 2013 Serebryany et al . 6 / 2014 Beigelman et al . 6 / 2014 Beigelman et al .

10 / 2014 Beigelman et al . 10 / 2014 Krop et al .

1 / 2015 Beigelman et al . 2 / 2015 Smith et al . 2 / 2015 Wang et al . 4 / 2015 Beigelman et al . 5 / 2015 Wang et al . 6 / 2015 Kuldipkumar et al .

( Continued )

@ ( 73 ) Assignee : Alios BioPharma , Inc . , South San Francisco , CA ( US )

( * ) Notice : Subject to any disclaimer , the term of this patent is extended or adjusted under 35 U . S . C . 154 ( b ) by 317 days . FOREIGN PATENT DOCUMENTS

( 21 ) Appl . No . : 14 / 313 , 043 WO WO

WO 2008 / 082601 7 / 2008 WO 2010 / 091386 8 / 2010

( Continued ) ( 22 ) Filed : Jun . 24 , 2014 ( 65 ) OTHER PUBLICATIONS Prior Publication Data

US 2015 / 0011497 A1 Jan . 8 , 2015

Related U . S . Application Data ( 60 ) Provisional application No . 61 / 839 , 711 , filed on Jun .

26 , 2013 .

International Search Report and Written Opinion dated Sep . 1 , 2014 for PCT Application No . PCT / US2014 / 043836 , filed Jun . 24 , 2014 . Norovirus Clinical Overview ( Nov . 2012 ) . Obtained from https : / / web . archive . org / web / 20121113185824 / http : / / www . cdc . gov / norovi rus / hcp / clinicaloverview . html accessed Jun . 30 , 2016 ) . Norovirus - Preventing Norovirus Infection ( May 2014 ) . Obtained from https : / / web . archive . org / web / 20140526020356 / http : / / www . cdc . gov / norovirus / preventinginfection . html ( accessed Jun . 30 , 2016 ) . “ IUPAC - IUB Commission on Biochemical Nomenclature Abbre viated Nomenclature of Synthetic Polypeptides ( Polymerized Amino Acids ) Revised Recommendations ( 1971 ) ” Biochemistry . ( 1972 ) 11 ( 5 ) : 942 - 944 .

( Continued )

( 51 ) Int . CI . AOIN 43 / 04 ( 2006 . 01 ) A61K 31 / 70 ( 2006 . 01 ) CO7H 19 / 20 ( 2006 . 01 ) CO7H 19 / 06 ( 2006 . 01 ) CO7H 19 / 10 ( 2006 . 01 ) CO7H 19 / 16 ( 2006 . 01 ) C07H 19 / 11 ( 2006 . 01 )

( 52 ) U . S . CI . CPC . . . . . . . . . . . . CO7H 19 / 20 ( 2013 . 01 ) ; C07H 19 / 06

( 2013 . 01 ) ; C07H 19 / 10 ( 2013 . 01 ) ; C07H 19 / 11 ( 2013 . 01 ) ; CO7H 19 / 16 ( 2013 . 01 )

( 58 ) Field of Classification Search CPC . . . . . . . . C07H 19 / 11 ; C07H 19 / 10 ; CO7H 19 / 16 ;

C07H 19 / 06 ; CO7H 19 / 20 See application file for complete search history .

Primary Examiner - Lawrence E Crane ( 74 ) Attorney , Agent , or Firm — Knobbe , Martens , Olson & Bear , LLP ( 57 ) ABSTRACT Disclosed herein are nucleosides , nucleotides and analogs thereof , pharmaceutical compositions that include one or more of nucleosides , nucleotides and analogs thereof , and methods of synthesizing the same , of the Formula ( I ) .

( 56 ) References Cited U . S . PATENT DOCUMENTS

Raal Raa2 R140 BIA

R2411 . . " IR4 H LR54

R34 R44

5 , 432 , 272 A 7 / 1995 Benner 6 , 846 , 810 B21 / 2005 Martin et al . 7 , 125 , 855 B2 10 / 2006 Bhat et al . 8 , 609 , 627 B2 * 12 / 2013 Cho . . . . . . . . . . . . . . . . . . . A61K 31 / 7028

514 / 43 9 , 173 , 893 B2 * 11 / 2015 Cho . . . . . . . . . . . . . . . . . . . . . A61K 31 / 7076 9 , 296 , 719 B2 * 3 / 2016 Subba - Reddy . . . . . . A61K 31 / 381 9 , 441 , 007 B2 9 / 2016 Wang et al . 9 , 598 , 457 B2 3 / 2017 Smith et al . 9 , 603 , 864 B2 3 / 2017 Blatt et al . 9 , 605 , 018 B2 3 / 2017 Wang et al .

2007 / 0066815 A 3 / 2007 Sarma 2009 / 0280084 A1 11 / 2009 Schinazi et al . 2012 / 0070411 Al 3 / 2012 Beigelman et al . 2012 / 0070415 Al 3 / 2012 Beigelman et al . 2012 / 0071434 A1 3 / 2012 Smith et al .

Also disclosed herein are methods of ameliorating and / or treating a disease and / or a condition , including an infection from a norovirus , with a nucleoside , a nucleotide and an analog thereof .

17 Claims , 1 Drawing Sheet

US 9 , 815 , 864 B2 Page 2

( 56 ) References Cited U . S . PATENT DOCUMENTS

WO WO WO WO Wo

WO 2014 / 100498 WO 2014 / 134251 WO 2014 / 164533 WO 2014 / 209983 WO 2016 / 022464

6 / 2014 9 / 2014

10 / 2014 12 / 2014 2 / 2016 2015 / 0183819 A1

2015 / 0315228 A1 2015 / 0366887 Al 2015 / 0366888 A1 2015 / 0368286 A1 2016 / 0016987 AL 2016 / 0022724 Al 2016 / 0024136 Al 2016 / 0039858 Al 2016 / 0039861 A1 2016 / 0115190 A1 2016 / 0176910 Al 2016 / 0176911 A1 2016 / 0264610 A1 2016 / 0318967 AL 2016 / 0318969 Al 2016 / 0331770 A1 2017 / 0002037 AL 2017 / 0037075 Al 2017 / 0037077 AL 2017 / 0143749 Al 2017 / 0143751 Al

7 / 2015 Beigelman et al . 11 / 2015 Beigelman et al . 12 / 2015 Blatt et al . 12 / 2015 Blatt et al . 12 / 2015 Serebryany et al . 1 / 2016 Beigelman et al . 1 / 2016 Chanda et al . 1 / 2016 Beigelman et al . 2 / 2016 Beigelman et al . 2 / 2016 Smith et al . 4 / 2016 Serebryany et al . 6 / 2016 Wang et al . 6 / 2016 Beigelman et al . 9 / 2016 Beigelman et al .

11 / 2016 Dyatkina et al . 11 / 2016 Kuldipkumar et al . 11 / 2016 Beigelman et al .

1 / 2017 Beigelman et al . 2 / 2017 Beigelman et al . 2 / 2017 Beigelman et al . 5 / 2017 Blatt et al . 5 / 2017 Blatt et al .

OTHER PUBLICATIONS Greene , et al . , Protective Groups in Organic Synthesis , 3 . Ed . , John Wiley & Sons . ( 1999 ) Cover & Contents pages . McOmie , J . F . W . , Protective Groups in Organic Chemistry , Plenum Press , 1973 . Cover & Contents pages . Villard et al . , “ Phenyl phosphotriester derivatives of AZT : Varia tions upon the SATE moiety ” , Bioorg . Med . Chem . ( 2008 ) 15 : 7321 7329 . McGuigan et al . , “ Phosphate Prodrugs Derived fron N - Acetylglucosamine Have Enhanced Chondroprotective Activity in Explant Cultures and Represent a New Lead in Antiosteoarthritis Drug Discovery ” , J . Med . Chem . ( 2008 ) 51 : 5807 - 5812 . Reddy et al . , “ Stereoselective Synthesis of PSI - 352938 : AB - D - 20 Deoxy - 20 - r - fluoro - 20 - B - C - methyl - 30 , 50 - cyclic Phosphate Nucleo tide Prodrug for the Treatment of HCV ” , J . Org . Chem . ( 2011 ) 76 ( 10 ) , 3782 - 3790 . Bondada , L . et al . , “ Adenosine Dioxolane Nucleoside Phosphoramidates as Antiviral Agents for Human Immunodefi ciency and Hepatitis B Viruses ” , ACS Medicinal Chemistry Letters ( 2013 ) 4 ( 8 ) : 747 - 751 . Lefebvre et al . , “ Mononucleoside Phosphotriester Derivatives with S - Acyl - 2 - thioethyl Bioreversible Phosphate - Protecting Groups : Intracellular Delivery of 3 ' - Azido - 2 ' , 3 ' - dideoxythymidine 5 ' - Monophosphate ” , J . Med . Chem . ( 1995 ) 38 : 3941 - 3950 . Extended European Search Report dated Apr . 3 , 2017 for EP Application No . 14818480 . 7 , filed Jun . 24 , 2014 .

FOREIGN PATENT DOCUMENTS WO WO WO WO WO WO WO

WO 2010 / 108140 WO 2012 / 040124 WO 2012 / 158811 WO 2013 / 096680 WO 2013 / 142124 WO 2013 / 142159 WO 2013 / 142525

9 / 2010 3 / 2012 11 / 2012 6 / 2013 9 / 2013 9 / 2013 9 / 2013 * cited by examiner

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US 9 , 815 , 864 B2

US 9 , 815 , 864 B2

SUBSTITUTED NUCLEOSIDES , can include contacting a cell infected with the norovirus NUCLEOTIDES AND ANALOGS THEREOF infection with an effective amount of one or more com

pounds of Formula ( I ) , Formula ( II ) and / or Formula ( III ) , or INCORPORATION BY REFERENCE TO ANY a pharmaceutically acceptable salt of the foregoing , or a

PRIORITY APPLICATIONS 5 pharmaceutical composition that includes one or more com pounds of Formula ( I ) , Formula ( II ) and / or Formula ( III ) , or

Any and all applications for which a foreign or domestic a pharmaceutically acceptable salt of the foregoing . Some priority claim is identified , for example , in the Application embodiments disclosed herein relate to methods of inhibit Data Sheet or Request as filed with the present application , ing the replication of a norovirus that can include contacting are hereby incorporated by reference under 37 CFR 1 . 57 , 10 a cell infection with the norovirus with an effective amount and Rules 4 . 18 and 20 . 6 . of one or more compounds of Formula ( I ) , Formula ( II )

and / or Formula ( III ) , or a pharmaceutically acceptable salt SEQUENCE LISTING of the foregoing , or a pharmaceutical composition that includes one or more compounds of Formula ( I ) , Formula The present application is being filed along with a 15 ( II ) and / or Formula ( III ) , or a pharmaceutically acceptable Sequence Listing in electronic format . The Sequence Listing

is provided as a file entitled ALIOS066 . TXT , created Jun . salt of the foregoing . 23 , 2014 , which is 4 kb in size . The information in the electronic format of the Sequence Listing is incorporated BRIEF DESCRIPTION OF THE DRAWINGS herein by reference in its entirety . 20

FIG . 1 is a schematic of the genetic organization of BACKGROUND norovirus ( NV ) and first murine norovirus virus ( MNV - 1 ) .

Field DETAILED DESCRIPTION The present application relates to the fields of chemistry , 25

biochemistry and medicine . More particularly , disclosed Noroviruses are a member of the Caliciviridae family , and herein are nucleoside , nucleotides and analogs thereof , phar - positive single - stranded RNA , non - enveloped viruses that maceutical compositions that include one or more nucleo - are approximately 27 - 35 nm in diameter . To date , norovi sides , nucleotides and analogs thereof , and methods of ruses have been classified into 6 recognized genogroups , GI , synthesizing the same . Also disclosed herein are methods of 30 GII , GIII , GIV , GV and GVI , with GI , GII and GIV affecting ameliorating and / or treating a norovirus infection with one humans . Examples of the noroviruses include Norwalk or more nucleosides , nucleotides and analogs thereof . virus , Desert Shield virus , Southampton virus , Hawaii virus ,

Description Snow Mountain virus , Mexico virus , Toronto virus , Bristol Nucleoside analogs are a class of compounds that have virus and Lordsdale virus . The RNA genomes of the noro

been shown to exert antiviral activity both in vitro and in 35 viruses are organized into 3 major open reading frames vivo , and thus , have been the subject of widespread research ( OFR1 , OFR2 , and OFR3 ) with a polyadenylated 3 ' - end . for the treatment of viral infections . Nucleoside analogs are OFR1 enclosed a large polyprotein that is proteolytically usually therapeutically inactive compounds that are con processed into mature nonstructural proteins ; OFR2 verted by host or viral enzymes to their respective active enclosed the major capside protein ( VP1 ) ; and OFR3 anti - metabolites , which , in turn , may inhibit polymerases 40 involved in viral or cell proliferation . The activation occurs enclosed a minor structural protein ( VP2 ) .

Noroviruses are highly contagious . According to the U . S . by a variety of mechanisms , such as the addition of one or more phosphate groups and , or in combination with , other Center for Disease Control ( CDC ) , a person with a norovirus metabolic processes . infection can shed billions of norovirus particles , and it only

45 takes as few as 18 viral particles to infect another person . SUMMARY http : / / www . cdc . gov / norovirus / hcp / clinical - overview . html

( November 2012 ) . The virus is transmitted in various man Some embodiments disclosed herein relate to methods of ners , including contacting a contaminated person , consum

ameliorating , treating and / or preventing a norovirus infec - ing contaminated food and / or water , and contacting con tion that can include administering to a subject an effective 50 taminated surfaces , objects and / or substances . Outbreaks of amount of one or more compounds of Formula ( I ) , Formula norovirus infection can occur in closed or semi - closed ( II ) and / or Formula ( III ) , or a pharmaceutically acceptable spaces such as long - term facilities , overnight camps , hospi salt of the foregoing , or a pharmaceutical composition that tals , prisons , dorms , cruise ships and military settings . includes one or more compounds of Formula ( 1 ) , Formula Noroviruses have been attributed as being the leading cause ( II ) and / or Formula ( III ) , or a pharmaceutically acceptable 55 of gastroenteritis . Symptoms of gastroenteritis include salt of the foregoing . Other embodiments described herein abdominal cramps , nausea , diarrhea and vomiting ; and the relate to using one or more compounds of Formula ( I ) , diarrhea and vomiting associated with gastroenteritis can Formula ( II ) and / or Formula ( III ) , or a pharmaceutically lead to dehydration . The duration of illness can vary from a acceptable salt of the foregoing , in the manufacture of a couple of hours to several days . medicament for ameliorating , treating and / or preventing a 60 According to the CDC , there is no specific therapy to treat norovirus infection . Still other embodiments described or approved vaccine to prevent a norovirus infection . http : / / herein relate to compounds of Formula ( I ) , Formula ( II ) www . cdc . gov / norovirus / preventing - infection . html . Rather , and / or Formula ( III ) , or a pharmaceutically acceptable salt a person can try to prevent a norovirus infection by prac of the foregoing , that can be used for ameliorating , treating ticing proper hygiene ( including washing the hands with and / or preventing a norovirus infection . Yet still other 65 soap and water ) , washing fruits and vegetables , cooking embodiments disclosed herein relate to methods of amelio - seafood thoroughly , limiting exposure to others when rating , treating and / or preventing a norovirus infection that infected , cleaning and disinfecting contaminated surfaces ,

US 9 , 815 , 864 B2

washing laundry that may be contaminated and wearing of the aryl , ring ( s ) of the heteroaryl or ring ( s ) of the gloves when handling soiled items . heterocyclyl can contain from “ a ” to “ b ” , inclusive , carbon

atoms . Thus , for example , a “ C? to C4 alkyl ” group refers to DEFINITIONS all alkyl groups having from 1 to 4 carbons , that is , CH3 — ,

5 CH3CH2 – CH3CH2CH2 – ( CH3 ) 2CH — , Unless defined otherwise , all technical and scientific CH2CH2CH2CH2 - , CH2CH2CH ( CH3 ) and ( CH3 ) 3C — .

terms used herein have the same meaning as is commonly If no “ a ” and “ b ” are designated with regard to an alkyl , understood by one of ordinary skill in the art . All patents , alkenyl , alkynyl , cycloalkyl cycloalkenyl , aryl , heteroaryl or applications , published applications and other publications heterocyclyl group , the broadest range described in these referenced herein are incorporated by reference in their 10 definitions is to be assumed . entirety unless stated otherwise . In the event that there are a As used herein , “ alkyl ” refers to a straight or branched plurality of definitions for a term herein , those in this section hydrocarbon chain that comprises a fully saturated ( no prevail unless stated otherwise . double or triple bonds ) hydrocarbon group . The alkyl group

As used herein , any “ R ” group ( s ) such as , without limi may have 1 to 20 carbon atoms ( whenever it appears herein , tation , R4 , R14 , R24 , R34 , R44 , R54 , R64 , R74 , R8A , R94 , 15 a numerical range such as “ 1 to 20 ” refers to each integer in R104 , R11A , R 124 , R134 , R144 , R154 , R164 , R174 , R184 , R194 the given range ; e . g . , “ 1 to 20 carbon atoms ” means that the R204 , R214 , R224 , R234 , R244 , R2541 , R2542 , R264 , R274 alkyl group may consist of 1 carbon atom , 2 carbon atoms , R284 R294 R304 , R314 , R324 , R33A , R344 , R354 , R36A , R374 3 carbon atoms , etc . , up to and including 20 carbon atoms , R38A , RIB , R2B , R3B , RB , R5 , RÓB , R7B , R & B , RB , RIOB although the present definition also covers the occurrence of R11B1 , R11B2 , R12B , R13 R14B , RI? , R2? , R3? , R4C RSC 20 the term “ alkyl ” where no numerical range is designated ) . R6C , R7C , R & C . RºC , R10C , RII? , R12C , R13C , R14C , R1502 The alkyl group may also be a medium size alkyl having 1 R15?I , R16C , R17C , R18C , R19C , R20C , RAIC , R22C and R23? to 10 carbon atoms . The alkyl group could also be a lower represent substituents that can be attached to the indicated alkyl having 1 to 6 carbon atoms . The alkyl group of the atom . An R group may be substituted or unsubstituted . If two compounds may be designated as “ C1 - C4 alkyl ” or similar “ R ” groups are described as being “ taken together ” the R25 designations . By way of example only , “ C , - C4 alkyl ” indi groups and the atoms they are attached to can form a cates that there are one to four carbon atoms in the alkyl cycloalkyl , cycloalkenyl , aryl , heteroaryl or heterocycle . For chain , i . e . , the alkyl chain is selected from methyl , ethyl , example , without limitation , if R " and R of an NR “ R ” group propyl , iso - propyl , n - butyl , iso - butyl , sec - butyl , and t - butyl . are indicated to be taken together , " it means that they are Typical alkyl groups include , but are in no way limited to , covalently bonded to one another to form a ring : 30 methyl , ethyl , propyl , isopropyl , butyl , isobutyl , tertiary

butyl , pentyl and hexyl . The alkyl group may be substituted or unsubstituted . As used herein , " alkenyl ” refers to an alkyl group that

contains in the straight or branched hydrocarbon chain one 35 or more double bonds . Examples of alkenyl groups include

allenyl , vinylmethyl and ethenyl . An alkenyl group may be In addition , if two “ R ” groups are described as being “ taken u nsubstituted or substituted . together ” with the atom ( s ) to which they are attached to form As used herein , " alkyny? ” refers to an alkyl group that a ring as an alternative , the R groups are not limited to the contains in the straight or branched hydrocarbon chain one variables or substituents defined previously . 40 or more triple bonds . Examples of alkynyls include ethynyl

Whenever a group is described as being " optionally and propynyl . An alkynyl group may be unsubstituted or substituted ” that group may be unsubstituted or substituted substituted . with one or more of the indicated substituents . Likewise , As used herein , " cycloalkyl ” refers to a completely satu when a group is described as being “ unsubstituted or sub - rated ( no double or triple bonds ) mono - or multi - cyclic stituted ” if substituted , the substituent ( s ) may be selected 45 hydrocarbon ring system . When composed of two or more from one or more the indicated substituents . If no substitu - rings , the rings may be joined together in a fused fashion . ents are indicated , it is meant that the indicated “ optionally Cycloalkyl groups can contain 3 to 10 atoms in the ring ( s ) substituted ” or “ substituted ” group may be substituted with or 3 to 8 atoms in the ring ( s ) . A cycloalkyl group may be one or more group ( s ) individually and independently unsubstituted or substituted . Typical cycloalkyl groups selected from alkyl , alkenyl , alkynyl , cycloalkyl , cycloalk - 50 include , but are in no way limited to , cyclopropyl , cyclobu enyl , aryl , heteroaryl , heterocyclyl , aryl ( alkyl ) , heteroaryl tyl , cyclopentyl , cyclohexyl , cycloheptyl and cyclooctyl . ( alkyl ) , heterocyclyl ( alkyl ) , hydroxy , alkoxy , aryloxy , acyl , As used herein , " cycloalkenyl ” refers to a mono - or mercapto , alkylthio , arylthio , cyano , halogen , thiocarbonyl , multi - cyclic hydrocarbon ring system that contains one or O carbamyl , N - carbamyl , O - thiocarbamyl , N - thiocarbamyl , more double bonds in at least one ring ; although , if there is C - amido , N - amido , S - sulfonamido , N - sulfonamido , C - car - 55 more than one , the double bonds cannot form a fully boxy , protected C - carboxy , O - carboxy , isocyanato , thiocya delocalized pi - electron system throughout all the rings ( oth nato , isothiocyanato , azido , nitro , silyl , sulfenyl , sulfenyl , erwise the group would be “ aryl , ” as defined herein ) . When sulfonyl , haloalkyl , haloalkoxy , trihalomethanesulfonyl , tri composed of two or more rings , the rings may be connected halomethanesulfonamido , an amino , a mono - substituted together in a fused fashion . A cycloalkenyl can contain 3 to amino group and a di - substituted amino group , and pro - 60 10 atoms in the ring ( s ) or 3 to 8 atoms in the ring ( s ) . A tected derivatives thereof . cycloalkenyl group may be unsubstituted or substituted .

As used herein , " C . to C / " in which " a " and " b " are As used herein , " aryl ” refers to a carbocyclic ( all carbon ) integers refer to the number of carbon atoms in an alkyl , monocyclic or multicyclic aromatic ring system ( including alkenyl or alkynyl group , or the number of carbon atoms in fused ring systems where two carbocyclic rings share a the ring of a cycloalkyl , cycloalkenyl , aryl , heteroaryl or 65 chemical bond ) that has a fully delocalized pi - electron heterocyclyl group . That is , the alkyl , alkenyl , alkynyl , system throughout all the rings . The number of carbon atoms ring ( s ) of the cycloalkyl , ring ( s ) of the cycloalkenyl , ring ( s ) in an aryl group can vary . For example , the aryl group can

RO

US 9 , 815 , 864 B2

be a C . - C14 aryl group , a C . - C1o aryl group , or a Co aryl may be substituted or unsubstituted . Examples include but group . Examples of aryl groups include , but are not limited are not limited to benzyl , 2 - phenylalkyl ) , 3 - phenyl ( alkyl ) , to , benzene , naphthalene and azulene . An aryl group may be and naphthyl ( alkyl ) . substituted or unsubstituted . As used herein , “ heteroaralkyl ” and “ heteroaryl ( alkyl ) ” As used herein , " heteroaryl ” refers to a monocyclic , 5 refer to a heteroaryl group connected , as a substituent , via a

bicyclic and tricyclic aromatic ring system ( a ring system lower alkylene group . The lower alkylene and heteroaryl with fully delocalized pi - electron system ) that contain ( s ) one group of heteroaryl ( alkyl ) may be substituted or unsubsti or more heteroatoms ( for example , 1 to 5 heteroatoms ) , that tuted . Examples include but are not limited to 2 - thienyl is , an element other than carbon , including but not limited to , ( alkyl ) , 3 - thienyl ( alkyl ) , furyl ( alkyl ) , thienyl ( alkyl ) , pyrro nitrogen , oxygen and sulfur . The number of atoms in the 10 lyl ( alkyl ) , pyridyl ( alkyl ) , isoxazolyl ( alkyl ) , imidazolyl

( alkyl ) , and their benzo - fused analogs . ring ( s ) of a heteroaryl group can vary . For example , the A “ ( heteroalicyclyl ) alkyl ” and “ ( heterocyclyl ) alkyl ” refer heteroaryl group can contain 4 to 14 atoms in the ring ( s ) , 5 to a heterocyclic or a heteroalicyclylic group connected , as to 10 atoms in the ring ( s ) or 5 to 6 atoms in the ring ( s ) . • a substituent , via a lower alkylene group . The lower alkylene Furthermore , the term " heteroaryl ” includes fused ring sys - 15 and heterocyclvl of a heterocyclvl ( alkyl ) may be substituted tems where two rings , such as at least one aryl ring and at or unsubstituted . Examples include but are not limited least one heteroaryl ring , or at least two heteroaryl rings , tetrahydro - 2H - pyran - 4 - yl ( methyl ) , piperidin - 4 - yl ( ethyl ) , share at least one chemical bond . Examples of heteroaryl piperidin - 4 - yl ( propyl ) , tetrahydro - 2H - thiopyran - 4 - yl rings include , but are not limited to , furan , furazan , thio - ( methyl ) and 1 , 3 - thiazinan - 4 - yl ( methyl ) phene , benzothiophene , phthalazine , pyrrole , oxazole , ben - 20 “ Lower alkylene groups ” are straight - chained – CH2 – zoxazole , 1 , 2 , 3 - oxadiazole , 1 , 2 , 4 - oxadiazole , thiazole , 1 , 2 , tethering groups , forming bonds to connect molecular frag 3 - thiadiazole , 1 , 2 , 4 - thiadiazole , benzothiazole , imidazole , ments via their terminal carbon atoms . Examples include but benzimidazole , indole , indazole , pyrazole , benzopyrazole , are not limited to methylene CH2 – ) , ethylene isoxazole , benzoisoxazole , isothiazole , triazole , benzotriaz - A CH CH2 – ) , propylene ( CH , CH , CH , – ) , and buty ole , thiadiazole , tetrazole , pyridine , pyridazine , pyrimidine , 25 lene ( CH2CH2CH2CH2 - ) . A lower alkylene group can pyrazine , purine , pteridine , quinoline , isoquinoline , qui - be substituted by replacing one or more hydrogen of the nazoline , quinoxaline , cinnoline and triazine . A heteroaryl nazoline quinoxaline . cinnoline and triazine . A heteroarul lower alkylene group with a substituent ( s ) listed under the group may be substituted or unsubstituted . definition of “ substituted . ” As used herein , “ heterocyclyl ” or “ heteroalicyclyl ” refers As used herein , “ alkoxy ” refers to the formula — OR

to three - , four - , five - , six - , seven - , eight - , nine - , ten - , up to 30 wherein R is an alkyl , an alkenyl , an alkynyl , a cycloalkyl , a cycloalkenyl , aryl , heteroaryl , heteroalicyclyl , aralkyl , 18 - membered monocyclic , bicyclic , and tricyclic ring sys heteroaryl ( alkyl ) or heterocyclyl ( alkyl ) is defined herein . A tem wherein carbon atoms together with from 1 to 5 het non - limiting list of alkoxys are methoxy , ethoxy , n - propoxy , eroatoms constitute said ring system . A heterocycle may 1 - methylethoxy ( isopropoxy ) , n - butoxy , iso - butoxy , sec - bu

optionally contain one or more unsaturated bonds situated in 35 toxy , tert - butoxv . phenoxy and benzoxy . An alkoxy may be such a way , however , that a fully delocalized pi - electron substituted or unsubstituted . system does not occur throughout all the rings . The heteroa As used herein , " acyl ” refers to a hydrogen an alkyl , an tom ( s ) is an element other than carbon including , but not alkenyl , an alkynyl , a cycloalkyl , a cycloalkenyl , aryl , limited to , oxygen , sulfur , and nitrogen . A heterocycle may h eteroaryl , heteroalicyclyl , aralkyl , heteroaryl ( alkyl ) or het further contain one or more carbonyl or thiocarbonyl func - 40 erocyclyl ( alkyl ) connected , as substituents , via a carbonyl tionalities , so as to make the definition include oxo - systems group . Examples include formyl , acetyl , propanoyl , benzoyl , and thio - systems such as lactams , lactones , cyclic imides , and acryl . An acyl may be substituted or unsubstituted . cyclic thioimides and cyclic carbamates . When composed of As used herein , “ hydroxyalkyl ” refers to an alkyl group in two or more rings , the rings may be joined together in a which one or more of the hydrogen atoms are replaced by a fused fashion . Additionally , any nitrogens in a heteroalicy - 45 hydroxy group . Exemplary hydroxyalkyl groups include but clic may be quaternized . Heterocyclyl or heteroalicyclic are not limited to , 2 - hydroxyethyl , 3 - hydroxypropyl , 2 - hy groups may be unsubstituted or substituted . Examples of droxypropyl , and 2 , 2 - dihydroxyethyl . A hydroxyalkyl may such " heterocyclyl ” or “ heteroalicyclyl ” groups include but be substituted or unsubstituted . are not limited to , 1 , 3 - dioxin , 1 , 3 - dioxane , 1 , 4 - dioxane , As used herein , “ haloalkyl ” refers to an alkyl group in 1 , 2 - dioxolane , 1 , 3 - dioxolane , 1 , 4 - dioxolane , 1 , 3 - oxathiane , 50 which one or more of the hydrogen atoms are replaced by a 1 , 4 - oxathiin , 1 , 3 - oxathiolane , 1 , 3 - dithiole , 1 , 3 - dithiolane , halogen ( e . g . , mono - haloalkyl , di - haloalkyl and tri - ha 1 , 4 - oxathiane , tetrahydro - 1 , 4 - thiazine , 2H - 1 , 2 - oxazine , loalkyl ) . Such groups include but are not limited to , chlo maleimide , succinimide , barbituric acid , thiobarbituric acid , romethyl , fluoromethyl , difluoromethyl , trifluoromethyl , dioxopiperazine , hydantoin , dihydrouracil , trioxane , hexa - 1 - chloro - 2 - fluoromethyl and 2 - fluoroisobutyl . A haloalkyl hydro - 1 , 3 , 5 - triazine , imidazoline , imidazolidine , isoxazo - 55 may be substituted or unsubstituted . line , isoxazolidine , oxazoline , oxazolidine , oxazolidinone , As used herein , “ haloalkoxy ” refers to a O - alkyl group in thiazoline , thiazolidine , morpholine , oxirane , piperidine which one or more of the hydrogen atoms are replaced by a N - Oxide , piperidine , piperazine , pyrrolidine , pyrrolidone , halogen ( e . g . , mono - haloalkoxy , di - haloalkoxy and tri - ha pyrrolidione , 4 - piperidone , pyrazoline , pyrazolidine , 2 - ox - loalkoxy ) . Such groups include but are not limited to , opyrrolidine , tetrahydropyran , 4H - pyran , tetrahydrothiopy - 60 chloromethoxy , fluoromethoxy , difluoromethoxy , trifluo ran , thiamorpholine , thiamorpholine sulfoxide , thiamorpho - romethoxy , 1 - chloro - 2 - fluoromethoxy and 2 - fluoroisobu line sulfone , and their benzo - fused analogs ( e . g . , toxy . A haloalkoxy may be substituted or unsubstituted . benzimidazolidinone , tetrahydroquinoline , and 3 , 4 - methyl - A “ sulfenyl ” group refers to an “ _ SR ” group in which R enedioxyphenyl ) . can be hydrogen , alkyl , alkenyl , alkynyl , cycloalkyl , As used herein , “ aralkyl ” and “ aryl ( alkyl ) ” refer to an aryl 65 cycloalkenyl , aryl , heteroaryl , heterocyclyl , aryl ( alkyl ) , het

group connected , as a substituent , via a lower alkylene eroaryl ( alkyl ) or heterocyclyl ( alkyl ) . A sulfenyl may be group . The lower alkylene and aryl group of an aryl ( alkyl ) substituted or unsubstituted .

US 9 , 815 , 864 B2

A " sulfinyl ” group refers to an “ _ S ( = O ) - R ” group in hydrogen , alkyl , alkenyl , alkynyl , cycloalkyl , cycloalkenyl , which R can be the same as defined with respect to sulfenyl . aryl , heteroaryl , heterocyclyl , aryl ( alkyl ) , heteroaryl ( alkyl ) A sulfinyl may be substituted or unsubstituted . or heterocyclyl ( alkyl ) . An N - thiocarbamyl may be substi

A “ sulfonyl ” group refers to an “ SO , R ” group in which R tuted or unsubstituted . can be the same as defined with respect to sulfenyl . A 5 A " C - amido ” group refers to a “ CEO ) N ( RAR ) " sulfonyl may be substituted or unsubstituted . group in which RA and Rg can be independently hydrogen ,

An “ O - carboxy " group refers to a “ RCE00 — ” group alkyl , alkenyl , alkynyl , cycloalkyl , cycloalkenyl , aryl , het in which R can be hydrogen , alkyl , alkenyl , alkynyl , eroaryl , heterocyclyl , aryl ( alkyl ) , heteroaryl ( alkyl ) or het cycloalkyl , cycloalkenyl , aryl , heteroaryl , heterocyclyl , aryl erocyclyl ( alkyl ) . A C - amido may be substituted or unsub ( alkyl ) , heteroaryl ( alkyl ) or heterocyclyl ( alkyl ) , as defined 10 stituted . herein . An O - carboxy may be substituted or unsubstituted . An “ N - amido " group refers to a “ RC ( = O ) N ( R ) ”

The terms " ester ” and “ C - carboxy ” refer to a “ CEO group in which R and R , can be independently hydrogen , OR ” group in which R can be the same as defined with alkyl , alkenyl , alkynyl , cycloalkyl , cycloalkenyl , aryl , het respect to O - carboxy . An ester and C - carboxy may be eroaryl , heterocyclyl , aryl ( alkyl ) , heteroaryl ( alkyl ) or het substituted or unsubstituted . 15 erocyclyl ( alkyl ) . An N - amido may be substituted or unsub

A “ thiocarbonyl ” group refers to a “ _ C = S ) R ” group in stituted . which R can be the same as defined with respect to O - car - The term “ halogen atom ” or “ halogen ” as used herein , boxy . A thiocarbonyl may be substituted or unsubstituted . means any one of the radio - stable atoms of column 7 of the

A “ trihalomethanesulfonyl ” group refers to an Periodic Table of the Elements , such as , fluorine , chlorine , “ X2CS02 ” group wherein each X is a halogen . 20 bromine and iodine .

A “ trihalomethanesulfonamido ” group refers to an “ X CS Where the numbers of substituents is not specified ( e . g . ( 0 ) N ( RA ) ” group wherein each X is a halogen , and R haloalkyl ) , there may be one or more substituents present . hydrogen , alkyl , alkenyl , alkynyl , cycloalkyl , cycloalkenyl , For example “ haloalkyl ” may include one or more of the aryl , heteroaryl , heterocyclyl , aryl ( alkyl ) , heteroaryl ( alkyl ) same or different halogens . As another example , “ C , - C3 or heterocyclyl ( alkyl ) . 25 alkoxyphenyl ” may include one or more of the same or

The term “ amino " as used herein refers to a - NH2 group . different alkoxy groups containing one , two or three atoms . As used herein , the term “ hydroxy ” refers to a OH As used herein , the abbreviations for any protective

group . groups , amino acids and other compounds , are , unless A “ cyano " group refers to a “ _ CN ” group . indicated otherwise , in accord with their common usage , The term " azido ” as used herein refers to a — N , group . 30 recognized abbreviations , or the IUPAC - IUB Commission An " isocyanato ” group refers to a “ — NCO ” group . on Biochemical Nomenclature ( See , Biochem . 11 : 942 - 944 A “ thiocyanato " group refers to a “ _ CNS ” group . ( 1972 ) ) . An “ isothiocyanato ” group refers to an “ — NCS ” group . The term “ nucleoside ” is used herein in its ordinary sense A “ mercapto ” group refers to an “ GSH ” group . as understood by those skilled in the art , and refers to a A “ carbonyl ” group refers to a CEO group . 35 compound composed of an optionally substituted pentose An “ S - sulfonamido ” group refers to a “ — SO N ( R / RB ) ” moiety or modified pentose moiety attached to a heterocy

group in which RA and Rp can be independently hydrogen , clic base or tautomer thereof via a N - glycosidic bond , such alkyl , alkenyl , alkynyl , cycloalkyl , cycloalkenyl , aryl , het - as attached via the 9 - position of a purine - base or the eroaryl , heterocyclyl , aryl ( alkyl ) , heteroaryl ( alkyl ) or het - 1 - position of a pyrimidine - base . Examples include , but are erocyclyl ( alkyl ) . An S - sulfonamido may be substituted or 40 not limited to , a ribonucleoside comprising a ribose moiety unsubstituted . and a deoxyribonucleoside comprising a deoxyribose moi

An “ N - sulfonamido ” group refers to a “ RSO , N ( RA ) ” ety . A modified pentose moiety is a pentose moiety in which group in which R and R , can be independently hydrogen , an oxygen atom has been replaced with a carbon and / or a alkyl , alkenyl , alkynyl , cycloalkyl , cycloalkenyl , aryl , het carbon has been replaced with a sulfur or an oxygen atom . eroaryl , heterocyclyl , aryl ( alkyl ) , heteroaryl ( alkyl ) or het - 45 A “ nucleoside ” is a monomer that can have a substituted erocyclyl ( alkyl ) . An N - sulfonamido may be substituted or base and / or sugar moiety . Additionally , a nucleoside can be unsubstituted . incorporated into larger DNA and / or RNA polymers and

An “ O - carbamyl ” group refers to a “ OC ( O ) N oligomers . In some instances , the nucleoside can be a ( R , RR ) " group in which R , and R , can be independently nucleoside analog drug . hydrogen , alkyl , alkenyl , alkynyl , cycloalkyl , cycloalkenyl , 50 The term “ nucleotide ” is used herein in its ordinary sense aryl , heteroaryl , heterocyclyl , aryl ( alkyl ) , heteroaryl ( alkyl ) as understood by those skilled in the art , and refers to a or heterocyclyl ( alkyl ) . An O - carbamyl may be substituted or nucleoside having a phosphate ester bound to the pentose unsubstituted . moiety , for example , at the 5 ' - position . An “ N - carbamyl ” group refers to an “ ROCESON As used herein , the term " heterocyclic base ” refers to an

( RA ) ” group in which R and RA can be independently 55 optionally substituted nitrogen - containing heterocyclyl that hydrogen , alkyl , alkenyl , alkynyl , cycloalkyl , cycloalkenyl , can be attached to an optionally substituted pentose moiety aryl , heteroaryl , heterocyclyl , aryl ( alkyl ) , heteroaryl ( alkyl ) or modified pentose moiety . In some embodiments , the or heterocyclyl ( alkyl ) . An N - carbamyl may be substituted or heterocyclic base can be selected from an optionally sub unsubstituted . stituted purine - base , an optionally substituted pyrimidine

An “ O - thiocarbamyl ” group refers to a “ _ OC S - N 60 base and an optionally substituted triazole - base ( for ( R / RB ) " group in which RA and Rg can be independently example , a 1 , 2 , 4 - triazole ) . The term “ purine - base ” is used hydrogen , alkyl , alkenyl , alkynyl , cycloalkyl , cycloalkenyl , herein in its ordinary sense as understood by those skilled in aryl , heteroaryl , heterocyclyl , aryl ( alkyl ) , heteroaryl ( alkyl ) the art , and includes its tautomers . Similarly , the term or heterocyclyl ( alkyl ) . An O - thiocarbamyl may be substi - " pyrimidine - base " is used herein in its ordinary sense as tuted or unsubstituted . 65 understood by those skilled in the art , and includes its

An " N - thiocarbamyl ” group refers to an " ROCC — SN tautomers . A non - limiting list of optionally substituted ( RA ) ” group in which R and Rg can be independently purine - bases includes purine , adenine , guanine , hypoxan

ur

US 9 , 815 , 864 B2 10

SO 1 OH OH

" ILI maan S and

SH

I ??

30 LIH O - 14

and

thine , xanthine , alloxanthine , 7 - alkylguanine ( e . g . 7 - meth ylguanine ) , theobromine , caffeine , uric acid and isoguanine . Examples of pyrimidine - bases include , but are not limited to , cytosine , thymine , uracil , 5 , 6 - dihydrouracil and 5 - alky lcytosine ( e . g . , 5 - methylcytosine ) . An example of an option - 5 ally substituted triazole - base is 1 , 2 , 4 - triazole - 3 - carboxam ide . Other non - limiting examples of heterocyclic bases its protonated forms ( for example , include diaminopurine , 8 - oxo - N? - alkyladenine ( e . g . , 8 - oxo Nº - methyladenine ) , 7 - deazaxanthine , 7 - deazaguanine , 7 - deazaadenine , N4 , N4 - ethanocytosin , Nº , Nº - ethano - 2 , 6 - di - 10 aminopurine , 5 - halouracil ( e . g . , 5 - fluorouracil and 5 - bro SEP - 0 SEP - 04 mouracil ) , pseudoisocytosine , isocytosine , isoguanine , and other heterocyclic bases described in U . S . Pat . Nos . 5 , 432 , S and OH 272 and 7 , 125 , 855 , which are incorporated herein by refer 15 ence for the limited purpose of disclosing additional hetero - and its tautomers ( such as cyclic bases . In some embodiments , a heterocyclic base can be optionally substituted with an amine or an enol protecting group ( s ) .

The term “ — N - linked amino acid ” refers to an amino acid 20 O = P - 0 that is attached to the indicated moiety via a main - chain amino or mono - substituted amino group . When the amino ?? acid is attached in an — N - linked amino acid , one of the hydrogens that is part of the main - chain amino or mono As used herein , the term “ phosphate ” is used in its substituted amino group is not present and the amino acid is 25 ordinary sense as understood by those skilled in the art , and attached via the nitrogen . N - linked amino acids can be includes its protonated forms ( for example , substituted or unsubstituted .

The term “ — N - linked amino acid ester derivative ” refers to an amino acid in which a main - chain carboxylic acid OH group has been converted to an ester group . In some su 0 = - 0 O = P - 0 embodiments , the ester group has a formula selected from alkyl - 0 C ( O ) - cycloalkyl - 0 C ( O ) - aryl - O C o sand OH GO ) - and aryl ( alkyl ) - 0 _ C 0 — . A non - limiting list of ester groups include substituted and unsubstituted ver - 35 As used herein , the terms “ monophosphate , ” “ diphosphate , ” sions of the following : methyl - 0 _ C ( 0 ) — , ethyl - 0 C and “ triphosphate ” are used in their ordinary sense as Go ) . n - propyl - O C ( O ) - , isopropyl - 0 _ C ( O ) - , understood by those skilled in the art , and include protonated n - butyl - 0 _ C ( = O ) — , isobutyl - 0 — C — 0 ) — , tert - butyl - forms . 0 - C ( O ) - , neopentyl - 0 _ CEO ) — , cyclopropyl - 0 The terms “ protecting group ” and “ protecting groups ” as C ( O ) - , cyclobutyl - 0 _ C = O ) - , cyclopentyl - 0 C 40 used herein refer to any atom or group of atoms that is added GO ) , cyclohexyl - O - C ( O ) - , phenyl - O - C ( O ) - , to a molecule in order to prevent existing groups in the benzyl - 0 _ C ( = O ) , and naphthyl - 0 _ C40 ) — . molecule from undergoing unwanted chemical reactions . N - linked amino acid ester derivatives can be substituted or Examples of protecting group moieties are described in T . unsubstituted . W . Greene and P . G . M . Wuts , Protective Groups in Organic

The term “ _ O - linked amino acid ” refers to an amino acid 45 Synthesis , 3 . Ed . John Wiley & Sons , 1999 , and in J . F . W . that is attached to the indicated moiety via the hydroxy from McOmie , Protective Groups in Organic Chemistry Plenum its main - chain carboxylic acid group . When the amino acid Press , 1973 , both of which are hereby incorporated by is attached in an O - linked amino acid , the hydrogen that reference for the limited purpose of disclosing suitable is part of the hydroxy from its main - chain carboxylic acid protecting groups . The protecting group moiety may be group is not present and the amino acid is attached via the 50 chosen in such a way , that they are stable to certain reaction oxygen . O - linked amino acids can be substituted or unsub - conditions and readily removed at a convenient stage using stituted . methodology known from the art . A non - limiting list of As used herein , the term “ amino acid ” refers to any amino protecting groups include benzyl ; substituted benzyl ; alky

acid ( both standard and non - standard amino acids ) , includ - lcarbonyls and alkoxycarbonyls ( e . g . , t - butoxycarbonyl ing , but not limited to , a - amino acids , B - amino acids , 55 ( BOC ) , acetyl , or isobutyryl ) ; arylalkylcarbonyls and aryl y - amino acids and d - amino acids . Examples of suitable alkoxycarbonyls ( e . g . , benzyloxycarbonyl ) ; substituted amino acids include , but are not limited to , alanine , aspara - methyl ether ( e . g . methoxymethyl ether ) ; substituted ethyl gine , aspartate , cysteine , glutamate , glutamine , glycine , pro - ether ; a substituted benzyl ether ; tetrahydropyranyl ether ; line , serine , tyrosine , arginine , histidine , isoleucine , leucine , silyls ( e . g . , trimethylsilyl , triethylsilyl , triisopropylsilyl , lysine , methionine , phenylalanine , threonine , tryptophan 60 t - butyldimethylsilyl , tri - iso - propylsilyloxymethyl , [ 2 - ( trim and valine . Additional examples of suitable amino acids ethylsilyl ) ethoxy ] methyl or t - butyldiphenylsilyl ) ; esters include , but are not limited to , ornithine , hypusine , 2 - ami - ( e . g . benzoate ester ) ; carbonates ( e . g . methoxymethylcar noisobutyric acid , dehydroalanine , gamma - aminobutyric bonate ) ; sulfonates ( e . g . tosylate or mesylate ) ; acyclic ketal acid , citrulline , beta - alanine , alpha - ethyl - glycine , alpha - pro - ( e . g . dimethyl acetal ) ; cyclic ketals ( e . g . , 1 , 3 - dioxane , 1 , 3 pyl - glycine and norleucine . 65 dioxolanes , and those described herein ) ; acyclic acetal ;

The terms " phosphorothioate ” and “ phosphothioate ” refer cyclic acetal ( e . g . , those described herein ) ; acyclic hemiac to a compound of the general formula etal ; cyclic hemiacetal ; cyclic dithioketals ( e . g . , 1 , 3 - dithiane

US 9 , 815 , 864 B2 12

an

or 1 , 3 - dithiolane ) ; orthoesters ( e . g . , those described herein ) singular to the plural as is appropriate to the context and / or and triarylmethyl groups ( e . g . , trityl ; monomethoxytrityl application . The various singular / plural permutations may ( MMTr ) ; 4 , 4 ' - dimethoxytrityl ( DMTr ) ; 4 , 4 ' , 4 " be expressly set forth herein for sake of clarity . The indefi trimethoxytrityl ( TMTr ) ; and those described herein ) . nite article “ a ” or “ an ” does not exclude a plurality . A single

The term “ pharmaceutically acceptable salt ” refers to a 5 processor or other unit may fulfill the functions of several salt of a compound that does not cause significant irritation items recited in the claims . The mere fact that certain to an organism to which it is administered and does not measures are recited in mutually different dependent claims abrogate the biological activity and properties of the com does not indicate that a combination of these measures pound . In some embodiments , the salt is an acid addition salt cannot be used to advantage . Any reference signs in the of the compound . Pharmaceutical salts can be obtained by 10 claims should not be construed as limiting the scope . reacting a compound with inorganic acids such as hydro It is understood that , in any compound described herein halic acid ( e . g . , hydrochloric acid or hydrobromic acid ) , having one or more chiral centers , if an absolute stereo sulfuric acid , nitric acid and phosphoric acid . Pharmaceuti chemistry is not expressly indicated , then each center may cal salts can also be obtained by reacting a compound with organic acid such as aliphatic or aromatic carboxylic or 15 independently be of R - configuration or S - configuration or a sulfonic acids , for example formic , acetic , succinic , lactic , mixture thereof . Thus , the compounds provided herein may malic , tartaric , citric , ascorbic , nicotinic , methanesulfonic , be enantiomerically pure , enantiomerically enriched , race ethanesulfonic , p - toluensulfonic , salicylic or naphthalene mic mixture , diastereomerically pure , diastereomerically sulfonic acid . Pharmaceutical salts can also be obtained by enriched , or a stereoisomeric mixture . In addition it is reacting a compound with a base to form a salt such as an 20 understood that , in any compound described herein having ammonium salt , an alkali metal salt , such as a sodium or a one or more double bond ( s ) generating geometrical isomers potassium salt , an alkaline earth metal salt , such as a calcium that can be defined as E or Z , each double bond may or a magnesium salt , a salt of organic bases such as dicy - independently be E or Z a mixture thereof . clohexylamine , N - methyl - D - glucamine , tris ( hydroxymeth Likewise , it is understood that , in any compound yl ) methylamine , C . - C , alkylamine , cyclohexylamine , tri - 25 described , all tautomeric forms are also intended to be ethanolamine , ethylenediamine , and salts with amino acids included . For example all tautomers of a phosphate and a such as arginine and lysine . phosphorothioate groups are intended to be included .

Terms and phrases used in this application , and variations Examples of tautomers of a phosphorothioate include the thereof , especially in the appended claims , unless otherwise following : expressly stated , should be construed as open ended as 30 opposed to limiting . As examples of the foregoing , the term ‘ including should be read to mean ' including , without OH ??

limitation , including but not limited to , ' or the like ; the - S - P - 0 SEP — 0 HS - P - 0 term ' comprising ' as used herein is synonymous with ‘ including , ' ' containing , ' or ' characterized by , ' and is inclu - 35 0 m

sive or open - ended and does not exclude additional , unre cited elements or method steps ; the term “ having ’ should be S = P - 0 interpreted as ' having at least ; ' the term “ includes ' should be interpreted as “ includes but is not limited to ; ' the term ' example ’ is used to provide exemplary instances of the item 40 in discussion , not an exhaustive or limiting list thereof ; and use of terms like “ preferably , ' ' preferred , ' ' desired , or Furthermore , all tautomers of heterocyclic bases known in ' desirable , ' and words of similar meaning should not be the art are intended to be included , including tautomers of understood as implying that certain features are critical , natural and non - natural purine - bases and pyrimidine - bases . essential , or even important to the structure or function , but 45 It is to be understood that where compounds disclosed instead as merely intended to highlight alternative or addi - herein have unfilled valencies , then the valencies are to be tional features that may or may not be utilized in a particular filled with hydrogens or isotopes thereof , e . g . , hydrogen - 1 embodiment . In addition , the term “ comprising " is to be ( protium ) and hydrogen - 2 ( deuterium ) . interpreted synonymously with the phrases “ having at least " It is understood that the compounds described herein can or " including at least ” . When used in the context of a 50 be labeled isotopically . Substitution with isotopes such as process , the term " comprising ” means that the process deuterium may afford certain therapeutic advantages result includes at least the recited steps , but may include additional ing from greater metabolic stability , such as , for example , steps . When used in the context of a compound , composition increased in vivo half - life or reduced dosage requirements . or device , the term “ comprising ” means that the compound , Each chemical element as represented in a compound struc composition or device includes at least the recited features 55 ture may include any isotope of said element . For example , or components , but may also include additional features or in a compound structure a hydrogen atom may be explicitly components . Likewise , a group of items linked with the disclosed or understood to be present in the compound . At conjunction ' and ’ should not be read as requiring that each any position of the compound that a hydrogen atom may be and every one of those items be present in the grouping , but present , the hydrogen atom can be any isotope of hydrogen , rather should be read as ' and / or unless expressly stated 60 including but not limited to hydrogen - 1 ( protium ) and otherwise . Similarly , a group of items linked with the hydrogen - 2 ( deuterium ) . Thus , reference herein to a com conjunction ' or ’ should not be read as requiring mutual pound encompasses all potential isotopic forms unless the exclusivity among that group , but rather should be read as context clearly dictates otherwise . ‘ and / or ' unless expressly stated otherwise . It is understood that the methods and combinations

With respect to the use of substantially any plural and / or 65 described herein include crystalline forms ( also known as singular terms herein , those having skill in the art can polymorphs , which include the different crystal packing translate from the plural to the singular and / or from the arrangements of the same elemental composition of a com

po HS - Phon ? Share Oh nor ?? and and mw OH we

?? OH wi .

US 9 , 815 , 864 B2 13 14

pound ) , amorphous phases , salts , solvates , and hydrates . In abdominal cramps , nausea , diarrhea , vomiting , dehydration , some embodiments , the compounds described herein exist in fever , headache , chills , myalgia and sore throat . solvated forms with pharmaceutically acceptable solvents The one or more compounds of Formula ( I ) or a phar such as water , ethanol , or the like . In other embodiments , the maceutically acceptable salt thereof , one or more com compounds described herein exist in unsolvated form . Sol - 5 pounds of Formula ( II ) , or a pharmaceutically acceptable vates contain either stoichiometric or non - stoichiometric salt thereof , and / or one or more compounds of Formula ( III ) , amounts of a solvent , and may be formed during the process or a pharmaceutically acceptable salt thereof , that can be of crystallization with pharmaceutically acceptable solvents used to treat , ameliorate and / or prevent a norovirus infection such as water , ethanol , or the like . Hydrates are formed when can be a compound of Formula ( I ) , or pharmaceutically the solvent is water , or alcoholates are formed when the 10 acceptable salt thereof , and / or a compound of Formula ( II ) ,

or a pharmaceutically acceptable salt thereof , and / or a solvent is alcohol . In addition , the compounds provided compound of Formula ( III ) , or a pharmaceutically accept herein can exist in unsolvated as well as solvated forms . In able salt thereof , provided in any of the embodiments general , the solvated forms are considered equivalent to the described in the section under the “ Compounds ” heading unsolvated forms for the purposes of the compounds and 15 below methods provided herein . As used herein , the terms " prevent ” and “ preventing , "

Where a range of values is provided , it is understood that mean a subject does not develop an infection because the the upper and lower limit , and each intervening value subject has an immunity against the infection , or if a subject between the upper and lower limit of the range is encom - becomes infected , the severity of the disease is less com passed within the embodiments . 20 pared to the severity of the disease if the subject has not been Methods of Use : administered / received the compound . Examples of forms of

Some embodiments described herein relate to a method of prevention include prophylactic administration to a subject ameliorating and / or treating a norovirus infection , which can who has been or may be exposed to an infectious agent , such include administering an effective amount of one or more as a norovirus . compounds described herein , or a pharmaceutical composi - 25 As used herein , the terms " treat , " " treating , " " treatment , " tion that includes one or more compounds described herein " therapeutic , ” and “ therapy ” do not necessarily mean total ( e . g . , a compound of Formula ( I ) , a compound of Formula cure or abolition of the disease or condition . Any alleviation ( II ) and / or a compound of Formula ( III ) , or a pharmaceuti - of any undesired signs or symptoms of a disease or condi cally acceptable salt of the foregoing ) . Other embodiments tion , to any extent can be considered treatment and / or described herein relate to a method of preventing a norovirus 30 therapy . Furthermore , treatment may include acts that may infection , which can include administering an effective worsen the subject ' s overall feeling of well - being or appear amount of one or more compounds described herein , or a ance . pharmaceutical composition that includes one or more com - The terms “ therapeutically effective amount ” and “ effec pounds described herein ( e . g . , a compound of Formula ( I ) , tive amount ” are used to indicate an amount of an active a compound of Formula ( II ) and / or a compound of Formula 35 compound , or pharmaceutical agent , that elicits the biologi ( III ) , or a pharmaceutically acceptable salt of the foregoing ) . cal or medicinal response indicated . For example , a thera

Other embodiments described herein relate to a method of peutically effective amount of compound can be the amount inhibiting viral replication of a norovirus virus , which can needed to prevent , alleviate or ameliorate symptoms of include contacting a cell infected with the norovirus virus disease or prolong the survival of the subject being treated with an effective amount of a compound of Formula ( 1 ) , or 40 This response may occur in a tissue , system , animal or a pharmaceutically acceptable salt thereof , an effective human and includes alleviation of the signs or symptoms of amount of a compound of Formula ( II ) , or a pharmaceuti - the disease being treated . Determination of an effective cally acceptable salt thereof , an effective amount of a amount is well within the capability of those skilled in the compound of Formula ( III ) , or a pharmaceutically accept - art , in view of the disclosure provided herein . The thera able salt thereof , and / or a pharmaceutical composition that 45 peutically effective amount of the compounds disclosed includes one or more compounds described herein ( e . g . , a herein required as a dose will depend on the route of compound of Formula ( I ) , a compound of Formula ( II ) administration , the type of animal , including human , being and / or a compound of Formula ( III ) , or a pharmaceutically treated , and the physical characteristics of the specific ani acceptable salt of the foregoing ) . Still other embodiments mal under consideration . The dose can be tailored to achieve described herein related to a method of inhibiting at least one 50 a desired effect , but will depend on such factors as weight , of the following in the norovirus replication : polymerase diet , concurrent medication and other factors which those protease and helicase . skilled in the medical arts will recognize .

In some embodiments , an effective amount of one or more Various indicators for determining the effectiveness of a compounds of Formula ( I ) , or a pharmaceutically acceptable method for treating a viral infection , such as a norovirus salt thereof , an effective amount of one or more compounds 55 infection , are known to those skilled in the art . Example of of Formula ( II ) , or a pharmaceutically acceptable salt suitable indicators include , but are not limited to , a reduction thereof , an effective amount of one or more compounds of in viral load , a reduction in viral replication , a reduction in Formula ( III ) , or a pharmaceutically acceptable salt thereof , time to seroconversion ( virus undetectable in patient serum ) , and / or a pharmaceutical composition that includes one or a reduction of morbidity or mortality in clinical outcomes , more compounds described herein ( e . g . , a compound of 60 and / or other indicator of disease response . Formula ( I ) , a compound of Formula ( II ) and / or a compound In some embodiments , an effective amount of a com of Formula ( III ) , or a pharmaceutically acceptable salt of the pound of Formulae ( I ) , ( II ) and / or ( III ) , or a pharmaceuti foregoing ) can be used treat , ameliorate and / or prevent one cally acceptable salt of the foregoing , is an amount that is more symptoms of an infection caused by a norovirus . For effective to reduce viral titers to undetectable levels , for example , a compound of Formulae ( I ) , ( II ) and / or ( III ) can 65 example , to about 1000 to about 5000 , to about 500 to about be used to treat , ameliorate and / or prevent one or more of the 1000 , or to about 100 to about 500 genome copies / mL following symptoms caused by a norovirus infection : serum . In some embodiments , an effective amount of a

15

US 9 , 815 , 864 B2 15 16

compound of Formulae ( I ) , ( II ) and / or ( III ) , or a pharma - priate values derived from in vitro or in vivo studies , as ceutically acceptable salt of the foregoing , is an amount that qualified by toxicity studies and efficacy studies in animals . is effective to reduce viral load compared to the viral load In cases of administration of a pharmaceutically accept before administration of the compound of Formulae ( 1 ) , ( II ) able salt . dosages may be calculated as the free base . As will and / or ( III ) , or a pharmaceutically acceptable salt of the 3 be understood by those of skill in the art , in certain situations foregoing . In some embodiments , an effective amount of a it may be necessary to administer the compounds disclosed compound of Formulae ( 1 ) , ( II ) and / or ( III ) , or a pharma - herein in amounts that exceed , or even far exceed , the ceutically acceptable salt of the foregoing , is an amount that above - stated , preferred dosage range in order to effectively is effective to achieve a reduction in viral titer in the serum 10 and aggressively treat particularly aggressive diseases or of the subject in the range of about 1 . 5 - log to about a 2 . 5 - log infections . reduction , about a 3 - log to about a 4 - log reduction , or a Dosage amount and interval may be adjusted individually greater than about 5 - log reduction compared to the viral load before administration of the compound of Formulae ( I ) , ( II ) to provide plasma levels of the active moiety which are and / or ( III ) , or a pharmaceutically acceptable salt of the 15 sufficient to maintain the modulating effects , or minimal foregoing . For example , wherein the viral load is measure effective concentration ( MEC ) . The MEC will vary for each before administration of the compound of Formulae ( I ) , ( II ) compound but can be estimated from in vitro data . Dosages and / or ( III ) , or a pharmaceutically acceptable salt of the necessary to achieve the MEC will depend on individual foregoing , and again after completion of the treatment characteristics and route of administration . However , HPLC regime with the compound of Formulae ( 1 ) , ( II ) and / or ( III ) , 20 assays or bioassays can be used to determine plasma con or a pharmaceutically acceptable salt of the foregoing ( for centrations . Dosage intervals can also be determined using example , 1 week after completion ) . In some embodiments , MEC value . Compositions should be administered using a a compound of Formulae ( I ) , ( II ) and / or ( III ) , or a pharma ceutically acceptable salt of the foregoing , can result in at regimen which maintains plasma levels above the MEC for least a 1 , 2 , 3 , 4 , 5 , 10 , 15 , 20 , 25 , 50 , 75 , 100 - fold or more 25 10 - 90 % of the time , preferably between 30 - 90 % and most reduction in the replication of a norovirus relative to pre - preferably between 50 - 90 % . In cases of local administration treatment levels in a subject , as determined after completion or selective uptake , the effective local concentration of the of the treatment regime ( for example , 1 week after comple drug may not be related to plasma concentration . tion ) . In some embodiments , a compound of Formulae ( 1 ) , ( II ) and / or ( III ) , or a pharmaceutically acceptable salt of the 30 It should be noted that the attending physician would foregoing , can result in a reduction of the replication of a know how to and when to terminate , interrupt , or adjust norovirus relative to pre - treatment levels in the range of administration due to toxicity or organ dysfunctions . Con about 2 to about 5 fold , about 10 to about 20 fold , about 15 versely , the attending physician would also know to adjust to about 40 fold , or about 50 to about 100 fold . treatment to higher levels if the clinical response were not

As will be readily apparent to one skilled in the art , the 35 adequate ( precluding toxicity ) . The magnitude of an admin useful in vivo dosage to be administered and the particular istrated dose in the management of the disorder of interest mode of administration will vary depending upon the age , will vary with the severity of the condition to be treated and weight , the severity of the affliction , and mammalian species to the route of administration . The severity of the condition treated , the particular compounds employed , and the specific may , for example , be evaluated , in part , by standard prog use for which these compounds are employed . The deter - 40 nostic evaluation methods . Further , the dose and perhaps mination of effective dosage levels , that is the dosage levels dose frequency , will also vary according to the age , body necessary to achieve the desired result , can be accomplished weight , and response of the individual patient . A program by one skilled in the art using routine methods , for example , comparable to that discussed above may be used in veteri human clinical trials and in vitro studies . nary medicine . The dosage may range broadly , depending upon the 45 desired effects and the therapeutic indication . Alternatively Compounds disclosed herein can be evaluated for efficacy dosages may be based and calculated upon the surface area and toxicity using known methods . For example , the toxi of the patient , as understood by those of skill in the art . cology of a particular compound , or of a subset of the Although the exact dosage will be determined on a drug compounds , sharing certain chemical moieties , may be by - drug basis , in most cases , some generalizations regarding 50 established by determining in vitro toxicity towards a cell the dosage can be made . The daily dosage regimen for an line , such as a mammalian , and preferably human , cell line . adult human patient may be , for example , an oral dose of The results of such studies are often predictive of toxicity in between 0 . 01 mg and 3000 mg of each active ingredient , animals , such as mammals , or more specifically , humans . preferably between 1 mg and 700 mg , e . g . 5 to 200 mg . The Alternatively , the toxicity of particular compounds in an dosage may be a single one or a series of two or more given 55 animal model , such as mice , rats , rabbits , or monkeys , may in the course of one or more days , as is needed by the be determined using known methods . The efficacy of a subject . In some embodiments , the compounds will be particular compound may be established using several rec administered for a period of continuous therapy , for example ognized methods , such as in vitro methods , animal models , for a week or more , or for months or years . or human clinical trials . When selecting a model to deter In instances where human dosages for compounds have 60 mine efficacy , the skilled artisan can be guided by the state been established for at least some condition , those same of the art to choose an appropriate model , dose , route of dosages may be used , or dosages that are between about administration and / or regime . 0 . 1 % and 500 % , more preferably between about 25 % and 250 % of the established human dosage . Where no human Compounds dosage is established , as will be the case for newly - discov - 65 Some embodiments disclosed herein relate to a compound ered pharmaceutical compositions , a suitable human dosage selected from Formula ( I ) , Formula ( II ) and Formula ( III ) , or can be inferred from ED50 or ID50 values , or other appro - a pharmaceutically acceptable salt of the foregoing :

17 US 9 , 815 , 864 B2

18 an optionally substituted N - linked amino acid and an option ally substituted N - linked amino acid ester derivative ; RIC and R2C can be independently selected from O " , OH , an optionally substituted C1 - 6 alkoxy ,

( 1 ) Raal Raa2

R140 BA 5 R24 . 1 . KummyR *

H RSA

Illll SR°C R100 R3 R44 RIC m

( II ) BIB 10

0 R2Bm . 2B m . O . . . TH S R120 R13CO zlB = P

RII R38 www R14C

210 RIB 15 men RIC R70 R15C2

- R8C w

BC B Cac BIC B O 20

RS HC 2 . II?

H ROC an optionally substituted N - linked amino acid and an option ally substituted N - linked amino acid ester derivative ; or RIC can be R4 R5C

LE + an

NA - JEN R640 = A 840 - R104

ORTA RYA and RIIA

wherein : B14 , B1B and B1C can be independently an option - 25 O OH 1 ally substituted heterocyclic base or an optionally substi tuted heterocyclic base with a protected amino group ; Raal R16C0 — P - o + P - 0 + and Raa2 can be independently hydrogen or deuterium ; R4 OR170 L OR 18C can be hydrogen , deuterium , an unsubstituted C1 - z alkyl , an unsubstituted C2 - 4 alkenyl , an unsubstituted C2 - 3 alkynyl or 30 cyano ; RlA can be selected from hydrogen , an optionally and R2C can be o or OH ; R2B and R3C can be independently substituted acyl , an optionally substituted O - linked amino selected from halogen , an optionally substituted C1 - 6 alkyl , acid , an optionally substituted C2 - 6 alkenyl , an optionally substi

tuted C2 - 6 alkynyl , an optionally substituted 0 C1 - 6 35 alkyl , an optionally substituted 0 C3 - 6 alkenyl , an

optionally substituted - 0 _ C3 - 6 alkynyl , an optionally sub stituted C3 - 6 cycloalkyl and cyano ; R4C can be selected from OH , OC ( O ) R " and an optionally substituted O - linked amino acid ; R44 , R3B and RSC can be independently selected

40 from hydrogen , halogen , ORD , an optionally substituted O - linked amino acid , azido and NR2DR3D ; RID can be

R24 can be selected from hydrogen , halogen , azido , an hydrogen or C ( O ) R " D ; R2D and R3D can be indepen optionally substituted C1 - 6 alkyl , an optionally substituted dently hydrogen or an optionally substituted C1 - 6 alkyl ; RS4 , C2 - 6 alkenyl , an optionally substituted C2 - 6 alkynyl , an RS and RºC can be independently selected from hydrogen , optionally substituted Cz . cycloalkyl , an optionally substi - 45 halogen , an optionally substituted C1 - 6 alkyl , an optionally tuted O - C1 - 6 alkyl , an optionally substituted O _ C3 . 6 . substituted C2 - 6 alkenyl and an optionally substituted C2 - 6 alkenyl , an optionally substituted O _ C3 - 6 alkynyl and alkynyl ; RØA , R74 and R8A can be independently selected cyano ; R34 can be selected from halogen , OH , OCEO ) from absent , hydrogen , an optionally substituted C1 - 24 alkyl , R " 4 and an optionally substituted O - linked amino acid ; R1B an optionally substituted C2 - 24 alkenyl , an optionally sub can be selected from 0 - , OH , an optionally substituted C1 - 6 sostituted C2 - 24 alkynyl , an optionally substituted C3 - 6 alkoxy , cycloalkyl , an optionally substituted C3 - 6 cycloalkenyl , an

optionally substituted aryl , an optionally substituted het eroaryl , an optionally substituted aryl ( C1 - 6 alkyl ) , an option

R5B R6B ally substituted * ( CR1SAR164 ) , 0 C1 - 24 alkyl , an se optionally substituted * _ ( CR174R184 ) 0 - C , w alkenvl . 1 - 24

min R194 R204 s R224 R23A O

R & B ROBO $ min R214 R244 - R 10B mi o 741 50 220 XXXX Hortik yoshlar mm mm RIIBI RIB2 R 2542

65 vi W1

US 9 , 815 , 864 B2 19 20

- R284 and

mm R294

10

O

=

A

ORIO OR Jm

- continued R2541 , R2542 , R294 , R11B1 , R11B2 , R15C1 and R1502 can be independently selected from hydrogen , an optionally sub stituted C1 - 24 alkyl and an optionally substituted aryl ; R16C , R17C and R18C can be independently absent or hydrogen ;

5 R264 and R274 can be independently C = N or an option ally substituted substituent selected from C2 - 3 organylcar

R264 R274 bonyl , C2 - 8 alkoxycarbonyl and C2 - 8 organylaminocarbonyl ; R284 can be selected from hydrogen , an optionally substi

or RÓA can be tuted C1 - 24 - alkyl , an optionally substituted C2 - 24 alkenyl , an optionally substituted C2 - 24 alkynyl , an optionally substi tuted Cz - cycloalkyl and an optionally substituted C3 - 6 cycloalkenyl ; R304 and R314 can be independently selected from hydrogen , an optionally substituted C1 - 24 - alkyl , an

R1240 15 optionally substituted C2 - 24 alkenyl , an optionally substi tuted C2 - 24 alkynyl , an optionally substituted C3 - 6 cycloalkyl and an optionally substituted C3 - 6 cycloalkenyl ; for Formula ( III ) , - - - - - - - can be a single bond or a double bond ;

and R74 can be absent or hydrogen ; or R64 and R74 can be when - - - - - - - is a single bond , each R7C and each R & C can be taken together to form a moiety selected from an optionally independently hydrogen or halogen ; and when - - - - - - - is a substituted double bond , each R7C is absent and each R & C can be

independently hydrogen or halogen ; R " 4 , R " C and R " P can be independently an optionally substituted C1 - 24 - alkyl ; d , j and h can be independently 1 or 2 ; el , kl and wl can be

25 independently 0 or 1 ; e2 , k2 and w2 can be independently 3 , 4 or 5 ; m and n can be independently 0 or 1 ; p and q can be independently selected from 1 , 2 and 3 ; r can be 1 or 2 ; and Z14 , 224 , 234 , 244 , z1B , Z2B and zic can be independently

and an optionally substituted O or S . 30 In some embodiments , the compound can be a compound

of Formula ( I ) , or a pharmaceutically acceptable salt thereof , wherein : BlA can be an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with a protected amino group ; Raal and Raa2 can be independently hydrogen or deuterium ; R4 can be hydrogen , deuterium , an unsubstituted C1 - z alkyl , an unsubstituted C2 - 4 alkenyl , an

wherein the oxygens connected to R6A and R74 , the phos - unsubstituted Co , alkynyl or cyano ; R1A can be selected phorus and the moiety form a six - membered to ten - mem from hydrogen , bered ring system ; R94 can be independently selected from an optionally substituted C1 - 24 alkyl , an optionally substi tuted C2 - 24 alkenyl , an optionally substituted C2 - 24 alkynyl , an optionally substituted C3 - 6 cycloalkyl , an optionally sub

R640 P R840 — P and stituted C3 - 6 cycloalkenyl , NR304R314 an optionally substi R10A — P

tuted N - linked amino acid and an optionally substituted R1143 N - linked amino acid ester derivative ; R104 and RlA can be us independently an optionally substituted N - linked amino acid or an optionally substituted N - linked amino acid ester R24 can be selected from hydrogen , halogen , an optionally derivative ; R124 , R134 and R144 can be independently absent substituted C1 - 6 alkyl , an optionally substituted C2 - 4 alkenyl , or hydrogen ; each R154 , each R 164 , each R174 and each R184 an optionally substituted C2 alkynyl , an optionally substi can be independently hydrogen , an optionally substituted 50 tuted - 0 C1 - 6 alkyl , an optionally substituted - 0 C3 - 6 C - 24 alkyl or alkoxy ; R194 , R204 , R224 , R234 , R5B , RB , R & B , RB , R°C , RIOC , ?12C and Ri3C can be independently alkenyl , an optionally substituted O - C3 - 6 alkynyl and

cyano ; R34 is halogen , OH , OC ( O ) R " A and an option selected from hydrogen , an optionally substituted C1 - 24 alkyl ally substituted O - linked amino ; R44 can be selected from and an optionally substituted aryl ; R214 , R244 , R7B , R10L hydrogen , halogen , ORD , an optionally substituted Rlic and R14C can be independently selected from hydro 0 - 55 O - linked amino acid , azido and NR2DR3D ; RID can be gen , an optionally substituted C1 - 24 alkyl , an optionally hydrogen or C ( = O ) R " D ; R2D and R3D can be indepen substituted aryl , an optionally substituted 0 - 01 - 24 alkyl , dently hydrogen or an optionally substituted C1 - 6 alkyl ; RSA an optionally substituted O - aryl , an optionally substituted can be selected from hydrogen , halogen , an optionally - O - heteroaryl , an optionally substituted O - monocyclic substituted C1 - 6 alkyl , an optionally substituted C2 - 6 alkenyl heterocyclyl and 60 and an optionally substituted C2 - 6 alkynyl ; R6A , R14 and RSA can be independently selected from absent , hydrogen , an optionally substituted C1 - 24 alkyl , an optionally substituted C2 - 24 alkenyl , an optionally substituted C2 - 24 alkynyl , an optionally substituted C3 - 6 cycloalkyl , an optionally substi

65 tuted C3 - 6 cycloalkenyl , an optionally substituted aryl , an optionally substituted heteroaryl , an optionally substituted aryl ( C1 - 6 alkyl ) , an optionally substituted * — ( CR154R164 )

14

- NA - - - win RIAS 45 ORA

Iyo w

21 alkyl , an optionally

* ( CRIŽAR184 ) , 0 C1 - 24 alkenyl , V1 - 24

US 9 , 815 , 864 B2 22

substituted can be independently hydrogen , an optionally substituted C1 - 24 alkyl or alkoxy ; R194 , R204 , R224 and R234 can be independently selected from hydrogen , an optionally sub stituted C1 - 24 alkyl and an optionally substituted aryl ; R214

5 and R244 can be independently selected from hydrogen , an optionally substituted C1 - 24 alkyl , an optionally substituted aryl , an optionally substituted — O _ C1 - 24 alkyl , an option ally substituted O - aryl , an optionally substituted - O heteroaryl , an optionally substituted - O - monocyclic het erocyclyl and

R19A R204 R22 R234 0 ww RIA R244

R2541 www tot 15 R284 ma Kaltri O 1 s R2542 R254 R264 R27A and and

20

m

R294

or R64 can be

R254 , R2542 and R294 can be independently selected from hydrogen , an optionally substituted C1 - 24 alkyl and an optionally substituted aryl ; R264 and R274 can be indepen dently C = N or an optionally substituted substituent selected from C2 - 8 organylcarbonyl , C2 - 8 alkoxycarbonyl and C2 - 8 organylaminocarbonyl ; R284 can be selected from hydrogen , an optionally substituted C1 - 24 - alkyl , an option ally substituted C2 - 24 alkenyl , an optionally substituted C2 - 24 alkynyl , an optionally substituted C3 - 6 cycloalkyl and an optionally substituted C3 - 6 cycloalkenyl ; R304 and R314 can be independently selected from hydrogen , an optionally substituted C1 - 24 - alkyl , an optionally substituted C2 - 24 alk enyl , an optionally substituted C2 - 24 alkynyl , an optionally substituted Cz , cycloalkyl and an optionally substituted C3 - 6 cycloalkenyl ; R " 4 and R " D can be independently an optionally substituted C1 - 94 - alkyl ; h can be 1 or 2 ; w1 can be O or 1 ; w2 can be 3 , 4 or 5 ; m can be 0 or 1 ; p and q can be independently selected from 1 , 2 and 3 ; r can be 1 or 2 ; and ZA , Z - 4 , Z A and Z44 can be independently O or S .

In some embodiments , a compound of Formula ( 1 ) can have a structure shown herein , provided that when R14 is

30

R1240 - P 11h - + 0 - P

OR13A OR 14AS

and R7A can be absent or hydrogen ; or R64 and R74 can be taken together to form a moiety selected from an optionally substituted

40

JEN R8407 R9A 3 45

and an optionally substituted wherein R & A is an unsubstituted C - 4 alkyl or phenyl option ally para - substituted with a halogen or methyl and R94 is methyl ester , ethyl ester , isopropyl ester , n - butyl ester ,

50 benzyl ester or phenyl ester of an amino acid selected from glycine , alanine , valine , leucine , phenylalanine , tryptophan , methionine and proline ; R34 is OH ; R44 is fluoro ; R34 is fluoro or hydrogen ; and B14 is an unsubstituted uracil ; then R24 cannot be — OCHz . In some embodiments , a compound

wherein the oxygens connected to R6A and R74 , the phos - 55 of Formula ( 1 ) can have a structure shown herein , provided phorus and the moiety form a six - membered to ten - mem - that when R14 is H ; R34 is OH ; R44 is fluoro ; RSA is fluoro ; bered ring system ; R94 can be independently selected from and B14 is an unsubstituted cytosine ; then R24 cannot be an optionally substituted C1 - 24 alkyl , an optionally substi allenyl . In some embodiments , a compound of Formula ( 1 ) tuted C2 - 24 alkenyl , an optionally substituted C2 - 24 alkynyl , can have a structure shown herein , provided that when R14 an optionally substituted C3 - 6 cycloalkyl , an optionally sub - 60 is H ; R34 is OH ; R44 is fluoro ; R54 is hydrogen ; and B14 is stituted C3 - 6 cycloalkenyl , NR304R314 , an optionally substi an unsubstituted thymine ; then R24 cannot be C , alkyl tuted N - linked amino acid and an optionally substituted substituted with an N - amido ( for example , — NC O CF2 ) . N - linked amino acid ester derivative ; R104 and R114 can be In some embodiments , a compound of Formula ( I ) can have independently an optionally substituted N - linked amino acid a structure shown herein , provided that when R14 is H ; R34 or an optionally substituted N - linked amino acid ester 65 is OH ; R44 is fluoro ; RSA is fluoro ; and BA is an unsubsti derivative ; R124 , R134 and R 144 can be independently absent tuted cytosine ; then R24 cannot be ethynyl . In some embodi or hydrogen ; each R154 , each R16A , each R174 and each R184 ments , R24 cannot be hydrogen . In some embodiments ,

US 9 , 815 , 864 B2 23 24

10 - 11 OR7A .

when R24 is hydrogen , then RS4 can be selected from ( for example , benzoxy ) . In some embodiments , p can be 1 . halogen , an optionally substituted C1 - 6 alkyl , an optionally In other embodiments , p can be 2 . In still other embodi substituted C2 - 6 alkenyl and an optionally substituted C2 - 6 ments , p can be 3 . alkynyl . In some embodiments , at least one of RÓA and R74 can be In some embodiments , R14 can be * % ( CR174R184 ) , 0 - C2 - 24 alkenyl . In other embodi

ments , R64 and R74 can be both * — ( CR174R184 ) , C2 - 24 alkenyl . In some embodiments , each R174 and each R184 can be hydrogen . In other embodiments , at least one of

R640 — P 10 R174 and R 184 can be an optionally substituted C1 - 24 alkyl . In some embodiments , q can be 1 . In other embodiments , q can be 2 . In still other embodiments , q can be 3 . When at least one of R64 and R74 is * — ( CR154R164 ) , 0 C1 - 24

In some embodiments , R64 and R 74 can be both hydrogen . alkyl or * % ( CR174R184 ) , O _ C2 - 24 alkenyl , the C1 - 24 In other embodiments , RÓA and R74 can be both absent . In 15 alkyl can be selected from caprylyl , capryl , lauryl , myristyl , still other embodiments , at least one R64 and R74 can be palmityl , stearyl , arachidyl , behenyl , lignoceryl , and cerotyl , absent . In yet still other embodiments , at least one R?A and and the C2 - 24 alkenyl can be selected from myristoleyl , R 4 can be hydrogen . Those skilled in the art understand that palmitoleyl , sapienyl , oleyl , elaidyl , vaccenyl , linoleyl , a - li when RÓA and / or R74 are absent , the associated oxygen ( s ) nolenyl , arachidonyl , eicosapentaenyl , erucyl and docosa will have a negative charge . For example , when R4 is 20 hexaenyl . absent , the oxygen associated with R64 will have a negative In some embodiments , when R14 is charge . In some embodiments , ZlA can be O ( oxygen ) . In other embodiments , Zl4 can be S ( sulfur ) . In some embodi ments , R14 can be a monophosphate . In other embodiments , R14 can be a monothiophosphate .

In some embodiments , when R14 is R640 — P UN OR

JEN 30 R640 — P at least one of RÓA and R74 can be selected from

? ORA

R21A walan XXoy R24A and min

w - R28A

R194 R204 one of RÓA and R7A can be hydrogen , and the other of RA 35 and R74 can be selected from an optionally substituted C1 - 24 alkyl , an optionally substituted C2 - 24 alkenyl , an optionally substituted C2 - 24 alkynyl , an optionally substituted C3 - 6 cycloalkyl , an optionally substituted C3 - 6 cycloalkenyl , an R22A R23A optionally substituted aryl , an optionally substituted het - 40 eroaryl and an optionally substituted aryl ( C1 - 6 alkyl ) . In some embodiments , one of RA and R74 can be hydrogen , and the other of RA and R7A can be an optionally substituted C1 - 24 alkyl . In other embodiments , both RÓA and R74 can be independently selected from an optionally substituted C1 - 24 alkyl , an optionally substituted C2 - 24 alkenyl , an optionally substituted C2 - 24 alkynyl , an optionally substituted C3 - 6 R26A R271 cycloalkyl , an optionally substituted C3 - 6 cycloalkenyl , an optionally substituted aryl , an optionally substituted het - 50 eroaryl and an optionally substituted aryl ( C - alkyl ) . In and the other of RÓA and R74 can be selected from absent , some embodiments , both RØA and R74 can be an optionally hydrogen , an optionally substituted C1 - 24 alkyl , an option substituted C1 - 24 alkyl . In other embodiments , both R64 and ally substituted C2 - 24 alkenyl , an optionally substituted C2 - 24 R74 can be an optionally substituted C2 - 24 alkenyl . In some alkynyl , an optionally substituted C3 - 6 cycloalkyl , an option embodiments , R6A and R74 can be independently an option - 55 ally substituted C3 - 6 cycloalkenyl , an optionally substituted ally substituted version of the following : myristoleyl , myri aryl , an optionally substituted heteroaryl and an optionally styl , palmitoleyl , palmityl , sapienyl , oleyl , elaidyl , vaccenyl , substituted aryl ( C1 - 6 alkyl ) . linoleyl , a - linolenyl , arachidonyl , eicosapentaenyl , erucyl , In some embodiments , at least one of R64 and R74 can be docosahexaenyl , caprylyl , capryl , lauryl , stearyl , arachidyl , behenyl , lignoceryl , and cerotyl .

In some embodiments , at least one of R64 and R74 can be R 194 R204 s R224 R23A O * _ ( CR154R164 ) . – O C . 34 alkyl . In other embodiments , R6A and R74 can be both * _ ( CR154R164 ) , - 0 - 01 - 24 R21A or X

24A alkyl . In some embodiments , each R154 and each R164 can be hydrogen . In other embodiments , at least one of R154 and 65 R164 can be an optionally substituted C1 - 24 alkyl . In other embodiments , at least one of R15A and R164 can be an alkoxy

R 24A - - 8 mi mi o

25 US 9 , 815 , 864 B2

26 In some embodiments , both R64 and R74 can be R224 and R234 can be independently selected from hydrogen ,

an optionally substituted C1 - 24 alkyl and an optionally sub stituted aryl ; R244 can be independently selected from

R194 R204 hydrogen , an optionally substituted C1 - 24 alkyl , an option C R214 5 ally substituted aryl , an optionally substituted 0 C1 - 24

alkyl , an optionally substituted — O - aryl , an optionally substituted O - heteroaryl , an optionally substituted - O monocyclic heterocyclyl and

When one or both of R64 and R74 are

drogen , an oparyl , an optionad 40 - aryl , an tuled man O = 0 10

R 194 R20A man tot w C R214 ,

and Z44 can be independently O ( oxygen ) or S ( sulfur ) . In some embodiments , R224 and R234 can be hydrogen . In other

R19A and R204 can be independently selected from hydrogen , embodiments , at least one of R4A and R SA can be an an optionally substituted C , alkyl and an optionally sub - 20 optionally substituted C1 - 24 alkyl or an optionally substituted stituted aryl ; and R214 can be selected from hydrogen , an aryl . In some embodiments , R244 can be an optionally optionally substituted C1 - 24 alkyl , an optionally substituted substituted C1 - 24 alkyl . In other embodiments , R244 can be aryl , an optionally substituted O C 24 alkyl , an option an optionally substituted aryl . In still other embodiments , ally substituted O - aryl , an optionally substituted 0 - 25 R244 can be an optionally substituted O - C1 - 24 alkyl , an heteroaryl , an optionally substituted O - monocyclic het optionally substituted - O - aryl , an optionally substituted erocyclyl and - O - heteroaryl or an optionally substituted O - monocyclic

heterocyclyl . In yet still other embodiments , R244 can be

30 mw tot 11

ma ' In some embodiments , R194 and R204 can be hydrogen . In 35 other embodiments , at least one of R194 and R204 can be an In some embodiments , h can be 1 . In other embodiments , h optionally substituted C1 - 24 alkyl or an optionally substituted aryl . In some embodiments , R214 can be an optionally can be 2 . In some embodiments , Z44 can be O ( oxygen ) . In substituted C1 - 24 alkyl . In other embodiments , R214 can be other embodiments , Z44 can be or S ( sulfur ) . In some an optionally substituted aryl . In still other embodiments , 40 embodiments , one or both of RÓA and R74 can be isopropy R21A can be an optionally substituted - O _ C1 - 24 alkyl , an loxycarbonyloxymethyl . In some embodiments , one or both optionally substituted — O - aryl , an optionally substituted of R64 and R74 can be pivaloyloxymethyl . In some embodi - O - heteroaryl or an optionally substituted - O - monocyclic ments , R64 and R74 can be both a isopropyloxycarbony heterocyclyl . In yet still other embodiments , R214 can be loxymethyl group , and form a bis ( isopropyloxycarbony

loxymethyl ) ( bis ( POC ) ) prodrug . In some embodiments , R64 and R74 can be both a pivaloyloxymethyl group , and form a bis ( pivaloyloxymethyl ) ( bis ( POM ) ) prodrug .

In some embodiments , both R64 and R74 can be mm Vynot 50

In some embodiments , both R6A and R74 can be R284 man R22A R23A O 55

R24A mi o 744 to R264 R27A

When one or both of R64 and R74 are

R22A R234 0 XXL mm wherein R264 and R274 can be independently C = N or an optionally substituted substituent selected from C2 - 8 orga nylcarbonyl , C2 - 8 alkoxycarbonyl and C2 - 8 organylamin ocarbonyl ; R284 can be selected from hydrogen , an option ally substituted C1 - 24 - alkyl , an optionally substituted C2 - 24

65 alkenyl , an optionally substituted C2 - 24 alkynyl , an option ally substituted C3 - 6 cycloalkyl and an optionally substituted C3 - 6 cycloalkenyl ; and r can be 1 or 2 . Example of

R244

US 9 , 815 , 864 B2

27 28 - çontinued

OCH2CH3 R284

wan mo OCH2CH3 .

R264 R274 H3C

include , but are not limited to the following : 10

man H3 - OCH3

- OCH3 , NFC , - OCH3 noz H3C

In some embodiments , R64 and R74 can be both an optionally substituted aryl . In some embodiments , at least one of RA and R7A can be an optionally substituted aryl . For

15 example , both RÓA and R74 can be an optionally substituted phenyl or an optionally substituted naphthyl . When substi tuted , the substituted aryl can be substituted with 1 , 2 , 3 or more than 3 substituents . When more the two substituents are present , the substituents can be the same or different . In

20 some embodiments , when at least one of RÓA and R74 is a substituted phenyl , the substituted phenyl can be a para - , ortho - or meta - substituted phenyl .

In some embodiments , R64 and R74 can be both an optionally substituted aryl ( C - 6 alkyl ) . In some embodi ments , at least one of RÓA and R74 can be an optionally substituted aryl ( C1 - 6 alkyl ) . For example , both R64 and R74 can be an optionally substituted benzyl . When substituted , the substituted benzyl group can be substituted with 1 , 2 , 3 or more than 3 substituents . When more the two substituents are present , the substituents can be the same or different . In

30 some embodiments , the aryl group of the aryl ( C1 - 6 alkyl ) can be a para - , ortho - or meta - substituted phenyl .

In some embodiments , R64 and R74 can be both

CH3 mu w - CH3

- CH3 , NE NHCH2CH3 , H3C

35 NE CH3 ,

mino Hul 40 * In some embodiments , at least one of R64 and R74 can be

45 - CH3 wa s R2541

On - CH3 ,

- OCH2CH3

In some embodiments , R2541 can be hydrogen . In other 50 embodiments , R2541 can be an optionally substituted C - 24

alkyl . In still other embodiments , R2541 can be an optionally substituted aryl . In some embodiments , R2541 can be a C1 . 6 alkyl , for example , methyl , ethyl , n - propyl , isopropyl , n - bu tyl , isobutyl , tert - butyl , pentyl ( branched and straight chained ) and hexyl ( branched and straight - chained ) . In some embodiments , wl can be 0 . In other embodiments , wl can be 1 . In some embodiments , RA and R7A can be both a S - acylthioethyl ( SATE ) group and form a SATE ester pro drug .

60 In some embodiments , R64 and R74 can be both

OCH2CH3 , H3C

- OCH2CH3

too - OCH CH , and ma 65 w2s R2542

mm

US 9 , 815 , 864 B2 29 30

In some embodiments , at least one of R64 and R74 can be some embodiments , m can be 0 , and R74 , R124 and R134 can be independently absent or hydrogen . In other embodiments , m can be 1 , and R74 , R124 , R134 and R144 can be indepen dently absent or hydrogen . Those skilled in the art under

5 stand that when m is 0 , R64 can be diphosphate , when Z14 is oxygen , or an alpha - thiodiphosphate , when Z14 is sulfur . Ww2 s R2542 . Likewise , those skilled in the art understand that when m is 1 , RÓA can be triphosphate , when Z14 is oxygen , or an

In some embodiments , R25A2 can be hydrogen . In other alpha - thiotriphosphate , when Z ' * is sulfur . embodiments , R2542 can be an optionally substituted C1 - 24 10 In some embodiments , R64 and R74 can be taken together alkyl . In still other embodiments , R2542 can be an optionally to form an optionally substituted substituted aryl , for example , an optionally substituted phe nyl . In some embodiments , R2542 can be an optionally substituted C1 - 6 alkyl . In some embodiments , R2542 can be an unsubstituted C1 - 6 alkyl . In some embodiments , w2 can 15 be 3 . In other embodiments , w2 can be 4 . In still other embodiments , w2 can be 5 .

In some embodiments , R64 and R74 can be both For example , R14 can be an optionally substituted 20

N

=

mm 25

R294

In some embodiments , at least one of R64 and R74 can be When substituted , the ring can be substituted 1 , 2 , 3 or 3 or more times . When substituted with multiple substituents , the

30 substituents can be the same or different . In some embodi ments , when R1A is

35 mm R 29A

In some embodiments , R294 can be hydrogen . In other embodiments , R294 can be an optionally substituted C1 . 34 " the ring can be substituted with an optionally substituted aryl alkyl . In some embodiments , R294 can be a C1 - 4 alkyl , such group and / or an optionally substituted heteroaryl . An as methyl , ethyl , n - propyl , iso - propyl , n - butyl , iso - butyl and example of a suitable heteroaryl is pyridinyl . In some t - butyl . In still other embodiments , R294 can be an optionally embodiments , R A and R ' A can be taken together to form an substituted aryl , such as an optionally substituted phenyl or optionally substituted an optionally substituted naphthyl . In some embodiments , R6A and R7A can be both a dioxolenone group and form a dioxolenone prodrug .

In some embodiments , R ' A can be 50

10 JEN such as R640 — P

ORTA s 55 R32A

R6A can be

60 = mm -

A R1240 — P - TO - P -

OR 134 | OR 144 , 3 ;

wherein R324 can be an optionally substituted aryl , an optionally substituted heteroaryl or an optionally substituted heterocyclyl . In some embodiments , R64 and R74 can form a cyclic 1 - aryl - 1 , 3 - propanyl ester ( Hep Direct ) prodrug moi

65 ety . In some embodiments , R64 and R74 can be taken together

to form an optionally substituted R74 can be absent or hydrogen ; R124 , R134 and R144 can be independently absent or hydrogen ; and m can be 0 or 1 . In

US 9 , 815 , 864 B2 31 32

10

C1 - 6 alkyls include methyl , ethyl , n - propyl , isopropyl , n - bu tyl , isobutyl , tert - butyl , pentyl ( branched and straight chained ) and hexyl ( branched and straight - chained ) . In other embodiments , R8A can be hydrogen , and R94 can be

5 NR304R314 , wherein R30 and R31 can be independently selected from hydrogen , an optionally substituted C1 - 24

wherein the oxygens connected to R6A and R74 , the phos - alkyl , an optionally substituted C2 - 24 alkenyl , an optionally phorus and the moiety form a six - membered to ten - mem substituted C2 - 24 alkynyl , an optionally substituted C3 - 6 bered ring system . Example of an optionally substituted cycloalkyl and an optionally substituted C3 - 6 cycloalkenyl .

In some embodiments , R8A can be absent or hydrogen ; and R94 can be an optionally substituted N - linked amino acid or an optionally substituted N - linked amino acid ester derivative . In other embodiments , R8A can be an optionally substituted aryl ; and R9A can be an optionally substituted N - linked amino acid or an optionally substituted N - linked amino acid ester derivative . In still other embodiments , RSA

include can be an optionally substituted heteroaryl ; and R94 can be an optionally substituted N - linked amino acid or an option ally substituted N - linked amino acid ester derivative . In some embodiments , R94 can be selected from alanine , asparagine , aspartate , cysteine , glutamate , glutamine , gly cine , proline , serine , tyrosine , arginine , histidine , isoleucine , leucine , lysine , methionine , phenylalanine , threonine , tryp

25 tophan , valine and ester derivatives thereof . Examples of an optionally substituted N - linked amino acid ester derivatives

CO2CH3 include optionally substituted versions of the following : alanine isopropyl ester , alanine cyclohexyl ester , alanine neopentyl ester , valine isopropyl ester and leucine isopropyl

sester . In some embodiments , R94 can have the structure

CH3

*

and

*

R3340 R344 R354

35 HN - ?

72A

wherein R334 can be selected from hydrogen , an optionally 40 substituted C1 - 6 - alkyl , an optionally substituted C3 - 6

cycloalkyl , an optionally substituted aryl , an optionally In some embodiments , Rº ̂ and R ' ̂ can form a cyclosalig - substituted aryl ( C , alkyl ) and an optionally substituted enyl ( cycloSal ) prodrug . haloalkyl ; R344 can be selected from hydrogen , an optionally

In some embodiments , Rº4 and R ' ̂ can be the same . In substituted C , alkyl , an optionally substituted C . some embodiments , RÓA and R7A can be different . 45 haloalkyl , an optionally substituted C2 . 6 cycloalkyl , an

In some embodiments , Z14 can be oxygen . In other optionally substituted C aryl , an optionally substituted C10 embodiments , Z14 can be sulfur . aryl and an optionally substituted aryl ( C . alkyl ) ; and R35

In some embodiments , R14 can be can be hydrogen or an optionally substituted C - 4 - alkyl ; or R344 and R354 can be taken together to form an optionally

50 substituted Cz - cycloalkyl . When R344 is substituted , R344 can be substituted with

one or more substituents selected from N - amido , mercapto , R840 — P alkylthio , an optionally substituted aryl , hydroxy , an option

ally substituted heteroaryl , O - carboxy and amino . In some 55 embodiments , R344 can be an unsubstituted C1 - 6 - alkyl , such

as those described herein . In some embodiments , R344 can In some embodiments , R8A can be selected from absent , be hydrogen . In other embodiments , R344 can be methyl . In hydrogen , an optionally substituted C1 - 24 alkyl , an option - some embodiments . R33A can be an optionally substituted ally substituted C2 - 24 alkenyl , an optionally substituted C2 - 24 C alkyl . Examples of optionally substituted Cic - alkyls alkynyl , an optionally substituted C3 - 6 cycloalkyl and an 60 include optionally substituted variants of the following : optionally substituted C2 - 6 cycloalkenyl ; and R ' A can be methyl , ethyl , n - propyl , isopropyl , n - butyl , isobutyl , tert independently selected from an optionally substituted C1 - 24 butyl , pentyl ( branched and straight - chained ) and hexyl alkyl , an optionally substituted C2 - 24 alkenyl , an optionally ( branched and straight - chained ) . In some embodiments , substituted C2 - 24 alkynyl , an optionally substituted C3 - 6 R334 can be methyl or isopropyl . In some embodiments , cycloalkyl and an optionally substituted C3 - 6 cycloalkenyl . 65 R334 can be ethyl or neopentyl . In other embodiments , R334

In some embodiments , R84 can be hydrogen , and R94 can can be an optionally substituted C3 - 6 cycloalkyl . Examples be an optionally substituted C1 - 6 alkyl . Examples of suitable of optionally substituted C3 - 6 cycloalkyl include optionally

mimi RYA

US 9 , 815 , 864 B2 33 34

HN

25

NA 30 18A

RIA

substituted variants of the following : cyclopropyl , cyclobu - dine , isoleucine , leucine , lysine , methionine , phenylalanine , tyl , cyclopentyl , and cyclohexyl . In an embodiment , R334 threonine , tryptophan , valine and ester derivatives thereof . can be an optionally substituted cyclohexyl . In still other In some embodiments , R104 and R114 can be an optionally embodiments , R334 can be an optionally substituted aryl , substituted version of the following : alanine isopropyl ester , such as phenyl and naphthyl . In yet still other embodiments , 5 alanine cyclohexyl ester , alanine neopentyl ester , valine R334 can be an optionally substituted aryl ( C1 - 6 alkyl ) . In isopropyl ester and leucine isopropyl ester . In some embodi some embodiments , R334 can be an optionally substituted ments , R104 and R114 can independently have the structure benzyl . In some embodiments , R334 can be an optionally substituted C1 - 6 haloalkyl , for example , CF3 . In some embodiments , R35A can be hydrogen . In other embodiments , 10 R3640 R37A R384 R35A can be an optionally substituted C1 - 4 - alkyl , such as methyl , ethyl , n - propyl , isopropyl , n - butyl , isobutyl and tert - butyl . In an embodiment , R35A can be methyl . In some embodiments , R344 and R35A can be taken together to form 15 an optionally substituted C3 - 6 cycloalkyl . Examples of optionally substituted C3 - 6 cycloalkyl include optionally wherein R364 can be selected from hydrogen , an optionally substituted variants of the following : cyclopropyl , cyclobu substituted C1 - 6 - alkyl , an optionally substituted C3 - 6 tyl , cyclopentyl , and cyclohexyl . Depending on the groups cycloalkyl , an optionally substituted aryl , an optionally that are selected for Rº ̂ and Rº * , the carbon to which Rº * * 20 substituted aryl ( C . alkyl ) and an optionally substituted and RVA are attached may be a chiral center . In some haloalkyl ; R374 can be selected from hydrogen , an optionally embodiment , the carbon to which R344 and R354 are attached substituted C1 - 6 alkyl , an optionally substituted C1 - 6 may be a ( R ) - chiral center . In other embodiments , the carbon haloalkyl , an optionally substituted C3 - 6 cycloalkyl , an to which R344 and R354 are attached may be a ( S ) - chiral optionally substituted Co aryl , an optionally substituted C10 center . aryl and an optionally substituted aryl ( C1 - 6 alkyl ) ; and R38A In some embodiments , when R14 is can be hydrogen or an optionally substituted C1 - 4 - alkyl ; or

R374 and R384 can be taken together to form an optionally substituted C3 - 6 cycloalkyl . When R374 is substituted , R374 can be substituted with

one or more substituents selected from N - amido , mercapto , alkylthio , an optionally substituted aryl , hydroxy , an option ally substituted heteroaryl , O - carboxy and amino . In some embodiments , R374 can be an unsubstituted C1 - 6 - alkyl , such Z24 can be O ( oxygen ) . In other embodiments , when RlA is 18 35 as those described herein . In some embodiments , R374 can be hydrogen . In other embodiments , R37A can be methyl . In some embodiments , R364 can be an optionally substituted C1 - 6 alkyl . Examples of optionally substituted C1 - 6 - alkyls

R840 include optionally substituted variants of the following : 40 methyl , ethyl , n - propyl , isopropyl , n - butyl , isobutyl , tert

butyl , pentyl ( branched and straight - chained ) and hexyl ( branched and straight - chained ) . In some embodiments ,

Z24 can be S ( sulfur ) . In some embodiments , when R14 is R36A can be methyl or isopropyl . In some embodiments , R364 can be ethyl or neopentyl . In other embodiments , R364

45 can be an optionally substituted Cz _ cycloalkyl . Examples of optionally substituted Cz , cycloalkyl include optionally

R840 — P substituted variants of the following : cyclopropyl , cyclobu tyl , cyclopentyl , and cyclohexyl . In an embodiment , R364

R9A5 can be an optionally substituted cyclohexyl . In still other 50 embodiments , R36A can be an optionally substituted aryl ,

such as phenyl and naphthyl . In yet still other embodiments , a compound of Formula ( 1 ) can be a phosphoramidate R364 can be an optionally substituted aryl ( C . , alkyl ) . In prodrug , such as an aryl phosphoramidate prodrug . some embodiments , R364 can be an optionally substituted In some embodiments , R1A can be benzyl . In some embodiments , R36A can be an optionally 55 substituted C1 - 6 haloalkyl , for example , CF3 . In some

embodiments , R384 can be hydrogen . In other embodiments , R38A can be an optionally substituted C - 4 - alkyl , such as methyl , ethyl , n - propyl , isopropyl , n - butyl , isobutyl and tert - butyl . In an embodiment , R38A can be methyl . In some

60 embodiments , R374 and R38A can be taken together to form an optionally substituted C3 - 6 cycloalkyl . Examples of

In some embodiments , R104 and R 14 can be both an optionally substituted C3 . 6 cycloalkyl include optionally optionally substituted N - linked amino acid or an optionally substituted variants of the following : cyclopropyl , cyclobu substituted N - linked amino acid ester derivative . In some tyl , cyclopentyl , and cyclohexyl . Depending on the groups embodiments , R10A and R114 can be independently selected 65 that are selected for R374 and R384 , the carbon to which R374 from alanine , asparagine , aspartate , cysteine , glutamate , and R384 are attached may be a chiral center . In some glutamine , glycine , proline , serine , tyrosine , arginine , histi embodiment , the carbon to which R374 and R384 are attached

NA R94

724 2017 E

R 10A - P -

R1143

US 9 , 815 , 864 B2 35

may be a ( R ) - chiral center . In other embodiments , the carbon to which R374 and R384 are attached may be a ( S ) - chiral center .

Examples of suitable

36 - continued

- H3C H = = 84 - 27

5 wire HN NH OG R3310 R344 R354 R3640 R37A R384

I

and © HN? 11111

H

N N

groups include the following :

and R3310 R34A R354 R3640 R37A R38A

NH Ó HN HN ? HN HN * xerant XX . MA R3302 R344 R354 R3640 R374 R384

HN HN

H3CO H3CO H3CH wenn weni HN mun HN

In some embodiments , R104 and R114 can be the same . In 30 some embodiments , R104 and R 14 can be different .

In some embodiments , Z3A can be O ( oxygen ) . In other embodiments , Z34 can be S ( sulfur ) . In some embodiments , when R14 is

H3CO HzCH 35

min HN R104 _ P man -

40 - O HZC H - O HC H

HN

liit

HN HN

?? , ??

HN ? ' ?? XXXT XXXXX

a compound of Formula ( 1 ) can be a phosphonic diamide prodrug .

In some embodiments , R14 can be hydrogen . In some 45 embodiments , R1A can be an optionally substituted acyl . In

other embodiments , R14 can be — CEO ) R394 , wherein R394 can be selected from an optionally substituted C . 12 alkyl , an optionally substituted C2 - 12 alkenyl , an optionally substituted C2 - 12 alkynyl , an optionally substituted C3 - 8

50 cycloalkyl , an optionally substituted C5 - 8 cycloalkenyl , an optionally substituted C6 - 10 aryl , an optionally substituted heteroaryl , an optionally substituted heterocyclyl , an option ally substituted aryl ( C1 - 6 alkyl ) , an optionally substituted heteroaryl ( C1 - 6 alkyl ) and an optionally substituted hetero

55 cyclyl ( C1 - 6 alkyl ) . In some embodiments , R394 can be a substituted C1 - 12 alkyl . In other embodiments , R394 can be an unsubstituted C1 - 12 alkyl . In still other embodiments , R394 can be an unsubstituted C2 - 12 alkyl . In yet still other embodiments , R394 can be an unsubstituted C2 - 6 alkyl .

60 In still other embodiments , R14 can be an optionally substituted O - linked amino acid . Examples of suitable O - linked amino acids include alanine , asparagine , aspartate , cysteine , glutamate , glutamine , glycine , proline , serine , tyrosine , arginine , histidine , isoleucine , leucine , lysine ,

65 methionine , phenylalanine , threonine , tryptophan and valine . Additional examples of suitable amino acids include , but are not limited to , ornithine , hypusine , 2 - aminoisobu

- OH L - H3C

HN # N non - 0 HgC H

. . . / m

^

HN winni HN

US 9 , 815 , 864 B2 37 38 38

include the following : following tyric acid , dehydroalanine , gamma - aminobutyric acid , cit - rulline , beta - alanine , alpha - ethyl - glycine , alpha - propyl - gly cine and norleucine . In some embodiments , the O - linked amino acid can have the structure

R 404 404 R41A ity ty ty ty

NH2 NH2 - 0 R404 R414

mm 10

NH2 NH2 , NH2 ,

IV * till

NH ,

tyyty mm and n

NH2

?

wherein R404 can be selected from hydrogen , an optionally substituted C1 - 6 alkyl , an optionally substituted C1 - 6 haloalkyl , an optionally substituted C3 - 6 cycloalkyl , an optionally substituted Co aryl , an optionally substituted C10

NH2 aryl and an optionally substituted aryl ( C1 - 6 alkyl ) ; and R414 can be hydrogen or an optionally substituted C1 - 4 - alkyl ; or R404 and R414 can be taken together to form an optionally substituted C3 - 6 cycloalkyl . Those skilled in the art under stand that when R14 is an optionally substituted O - linked NH2 amino acid , the oxygen of R140 of Formula ( I ) is part of the optionally substituted O - linked amino acid . For example , 25 when R1A is In some embodiments , R24 can be selected from an

optionally substituted C1 - 6 alkyl , an optionally substituted C2 - 6 alkenyl , an optionally substituted C2 - 6 alkynyl , an optionally substituted 0 C . alkyl , an optionally sub stituted 0 C3 - 6 alkenyl , an optionally substituted - 0 R404 R414 0 Cz . , alkynyl and cyano , and R34 can be selected from OH , OCCOR " A and an optionally substituted O - linked amino acid .

NH2 Various groups can be attached to the 4 ' - position of the pentose ring . In some embodiments , R24 can be hydrogen . In

35 other embodiments , R24 can be halogen , such as fluoro . In the oxygen indicated with “ * ” is the oxygen of R140 — of still other embodiments , R24 can be azido . In some embodi Formula ( I ) . ments , R24 can be an optionally substituted C1 - 6 alkyl . When R404 is substituted , R404 can be substituted with Examples of suitable C1 - 6 alkyls include methyl , ethyl ,

one or more substituents selected from N - amido , mercapto , n - propyl , isopropyl , n - butyl , isobutyl , tert - butyl , pentyl ' 40 ( branched and straight - chained ) and hexyl ( branched and alkylthio , an optionally substituted aryl , hydroxy , an option straight - chained ) . In some embodiments , R24 can be an

ally substituted heteroaryl , O - carboxy and amino . In some unsubstituted C1 - 6 alkyl . In other embodiments , R24 can be embodiments , R404 can be an unsubstituted C1 - 6 - alkyl , such a substituted Cl - , alkyl . For example , R24 can be a halogen as those described herein . In some embodiments , R404 can substituted C1 - 6 alkyl , a hydroxy substituted C1 - 6 alkyl ( such be hydrogen . In other embodiments , R404 can be methyl . In 45 as , ments R404 can he methyl In 45 as , CH2OH ) , an alkoxy substituted C1 - 6 alkyl ( such as ,

C1 - 6 alkyl - 0 C1 - 6 alkyl and CHOCHZ ) , a sulfenyl sub some embodiments , R414 can be hydrogen . In other embodi stituted C1 - 6 alkyl ( for example , C1 - 6 alkyl - S _ C1 - 6 alkyl ments , R414 can be an optionally substituted C - 4 - alkyl , such and CH SCHZ ) , an azido substituted C1 - 6 alkyl or amino as methyl , ethyl , n - propyl , isopropyl , n - butyl , isobutyl and substituted C1 - 6 alkyl . In some embodiments , R24 can be a tert - butyl . In an embodiment , R414 can be methyl . Depend - 50 C1 - 6 haloalkyl . For example , R - 4 can be a C1 - 6 bromoalkyl ing on the groups that are selected for R404 and R414 , the C1 - 6 chloroalkyl or a C1 - 6 fluoroalkyl , such as CH Br ,

CH , C1 , CH , F , CHF , or CHFCHz . In other embodiments , carbon to which R404 and R414 are attached may be a chiral R24 can be a C1 - 6 azidoalkyl ( for example , N3CH2 – ) . In center . In some embodiment , the carbon to which R + 0A and still other embodiments , R24 can be a C1 - 6 aminoalkyl ( for R414 are attached may be a ( R ) - chiral center . In other example , NH CH2 – ) . In some embodiments , R24 can be an embodiments , the carbon to which R404 and R414 are » optionally substituted C2 - 6 alkenyl . In some embodiments ,

R24 can be a substituted C2 - 6 alkenyl . In other embodiments , attached may be a ( S ) - chiral center . R24 can be an unsubstituted C2 - 6 alkenyl . For example , R24 Examples of suitable can be ethenyl , propenyl or allenyl . In still other embodi

ments , R24 can be an optionally substituted C2 - 6 alkynyl . In some embodiments , R ' A can be a substituted C2 alkynyl . In other embodiments , R24 can be an unsubstituted C2 - 6 alky

R404 R414 nyl . Suitable C2 - 6 alkynyls include ethynyl and propynyl . In yet still other embodiments , R24 can be an optionally sub stituted C3 - 6 cycloalkyl . In some embodiments , R24 can be

NH2 65 a substituted C3 - 6 cycloalkyl . In other embodiments , R24 can be an unsubstituted C2 cycloalkyl . A non - limiting list of C3 - 6 cycloalkyls include cyclopropyl , cyclobutyl , cyclopen

man

39

x NH

15

US 9 , 815 , 864 B2 40

tyl and cyclohexyl . In some embodiments , R24 can be an R434 are attached may be a ( R ) - chiral center . In other optionally substituted 0 C1 - 6 alkyl . In some embodi embodiments , the carbon to which R424 and R434 are ments , R24 can be a substituted 0 C1 - 6 alkyl . In other attached may be a ( S ) - chiral center . embodiments , R24 can be an unsubstituted O _ C1 - 6 alkyl . Examples of suitable Examples of suitable 0 C1 - 6 alkyl groups include 5 methoxy , ethoxy , n - propoxy , iso - propoxy , n - butoxy , isobu toxy , tert - butoxy , pentoxy ( branched and straight - chained ) and hexoxy ( branched and straight - chained ) . In other 0 R42A R 434 embodiments , R24 can be an optionally substituted - O _ C3 - 6 alkenyl . In some embodiments , R24 can be a 10 substituted 0 Cz . , alkenyl . In other embodiments , R24 can be an unsubstituted O _ C3 - 6 alkenyl . In still other embodiments , R24 can be an optionally substituted include the following : - O - C3 - 6 alkynyl . In some embodiments , R24 can be a

substituted 0 C3 - 6 alkynyl . In other embodiments , R24 can be an unsubstituted 0 C3 - 6 alkynyl . In still other embodiments , R24 can be cyano .

The groups attached to the 3 ' - position of the pentose ring can vary . In some embodiments , including those of the 20 preceding paragraph ( that begins with the sentence “ Various groups can be attached to the 4 ' - position of the pentose ring ” ) , R34 can be halogen , for example , fluoro . In other embodiments , including those of the preceding paragraph , R34 can be OH . In still other embodiments , including those of the preceding paragraph , R34 can be an optionally sub stituted O - linked amino acid . Examples of suitable O - linked amino acids include alanine , asparagine , aspartate , cysteine , glutamate , glutamine , glycine , proline , serine , tyrosine , argi nine , histidine , isoleucine , leucine , lysine , methionine , phe nylalanine , threonine , tryptophan and valine . Additional 30

NH examples of suitable amino acids include , but are not limited to , ornithine , hypusine , 2 - aminoisobutyric acid , dehydroala nine , gamma - aminobutyric acid , citrulline , beta - alanine , alpha - ethyl - glycine , alpha - propyl - glycine and norleucine . In some embodiments , the O - linked amino acid can have the " NH2 structure

R 424 43A 42A R43A

NH2 NH2 ty by txt ty ty

? NH2 , NH2 ,

mm NH2

# BINY and n

NH2

w

40 In still other embodiments , including those described

above ( in the paragraph that begins with the sentence - R424 R434 “ Various groups can be attached to the 4 ' - position of the

pentose ring ” ) , R34 can be OC ( O ) R " 4 , wherein R " 4 can be an optionally substituted C , 4 alkyl . In some embodi

NH2 ments , R " 4 can be a substituted C - s alkyl . In other embodi 45 ments , R " 4 can be an unsubstituted C - s alkyl . In still other

wherein R424 can be selected from hydrogen , an optionally embodiments , including those described above ( in the para substituted C1 - 6 alkyl , an optionally substituted C1 - 6 graph that begins with the sentence “ Various groups can be haloalkyl , an optionally substituted C3 - 6 cycloalkyl , an attached to the 4 ’ - position of the pentose ring ” ) , R34 can be optionally substituted Cearyl , an optionally substituted C , an optionally substituted O - acyl . In yet still other embodi aryl and an optionally substituted aryl ( C1 - 6 alkyl ) ; and R434 50 ments , including those described above ( in the paragraph can be hydrogen or an optionally substituted C1 - 4 - alkyl ; or that begins with the sentence “ Various groups can be R424 and R434 can be taken together to form an optionally attached to the 4 ’ - position of the pentose ring ” ) , R34 can be substituted C3 - 6 cycloalkyl . OC ( O ) R444 , wherein R444 can be selected from an When R424 is substituted , R424 can be substituted with optionally substituted C1 - 12 alkyl , an optionally substituted

one or more substituents selected from N - amido , mercapto , 55 C2 - 12 alkenyl , an optionally substituted C2 - 12 alkynyl , an alkylthio , an optionally substituted aryl , hydroxy , an option optionally substituted C3 - 8 cycloalkyl , an optionally substi ally substituted heteroaryl , O - carboxy and amino . In some tuted C5 - 8 cycloalkenyl , an optionally substituted C6 - 10 aryl , embodiments , R424 can be an unsubstituted C1 - 6 - alkyl , such an optionally substituted heteroaryl , an optionally substi as those described herein . In some embodiments , R424 can tuted heterocyclyl , an optionally substituted aryl ( C1 - 6 alkyl ) , be hydrogen . In other embodiments , R42A can be methyl . In 60 an optionally substituted heteroaryl ( C1 - 6 alkyl ) and an some embodiments , R434 can be hydrogen . In other embodi optionally substituted heterocyclyl ( C1 - 6 alkyl ) . In some ments , R434 can be an optionally substituted C1 - 4 - alkyl , such embodiments , R444 can be a substituted C1 - 12 alkyl . In other as methyl , ethyl , n - propyl , isopropyl , n - butyl , isobutyl and embodiments , R444 can be an unsubstituted C1 - 12 alkyl . tert - butyl . In an embodiment , R434 can be methyl . Depend Various substituents can be present at the 2 ' - position of ing on the groups that are selected for R424 and R434 , the 65 the pentose ring . In some embodiments , RSA can be hydro carbon to which R424 and R434 are attached may be a chiral g en . In other embodiments , R5A can be halogen , for center . In some embodiment , the carbon to which R424 and example , fluoro . In still other embodiments , R " A can be an

42

10 acyl .

US 9 , 815 , 864 B2 41

optionally substituted C - 6 alkyl . In some embodiments , RSA A variety of substituents can also be present at the can be an unsubstituted C alkyl . In some embodiments , 5 ' - position of the pentose ring . In some embodiments , both R ” A can be a substituted C1 - 6 alkyl . In yet still other embodi - Raal and Raa2 can be hydrogen . In other embodiments , Raal ments , R54 can be an optionally substituted C2 - 6 alkenyl . In can be hydrogen and Raa2 can be deuterium . In still other some embodiments , R ^ can be an unsubstituted C2 - 6 alk - 5 embodiments , both Raal and Raa2 can be deuterium . enyl . In some embodiments , R5A can be a substituted C , alkenyl . In some embodiments , RSA can be an optionally In some embodiments , R24 can be a C1 - 6 haloalkyl , R34 substituted C2 - 6 alkynyl . In some embodiments , R34 can be can be OH or an optionally substituted acyl , R44 can be a an unsubstituted C2 - 6 alkynyl . In some embodiments , RSA halogen ( for example , fluoro or chloro ) . In some embodi

ments , R3A and R5A can each be an optionally substituted can be a substituted C2 - 6 alkynyl . In some embodiments , R44 can be hydrogen . In other

embodiments , R44 can be halogen , such as fluoro or chloro . In some embodiments , R24 cannot be hydroxy . In some In still other embodiments , R44 can be ORID . For example , embodiments , when R44 is hydroxy , amino or fluoro and RS4 R44 can be OH . In some embodiments , R44 can be OC ( = O ) is hydrogen or methyl , then R24 cannot be hydrogen . In R " ) . In other embodiments , R44 can be an optionally sub some embodiments , R24 cannot be hydrogen . In some stituted O - linked amino acid . In still other embodiments , embodiments , R24 cannot be halogen ( for example , fluoro ) . R44 can be azido . In yet still other embodiments , R44 can be In some embodiments , R24 cannot be azido . In some NR2DR3D . For example , R44 can be amino , a mono - substi embodiments , R24 cannot be methoxy . In some embodi tuted amine or a di - substituted amine . Examples of suitable ments , R24 cannot be methoxy when B14 is substituted or O - linked amino acids for R44 include , but are not limited to : 30 unsubstituted uracil . In some embodiments , B1A is a substi

20 tuted or an unsubstituted cytosine . In other embodiments , BlA is a substituted or an unsubstituted thymine . In still other embodiments , B14 cannot be a substituted or an unsubsti tuted uracil . In some embodiments , R - A cannot be methoxy

- O RD4 RD5 when Z1A is ml 25

NH2

R840 — P = men include the following :

30

tx tx wherein R84 is an unsubstituted C1 - 6 alkyl or a para - substi tuted phenyl ; and R94 is an optionally substituted N - linked

35 amino acid or an optionally substituted N - linked amino acid ester derivative . In some embodiments , R24 cannot be methoxy when Z14 is NH2 , NH2 ,

to ty [ 3CH

40 . NH2 NH2 , R840 minn - 0 H CH? , num TX mm 45 In some embodiments , R24 cannot be an alkoxy ( for

example , when Z14 is ya kutengen eza come se nalang sa NH2 NH2

an min and - 0 H

. 50 50 R840 — P - s Ó NH2 NH2

R945 ) . In some embodiments , R54 can be hydrogen and R44 can

be halogen . In other embodiments , R44 and RSA can both be 55 In some embodiments , BlA cannot be cytosine when R24 is halogen . an unsubstituted alkenyl or an unsubstituted alkynyl . In

A variety of substituents can be present at the 1 ' - position some embodiments , BlA cannot be thymine when R24 is an of the pentose ring . In some embodiments , R4 can be optionally substituted alkyl . In some embodiments , R24 hydrogen . In some embodiments , R4 can be deuterium . In cannot be an unsubstituted alkoxy ( such as methoxy ) , an still other embodiments , R4 can be an unsubstituted C . z . 60 optionally substituted alkenyl ( such as allenyl ) , an unsub alkyl ( such as methyl , ethyl , n - propyl and iso - propyl ) . In yet stituted alkynyl ( such as ethynyl ) or a C , alkyl substituted still other embodiments , R4 can be an unsubstituted C2 - 4 with a non - halogen substituent . In some embodiments , R24 alkenyl ( for example , ethenyl , propenyl ( branched or cannot be an unsubstituted alkoxy ( such as methoxy ) , an straight ) and butenyl ( branched or straight ) ) . In some optionally substituted alkenyl ( such as allenyl ) , an option embodiments , R4 can be an unsubstituted C2 - 3 alkynyl ( such 65 ally substituted alkynyl ( such as ethynyl ) or a C1 - 4 alkyl as ethynyl and propynyl ( branched or straight ) ) . In other substituted with a non - halogen substituent . In some embodi embodiments , R4 can be an unsubstituted cyano . ments , R24 cannot be an optionally substituted alkynyl ( such

44 US 9 , 815 , 864 B2

43 as ethynyl ) , CHz or CF3 . In some embodiments , when B14 from hydrogen , hydroxy , an optionally substituted C1 - 6 is a substituted or unsubstituted cytosine , then R24 can be alkyl , an optionally substituted C3 - 8 cycloalkyl , - C ( O ) azido . In some embodiments R14 cannot be H . In some RR2 and C ( O ) ORS2 ; RF2 can be selected from hydro embodiments R14 cannot be H when B14 is an optionally gen , halogen , an optionally substituted C1 - 6 alkyl , an option substituted cytosine or an optionally substituted thymine . In 5 ally substituted C2 - 6 alkenyl and an optionally substituted

Ce alkynyl ; Y2 and Y ' can be independently N ( nitrogen ) some embodiments , R44 cannot be bromo . In some embodi or CR " , wherein Rl2 can be selected from hydrogen , halo ments , a compound of Formula ( I ) , or a pharmaceutically gen , an optionally substituted C1 - 6 - alkyl , an optionally sub acceptable salt , cannot be 2 - C - methylcytidine , ribavirin , stituted Co . g - alkenyl and an optionally substituted C2 - 6 B - d - N4 - hydroxycytidine , 2 - F - 2 ' - methylcytidine , 2 - thiouri alkynyl ; Wl can be NH or — NCH OC ( = O ) CH ( NH ) dine , 6 - aza - uridine , 5 - nitrocytidine and / or 2 - amino - 2 ' - de - CH ( CH3 ) 2 ; RG2 can be an optionally substituted C1 - 6 alkyl ; oxycytidine , or a mono - , a di - and / or a tri - phosphate of the RH2 can be hydrogen or NHR72 , wherein R72 can be inde foregoing . pendently selected from hydrogen , - C ( O ) RU2 and

Various optionally substituted heterocyclic bases can be C OOR " ; and RK2 , RX2 , RM2 , RN2 , RP2 , RO2 , RR2 , attached to the pentose ring . In some embodiments , one or RS2 , RU2 and Rº2 can be independently selected from hydro more of the amine and / or amino groups may be protected 13 gen , C1 - 6 alkyl , C2 - 6 alkenyl , C2 - 6 alkynyl , C3 - 6 cycloalkyl , with a suitable protecting group . For example , an amino C3 - 6 cycloalkenyl , C6 - 10 aryl , heteroaryl , heteroalicyclyl , group may be protected by transforming the amine and / or aryl ( C1 - 6 alkyl ) , heteroaryl ( C1 - 6 alkyl ) and heteroalicyclyl amino group to an amide or a carbamate . In some embodi - ( C - , alkyl ) . In some embodiments , the structures shown ments , an optionally substituted heterocyclic base or an above can be modified by replacing one or more hydrogens optionally substituted heterocyclic base with one or more 20 with substituents selected from the list of substituents pro protected amino groups can have one of the following vided for the definition of “ substituted . ” structures : In some embodiments , BlA can be

25

NH NH NH

N N N R42 N R N SN7 CNH5 . NH2 RC2 30

mm nem mi

?HRE2 In other embodiments , B14 can be RD2

NH N 35

N wa NH .

40

OR G2 RE2

ni

45 In still other embodiments , B14 can be ' N RH2 and

nu

RF2 NH2 ; 50 NH

muun

55 such as wherein : R42 can be selected from hydrogen , halogen and

NHR12 , wherein R12 can be selected from hydrogen , - C ( O ) RK2 and CEO ) ORL2 ; RB2 can be halogen or NHRW , wherein RW2 can be selected from hydrogen , an optionally substituted C1 - 6 alkyl , an optionally substituted 60 C2 - 6 alkenyl , an optionally substituted C3 - 8 cycloalkyl , - C ( = O ) RM2 and — C ( = O ) ORN2 ; RC2 can be hydrogen or NHRO2 , wherein Rº2 can be selected from hydrogen , - C ( O ) RP2 and - C ( O ) OR22 ; RD2 can be selected from hydrogen , deuterium , halogen , an optionally substi - 65 tuted C - alkyl , an optionally substituted C2 - alkenyl and an optionally substituted C2 - 6 alkynyl ; RE2 can be selected

NH NH

from bo omo alkysubstitute mi

US 9 , 815 , 864 B2 46 45

In yet still other embodiments , BlA can be R140 B14 , R140 BIA

?HRE2 H3C ! ! ! HO

H3C ) * * * HOA

R140 – costul

RD2 OH BHA N RIA R140 mo mommy

E H3C12 HO

R140 R1404

CH3 , H3C " . OH HO

B14 , R1407 10 OH

B1A min RIA BIA

.

for example , * * * 11111 * * 1111

O11 15 R140 B14 , R140 – RIA

NH2 NH2 F

* 11110 NH

20 R140 % BA RIAO

Oor N o . win ni * * 1111 till * * till

25 R140 B1A , R140 RIA In some embodiments , RD2 can be hydrogen . In other embodiments , B14 can be 11111 * * *

* 11111 11111 RB2 30

R150 RIA

F titlll * 11111 1111 35

man R140 B14 R140 B1A ,

* * 111111 * * 1111 1111 11111 In some embodiments , RB2 can be NH , . In other embodi

ments , RB2 can be NHRW2 , wherein RW2 can be CEO ) 40 RM2 or - C ( O ) ORN2 . In still other embodiments , BlA can be

RIAO B14 , R140 45 * * * inil ORG2 011111 till 1113 .

W

R140 BIA

RH2 50 11

when

R140 B1A , R140 – BIA

In some embodiments , B14 can be 11011 * * illlll 55 HO * 11111

ORG2 RIA RIAO

YN 11ttill * 1111 111111 *

tul 11 .

N NH2 NH2 . R1407 B4 , RIO min

> . nttill 65 011 FHC illo 1111 In some embodiments , a compound of Formula ( 1 ) can

have a structure selected from one of the following :

US 9 , 815 , 864 B2 48 47

- continued B1A , R140

- continued B14 R140 R140 BIA R140 BIA

* 111111 F CH3 atllll 111 Bry CH3 , CH3 , tillo Fill int 5 . Ins .

R34 HC R140 RIA B14 , R140 R140 BIA R140 – BIA

LCH3 , * * . * * llll * * * 111il * * CH3 ,

all CH3 , •111110 FISCH , OU cu 11 R3A OH TRICE 10 R1404 10 R140 – RIAO B14 R140 – B14 R140 B14 od

LCH3 , 1114 fona o Club HOW

???? ?? ?? OH

c = CH , ?? | B ' ,

R34 R34 R34 Red R34 OH F , OH H BHA R140

, R140 Bl4 , R140 15 RAO B1A

. Filler 11 * * Anne psill160 HO R3A H RW010

\ R34 B14 R140 R140 – R34 R140 R14 BWA 20R Low CH3 , LCH3 ,

?? ins

F F R34 F R3A OH HO " IC C . BIA

O Julia CECH , SH ?? Rii R34 RŠA R140 BIA RIAO Rico B RWO4

25 CH3 * * * llll face CH3 , F " 1111 F * * 1111 Fill All ??

LC = CH HOH POH

R140 B14

FH LECH , R34 F

R140 – R140 Bl? RM40 . HOR B14 R140 – BIA Mb RIN po us 11 . CH3 , n . Pt . 111

HO R34 OH F . B14 R140 –

SCH , POH

BHA R14 R34 . . . 111 . 25

R140 R140 RIA

will * * 111111 S Lachs , 11111 * * * F till F u 35

R34 R140 – BlA R140 – BIA B14 OR

* * * iiill * * 111 " CH3 , LCH3 ,

R34 til ?? 40 40 HOSH Olinto R140 B14 , R140 R40 BIA B1A , ????? RIAO R BIA RIO 0 .

fo 1111111 F7 ! " F HOW wilt R34 HOS LSCH OH

B14

các CH HOSH RA B IA B14 R ! 45 45 R140 RIA

no ? ?? ??? ????? ??? " CN , HzCouro HzCOM CECH F . tilll

?? C = C — 1 ,

?? RAO OH Yu1111 HO R140 BIA

50 ? ??? ??? .

NECA NECE . n111 1116 N3 NE HO

RIA

111 UH

R140 RIA B1A 55

. LCH3 , and 11111 * V3 On H2N 3 HO OH HOOH . H2N R140 B14 , R140 BIA

B1A Nzelunto [ ? ? .

R140 - V R241 . . .

H N31 " HITRA

DSA IRSA * R140 BIA R " La HOMH HOME

B14 R140

ZOH , FACH3 , 44 R34 R44

11 13 65

R3A OH or a pharmaceutically acceptable salt of the foregoing . In some embodiments of this paragraph , B14 can be an option

US 9 , 815 , 864 B2 49 50

ally substituted purine base . In other embodiments of this alkyl , an optionally substituted - O - aryl , an optionally paragraph , B14 can be an optionally substituted pyrimidine substituted O - heteroaryl and an optionally substituted base . In some embodiments of this paragraph , B14 can be O - monocyclic heterocyclyl ; Rllbl and Rl1B2 can be guanine . In other embodiments of this paragraph , Bl4 can be selected from hydrogen , an optionally substituted C1 - 24 alkyl thymine . In still other embodiments of this paragraph , B14 5 and an optionally substituted aryl ; j can be 1 or 2 ; kl can be can be cytosine . In yet still other embodiments of this 0 or 1 ; k2 can be 3 , 4 or 5 ; RWD can be an optionally paragraph , B14 can be uracil . In some embodiments of this substituted C1 - 24 - alkyl and Zlo and Z2B can be indepen paragraph , BlA can be adenine . In some embodiments of this dently O or S . paragraph , R1A can be hydrogen . In other embodiments of In some embodiments , RlB can be 0 . In other embodi In some embodiments R1B con he this paragraph , R " ̂ can be an optionally substituted acyl . In 10 ments . R1B can be OH . In still other embodiments , RIB can still other embodiments of this paragraph , R ^ can be mono - , be an optionally substituted C , alkoxy . For example , RD di - or tri - phosphate . In yet other embodiments of this can be methoxy , ethoxy , n - propoxy , iso - propoxy , n - butoxy , paragraph , R14 can be phosphoramidate prodrug , such as an iso - butoxy , tert - butoxy , straight or branched pentoxy or aryl phosphoramidate prodrug . In some embodiments of this 15 straight or branched hexoxy . paragraph , RlA can be an acyloxyalkyl ester phosphate 15 In some embodiments , RIB can be prodrug . In other embodiments of this paragraph , R A can be a S - acylthioethyl ( SATE ) prodrug . In still other embodi ments , R14 can be a phosphonic diamide prodrug . In yet still R5B R6B other embodiments , of this paragraph , R14 can be a cyclic 1 - aryl - 1 , 3 - propanyl ester ( Hep Direct ) prodrug moiety . In 20 some embodiments of this paragraph , R14 be a cyclosalig enyl ( cycloSal ) prodrug .

In some embodiments , the compound can be a compound of Formula ( II ) , or a pharmaceutically acceptable salt thereof , wherein : B1B can be an optionally substituted het - 25 wherein R and Rº can be independently selected from erocyclic base or an optionally substituted heterocyclic base hydrogen , an optionally substituted C1 - 24 alkyl and an with a protected amino group ; R1B can be selected from O " , optionally substituted aryl ; and R ' " can be selected from OH , an optionally substituted C1 - 6 alkoxy , hydrogen , an optionally substituted C1 - 24 alkyl , an option

ally substituted aryl , an optionally substituted O - C1 - 24 30 alkyl , an optionally substituted — O - aryl , an optionally

substituted — O - heteroaryl or an optionally substituted — O monocyclic heterocyclyl . In some embodiments , RSB and RB can be hydrogen . In other embodiments , at least one of RSB and RB can be an optionally substituted C1 - 24 alkyl or

35 an optionally substituted aryl . In some embodiments , RTB can be an optionally substituted C1 - 24 alkyl . In other embodi ments , R7B can be an optionally substituted aryl . In still other embodiments , R7B can be an optionally substituted

O _ C1 - 24 alkyl , an optionally substituted O - aryl , an 40 optionally substituted — O - heteroaryl or an optionally sub

stituted O - monocyclic heterocyclyl . s R1101 In some embodiments , R1B can be

R7B

RB R6B Ro

XX y RIOB 72B

House ma 45 s R & B ROBO

es R11B2 RIOB tur 22B

an optionally substituted N - linked amino acid and an option ally substituted N - linked amino acid ester derivative ; R2B 50 wherein R & B and RB can be independently selected from can be selected from an optionally substituted C1 - 6 alkyl , an hydrogen , an optionally substituted C1 - 24 alkyl and an optionally substituted C2 - 6 alkenyl , an optionally substituted optionally substituted aryl ; RIOB can be independently C2 - 6 alkynyl , an optionally substituted O _ C1 - 6 alkyl , an selected from hydrogen , an optionally substituted C1 - 24 optionally substituted O _ C3 - 6 alkenyl , an optionally sub alkyl , an optionally substituted aryl , an optionally substi stituted O C3 - 6 alkynyl and cyano ; R3B can be selected 55 tuted O _ C1 - 24 alkyl , an optionally substituted O - aryl , from hydrogen , halogen , ORD , an optionally substituted an optionally substituted - O - heteroaryl and an optionally O - linked amino acid , azido and NR2DR3D ; RD can be substituted O - monocyclic heterocyclyl ; and Z2B can be hydrogen or - C ( O ) R " D ; R2D and R3D can be indepen independently O ( oxygen ) or S ( sulfur ) . In some embodi dently hydrogen or an optionally substituted C1 - 6 alkyl ; R4B ments , R & B and R9B can be hydrogen . In other embodiments , can be selected from hydrogen , halogen , an optionally 60 at least one of R & B and RB can be an optionally substituted substituted C1 - 6 alkyl , an optionally substituted C2 - 6 alkenyl C1 - 24 alkyl or an optionally substituted aryl . In some and an optionally substituted Coalkynyl ; R5B , RB , R & B and embodiments , R10B can be an optionally substituted C1 - 24 RB can be independently selected from hydrogen , an alkyl . In other embodiments , R10B can be an optionally optionally substituted C1 - 24 alkyl and an optionally substi - substituted aryl . In still other embodiments , ROB can be an tuted aryl ; RTB and RIOB can be independently selected from 65 optionally substituted - 0 C1 - 24 alkyl , an optionally sub hydrogen , an optionally substituted C1 - 24 alkyl , an option stituted — O - aryl , an optionally substituted O - heteroaryl ally substituted aryl , an optionally substituted - O C1 - 24 or an optionally substituted O - monocyclic heterocyclyl .

52

mu RIIBI

US 9 , 815 , 864 B2 51

In some embodiments , j can be 1 . In other embodiments , j cycloalkyl , an optionally substituted aryl , an optionally can be 2 . In some embodiments , Z2B can be O ( oxygen ) . In substituted aryl ( C1 - 6 alkyl ) and an optionally substituted other embodiments , Z2B can be or S ( sulfur ) . In some haloalkyl ; R13B can be selected from hydrogen , an optionally embodiments , RIB can be isopropyloxycarbonyloxymethyl - substituted C1 - 6 alkyl , an optionally substituted C1 - 6 oxy , and form a bis ( isopropyloxycarbonyloxymethyl ) ( bis 5 haloalkyl , an optionally substituted C3 - 6 cycloalkyl , an ( POC ) ) prodrug . In some embodiments , R1B can be pivaloy optionally substituted Co aryl , an optionally substituted C10 loxymethyloxy , and form a bis ( pivaloyloxymethyl ) ( bis aryl and an optionally substituted aryl ( C1 - 6 alkyl ) ; and R14B ( POM ) ) prodrug . can be hydrogen or an optionally substituted C1 - 4 - alkyl ; or

R13B and R14B can be taken together to form an optionally In some embodiments , RIB can be 10 substituted Cza cycloalkyl . When R13B is substituted , R13B can be substituted with

one or more substituents selected from N - amido , mercapto , alkylthio , an optionally substituted aryl , hydroxy , an option ally substituted heteroaryl , O - carboxy and amino . In some

5 embodiments , RTSP can be an unsubstituted C1 . 6 - alkyl , such as those described herein . In some embodiments , R 3 can be hydrogen . In other embodiments , R13B can be methyl . In some embodiments , R12B can be an optionally substituted In some embodiments , R11Bl can be hydrogen . In other C1 - 6 alkyl . Examples of optionally substituted C1 . 6 - alkyls

embodiments , R11Bl can be an optionally substituted C1 - 24 be an optionally substituted C1 - 24 include optionally substituted variants of the following : alkyl . In still other embodiments , R11Bl can be an optionally 20 methyl , ethyl , n - propyl , isopropyl , n - butyl , isobutyl , tert substituted aryl . In some embodiments , R11B1 can be a C1 - 6 butyl , pentyl ( branched and straight - chained ) and hexyl alkyl , for example , methyl , ethyl , n - propyl , isopropyl , n - bu - ( branched and straight - chained ) . In some embodiments , tyl , isobutyl , tert - butyl , pentyl ( branched and straight R12B can be methyl or isopropyl . In some embodiments ,

R12B can be ethyl or neopentyl . In other embodiments , R12B chained ) and hexyl ( branched and straight - chained ) . In some embodiments , kl can be 0 . In other embodiments , kl can be 25 can be an optionally substituted C3 . 6 cycloalkyl . Examples

of optionally substituted Cz . cycloalkyl include optionally 1 . In some embodiments , RIB can be a S - acylthioethoxy substituted variants of the following : cyclopropyl , cyclobu ( SATE ) group and form a SATE ester prodrug . tyl , cyclopentyl , and cyclohexyl . În an embodiment , R12B In some embodiments RIB can be can be an optionally substituted cyclohexyl . In still other

embodiments , R12B can be an optionally substituted aryl , such as phenyl and naphthyl . In yet still other embodiments , R12B can be an optionally substituted aryl ( Ci - , alkyl ) . In some embodiments , R12B can be an optionally substituted

12 ' s R1132 benzyl . In some embodiments , R12B can be an optionally substituted C1 - 6 haloalkyl , for example , CF3 . In some

35 embodiments , R14B can be hydrogen . In other embodiments , In some embodiments , R11B2 can be hydrogen . In other R14B can be an optionally substituted C - 4 - alkyl , such as embodiments , R11B2 can be an optionally substituted C1 - 24 methyl , ethyl , n - propyl , isopropyl , n - butyl , isobutyl and alkyl . In still other embodiments , R11B2 can be an optionally tert - butyl . In an embodiment , R14B can be methyl . In some

embodiments , R13B and R14B can be taken together to form substituted aryl , for example , an optionally substituted phe 40 an optionally substituted C3 - 6 cycloalkyl . Examples of nyl . In some embodiments , R11B2 can be an optionally 4 optionally substituted Cz , cycloalkyl include optionally substituted C . alkyl . In some embodiments , R11B2 can be substituted variants of the following : cyclopropyl , cyclobu an unsubstituted C1 - 6 alkyl . In some embodiments , k2 can be tyl , cyclopentyl , and cyclohexyl . Depending on the groups 3 . In other embodiments , k2 can be 4 . In still other embodi - that are selected for R13B and R14B , the carbon to which R130 ments , k2 can be 5 . and R14B are attached may be a chiral center . In some

In some embodiments , RIB can be an optionally substi - * » embodiment , the carbon to which R13B and R14B are attached tuted N - linked amino acid or an optionally substituted may be a ( R ) - chiral center . In other embodiments , the carbon N - linked amino acid ester derivative . For example , RIB can to which R13B and R14B are attached may be a ( S ) - chiral be optionally substituted version of the following : alanine , center . asparagine , aspartate , cysteine , glutamate , glutamine , gly Examples of suitable cine , proline , serine , tyrosine , arginine , histidine , isoleucine , leucine , lysine , methionine , phenylalanine , threonine , tryp tophan , valine and ester derivatives thereof . In some R12B0 R13 R14B embodiments , R1B can be selected from alanine isopropyl ester , alanine cyclohexyl ester , alanine neopentyl ester , valine isopropyl ester and leucine isopropyl ester . In some » embodiments , RIB can have the structure

w

" Cine , 50

HN

groups include the following : R12B0 R13B R14B 60

R12B0 R13B R14B R12B0 R13B R14B HN 1111

HN HN 05 wherein R12B can be selected from hydrogen , an optionally substituted C1 - 6 - alkyl , an optionally substituted C3 - 6

US 9 , 815 , 864 B2 53 54

- continued H3CO H3CH HzCO FZ HN HN 2134

H4X4 H3CO H3C H

10 HN wa

- O HZC H - OH CH X y

an mutno - H3C H

HN

– 0 H?C H .

Y HN OHN HN

HzC - ?? ; ?? n XXXX Fm . .

mri waris

A variety of substituents can be present at the 4 ' - position of the pentose ring . In some embodiments , R2B can be an optionally substituted C1 - 6 alkyl . Examples of suitable C1 - 6 alkyls include methyl , ethyl , n - propyl , isopropyl , n - butyl ,

5 isobutyl , tert - butyl , pentyl ( branched and straight - chained ) and hexyl ( branched and straight - chained ) . In some embodi ments , R2B can be an unsubstituted C1 - 6 alkyl . In other embodiments , R2B can be a substituted C1 - 6 alkyl . For example , R2B can be a halogen substituted C1 - 6 alkyl , a hydroxy substituted C1 - 6 alkyl ( such as , CH2OH ) , an alkoxy substituted C1 - 6 alkyl ( such as , C1 - 6 alkyl - 0 C1 - 6 alkyl and CHOCHZ ) , a sulfenyl substituted C1 - 6 alkyl ( for example , C1 - 6 alkyl - S _ C1 - 6 alkyl and CH SCH3 ) , an azido substituted Cl . alkyl or amino substituted C1 - 6 alkyl . In some embodiments , R2B can be a C1 - 6 haloalkyl . For example , R2B can be a C1 - 6 bromoalkyl C1 - 6 chloroalkyl or a C1 - 6 fluoroalkyl , such as CH Br , CH C1 , CH2F , CHF , or CHFCHz . In other embodiments , R2B can be a C1 - 6 azido

20 alkyl ( for example , N3CH2 - ) . In still other embodiments , R2B can be a Cl . aminoalkyl ( for example , NH CH2 – ) . In some embodiments , R2B can be an optionally substituted C2 - 6 alkenyl . In some embodiments , R2B can be a substituted C2 alkenyl . In other embodiments , R2B can be an unsub

25 stituted C2 - 6 alkenyl . For example , R2B can be ethenyl , propenyl or allenyl . In still other embodiments , R2B can be an optionally substituted C2 - 6 alkynyl . In some embodi ments , R2B can be a substituted C2 - 6 alkynyl . In other embodiments , R2B can be an unsubstituted C2 . alkynyl .

30 Suitable C2 - 6 alkynyls include ethynyl and propynyl . In yet still other embodiments , R2B can be an optionally substituted Cz . , cycloalkyl . In some embodiments , R2B can be a sub stituted C3 . 6 cycloalkyl . In other embodiments , R2B can be an unsubstituted 3 - 6 cycloalkyl . A non - limiting list of C3 - 6

35 cycloalkyls include cyclopropyl , cyclobutyl , cyclopentyl and cyclohexyl . In some embodiments , R2B can be an optionally substituted O _ C1 - 6 alkyl . In some embodi ments , R²B can be a substituted O _ C1 - 6 alkyl . In other embodiments , R2B can be an unsubstituted 0 C . , alkyl .

40 Examples of suitable 0 - C1 - 6 alkyl groups include methoxy , ethoxy , n - propoxy , iso - propoxy , n - butoxy , isobu toxy , tert - butoxy , pentoxy ( branched and straight - chained ) and hexoxy ( branched and straight - chained ) . In other embodiments , R2B can be an optionally substituted

450 C3 - 6 alkenyl . In some embodiments , R2B can be a substituted 0 C3 - 6 alkenyl . In other embodiments , R2B can be an unsubstituted - 0 Cz . alkenyl . In still other embodiments , R2B can be an optionally substituted - 0 - C2 alkynyl . In some embodiments , R2B can be a

50 substituted 0 C3 - 6 alkynyl . In other embodiments , R2B can be an unsubstituted — O - Cz - , alkynyl . In still other embodiments , R2B can be cyano . In yet still other embodi ments , R2B can be halogen , such as fluoro .

Various substituents can be present at the 2 ' - position of 55 the pentose ring . In some embodiments , R4B can be hydro

gen . In other embodiments , R4B can be halogen , for example , fluoro . In still other embodiments , R4B can be an optionally substituted C1 - 6 alkyl . In some embodiments , R4B can be an unsubstituted C1 - 6 alkyl . In some embodiments ,

60 R4B can be a substituted C - alkyl . In yet still other embodi ments , R4B can be an optionally substituted C2 - 6 alkenyl . In some embodiments , R4B can be an unsubstituted C26 alk enyl . In some embodiments , R4B can be a substituted C2 - 6 alkenyl . In some embodiments , R4B can be an optionally

65 substituted C2 - 6 alkynyl . In some embodiments , R4B can be an unsubstituted C2 - 6 alkynyl . In some embodiments , RAB can be a substituted C2 - 6 alkynyl .

- O H3CH Film

HN

- HzÇ , H Oxir N min the

* * 1111 * * 1110ll muna N FO !

and and

- N IZ man H .

US 9 , 815 , 864 B2 55 56

RBB2

- 2 NH

N N N RAB2 RAB2 , N R CB2 , ww

In some embodiments , R3B can be hydrogen . In other embodiments , R * D can be halogen , such as fluoro or chloro . In still other embodiments , R3B can be ORD . For example , R3B can be OH . In some embodiments , R3B can be OC ( O ) R " ) . In other embodiments , R3B can be an optionally sub - 5 stituted O - linked amino acid . In still other example , R3B can be amino , a mono - substituted amine or a di - substituted amine . When R3B is an optionally substituted O - linked amino acid , in some embodiments , RD4 can be selected from hydrogen , an optionally substituted C1 - 6 alkyl , an optionally substituted C1 - 6 haloalkyl , an optionally substituted C3 - 6 cycloalkyl , an optionally substituted Co aryl , an optionally substituted C10 aryl and an optionally substituted aryl ( C1 - 6 alkyl ) ; and RDS can be hydrogen or an optionally substituted C , 4 - alkyl , or RD4 and Rºs can be taken together to form an is optionally substituted C3 - 6 cycloalkyl . Examples of suitable O - linked amino acids for R3B include , but are not limited to :

NHREB2 RDB2

NH

y3B

ma

OR GB2

RFB2 NH 20

- 0 RD4 RD5 N N RHB2 and

NH ) NH2 ma nuu

25

include the following : NH2 ;

N N m

mah RD4 D4 RDS 30

1111 *

tx tx tx tx tx ???? tyttur

wm ni mu

nmn NH2 NH2 ,

man In

NH2 ,

> IU and w

NH2

wherein : RAB2 can be selected from hydrogen , halogen and NH2 , NHRTB2 , wherein RJB2 can be selected from hydrogen , C ( O ) RKB2 and CEO ) ORLB2 ; RBB2 can be halogen

or NHRWB2 , wherein RWB2 can be selected from hydrogen , an optionally substituted C1 - 6 alkyl , an optionally substituted

? NH2 , C2 - 6 alkenyl , an optionally substituted C3 - 8 cycloalkyl , - C ( O ) RMB2 and _ C ( O ) ORNB2 ; RCB2 can be hydro

40 gen or NHROB2 ; wherein ROB2 can be selected from hydro gen , CEO ) RPB2 and C = O ) OROB2 ; RDB2 can be selected from hydrogen , deuterium , halogen , an optionally

NH2 , substituted C1 - 6 alkyl , an optionally substituted C2 - 6 alkenyl and an optionally substituted C2 - 6 alkynyl ; REB2 can be

45 selected from hydrogen , hydroxy , an optionally substituted Cl - 6 alkyl , an optionally substituted C3 - 8 cycloalkyl , - C ( O ) RRB2 and C ( O ) ORSB2 ; RFB2 can be selected

NH2 from hydrogen , halogen , an optionally substituted C1 - 6 alkyl , an optionally substituted C2 - 6 alkenyl and an option ally substituted C2 - 6 alkynyl ; Y2B and Y3B can be indepen

In some embodiments , RB can be halogen , such as fluoro dently N ( nitrogen ) or CRIB2 , wherein RIB2 can be selected or chloro . In some embodiments , R4B can be hydrogen and from hydrogen , halogen , an optionally substituted C1 - 6 R3B can be halogen . In other embodiments , R3B and R4B can alkyl , an optionally substituted C2 - ? - alkenyl and an option be both halogen . For example , R3B and R4B can be both ally substituted C2 - ? - alkynyl ; RB2 can be an optionally fluoro . 55 In some embodiments , ZlB can be O ( oxygen ) . In other substituted C1 - 6 alkyl ; RAB2 can be hydrogen or NHR7B2 ;

embodiments , zB can be S ( sulfur ) . wherein RTB2 can be independently selected from hydrogen , C ( O ) RUB2 and C ( O ) ORVB2 ; and RKB2 , RLB2 , Various optionally substituted heterocyclic bases can be

attached to the pentose ring . In some embodiments , one or RMB2 , RNB2 , RPB2 , RQB2 , RRB2 , RSB2 , RUB2 and RVB2 can be R more of the amine and / or amino groups may be protected 60 independently selected from C1 - 6 alkyl , C2 - 6 alkenyl , C2 . 6 with a suitable protecting group . For example , an amino alkynyl , C3 - 6 cycloalkyl , C3 - 6 cycloalkenyl , C6 - 10 aryl , het group may be protected by transforming the amine and / or eroaryl , heteroalicyclyl , aryl ( C1 - 6 alkyl ) , heteroaryl ( C1 - 6 amino group to an amide or a carbamate . In some embodi - alkyl ) and heteroalicyclyl ( C1 - 6 alkyl ) . In some embodi ments , an optionally substituted heterocyclic base or an ments , the structures shown above can be modified by optionally substituted heterocyclic base with one or more 65 replacing one or more hydrogens with substituents selected protected amino groups can have one of the following from the list of substituents provided for the definition of structures : “ substituted . ”

- 6

57 US 9 , 815 , 864 B2

58 In some embodiments , RDB2 can be hydrogen . In other embodiments , BlB can be

In some embodiments , B1B can be

RBB2 y NH NH

N .

CN CNH ) . N wa 10

win In other embodiments , BlB can be

15 In some embodiments , RBB2 can be NH . In other embodi ments , RBB2 can be NHRWB2 , wherein RWB2 can be

C ( = O ) RMB2 or C ( O ) ORNB2 . In still other embodi ments , BB can be

ORGB2 å

moins

In still other embodiments , B1B can be N N RHB2 . mun

O

In some embodiments , BlB can be RFB2 NH

30 ORGB2 N

mu : such as 35 CN CNH ) . waar

In some embodiments , a compound of Formula ( II ) can be 40 selected from : NH

' N o BIB BlB , ataan OF 0 - O

CH3 5 In yet still other embodiments , B1B can be ZlB = p 11111 * * ZlB = p ?? RIB NHREB2

RIB BIB

RDB2 4 IN CH3 and A1111 and

z1B - P — y3B - 0 OH

RIB un 3

O for example , 11 CH3 , * * * 111

zlB = P NH , NH2 RIB 3

SN

or

or a pharmaceutically acceptable salt of the foregoing . In some embodiments of this paragraph , B ' can be an option ally substituted purine base . In other embodiments of this

65 paragraph , B1B can be an optionally substituted pyrimidine base . In some embodiments of this paragraph , BB can be guanine . In other embodiments of this paragraph , B1B can be

mu

59

RICO R7C ZR8C Réc BIC R7C1 10

RSC R3CO Hm p4

US 9 , 815 , 864 B2 60

thymine . In still other embodiments of this paragraph , BIB In some embodiments , - - - - - - - can be a single bond such can be cytosine . In yet still other embodiments of this that Formula ( III ) has the structure paragraph , BlB can be uracil . In some embodiments of this paragraph , BB can be adenine . In some embodiments of this paragraph , Z1B can be oxygen . In some embodiments of this 5 paragraph , zB can be sulfur . In still other embodiments of this paragraph , R1B can be alkylcarbonyloxyalkoxy . In yet still other embodiments of this paragraph , RIB can be alkoxycarbonyloxyalkoxy . In some embodiments of this III? paragraph , RB can be a C1 - alkoxy . LRC ,

In some embodiments , the compound can be a compound of Formula ( III ) , or a pharmaceutically acceptable salt thereof , wherein : BC can be an optionally substituted het erocyclic base or an optionally substituted heterocyclic base wherein each R7C and each RSC can be independently hydro with a protected amino group ; R1C and R2C can be indepen - 15 gen or halogen . In some embodiments , the RTC and the R & C dently selected from 0 - , OH , an optionally substituted C1 - 6 groups can all be hydrogen . In other embodiments , one R7C alkoxy , can be halogen , one R7C can be hydrogen and both R & C

groups can be hydrogen . In still other embodiments , one R7C can be halogen , one R ' can be hydrogen , one R can be

20 halogen and one R & C can be hydrogen . In some embodi ments , the carbon adjacent to the phosphorus and the 5 ' - car bon can each be independently a ( S ) - chiral center . In some embodiments , the carbon adjacent to the phosphorus and the 5 ' - carbon can each be independently a ( R ) - chiral center .

25 In some embodiments , - - - - - - - can be a double bond such that Formula ( III ) has the structure

RSC

SR°C R10C

mm S R120 R13CO

R14C XXL Houtlet RIC ww s R15CI , ' s R1502 30 OS R7C ZR8C BIC

- 11110 R4C

RSC R3C . . . . . 1H an optionally substituted N - linked amino acid and an option H R6C ally substituted N - linked amino acid ester derivative ; R3C 35 R5C can be selected from an optionally substituted C1 - 6 alkyl , an optionally substituted C2 - 6 alkenyl , an optionally substituted C2 - 6 alkynyl , an optionally substituted O _ C1 - 6 alkyl , an wherein each R ' C is absent and each R & C can be indepen optionally substituted - O _ C3 - 6 alkenyl , an optionally sub - dently hydrogen or halogen . In some embodiments , both stituted O _ C3 - 6 alkynyl , an optionally substituted C2 . 6 40 R $ groups can be hydrogen . In other embodiments , one R $ C cycloalkyl and cyano ; R4C can be selected from OH , OC can be halogen and the other R $ can be hydrogen . In some FOR " C and an optionally substituted O - linked amino embodiments , both Rº groups can be halogen . In some acid ; R * can be selected from hydrogen , halogen , ORID , an embodiments , the double bond has a ( Z ) - configuration . In optionally substituted O - linked amino acid , azido and some embodiments , the double bond has a ( E ) - configura NR2DR3 , R1D can be hydrogen or - C ( O ) R " D ; R2D and 45 tion . RD can be independently hydrogen or an optionally sub - In some embodiments , RC and / or R2C can be 0 . In other stituted C . alkyl ; ROC can be selected from hydrogen , embodiments , Riº and / or R2C can be OH . In some embodi halogen , an optionally substituted C1 - 6 alkyl , an optionally ments , RC and R2C can be both OH . substituted C2 - alkenyl and an optionally substituted Co . In some embodiments , R1C and / or R2C can be alkynyl ; RºC , RIOC , R12C and R13C can be independently 50 selected from hydrogen , an optionally substituted C1 - 94 alkyl and an optionally substituted aryl ; RIIC and R14C can be independently selected from hydrogen , an optionally sub stituted C1 - 24 alkyl , an optionally substituted aryl , an option ally substituted 0 C1 - 24 alkyl , an optionally substituted 55 - O - aryl , an optionally substituted O - heteroaryl or an

optionally substituted - O - monocyclic heterocyclyl ; R15C1 and R15C2 can be independently selected from hydrogen , an wherein RºC and ROC can be independently selected from optionally substituted C1 - 24 alkyl and an optionally substi - hydrogen , an optionally substituted C1 - 24 alkyl and an tuted aryl ; - - - - - - - can be a single bond or a double bond ; 60 optionally substituted aryl ; and Rll can be selected from when - - - - - - - is a single bond , each R7C and each RSC can be hydrogen , an optionally substituted C1 - 24 alkyl , an option independently hydrogen or halogen ; and when - - - - - - - is a ally substituted aryl , an optionally substituted O _ C1 - 24 double bond , each R7C is absent and each R $ C can be alkyl , an optionally substituted O - aryl , an optionally independently hydrogen or halogen ; d can be 1 or 2 ; el can substituted O - heteroaryl and an optionally substituted be 0 or 1 ; e2 can be 3 , 4 or 5 ; R " C and R " can be 65 _ O - monocyclic heterocyclyl . In some embodiments , RºC independently an optionally substituted C1 - 24 - alkyl and ZlC and R10C can be hydrogen . In other embodiments , at least can be O ( oxygen ) or S ( sulfur ) . one of RºC and RIOC can be an optionally substituted C1 - 24

S R9C R10C RIIC

US 9 , 815 , 864 B2 62

www Houthu alkyl or an optionally substituted aryl . In some embodi In some embodiments , R1C and / or R2C can be ments , R11C can be an optionally substituted C1 - 24 alkyl . In other embodiments , RIIC can be an optionally substituted aryl . In still other embodiments , R11C can be an optionally substituted 0 C1 - 24 alkyl , an optionally substituted O - 5 aryl , an optionally substituted O - heteroaryl or an option s R1501 ally substituted O - monocyclic heterocyclyl . In some embodiments , R1C and R2C can be both

In some embodiments , R15C1 can be hydrogen . In other embodiments , RISC1 can be an optionally substituted C1 - 24 R9C R100 alkyl . In still other embodiments , Risc1 can be an option ally substituted aryl . In some embodiments , R15C1 can be a C1 - 6 alkyl , for example , methyl , ethyl , n - propyl , isopropyl , n - bu

15 tyl , isobutyl , tert - butyl , pentyl ( branched and straight chained ) and hexyl ( branched and straight - chained ) . In some embodiments , R1C and R2C can be both

In some embodiments , R1C and / or R2C can be

10

mm R11C

20 S R12 R13C O Hotels R14C ' s R1501

z !

25

mm RISC2

KAL

> In some embodiments , el can be 0 . In other embodiments , wherein R12C and R13C can be independently selected from el can be 1 . In some embodiments , R1C and R2C can be both hydrogen , an optionally substituted C1 - 24 alkyl and an a S - acylthioethoxy ( SATE ) group and form a SATE ester optionally substituted aryl ; R14C can be independently prodrug . selected from hydrogen , an optionally substituted C1 - 24 In some embodiments , R1C and R2C can be both alkyl , an optionally substituted aryl , an optionally substi tuted - O - C1 - 24 alkyl , an optionally substituted - O - aryl , an optionally substituted O - heteroaryl and an optionally substituted O - monocyclic heterocyclyl ; and zic can be independently O ( oxygen ) or S ( sulfur ) . In some embodi ments , R12C and R13C can be hydrogen . In other embodi ments , at least one of R12C and R13C can be an optionally substituted C1 - 24 alkyl or an optionally substituted aryl . In In some embodiments , at least one of R1C and R2C can be some embodiments , R14C can be an optionally substituted C1 - 24 alkyl . In other embodiments , R14C can be an optionally 40 substituted aryl . In still other embodiments , R14C can be an optionally substituted 0 C1 - 24 alkyl , an optionally sub stituted — O - aryl , an optionally substituted O - heteroaryl or an optionally substituted - O - monocyclic heterocyclyl . In some embodiments , d can be 1 . In other embodiments , d 45 In some embodiments , R15C2 can be hydrogen . In other can be 2 . In some embodiments , Z " can be O ( oxygen ) . In embodiments , R15C2 can be an optionally substituted C , other embodiments , ZC can be or S ( sulfur ) . In some alkyl . In still other embodiments , R15C2 can be an optionally embodiments , RIC and / or R2C can be isopropyloxycarbony substituted aryl , for example , an optionally substituted phe loxymethoxy . In some embodiments , RC and / or R2C can be nyl . In some embodiments , R15C2 can be an optionally pivaloyloxymethoxy . In some embodiments , RIC and R2C 30 substituted C1 - 6 alkyl . In some embodiments , R15C2 can be can be both an unsubstituted C1 - 6 alkyl . In some embodiments , e2 can be

3 . In other embodiments , e2 can be 4 . In still other embodi ments , e2 can be 5 . R120 R13C 0 55 In some embodiments , R1C and / or R2C can be an option ally substituted N - linked amino acid or an optionally sub stituted N - linked amino acid ester derivative . For example , RIC and / or R2C can be optionally substituted version of the following : alanine , asparagine , aspartate , cysteine , gluta

In some embodiments , R1C and R2C can be both isopropy - 60 mate , glutamine , glycine , proline , serine , tyrosine , arginine , loxycarbonyloxymethoxy . In other embodiments , R ' and histidine , isoleucine , leucine , lysine , methionine , phenylala RC can be both pivaloyloxymethoxy . In some embodi - nine , threonine , tryptophan , valine and ester derivatives ments , R1C and R2C can be both a isopropyloxycarbony - thereof . In some embodiments , RIC and / or R2C can be loxymethoxy group , and form a bis ( isopropyloxycarbony - selected from alanine isopropyl ester , alanine cyclohexyl loxymethyl ) ( bis ( POC ) ) prodrug . In some embodiments , 65 ester , alanine neopentyl ester , valine isopropyl ester and RiC and R2C can be both a pivaloyloxymethoxy group , and leucine isopropyl ester . In some embodiments , RIC and / or form a bis ( pivaloyloxymethyl ) ( bis ( POM ) ) prodrug . R2C can have the structure

LR14C 71C

US 9 , 815 , 864 B2 63 64

groups include the following : R1900 R200 R210

R19C0 R200 R210 R1900 R200 R210 HN

y

HN 47747 " X1 H3CO H3CO H3C , H wir mi v

0 HN

H3CO H3CH

HN HN

- H3C - ?? ; ?? 111 ) IE HN Ó HN

- H3CH

HN 3

wherein R19C can be selected from hydrogen , an optionally substituted C1 - 6 - alkyl , an optionally substituted C3 - 6 cycloalkyl , an optionally substituted aryl , an optionally substituted aryl ( C . , alkyl ) and an optionally substituted haloalkyl ; R20C can be selected from hydrogen , an option ally substituted C1 - 6 alkyl , an optionally substituted C1 - 6 haloalkyl , an optionally substituted C3 - 6 cycloalkyl , an optionally substituted C , aryl , an optionally substituted C10 15 aryl and an optionally substituted aryl ( C1 - 6 alkyl ) ; and R21C can be hydrogen or an optionally substituted C1 - 4 - alkyl ; or R20C and R210 can be taken together to form an optionally substituted Cz , cycloalkyl . When R20C is substituted , R20C can be substituted with 20

one or more substituents selected from N - amido , mercapto , alkylthio , an optionally substituted aryl , hydroxy , an option ally substituted heteroaryl , O - carboxy and amino . In some embodiments , R200 can be an unsubstituted C . 6 - alkyl , such as those described herein . In some embodiments , R200 can 25 be hydrogen . In other embodiments , R200 can be methyl . In some embodiments , R19C can be an optionally substituted C1 - 6 alkyl . Examples of optionally substituted C1 - 6 - alkyls include optionally substituted variants of the following : methyl , ethyl , n - propyl , isopropyl , n - butyl , isobutyl , tert butyl , pentyl ( branched and straight - chained ) and hexyl 30 ( branched and straight - chained ) . In some embodiments , R19C can be methyl or isopropyl . In some embodiments , R19C can be ethyl or neopentyl . In other embodiments , R190 can be an optionally substituted Cz , cycloalkyl . Examples of optionally substituted Cz , cycloalkyl include optionally 35 substituted variants of the following : cyclopropyl , cyclobu tyl , cyclopentyl , and cyclohexyl . In an embodiment , R19 can be an optionally substituted cyclohexyl . In still other embodiments , Ri % can be an optionally substituted aryl , such as phenyl and naphthyl . In yet still other embodiments , 10 R19 can be an optionally substituted aryl ( C1 - 6 alkyl ) . In some embodiments , R C can be an optionally substituted benzyl . In some embodiments , R19C can be an optionally substituted C1 - 6 haloalkyl , for example , CFz . In some embodiments , R21 can be hydrogen . In other embodiments , R21C can be an optionally substituted C1 - 4 - alkyl , such as 45 methyl , ethyl , n - propyl , isopropyl , n - butyl , isobutyl and tert - butyl . In an embodiment , R21C can be methyl . In some embodiments , R20C and R21C can be taken together to form an optionally substituted Cz cycloalkyl . Examples of optionally substituted Cz , cycloalkyl include optionally 50 substituted variants of the following : cyclopropyl , cyclobu tyl , cyclopentyl , and cyclohexyl . Depending on the groups that are selected for R20C and R21C , the carbon to which R20C and R21 are attached may be a chiral center . In some embodiment , the carbon to which R200 and R210 are attached may be a ( R ) - chiral center . In other embodiments , » . the carbon to which R20 and R 1° are attached may be a ( S ) - chiral center .

Examples of suitable

?? ; ? ? w

Systy x x X 4X4

x84x844 1 . 0x104

– 0 H?C , H - HzCH w

HN

- H3C

HN HN

- H3C H

HN O

60

R1900 . R200 R210 I

IZ 65

65

5 YYYYY and 10

? 1111 *

260 - LILL 2

US 9 , 815 , 864 B2 66

- continued an unsubstituted C3 - 6 cycloalkyl . A non - limiting list of C3 - 6 cycloalkyls include cyclopropyl , cyclobutyl , cyclopentyl and cyclohexyl . In some embodiments , RC can be an optionally substituted O _ C1 - 6 alkyl . In some embodi ments , R3C can be a substituted - 0 C1 - 6 alkyl . In other embodiments , R3C can be an unsubstituted - 0 C1 - 6 alkyl . Examples of suitable 0 C1 - 6 alkyl groups include methoxy , ethoxy , n - propoxy , iso - propoxy , n - butoxy , isobu toxy , tert - butoxy , pentoxy ( branched and straight - chained ) and hexoxy ( branched and straight - chained ) . In other embodiments , R3C can be an optionally substituted - 0 _ C3 - 6 alkenyl . In some embodiments , RºC can be a

substituted — O - Cz alkenyl . In other embodiments , R3C can be an unsubstituted - 0 C2 alkenyl . In still other embodiments , R3C can be an optionally substituted - 0 Cz . , alkynyl . In some embodiments , R3C can be a

In some embodiments , R1C and R2C can be the same . In substituted 0 C3 - 6 alkynyl . In other embodiments , R3 other embodiments , R1C and R2C can be different . can be an unsubstituted - O C2 . alkynyl . In still other

In some embodiments , R1C can be embodiments , R ' can be cyano . 20 The substituents that can be present on the 3 ' - position of the pentose ring can vary . In some embodiments , R4C can be OH . In other embodiments , R4C can be an optionally sub stituted O - linked amino acid . Examples of suitable O - linked

R16C0 — P - 0 + P — 0 os amino acids include alanine , asparagine , aspartate , cysteine , OR17C OR 18C glutamate , glutamine , glycine , proline , serine , tyrosine , argi

nine , histidine , isoleucine , leucine , lysine , methionine , phe nylalanine , threonine , tryptophan and valine . Additional

and R2C can be o or OH , wherein R16C , R17C and R18C can examples of suitable amino acids include , but are not limited be absent or hydrogen : and n can be 0 or 1 . Those skilled in 20 to , ornithine , hypusine , 2 - aminoisobutyric acid , dehydroala the art understand that when R16C , R17C and / or R18C are nine , gamma - aminobutyric acid , citrulline , beta - alanine , absent , the associated oxygen will be negatively charge . In alpha - ethyl - glycine , alpha - propyl - glycine and norleucine . In

some embodiments , the O - linked amino acid can have the some embodiments , when n is 0 , the compound of Formula structure ( III ) will be a diphosphate . In other embodiments , when n is 1 , the compound of Formula ( III ) will be a triphosphate . 35

A variety of substituents can be present at the 4 ' - position of the pentose ring . In some embodiments , R3C can be an optionally substituted C1 - 6 alkyl . Examples of suitable C1 - 6 - R220 R23C alkyls include methyl , ethyl , n - propyl , isopropyl , n - butyl , isobutyl , tert - butyl , pentyl ( branched and straight - chained ) 40 NH2 and hexyl ( branched and straight - chained ) . In some embodi ments , RC can be an unsubstituted C - alkyl . In other embodiments , R3C can be a substituted C1 - 6 alkyl . For wherein R22C can be selected from hydrogen , an optionally example , RC can be a halogen substituted C1 - 6 alkyl , a substituted C1 - 6 alkyl , an optionally substituted C1 - 6 hydroxy substituted C1 - 6 alkyl ( such as , CH2OH ) , an alkoxy 45 haloalkyl , an optionally substituted C3 - 6 cycloalkyl , an substituted C1 - 6 alkyl ( such as , C1 - 6 alkyl - O _ C1 - 6 alkyl optionally substituted Co aryl , an optionally substituted C10 and CHOCHZ ) , a sulfenyl substituted C1 - 6 alkyl ( for aryl and an optionally substituted aryl ( C1 - 6 alkyl ) ; and R230 example , C1 - 6 alkyl - s - C1 - 6 alkyl and CH SCHZ ) , an can be hydrogen or an optionally substituted C1 - 4 - alkyl ; or azido substituted C - alkyl or amino substituted C - alkyl . R22C and R23C can be taken together to form an optionally In some embodiments , RC can be a C1 - 6 haloalkyl . For 50 substituted C3 . 0 cycloalkyl . example , R3C can be a C1 - 6 bromoalkyl C1 - 6 chloroalkyl or When R22C is substituted , R22C can be substituted with a C - fluoroalkyl , such as CH Br , CH , C1 , CH F , CHF , or one or more substituents selected from N - amido , mercapto , CHFCH3 . In other embodiments , R3C can be a C1 - 6 azido alkylthio , an optionally substituted aryl , hydroxy , an option alkyl ( for example , N2CH2 - ) . In still other embodiments , ally substituted heteroaryl , O - carboxy and amino . In some R3C can be a C1 - 6 aminoalkyl ( for example , NH CH2 – ) . In 55 embodiments , R22C can be an unsubstituted C1 - 6 - alkyl , such other embodiments , RC can be an optionally substituted as those described herein . In some embodiments , R22C can C2 alkenyl . In some embodiments , R3C can be a substituted be hydrogen . In other embodiments , R22C can be methyl . In C2 - 6 alkenyl . In other embodiments , RC can be an unsub some embodiments , R230 can be hydrogen . In other embodi stituted C2 - 6 alkenyl . For example , RC can be ethenyl , ments , R230 can be an optionally substituted C1 - 4 - alkyl , such propenyl or allenyl . In still other embodiments , RC can be 60 as methyl , ethyl , n - propyl , isopropyl , n - butyl , isobutyl and an optionally substituted C2 - 6 alkynyl . In some embodi - tert - butyl . In an embodiment , R23C can be methyl . Depend ments , RC can be a substituted Co . , alkynyl . In other ing on the groups that are selected for R22C and R23C , the embodiments , R3C can be an unsubstituted C2 - 6 alkynyl . carbon to which R22C and R23C are attached may be a chiral Suitable C2 - 6 alkynyls include ethynyl and propynyl . In yet center . In some embodiment , the carbon to which R22C and still other embodiments , R3C can be an optionally substituted 65 R23C are attached may be a ( R ) - chiral center . In other C3 - 6 cycloalkyl . In some embodiments , RºC can be a sub - embodiments , the carbon to which R22C and R23C are stituted C3 . 6 cycloalkyl . In other embodiments , R3C can be attached may be a ( S ) - chiral center .

mm

US 9 , 815 , 864 B2 67 68 Examples of suitable Examples of suitable

mm - 0 R220 R230 ,

NH2 NH , include the following :

an unsubstituted C2 - 6 alkynyl . In some embodiments , R?C can be a substituted C2 - 6 alkynyl .

In some embodiments , RSC can be hydrogen . In other embodiments , RSC can be halogen , such as fluoro or chloro .

5 In still other embodiments , R $ C can be ORID . For example , RSC can be OH . In some embodiments , R5C can be OC ( O ) R " D . In other embodiments , RSC can be an optionally sub stituted O - linked amino acid . In still other embodiments , RSC can be azido . In yet still other embodiments , RSC can be NR2DR3D . For example , RSC can be amino , a mono - substi tuted amine or a di - substituted amine . When RSC is an optionally substituted O - linked amino acid , in some embodi ments , RD4 can be selected from hydrogen , an optionally substituted C1 . 6 alkyl , an optionally substituted C1 . 6 haloalkyl , an optionally substituted C3 - 6 cycloalkyl , an optionally substituted Co aryl , an optionally substituted C10 aryl and an optionally substituted aryl ( C1 - 6 alkyl ) ; and RDS can be hydrogen or an optionally substituted C1 - 4 - alkyl ; or

20 RD4 and RDS can be taken together to form an optionally substituted C3 . 6 cycloalkyl . Examples of suitable O - linked amino acids for R include , but are not limited to :

w

R230

NH2 , NH2 ,

H

mm

tyyty txt byty

tyr

NH2 , NH2 ,

25 m - HC mm - 0 RD4 RDS

NH2 ) H2 NH2 , NH2

30

0 H m

* * * 141110

type " na sa kanilang txty

include the following :

NH2 , NH2 ,

ma mm mm mawa LO Hz

tyyty NH2 NH2

NH , NH2 and and NH2 . 35

- 0 RD4 RDS - 0 RD4 RDS In still other embodiments , R4C can be OCO R " C ,

wherein RC can be an optionally substituted C1 - 24 alkyl . In some embodiments , R " C can be a substituted C - 12 alkyl . In other embodiments , R " C can be an unsubstituted C1 - 12 alkyl . 40 In still other embodiments , R " C can be a substituted C1 - 8 0 H3C , H alkyl . In yet still other embodiments , R " C can be an unsub stituted C1 - 8 alkyl . In some embodiments , R4C can be an optionally substituted acyl . In other embodiments , R4C can be – OCO ) R " C , wherein R " C can be selected from an 45 optionally substituted C1 - 12 alkyl , an optionally substituted C2 - 12 alkenyl , an optionally substituted C2 - 12 alkynyl , an optionally substituted C3 - 8 cycloalkyl , an optionally substi tuted C5 - 8 cycloalkenyl , an optionally substituted C6 - 10 aryl , an optionally substituted heteroaryl , an optionally substi - 50 tuted heterocyclyl , an optionally substituted aryl ( C1 - 6 alkyl ) , an optionally substituted heteroaryl ( C1 - 6 alkyl ) and an optionally substituted heterocyclyl ( C1 - 6 alkyl ) . In some embodiments , R " C can be a substituted C1 - 12 alkyl . In other embodiments , R " C can be an unsubstituted C1 - 12 alkyl . 55 NH2 and

Various substituents can be present at the 2 ' - position of the pentose ring . In some embodiments , RÓC can be hydro gen . In other embodiments , RC can be halogen , for In some embodiments , R6C can be hydrogen and RSC can example , fluoro . In still other embodiments , RC can be an be halogen . In other embodiments , RSC and R6C can be both optionally substituted C , alkyl . In some embodiments , R6C 60 halogen . For example , R and Rº can be both fluoro . can be an unsubstituted C1 - 6 alkyl . In some embodiments , Various optionally substituted heterocyclic bases can be RC can be a substituted C . alkyl . In yet still other embodi - attached to the pentose ring . In some embodiments , one or ments , R?C can be an optionally substituted C2 - 6 alkenyl . In more of the amine and / or amino groups may be protected some embodiments , ROC can be an unsubstituted C , alk - with a suitable protecting group . For example , an amino enyl . In some embodiments , RÓC can be a substituted C2 - 6 65 group may be protected by transforming the amine and / or alkenyl . In some embodiments , R " can be an optionally amino group to an amide or a carbamate . In some embodi substituted C2 - 6 alkynyl . In some embodiments , RC can be ments , an optionally substituted heterocyclic base or an

- 0 H 11

NH2 .

US 9 , 815 , 864 B2 69 70

In some embodiments , B1C can be optionally substituted heterocyclic base with one or more protected amino groups can have one of the following structures :

RBC2 NH

NH N NH2 NH2 . 10 min

N RAC2 RAC2 N N RCC2

min In other embodiments , BIC can be NHREC2 O

RDC2 RFC2 WN NH

15 ANH 15

Y3C

un mus 20

ORGC2 In still other embodiments , B1C can be

NH2 25 25

N N RHC2

win and n on RFC2 NH

wherein : R4C2 can be selected from hydrogen , halogen and 30 NHRC2 , wherein RC2 can be selected from hydrogen , - C ( O ) RKC2 and C ( O ) OR C2 ; RBC2 can be halogen or NHRWC2 , wherein RWC2 can be selected from hydrogen , an optionally substituted C1 - 6 alkyl , an optionally substituted 35 Suc C2 - 6 alkenyl , an optionally substituted C3 - 8 cycloalkyl , - C ( O ) RMC2 and — CEO ) ORNC2 ; RCC2 can be hydro gen or NHR2C2 , wherein RDC2 can be selected from hydro gen , C ( O ) RPC2 and C ( O ) OROC2 ; RDC2 can be ?? selected from hydrogen , halogen , an optionally substituted C1 - 6 alkyl , an optionally substituted C2 - 6 alkenyl and an No . optionally substituted C2 - 6 alkynyl ; REC2 can be selected from hydrogen , hydroxy , an optionally substituted C1 - 6 alkyl , an optionally substituted C3 - 8 cycloalkyl , C ( 0 ) 45 In yet still other embodiments , B1C can be RRC2 and CEO ) ORSC2 ; RFC2 can be selected from hydrogen , halogen , an optionally substituted C1 - 6 alkyl , an optionally substituted C2 - 6 alkenyl and an optionally substi tuted C2 - 6 alkynyl ; Y2C and Y can be independently N 50 ( nitrogen ) or CRC2 , wherein RC2 can be selected from hydrogen , halogen , an optionally substituted C1 - 6 - alkyl , an optionally substituted C2 - 6 - alkenyl and an optionally sub ' N TO stituted C2 - ? - alkynyl ; RGC2 can be an optionally substituted C1 - 6 alkyl ; RHC2 can be hydrogen or NHRTC2 , wherein RTC2 can be independently selected from hydrogen , CEO ) for example , RUC2 and C OORVC2 ; and RKC2 , R2C2 , RMC2 , RNC2 , RPC2 , R2C2 , RRC ? , RSC ? , RUC2 and RVC2 can be indepen NH2 dently selected from C1 - 6 alkyl , C2 - 6 alkenyl , C2 - 6 alkynyl , 60 C3 - 6 cycloalkyl , C3 - 6 cycloalkenyl , C6 - 10 aryl , heteroaryl , heteroalicyclyl , aryl ( C1 - 6 alkyl ) , heteroaryl ( C1 - 6 alkyl ) and heteroalicyclyl ( C1 - 6 alkyl ) . In some embodiments , the struc oor N tures shown above can be modified by replacing one or more 65 hydrogens with substituents selected from the list of sub stituents provided for the definition of “ substituted . ”

NHREC2 RDC2 IN y3C

min

nin min

US 9 , 815 , 864 B2 71 72

In some embodiments , RDC2 can be hydrogen . In other embodiments , BIC can be

- continued

RICO BIC RBC2 20

nr 7 . 11111H . . 11H . R6C och RSC

NN 10

worten In some embodiments of this paragraph , BiC can be an optionally substituted purine base . In other embodiments of

In some embodiments , RBC2 can be NH , . In other embodi this paragraph , B1C can be an optionally substituted pyrimi ments , RBC2 can be NHRWC2 , wherein RWC2 can be 15 WC2 can he 15 dine base . In some embodiments of this paragraph , B1C can - C ( O ) RMC2 or - C ( O ) ORNC2 . In still other embodi be guanine . In other embodiments of this paragraph , BC can ments , B1C can be be thymine . In still other embodiments of this paragraph ,

BC can be cytosine . In yet still other embodiments of this paragraph , B ' can be uracil . In some embodiments of this

20 paragraph , B can be adenine . In some embodiments of this ORGC2 paragraph , RIC and R2C can each be an optionally substi tuted C - 4 alkyl . In other embodiments of this paragraph , R14 can be an optionally substituted acyl . In still other embodiments of this paragraph , RIC and R2C can form a

25 mono - , di - or tri - phosphate . In yet other embodiments of this paragraph , R1C and R2C can each be an alkylcarbonyloxy alkoxy . In some embodiments of this paragraph , R4C can be OH . In some embodiments of this paragraph , RSC can be F

In some embodiments , BIC can be or Cl , and RC can be hydrogen . 30 Examples of suitable compounds of Formula ( I ) include ,

but are not limited to the following : ORGC2

RHC2 mu

35 NH ,

N NH2 . HO N311 !

waar

40

In some embodiments , the compound of Formula ( III ) can have one of the following structures :

NH2 ,

HO 45 RICO RIC No .

016 Réel BIC : HT In YH , ROC 50 - NH2 ,

RSC HO

RIC OH H

BIC . 55

IV Y . 1111H , NH2 NH2 4 ARC ©

" 111050 RICO RIC / 60

LH ?? N o HO BIC

H . . Youll1H or 110 . SUH H ROC 65 . 11111 1111 *

R4C RSC HO

US 9 , 815 , 864 B2 73

- continued 74

- continued NH2

?? ?? HO ' N HOTO N N NH2 ,

111111 * * H3C

* * * 1116 11111 NH ) NH2 0

NH 15

O , HO HO OY HO í ó LOH - OH

HR Hz CLK ittills Hzci u CI C . * 11111 * 11111 HOW HOSE

1111 " E

NH2 NH

HN

HO - OH N O , HO — HO e N

Xullll - OH 11111

1111 1111 11107 NH NH2

AN - OH NH2 HO NO , HO

111111 F — TY * * * * * 1111 •1111 ,

NH2

?? - CN CNH ,

Best Boererate HOON HOM

HzCOHOL 111111 * 1111

NH2

HO - OH NNCNH NH2 ,

111113 H3COM " 1111 HO * 1111

US 9 , 815 , 864 B2 76 75

- continued - continued NH2

HOM N N NH2 , ??

* * NSPIRED ? 101

HO H? F NH2 NH2

NO LOH NÖ LOH - OH N '

* * tul

* + ! 1115 * 11111

NH2 NH2 NH2

?

- OH N ?? N o ?? N

H3C C1 11111 be

* 11116 H3C H3C Home Os * 1111 HzC ' HOW NH2

NH2 can

NH2 - OH

- SO ' H

•11111 HO — NH2 NH2

Cl

+ 38111

HO N o HO N ON

Br — * U1111 CI 11161

110 * 111 Olli .

HO . NH NH , NH

NY HO N O HO g ?? Ben . .

* * * 111111 ?

* 11110 * * 1111 HOW * * 1111

H?

_ US 9 , 815 , 864 B2 77

- continued - continued NH NH )

HN , ?

- OH N - UH _ H0 - r ?

{ iiitiir ? ?????? Cl 10

d°° •• MIHIC Hd ' 1f ; &

NH

_ c

H0 ?? 0 NH ,

M , clini - UH

? NH2 30 » MINI

HO 11116 NH ? 25

H

???? H } | NSNNH ) , - UH k 30

_ ? ? uftiil : - iiitito ?

, ifii ? » liil - X

HN 35

, N ? NH ,

H0 4f0

- ' iiliu ?

) . iiii ? ; _ $

" [ . fifiimo NH , 45 Iithuc

;

H } HgC - CH ; 50

F iiiuit ?

NH } - ino ?????

55 _

" N

NH { { { # # # # • 60 E 18

H } ) tiii ?

- liO ?? . . °HO 65 H , c

US 9 , 815 , 864 B2 08 79

- continued NH

- continued

HN

N ?? N NH2 ,

1113 N3 — 10141 WH 1111 . 1111

HOF NH ,

NH2

HO HOS H3C * + 1111

HONY CHz ul

HO - NH - OH N o NH2

je 1111ll NY

H3C6 * 1111 ?? HO ?? , HO N

NH2 N — Y Y N3 111111 Naz * * *

T ? + 1111

- OH - 0 , HOG .

11 i F HN NH2 1111 H3C 111 5

e

NH2 HO HOM HO - 10 * * * N ; — NH ill

111111 11 HO O , HOG ?? N to

110111 F

11 .

HOS •11111

NH

- OH _ N NX HO “ CHN .

N3 – 111111 Nz1000 * 1111

HOME

US 9 , 815 , 864 B2 87 82

- continued - continued NH2

NH , NH

HO . HO N N NH2 , "

0

AM HO - NO Una

10 1111 * y * + 1111 1110 Nz — , N2 - HO 1111 NH2

11111

NH2 HO NN

HN LECH 20

- OH N7 CNH , NH2

Ann 25 HOSH - OH 1 N " NH2

. F M Xo - CH3

30 HG ?? N o .

OCH2CH3 CH3 35 HOW OH

HO N NH2 , HN F 40

CH3 HO N N NH2 , HO POH H

LCH ; NH2 45

NH2 NH

NH HO N o , HO H0 – 50

- OH so , HO ?? P1111 P1111 CH3 CH ;

Fly yul . 2 A11025 CH S CH ; 55 1111 . •11111 55

HN NH

- OH N ?? NH2 ,

1113

111111 HOCH ;

US 9 , 815 , 864 B2 83 84

- continued - continued NH2

HN

- OH N N NH2 , HO N 0 .

felly A1111 10 CH3 1111

HO El HO NH2

?? 15 1 = HO - OH - OH

T pita F — - IHRE CN bach ; CN liiii .

20

HO NH , HOW OH NH ,

25 NH

- OH ??

. ! " F 111 11

30 CH3

HOW SHE HN 35

?? HO HO . " OHNN NH

40 * * 111110 HOS NH2 , 1111

NH2 NH2 NH2 45

HO HO ??

50

CI - UHR CH3 CH3

POH POH 55

NH2 NH2

NH NH

- OH OH ON OH LoH HO H0 N O , HO — OLOH N H0 VOY F — Llach 11111 HECHHO H3C1 LL CH3 a — had

HOMH HOSH HOMH

US 9 , 815 , 864 B2 85

- continued NH2 NH2 ,

0 0 NH

5 HO — P - 0 - P - 02P - 0

?? ?? ?? - OH HO 20 CH3

FK ) La FY U13 1111 * H? OH F 0 10 * 1111

NH2 NH2 NH2 O

N " ILIV 15 15 HO — P - 0 - 2 - 0 - 2 - 0

?? 9 -

O . ?? HO ?? HOG CH3

11 111111 F ( L . 20 NH2 11111 tull

NH2

25 HO — P - O - o = & _ 5 O - P - 0

H? | H? HO HOM NIIN F - 1 VT F

CH3 30 OE

NH

NH HO — P - O - P - O - P - 0 35

?? ?? ?? - OH

F11 11100 = 40

NH

HO — P - 04 P - 04 P - 0 NH 45

OH OH OH HO N O and and

. 491115 , A O WECH 50

110 POH NH

NH2 HO — P - 0 - P - 0 - P - 0 11 N NH2 ,

55 55 ?? ?? ?? DI

Ho Yo HOSH Nz — 119T 1110

09 NH

O OE 1111 -

HO HO — P - O - P - O - P - 0 1 N N NH2 , H ?? ?? ?? Nill 65 or a pharmaceutically acceptable salt of the foregoing .

Additional examples of a compound of Formula ( 1 ) include the following :

1111

US 9 , 815 , 864 B2 87 88

- continued - continued NH

5 C

i i i O =

HO — P - O - P - 0 - P - 04 N HO — P - O - P - - P - 02 N NH2 , HO HO HO OH ?? . flint .

M

4OH 10

NH , NH2

15 EO =

O = HO — P - O - P - O - P - 0

HO - o = 45 P - 0 - P - 0 - 0 - 0 HO HO HO

OH OH OH HO 11 . 00 | CA

20 111

NH2

25

HO - P - 0 - 0 - 0 - P - 0 N HO — O - P - O - P - 0 P -

OH HO HO HO OH 1111 * OH 30 * * 1111

11111 NH2

He tutte Ha Ha to the Hyttban # byth High tuote that

NH2 35

O O 0 0 = =

A A HO — P - 0 - 1 - 0 - P - 0 N = = = HO — P - O - P - O P - 0 – O HO ?? HO HO HO 40 1110 * *

HO HO HO

45

O

= =

A

50 HO — P - O - P - O - P - 0 N NH2 HO — P - 0 - P - 0 - P - 0 NCN CNH , HO HO HO

HO HO HO H3CORA * *

HOS 55

NH2

' N 60 60 O

HO — P - O - P - 0 - P — 0 – N " O , =

A HNNN HO — P - 0 - P - 0 - P - 07

?? ?? ?? HO HO HO ?co1141

re 65 HOW HOME

US 9 , 815 , 864 B2 68 90

- continued - continued NH2

0 0 0 0 0

HO — P - 0 - P - 0 - P - 0

?? ?? ??

o = N N NH2 , HO — P - 0 - P - - P - 0

VEC ?? ?? ?? 10

HzC * * ! ! 15

NH O

o = 15 =

HO — P - 0 - P - 0 - P - 0 A =

A _ . HO HO HO — P - O - P - O - P - 0 ?? HO ?? ?? HO 1111111

20

H2C NH2 HOME * 1111

NH2 25

O O

H0 — P - 0 — P - 0 - P — 0 O = 4 - 2 O , = =

A HO HO HO — P - 0 - P - 0 - P - 0 HO IN

H? HO H? HO H? ?? * * *

* + 1011 Br 30

. 2015 m U ' Hy Http Italia + the HHH Ha & . tytta

NH2 NH

35 O

HO — P - 0 - 0 - 0 - P - 0 0 0 = =

A HO — P - 0 - P - 0 - P - 0 O . HO HO ??

?? ?? ?? 40 11111 * * * 111

* 11116

NH ) 45

0 0 0 =

o = HO — P - 0 - P - 0 - P — 0 N

HO — P - O - P - O - P - 0 O , HO HO ?? HO HO 50

HO HO * + 1111

1111 *

55

NH2 NH2

SN 60 _

=

N A HO - P - 0 - P - 0 - P - 0 HO — P - 0 - - 0 - -

OH OH OH HO HO ?? Sun . 65

US 9 , 815 , 864 B2 91 92

- continued - continued NH2

HN .

5 O

= + -

A HO — P - O - P - O - P - 0 – O . HO — P - 0 - P — 0 - P - 0 – A No . ?? ?? OH ?? ?? ?? Ilm "

10 C1 - 1111 11111

NH2 7

15 il

HO — P - O - P - 0 - P - 04 N CN CNH , HO — P - 0 - - 0 - P - 0 N O Hit they ?? ?? ??

HO HO HO CL - - 20 11 .

. 1111 NH ,

0 0 NH 25 25 FO HO — P - O - P - 0 - P - 0 – HO — P - 0 - P - 0 - P - 0 N | CN CNH ) , NH2

HO ?? HO ?? HO ?? ?? ?? 30 . 111 * 111

NH2

N , 35 0 0

=

HO — P - O - P - O - P - 04 HO — P - O - P - 0 - P - 0 ON

?? ?? ?? HO HO HO Cl

40 11111 11111

NH2 NH2 h 45 45

= O o = =

Hi there Hytty

Hoy the HO — P - 0 - o = k _ 5 P - 0 - P - 0 HO — P - 0 - P - 0 - P - 0 NO

50 H? H? H? ?? Jinnas HO HO HO 11

* 1111

un 55

NH2 NH

EN , O 0 0 0 = = o .

HO — P - 0 - P - 0 - P - 04 HO — P - 04 P - 0 - P - 0 N

?? ???? HO HO HO ILO H * * 1116

65 11t .

US 9 , 815 , 864 B2 ? 93 94 - continued - continued

? H H0 HN .

0 + t , _ 0 $ - = ? H07 P - 0 - P - 0 - P - 0

- HO - P - 0 - - - 0 - - HO

- 0 HO HO 2 = ???? 0H _ 0HOH 10 riilimi ?

••11116 118

NH 15 _ 0 _ 0 0

HO - D - 0 - - - 0 - D - 0 S0 , + + + + + + + H0 - P 0 - - - 0 - - - 0 NNT HO HO H }

OH H } H } H _ 0H 20

" NN ANH 25 25

H0 - P - 0 s ?? ?? + + + + + + + - 0 - - 0 0 0

HO H ) HO H07 P - 0 - D - 0 - P - O - - 30 ? cHN ? N

HO HO H

35 " NH 35 NH Hh .

N N ?? NH ?? HO - P - 0 - P - 0 - P - 0 HO HO HO _ 0 _ 0

N : 40 _ H0 - - - 0 - - - 0 - - - 0 ? v

? ? OH OH _ 0H OH 93 iiiihit ?

HR IS llimo ? 45 45

HO - - 0 - - - 0 - - - 0 _ 0 _ 0 0

thy + + + + + + > 0 . + + + + + + + + + + S

50 HO HO H0 HO H0 H0 - P - 0 - D - 0 - - - 0 NV

HO H } HO H0 HO ifti ?

. 1

55

NH , HN

60 0 0 0 H0 - D - 0 - - - 0 - P 7 ? - 0 HO - P - 0 - - - 0 - - - 0 - - -

OH HO H0 H0 HO HO ?????? ?

111111 H , ; runt ???

65 ; vtifi & OH ?

US 9 , 815 , 864 B2 95 96

- continued - continued NH2

NH O

5 =

NH2 , HO — P - O - O = - . P - O - P - 0 –

HO — P - 0 - P - 04 P - 07

???? ?? HO HO 11llll HO , F2HC 10

1111 O

NH

?? 15 1 HO — HH P - 0 - P - 0 - P - 0 – i =

OH OH OH . HO — P - O - P - O - P - 0 Fit A

LCH3 HO HO HO 20 F2HC . nl

NH2 HN 0 0

Ork - E ou N N 25 HO 2 HO - P - 0 - P - 0 - P - 04

?? ?? ?? . NH2 , NE

denly LCH3 o = -

HO — P - 0 - P - 0 - P - 0 HOSH HO HO ?? 30 FH OLIMP

* * 1111 NH

0 0 0

HO — P - 0 - P40 - P - 0 N 35 35

NH ?? ?? ?? Pin = CH

HO — P - 0 - - 0 - - 0

OH HO 40

NH O O 0 S = = =

A - 0 - 0 - 0 - 0 - 0 - 0 - OH A A

45 45 H? H? H? AM

LaCH3 HN

=

HO — P - O - P - O - P - 04 50

?? ?? ?? O O

= =

A

0 H CN AN CNH , .

55 HO — P - 0 - P - 0 - P - 04

?? ?? ?? OH 55 OH Y " ? " 55 A111 ) C = CH ECH

NH2 HOSH O

/ N , 60 HN O

O =

= Hy Hyte HO — P - 0 - P - 0 - P - 0 HO — P - 04 P - 04 P

OH OH OH N NCNH ,

HO HO HO A1111 TECH 65 HOW SH HOSH

US 9 , 815 , 864 B2 97

- continued Usahawan 98 - continued

HN . O O = O 5 =

HO - P - O - P - O - P - 0 ?? ?? ?? HO — P - O - P - 0 - P - 0 Fv

H? OH OH 11l ACH3 10 HOCH

HN O O

= O =

= A NN NH2 , NH HO - P - O - P - O - P - 0 –

HO HO HO 0 O H? H? H? YY 15 15 0

=

LACH : HO — P - O - P - 0 - 0 - 02 HO - R - 01 . N NH2 , H? OH ?? ??? OH LacHz NH2

HOME 1111 20

NH2 = o

HO — P - O - P - O - P - 0 — O

HO HO HO 25 =

A HO — P - 0 - P - 0 - P - 0 N O CH HOMES 1111 OH ?? OH OH OH

CH3

Hur ty

How to that the that the end tutub

HOW TO 30

HN . NH2 N NH2 , HO — P - O - P - O - P - 0

?? ?? ?? 35 0 0 0

HO - P - 0 - P - 0 - P - 04 OH OH OH

LaCH3 NH2

40 40 ?? HN

CN CNH , NH NH2 , HO — P - 0 - P - 0 - P - 0 ?? ?? ??

O 0 0 N ON

L ECH C = CH 45 HO — P - O - P - 0 - - 0 ???? ??

NH2

N , O 0 50

NH HO — P - O - P - 0 - 0 - 0 O

=

?? ?? ?? HO — P - O - P - O - P - 04 o = - 6

55 OH OH OH CECH HOSPH

A1 . 111

HN 60 i i Cho HO — P - O - P - 0 - P - 0 N NH2 HO — P - 0 - P - 0 - P - O

???? ?? F CH ; P111 HOW OH 65

HO OH

HO OH * anillo 65 59 CHO H? H? H?

OH OH OH - 0 - 0 - 0 - 0 - 0 - 0 - OH

- 0 - - 0 - 0 - 0 - d - OH A

60

???

THE 11 + Hof 87 + ???

11 HO 55

H ] dilly OH OH OH | \ ?? H? ?? H? H? ?? NH2 , 0 - 0 - 0 - 0 - 0 - 0 - OH - A

- 0 - 0 - 0 - 0 - 0 - 0 - OH =

O = 0 O 50 50 = O NH NH

) O

NH2 HOSH 45

H? H? H? HO “ HNNN L 0 - 0 - 0 - 0 - 0 - 0 - OH 70 - 01 - 01 CH3

HN HN HOL Y ?? HO HO

2 - 0 - 40 HO HO

P - HO —

40 0 0 - O

O = HO ! ! HOM NH { HOT

35 HO HO HO NN - 0 - 0 - 0 - 0 - 0 - 0 - OH

OH HOW { H ]

* * * ill 30 HTH OH ?? ?? ?? CHN

- 0 - 0 - 0 - 0 - 0 - 0 - OH IL L L HO HO HO

HN É JO 25 - 0 - 0 - 0 - 0 - 0 - 0 - OH 0 = -

o = O

HOOH H 11110H CHN 20

?? ?? ?? HOOH - O - 0 - 0 - 0 - 0 - 0 - 0 - OH N = " , , HO HO ?? HO ??

ON - 0 - 0 - 0 - 0 - 0 - 0 - OH = =

O

HN HOW ZHN

HO , CH3 10 * * 111111 1

OH OH OH OH ! N = 1 , HO HO

N . - 0 - 0 - 0 - 0 - 0 - 0 - OH OH A

- 0 - 0 - 0 - 0 - 0 - 0 - OH O = _ E = 07 O

NH

HN - continued - continued

100 - 155 66 US 9 , 815 , 864 B2

US 9 , 815 , 864 B2 102 101

- continued 102

- continued NH2

AN 5 NH 0 0 O

u = H0 — P - 0 - - 0 - P - 0 HO — P - O - P - 0 — P - 0

HO HO HO 11111

2018 Hby tye Hype tyd

10 CH3 POH

?? NH

AN NH2 , NHA , HO — P - O - P - O - P - 0 HO HO HO HO — P - O - P - O - P - 0

CH ; HO HO HO 20 HOME HOW

-

HN 25

NH

O HO — P - 04 P - 0 - P — 0 5 - =

HO HO HO — P - 0 — P - - P - 0 HO H . CHY / CH3 HO HO ?? 30 IJ 11 * *

11 .

NH2

AN , 35

HO — P - O - P - O - P - 04 _ HO HO HO — P - O - P - O - P - 0 E _ = 0

40 HO HO HOF 11 1111111 F

yy ll

3

45

NH

0 0 =

o = o = A

HO — - P - HO — P - 0 - N P - 0 P - O - 0 - P - P - 0 0

HHH HHH Het

ovoj 50 - 2 50 HO HO HO HO HO HO

* * 1111

HOMH 55

NH

NH 60 0

0 = DEO A HO - P - 0 - P - 0 - P - 0 HO — P - 04 P - 0 - P - 0 _

OH OH HO HO HO 01 — 1C E

HOM 65 " 1111

US 9 , 815 , 864 B2 13 00 00 103 104 - continued - continued

NH2 NH2

LN 50 AN , 5

HO — P - 0 - - 0 - - 07 HO HO HO

_ = 0 HO — P - O - P - O - P - O

HO HO HO *

F lll CH ; LCH ;

HOW POH BH NH2

NS NH

o

o = HO — P - 0 - P - O - P - 04 O , HO — P - 0 - P - 0 - P - 0 — = - . _ HO HO HO HO HO HO

F

NH NH NH

N HO — P - 0 - P - 0 - P - 04 o HO - 1 - 0 - - 0 - - 09 HOW ?? ?? ??

30

CH3 HO POH OH °F

HHH Hutbe Hettad HH Hy Hy Het

35 HN . NH

O

= =

A HO — P - 0 - 0 - 0 - P - 0 HO — P - 0 - P - 0 - - 0 HO HO HO HO E ?? ?? ?? 111 * 40 All

100 ML OH °F NH2

45

HN .

0 0 0 DEA HO — P - 04 P - 04 P - 0 HO — P - O - P - O - P - 0 O .

HO HO HO HOF 50 HO HO HO HO F1 111111

HOS OH ' F

55

0

NH NH

60

HO — P - 0 - P - 0 - P - 0 HO — P - 04 HO HO HO F F - 1101 111111 1

.

HOW H , 65 11 HOME

US 9 , 815 , 864 B2 105 106

- continued NH2

=

HO — P - 0 Se SO . 0 - P - 0

H?C NH OH CH3

HOSH * 1111

H3C o total to

CO

HN ,

0 A 0 - P - 0 N De O

ON HO — P - 0 H?C H3C

NHÉ å

HO FH C " 1111

HzC O HOS 111

NH2 NH

NN 30

HO — P - 0 0 - P - 0

11 WCH3 35 Hiltic HOSH POH 11111

HC 07

40

NH NH O

= try these a HO — P - 0 - CN CNH , and and 45 45 O - P

?? OH FOLLACHz CH3

ANI . HzCNH H3C

HOS 11111 50 H3C 0

NH2

55

HN .

HO

O - P - 04 N F

1110H HOSH # 1111

or a pharmaceutically acceptable salt of the foregoing . 65 Further examples of a compound of Formula ( I ) include ,

but are not limited to the following :

US 9 , 815 , 864 B2 107

- continued 108

- continued NH2

HN

O = AO P — 02 O - P - 0 N

- 1 10 uns .

HOW * * ! 111

TO

NH2 E

NH2 OA 0 - P - OVO - P - 0 O , 20

* * 111lll

ZN O , 1111 HOF HzC / N - - 05 HzCN H _ 111 ) H?c , NH NH

25 11

NH2

30 NH

- JEO 0 O = e

- P - - 0 N NH2 ,

HzCOLLA 1111 1111

ä

t ??

NH O - P - 0

11111

FO * + 1111 0 - P - 0 HO

H?c , LNH ? 110111

* * * 111

NH2 ?

NH2

O N

§ 111111 . )

N TO * * 1111

* * *

lll

i 1111 *

US 9 , 815 , 864 B2 109 110

- continued - continued NH2 NH2

5

* * 100l Mitte

1116 111

NH2

HN way O - - 0 N N NH2 NH2 ,

111 *

* 1111

HN

NH2 4 0 HzC NN NH2 ,

CH3

To , 45 * * 111

•11111 ?? ?? .

N

1111111 .

1

NH2

11111

US 9 , 815 , 864 B2 112 111

- continued - continued NH2

NH

5

0 - P - 04 H3C \ / 17 - P - 0 NH2

Ó - Nat CI

10 * * 1111 1113

NH2

NH2 HC

N

20 CH3 C1 CILIH O - P - 0

•1111 NH2

25 1111

H3C M4 o

30

+ 1111

35 NH

Hz4 NH2

O - P - 04 40

HICO

- P - 0 . °CI — HAY 45

50

NH2

55

NH P — 0 N

0 - P - 0 A NH2 , 60

till * + 1111

65

US 9 , 815 , 864 B2 113 113 114

- continued - continued NH2

NH2

H2C N - P - _ _ o 0 H?CH NH NH . LO V31110 . 1111 + 1111

HOROS * 11111

OH NH2

HN . O ,

DEA O - P - 0

1111 . 13 * llll

101

HO 30 30 HO NH

O

=

0 - 0 A - 0 - 35 NH2 H? ' JH HN . stillil

H3C N

H3C HOW O = A

40 O - P - 0 N

? ?? ???

O = Unit - P - 0 45

* 1111

50

HO

HN 55

NH

- P - 0 =

03 - o = Az 0 N -

11111 1111

HOS

US 9 , 815 , 864 B2 115 116

- continued - continued NH ,

NH

N3 - 10 - P - 0 * * 1111 H3CN

- H?c , LNH . N3 INH

•11111

SO . NH

NH2 N3 Nz16 1100 20

119 .

NH2 N3 onill .

25

NH2

NH

0 . O 0 - - 0 - ?ó # tullo 11 NH 11111 N3

NH

N

NH

N37 =

0 - P - 0 1011 -

H3CNH 111111H 39

1111111 NH2

HN , lith

ON * * 11110 0

HOW * 1111

US 9 , 815 , 864 B2 118 117

- continued - continued NH2 NH2

O

=

0 — P - 0

11 N3

10 . 111 *

NH2 NH W

=

0 . - P - 0

- P - 02 N L ECH N2

HOW * 11111 NH2

0 - PC

NH

SCH

OH OH

??

- 0 N On = ASC ma N3 NH

HOT * * 1111 WA 0 - P - 0 N N NH2 , NH2

NH NH SCH

HO HO

HN .

is P - 04 NH , P — 0

lenne NH

HOW 111 TO | Lc = CH

ÕH OH

US 9 , 815 , 864 B2 119

- continued 120

- continued

" NH NH

=

0 - 20 0 - d - 0 ?? =

N

HN

CH 10 ? 3 = HD

OH OH OH OH

15

HN .

NH 0 d - 0 -

?? ???

?? 20 0 - P0

?? C = CH CH HN

ÕH ÕH ? C = C - CH , :

OH OH 25

F

???? ?? ?? ????

?? NH

NH =

= 0 . d - - 0 - 0 - 20

NH ??? NH

C = CH ??? C = CI ?? ,

OH OH OH OH

NH ) = NH

P0 SO =

0 d - - 0 NH

CH = ) ?? NH C = CH

c = CH OH OH " TTTTT IIIIII :

NH - NH

=

=

0P . 2 ?? 0 Nxx | CN CNH . NH2 ,

NH N NH

? c = CH c = CH : : ?? OH OH OH OH

US 9 , 815 , 864 B2 121 122

- continued - continued

NH HN . ? ?? 0 - P0 NS 0 0 - P - 0 ?

HN NH 0 11111 C = C ? 10 CH3

HQ HQ HO OH

NH ?

NH ???? 0 d - - 0 - 2 - P - 0

NH NH

FIIII ? 20 ? ? CH

C = CH ,

OH OH

25 HN . = (

0 0 - P - 0 50 .

| NH ?? = ??? 0 - 20 10 : 3 ) , CH ??

NH on ? ? c = C -

OH OH 35 NH

0 d - 0 - - No . | ( HN .

= / 11 / ?? 4 { CH , P - N

on NH

?? C = CH , 45 OH OH OCH2CH ,

NH - 0 - - 00 N 5 ( ) NH2 , = o

NH ????? - ? P - 0

CH ,

, CH ?? 55

OCH2CH ,

HN HN 09 NS 66 ) - (

- 0 - d - 00 00 - P - 0 N NH , , CN CNH , NH NH ???? ?? ????

CH3 C ?? Ho H

US 9 , 815 , 864 B2 123 124

- continued - continued OCH2CH3

NN NH

O = RG 0 - - 0 N O = A - 7 00 - P - 04 N . N NH2 ,

NH HN Flis 11 AnnA CH3 CH3 10 11 .

OH

NH NH

= 0

) 0 — P - 0 N . O 0 - P - 0

— NH F0000 ] Anita F A101 WSCH 20

HOW

NH " NH O 25

=

O A 0 - P - 0 0 . O - 0 - HNN NH HN FRON Ann

LCH3 30 * 111116 POH

OCH2CH3 NH 35 - 0 - 0 - 0 . O

NV NH NH NH2 , 00 - P - 07 111 "

NH240 NH OCH2CH3

A

* 11111 CH3 HI

- 0 - 0 - 00 45 N N NH2 , NH OCH2CH3 * ?? .

+ tul 1111 N O ??

50 OCH2CH3 O 0 - P - 0 - N IZ NS Ali

CH ; OO - P - 02 N NH2 , 55 NH

OCH2CH3 HOMH OCH CH3 ,

N 09 =

A OO - P - 07 N CN7 CNH , 00 - P - 02 NH HN

CH3 NH2 CH3 6 mus HO HOMECL

US 9 , 815 , 864 B2 125 126

- continued - continued

NH HN ,

HO — P - 0 O - O = A - O P - 0

NH 11117 A111111 CH3 10 CH3

?? HO

OCH2CH3

? 15 O = - Z

- 0 - 0 - 00 NH2 NH NH FIN

=

1111 ç 20 0 . O 0 - - 0 - OCH CH3 NH

LCH N OE B 25 - P - 04 NH2 NH

NH CH O

=

POH 30 O 0 - P - 0

HN

CH3 NH * * 11110 OH 35

= AO 1111

H3 40 HOMH ??

NH

O =

- P - 0 N . O A -

45 O

P111 * CH3

HOSH NH O

=

50 A O . O - O -

NH 1111

* 1501110 55

HN . O

=

A No . - HN C . O

A =

CH ; 00 - P - 0 A * 111tl HOC NH 111

CH ;

US 9 , 815 , 864 B2 127

- continued 128

- continued

HN O

= O 0 - P - 04 m O - P - 02 A

HN . A 10 NH , ,

# 1111

HOW CH ;

OH

00 - P - 0 N NH

HN 20 131 NH2 , A JA HN HN - PJ0n

NH NH - . A 1

LCH3 H 25 25 HOW

O 0 - P - 04

30 HN NH2 ,

* 1111 NH

HN 35

00 - P - 0 – 40

NH NH2 A1111

NH , 45

N

O

=

0 . O 0 - - 0 - A No OO - P - 0 50

HN NH 1111 " NH2 , CH3

* * 011

NH2

55

OSA 0 . O - 0 - - O - d - OO

NH NH NH NH2 , * * 11111

US 9 , 815 , 864 B2 129 130

- continued - continued

5 NH O

O = =

A O 0 - P - 0 0 P - 0 ' N

HN NH2 P1111 F - I

CH3 * 11111 . tillo

OO - P - 02

NH NH NH2 , 20 * 1111

NH O

=

A

NH2 ,

A Fin L Lach HOW OH

- 0 - 0 - 00 O NH

NH2 ,

* * 011

NH

- P - 0

O 111ly =

A 00 - P - 0 NH NH A1111 * NH ,

2011 met Thought OCH , CH3

55 NH

NS O

=

- P - 0 Na - P - 04 N NH2 ,

60 FLACH $ 11 . ga — L LCH3 CH3 * 1111 POH HOSH 65

US 9 , 815 , 864 B2

| 131 - continued ?i US 981 , 861 B2 132

- continued

OCH2CH3

HN ' N 5 5 O .

NN NH2 , O = P - 0

FI 10 CH3

OH HO POH

NH 15 15

O = P - 06 O . No , -

0

HN F La CH3 Ý BY DJEC 20

F •11110ll NH2 ,

L CH ; HOMH 25 25 AG

, { H ” HOOF

NH2

N .

0 = AO F 111111 . .

NH

HOSH A P - O N . ON -

0

CH ;

HOMH NH2

DA O - P - 04

eetttll

NH O =

HN A 09 O = P - 0 F

CH3 OH still

CH3 65 HOSH

US 9 , 815 , 864 B2 133 134

- continued - continued

OCH2CH3

NH 5 N

0 - P - 0 0 - P - 04 N N NH2 , P1 ) 011111 *

13 CH3 10 1111 OH

LNH5 , 15 NH . NH2

O = A

P - 0 - O

F 20 CH3 HOSH - P - 0

CH 25 POH

" ?? 30 NH2 ,

0 - P - 0 O

=

HO * 0 - P - 02 F -

0

35 / F / HOS OH CHZ

O X CH3 40

- DEA - 0 0

F - HVIT F NH

5 HO CH3

POH 45

0 - P - 0

F 11111 1 L CH3 CH3 50 OH

NH 55

- P - 0

CH ; HOH

60 and

CH3 HO OH

US 9 , 815 , 864 B2 136 135

- continued - continued OCHICH3

NH 5

CN CNH , - P - 0

10 CH3 F 10 10 PCH : * 4

NH )

20 or a pharmaceutically acceptable salt of the foregoing . Examples of a compound of Formula ( II ) include , but are

not limited to , the following : NH ,

( 114 tifA 25

NH

CN NHz ,

EP 4

NHz

INH3 , * *

*

0 - P | | K 011? A

0CH - CH3

XX - XS . xxxxx ¥ 9 xxxxx NON n - NH2 , and So , and

?? , CH FL ? CH3 .

OH 0

US 9 , 815 , 864 B2 138 137

- continued - continued 12

O " ??

H3CH2C0 H?CH _ CO

CI 1111111 CH3 10 10 •11111

ÓH

15 H3CH2C0 — P

H3CH2CO or a pharmaceutically acceptable salt of the foregoing . Examples of a compound of Formula ( III ) include , but are

not limited to , the following : Un

20 * * 1111

NH2 H3C H3C7 NH2

0 Hzc ' 25 =

=

No and H3CO — P O - and

OCH ; NI 8 111 11111

HOF NH2 H3CCHZ

CH3 O 7 NH2 =

=

H3C H307

HzC HzC0 — P

OCH3 nr .

Cl 6 * * 1111

.

TO * 1111

NH2 5

H3CCH CH3

HzC0 — P N "

4 OCH3

CIU Inn .

11111 or a pharmaceutically acceptable salt of the foregoing . Further examples of a compound of Formula ( III ) include ,

ss but are not limited to , the following :

NH2 NH2

=

A HzC0 — P Be the HO — P - O - P - 0 - P OCHZ

HO HO HO Cl J11111

111nn .

139 - continued

NH2

HO — P - O - P - - P = O

HO HO HO 111111

NH

US 9 , 815 , 864 B2 140

form of the drug for human or veterinary administration . Such notice , for example , may be the labeling approved by the U . S . Food and Drug Administration for prescription drugs , or the approved product insert . Compositions that can

5 include a compound described herein formulated in a com patible pharmaceutical carrier may also be prepared , placed in an appropriate container , and labeled for treatment of an indicated condition . Synthesis

10 Compounds of Formula ( I ) , Formula ( II ) and Formula ( III ) , and those described herein may be prepared in various ways . Some compounds of Formulae ( I ) , ( II ) and ( III ) can be obtained commercially and / or prepared utilizing known

15 synthetic procedures . General synthetic routes to the com o and and pounds of Formulae ( I ) , ( II ) and ( III ) , and some examples of

starting materials used to synthesize the compounds of Formulae ( I ) , ( II ) and ( III ) are shown and described herein . The routes shown and described herein are illustrative only

NH2 20 and are not intended , nor are they to be construed , to limit the scope of the claims in any manner whatsoever . Those skilled in the art will be able to recognize modifications of the disclosed syntheses and to devise alternate routes based on the disclosures herein ; all such modifications and alter

So , 25 nate routes are within the scope of the claims .

OA HO — P - O - P - 0 - P LIK N HO HO HO

NH2

HO — P - 0 — P - O - P HO HO HO HO HO

01 - 11 lini * 11111 Scheme 1

Ral Ra2 30

Bla YouRa

H 52 RS olul R3a R4a ( A )

Ral Bla

YnRa

_ _ I R5a 11

R3a R4a Ral Ra2

HO Bla

HO . . . . IR IR 5a

or a pharmaceutically acceptable salt of the foregoing . Compounds disclosed herein , for example compounds of

Formulae ( I ) , ( II ) and ( III ) , and pharmaceutically acceptable salts of the foregoing , can be administered in various ways . os Examples of suitable techniques for administration include , but not limited to , oral , rectal , topical , aerosol , injection and parenteral delivery , including intramuscular , subcutaneous , intravenous , intramedullary injections , intrathecal , direct intraventricular , intraperitoneal , intranasal and intraocular 10 injections . One may also administer the compound in a local rather

than systemic manner , for example , via injection of the compound directly into the infected area , often in a depot or sustained release formulation . Furthermore , one may admin - 45 ister the compound in a targeted drug delivery system , for example , in a liposome coated with a tissue - specific anti body . The liposomes will be targeted to and taken up selectively by the organ . In some embodiments , a compound described herein ( such as a compound of Formula ( 1 ) , a 50 compound of Formula ( II ) and / or a compound of Formula ( III ) , and pharmaceutically acceptable salts of the foregoing ) can be administered intranasally . In other embodiments , a compound described herein ( such as a compound of For mula ( I ) , a compound of Formula ( II ) and / or a compound of 55 Formula ( III ) , and pharmaceutically acceptable salts of the foregoing ) can be administered via an injection .

The compositions may , if desired , be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient . The pack may 60 for example comprise metal or plastic foil , such as a blister pack . The pack or dispenser device may be accompanied by instructions for administration . The pack or dispenser may also be accompanied with a notice associated with the container in form prescribed by a governmental agency 65 regulating the manufacture , use , or sale of pharmaceuticals , which notice is reflective of approval by the agency of the

3 RSR PX

( B ) Ral Ra2

PG ' 07 You ILIR YouRa

0 HP RS Die . . till ??

Ral Ra2 R140 B14 L0

R24 , . . . ) Y YRA

R 54 11 R34 R

o Bla . . . . . Rº " TIRO

HC Yosul HO or PG20 Rei D

5 ull 4a R *

R140 OBA

US 9 , 815 , 864 B2 141 142

As shown in Scheme 1 , compounds of Formula ( I ) can be - continued prepared from a nucleoside , for example , a nucleoside of Formula ( A ) . In Scheme 1 , R " , R34 , R40 , R54 , and Bla can be the same as R4 , R34 , R44 , R54 , and B14 as described herein for Formula ( I ) , and PG " is a suitable protecting 5 group . The 5 ' - position of the nucleoside can be oxidized to an aldehyde using methods known to those skilled in the art . Suitable oxidation conditions include , but are not limited to , Ral Ra2 Moffatt oxidation , Swern oxidation and Corey - Kim oxida tion ; and suitable oxidizing agents include , but are not limited to , Dess - Martin periodinane , IBX ( 2 - iodoxybenzoic acid ) , TPAP / NMO ( tetrapropylammonium perruthenate / N methylmorpholine N - oxide ) , Swern oxidation reagent , PCC

HO or PG - 0 ( pyridinium chlorochromate ) , PDC ( pyridinium dichro ( E ) mate ) , sodium periodate , Collin ' s reagent , ceric ammonium Ral Ra2 nitrate CAN , Na2Cr20 , in water , Ag2CO3 on celite , hot HNO3 in aqueous glyme , 02 - pyridine CuCl , Pb ( OAc ) - 4 pyridine and benzoyl peroxide - NiBr2 . A hydroxymethyl R24 . . . Y Y RA group can be added to the 4 ' - position of the pentose ring 20 R54 along with the reduction of the aldehyde to an alcohol . The hydroxymethyl group can be added via a condensation HOW 44 reaction using formaldehyde and a base , such as sodium hydroxide . After addition of the hydroxymethyl group , As shown in Scheme 2 , compounds of Formula ( I ) , where reduction of the intermediate compound with a 4 - hy - 25 R24 is an optionally substituted O - C , alkyl , an option droxymethyl group can be conducted using a reducing ally substituted O _ C3 - 6 alkenyl or an optionally substi reagent . Examples of suitable reducing agents include , but tuted _ O _ C , alkynyl , can be prepared from a nucleoside . are not limited to , NaBH4 and LiAlH4 . The oxygen attached for example , a nucleoside of Formula ( A ) . In Scheme 2 , Ra , to the 5 ' - carbon of Formula ( B ) can be protected , and the R2 R3 R4 R5a and Bla can be the same as R4 , R24 , R34 . hydroxymethyl group at the 4 ' - position can be oxidized to an > R44 , R5A and B14 as described herein for Formula ( I ) , and aldehyde using a suitable oxidizing agent ( s ) to form a PG2 can be a suitable protecting group . The nucleoside can compound of Formula ( C ) . Examples of suitable oxidizing undergo elimination and form an olefin having the general agent ( s ) are described herein . An optionally substituted C2 - 6 formula of Formula ( D ) . A compound of Formula ( D ) can be alkenyl or an optionally substituted C2 - 6 alkynyl can be 35 treated with an iodinating reagent in the presence of lead formed at the 4 ' - position using methods known to those carbonate and an alkoxy source to form a compound of skilled in the art , for example , Wittig reagent and n - BuLi , Formula ( E ) . A compound of Formula ( E ) can then be Wittig - type reactions , Peterson olefination reaction , and transformed to a compound of Formula ( I ) through displace Corey Fuchs reaction . An optionally substituted 1 - 6 alky m ent of the iodide with an oxygen nucleophile . can be obtained by hydrogenating the unsaturated group 40 attached to the 4 ' - position , for example , using hydrogen over palladium on carbon . Scheme 3

Alternatively , a compound of Formula ( B ) can be trans formed to a haloalkyl using a suitable agent ( s ) , for example , Ral Ra2 to an iodide using imidazole , triphenylphosphine and iodine ; 45 HO Bla to a fluoro using diethylaminosulfur trifluoride ( DAST ) ; or

YR to a chloro using triphenylphosphine and carbontetrachlo ride in dichloroethylene ( DCE ) . An iodoalkyl can be trans LR5a formed to an unsubstituted C1 - 6 alkyl group using methods known to those skilled in the art , for example , hydrogen over 50 palladium on carbon . A compound of Formula ( C ) can be Ral Ra2 reacted with hydroxylamine to form an oxime . The oxime can be transformed to a cyano group using methods known PG307 to those skilled in the art , for example , using methanesul LGlo . YouRa fonyl chloride .

ut

blo

R4a

0 Bla . R

55 H RS

Rhe Scheme 2 Ral Ra2

Ral Ra2 RAO 20 BA Bla N3 illuRA

IIIIR4 – RSA R $ R3A 14A

until . 65

Compounds of Formula ( I ) , where R24 is an azidoalkyl or haloalkyl can be prepared from a compound of Formula ( B ) .

144

Scheme 5

Ral Ra2

BA . . 11 R4 + R640 — P - Clor OH DEA — R54 R740

US 9 , 815 , 864 B2 143

In Scheme 3 , R " , R3a , R4a , R5a and Bla can be the same as R4 , R34 , R44 , RSA and Bl4 as described herein for Formula ( I ) , PG can be a suitable protecting group and LG can be a suitable leaving group . A suitable leaving group , such as a triflate , can be formed by replacing the hydrogen of the 5 HO hydroxymethyl group attached to the 4 ' - position , and the

R2A . . oxygen attached to the 5 ' - position can be protected with a suitable protecting group ( for example , by cyclization with H the base , Bla , or with a separate protecting group ) . The leaving group can be replaced with an azido or halo group 10 using a metal azide reagent or metal halide , respectively . An example of a suitable metal azide is sodium azide . An example of a suitable metal halide is lithium chloride . AC , azidoalkyl at the 4 ' - position can be reduced to a C - 6 aminoalkyl . Various reduction agents / conditions known to 15 those skilled in the art can be utilized . For example , the azido group can be reduced to an amino group via hydro genation ( for example , HZ - Pd / C or HCO , NH4 — Pd / C ) , Ral Ra2 Staudinger Reaction , NaBH _ / CoCl2 . 6 ; H20 , Fe / NH4Cl or Zn / NHACH .

unul 2 R44 ( G )

Ral Ra2 R640 — P - 04 B14

R740 R24 | | . . . YHIRA RS4

11ll pe

BIA . . . R4 + R8A0 — P — 01 — Y younge +

Scheme 4 H R54 R94 nu

R44 44 N 10 25 NH + POCl3

O

= 0 Ral Ra2

R840 — P - 04 A BIA R94 R24 , 1 . 4 YIHIRA

30 R54

Ral Ra2 R3G14LOOP R44 HO Bla INN

P - N Ral Ra2 Wato R2411 . . . YulRa N

35 BIA CHIR4 + H R2A . . . H R5a pub POCI ;

amino acid or amino acid ester 1111 amin - R3a R4a RSA ( B ) oy 4A Reg

40

? Ral Raz N N Ral Ra2 R104 — P - O - V Blo

NP Bla RIIA R24 , . . . .

O = RA YOUR 1111R4 R54 45 HN R $ 11

Ria

O Ral Ra2 BIA 0 / HO — P - O

R247Y O / HO YOUR H RS4 R34 R44

Compounds of Formula ( 1 ) having a phosphorus contain 50 ing group attached to the 5 ' - position of the pentose ring can

be prepared using various methods known to those skilled in the art . Examples of methods are shown in Schemes 4 and 5 . In Schemes 4 and 5 , Ra , R20 , R3a , R4a , R5a and Bla can be the same as R4 , R24 , R34 , R44 , R54 and B14 as described

55 herein for Formula ( I ) . A phosphorus containing precursor can be coupled to the nucleoside , for example , a compound of Formula ( F ) or a compound of Formula ( G ) . As shown in Scheme 4 , following the coupling of the phosphorus con taining precursor , any leaving groups can be cleaved under

60 suitable conditions , such as hydrolysis . Further phosphorus containing groups can be added using methods known to those skilled in the art , for example using a pyrophosphate .

In some embodiments , an alkoxide can be generated from a compound of Formula ( G ) using an organometallic

65 reagent , such as a Grignard reagent . The alkoxide can be coupled to the phosphorus containing precursor . Suitable Grignard reagents are known to those skilled in the art and

Ral Ra2 LEO R1240 — 1 — 10 — P - 1 0 BlA YURA OR 134 R2A . V R24111 OR 14A OR 14A 17

R 54 R3 R44

US 9 , 815 , 864 B2 145 146

include , but are not limited to , alkylmagnesium chlorides can be the same as R1B , R2B , R3B , R4B and BlB as described and alkylmagnesium bromides . In some embodiments , an herein for Formula ( II ) , each L ' can be a halogen , a sulfonate appropriate base can be used . Examples of suitable bases ester or an amine ( mono - or di - substituted ) , and X can be include , but are not limited to , an amine base , such as an oxygen or sulfur . As shown in Scheme 6 , a compound alkylamine ( including mono - , di - and tri - alkylamines ( e . g . , 5 having a hydroxy group attached to the 3 ' - carbon and a triethylamine ) ) , optionally substituted pyridines ( e . g . colli hydroxy group attached to the 5 ' - carbon can be reacted with dine ) and optionally substituted imidazoles ( e . g . , N - meth a compound having the formula , ( R1 ) P ( L ' ) 2 , in the pres ylimidazole ) ) . Alternatively , a phosphorus containing pre ence of a base , to produce a phosphite compound . Suitable cursor can be added to the nucleoside and form a phosphite . bases are known to those skilled in the art and described The phosphite can be oxidized to a phosphate using condi - herein . The phosphorus can then be oxidized to phosphorus tions known to those skilled in the art . Suitable conditions ( V ) using a suitable oxidizing agent , to produce a compound include , but are not limited to , meta - chloroperoxybenzoic where X is O ( oxygen ) . Alternatively , the phosphite com acid ( MCPBA ) and iodine as the oxidizing agent and water pound can be reacted with a sulfurization reagent to produce as the oxygen donor . a compound where X is S ( sulfur ) . Suitable oxidizing and

When compounds of Formula ( I ) have 214 , 224 or 234 - sulfurization agents are known to those skilled in the art . For being sulfur , the sulfur can be added in various manners example , the oxidation can be carried out using iodine as the known to those skilled in the art . In some embodiments , the oxidizing agent and water as the oxygen donor . Suitable sulfur can be part of the phosphorus containing precursor . sulfurization agents are described herein . for example ,

Scheme 7

HO Hono Blo =

- Kovo vo cause a moment R640 — P - Cl or OH or R840 — P - CI . R3C1 . . . HH + RC JIY . R3CH2 lllH 25 25 - R740 R94 RÓC R6C

11 "

Pure

Oce = 0 =

- Re R 2c pic Rio

R

Alternatively , the sulfur can be added using a sulfurization reagent . Suitable sulfurization agents are known to those skilled in the art , and include , but are not limited to , 30 elemental sulfur , Lawesson ' s reagent , cyclooctasulfur , 3H - 1 , 2 - Benzodithiole - 3 - one - 1 , 1 - dioxide ( Beaucage ' s reagent ) , 3 - ( ( N , N - dimethylaminomethylidene ) amino ) - 3H 1 , 2 , 4 - dithiazole - 5 - thione ( DDTT ) and bis ( 3 - triethoxysilyl ) propyl - tetrasulfide ( TEST ) . 35

Suitable phosphorus containing precursors can be com - mercially obtained or prepared by synthetic methods known to those skilled in the art . Examples of general structures of phosphorus containing precursors are shown in Schemes 4 and 5 .

O =

RIC - P . A RICE R2 = LO . BIC R2C OBIC R301 - YllH HRC

R4C R50

R3CY YH H R6C

RAC R5C 40

HO — Blo O . base

R43 R38

BB R20 UN

R46 R46 R38

Scheme 6 : A method for forming a compound of Formula ( III ) is shown in Scheme 7 . In Scheme 7 , RIC , R20 , R3c , R4c , R5c ,

45 R6c and Ble can be the same as R1C , R2C , R3C , R4C , R5C , RC R2010 ) . 11111H + R 16 and B1C as described herein for Formula ( III ) , and R7C and

R8C are not shown . The oxygen attached to the 5 ' - carbon of the compound of Formula ( H ) can be oxidized to a ketone using methods and reagents known to those skilled in the art .

50 For example , an oxidizing agent , such as Dess - Martin Yu111H periodinane , can be utilized . A phosphorus - containing

R15 — P . reagent can then be added to a compound of Formula ( 1 ) in the presence of a strong base ( e . g . , sodium hydride ) . The double bond can be hydrogenated , for example using hydro

55 gen gas or Pd / C , to a single bond . Additional phosphates can be added via phosphorylation to form a di - or tri - phosphate oxidation reagent ( Z1B = 0 )

sulfurization reagent ( Z1B = S ) | using suitable reagents , such as a pyrophosphate ( e . g . , tetrabutylammonium pyrophosphate ) .

0 An acyl group can be added to the 5 ' - position and / or the 60 3 ' - position of a compound of Formula ( 1 ) or ( III ) using

Z ! B / R2B 1 . 1 methods known to those skilled in the art . One suitable method is using an anhydride in pyridine .

During the synthesis of any of the compounds described herein , if desired , any hydroxy groups attached to the

65 pentose ring , and any — NH and / or NH , groups present on A method for forming a compound of Formula ( II ) is the Bla , Blb and Ble can be protected with one or more

shown in Scheme 6 . In Scheme 6 , R16 , R26 , R35 , R46 and B1b suitable protecting groups . Suitable protecting groups are

BIB Y . . 1H . HC

RIB csill

no a

US 9 , 815 , 864 B2 147 148

described herein . For example , when R3a and / or R4C is a The term “ physiologically acceptable ” defines a carrier , hydroxy group , R3a and / or R4e can be protected with a diluent or excipient that does not abrogate the biological triarylmethyl group or a silyl group . Likewise , any — NH activity and properties of the compound . and / or NH , groups present on the Bla , Blb and Ble can be As used herein , a “ carrier ” refers to a compound that protected , such as with a triarylmethyl and a silyl group ( s ) . 5 . s 5 facilitates the incorporation of a compound into cells or

tissues . For example , without limitation , dimethyl sulfoxide Examples of triarylmethyl groups include but are not limited ( DMSO ) is a commonly utilized carrier that facilitates the to , trityl , monomethoxytrityl ( MMTr ) , 4 , 4 ' - dimethoxytrityl uptake of many organic compounds into cells or tissues of ( DMTr ) , 4 , 4 , 4 " - trimethoxytrityl ( TMTr ) , 4 , 4 , 4 " - tris - ( ben a subject . zoyloxy ) trityl ( TBTr ) , 4 , 4 ' , 4 " - tris ( 4 , 5 - dichlorophthalimido ) As used herein , a " diluent ” refers to an ingredient in a trityl ( CPTr ) , 4 , 4 , 4 " - tris ( levulinyloxy ) trityl ( TLTr ) , p - ani pharmaceutical composition that lacks pharmacological syl - 1 - naphthylphenylmethyl , di - o - anisyl - 1 - naphthylmethyl , activity but may be pharmaceutically necessary or desirable . p - tolyldipheylmethyl , 3 - ( imidazolylmethyl ) - 4 , 4 ' - dime For example , a diluent may be used to increase the bulk of thoxytrityl , 9 - phenylxanthen - 9 - yl ( Pixyl ) , 9 - ( p - methoxy - a potent drug whose mass is too small for manufacture phenyl ) xanthen - 9 - yl ( Mox ) , 4 - decyloxytrityl , 4 - hexadecy - 15 and / or administration . It may also be a liquid for the loxytrityl , 4 , 4 ' - dioctadecyltrityl , 9 - ( 4 - octadecyloxyphenyl ) dissolution of a drug to be administered by injection , inges xanthen - 9 - yl , 1 , 1 ' - bis - ( 4 - methoxyphenyl ) - 1 - pyrenylmethyl . tion or inhalation . A common form of diluent in the art is a 4 , 4 ' , 4 " - tris - tert - butylphenyl ) methyl ( TTTr ) and 4 , 4 ' - di - 3 , 5 - buffered aqueous solution such as , without limitation , phos hexadienoxytrityl . Examples of silyl groups include , but are phate buffered saline that mimics the composition of human not limited to , trimethylsilyl ( TMS ) , tert - butyldimethylsilyl 20 blood . ( TBDMS ) , triisopropylsilyl ( TIPS ) , tert - butyldiphenylsilyl As used herein , an " excipient ” refers to an inert substance

that is added to a pharmaceutical composition to provide , ( TBDPS ) , tri - iso - propylsilyloxymethyl and [ 2 - ( trimethylsi lyl ) ethoxy ] methyl . Alternatively , R3a and R4Q and / or R4C and without limitation , bulk , consistency , stability , binding abil RSC can be protected by a single achiral or chiral protecting ity , lubrication , disintegrating ability etc . , to the composi group , for example , by forming an orthoester , a cyclic acetal 25 " stion . A “ diluent ” is a type of excipient . or a cyclic ketal . Suitable orthoesters include methoxym The pharmaceutical compositions described herein can be ethylene acetal , ethoxymethylene acetal , 2 - oxacyclopentyl administered to a human patient per se , or in pharmaceutical

compositions where they are mixed with other active ingre idene orthoester , dimethoxymethylene orthoester , 1 - methoxyethylidene orthoester , 1 - ethoxyethylidene orthoe dients , as in combination therapy , or carriers , diluents , ster , methylidene orthoester , phthalide orthoester 1 , 2 - dime - 30 excipients or combinations thereof . Proper formulation is thoxyethylidene orthoester , and alpha - methoxybenzylidene dependent upon the route of administration chosen . Tech

niques for formulation and administration of the compounds orthoester ; suitable cyclic acetals include methylene acetal , ethylidene acetal , t - butylmethylidene acetal , 3 - ( benzyloxy ) described herein are known to those skilled in the art . propyl acetal , benzylidene acetal , 3 , 4 - dimethoxyben The pharmaceutical compositions disclosed herein may zylidene acetal and p - acetoxybenzylidene acetal ; and suit - 35 be 5 be manufactured in a manner that is itself known , e . g . , by able cyclic ketals include 1 - t - butylethylidene ketal , means of conventional mixing , dissolving , granulating , dra 1 - phenylethylidene ketal , isopropylidene ketal , cyclopentyl gee - making , levigating , emulsifying , encapsulating , entrap idene ketal , cyclohexylidene ketal , cycloheptylidene ketal ping or tableting processes . Additionally , the active ingre and 1 - ( 4 - methoxyphenyl ) ethylidene ketal . Those skilled in dients are contained in an amount effective to achieve its the art will appreciate that groups attached to the pentose 40 intended purpose . Many of the compounds used in the ring and any — NH and / or NH , groups present on the Bla , pharmaceutical combinations disclosed herein may be pro Blb and Ble can be protected with various protecting groups , vided as salts with pharmaceutically compatible counteri

ons . and any protecting groups present can be exchanged for other protecting groups . The selection and exchange of the EXAMPLES protecting groups is within the skill of those of ordinary skill 45 in the art . Any protecting group ( s ) can be removed by Additional embodiments are disclosed in further detail in methods known in the art , for example , with an acid ( e . g . , a the following examples , which are not in any way intended mineral or an organic acid ) , a base or a fluoride source . Pharmaceutical Compositions to limit the scope of the claims . Some embodiments described herein relates to the use of 50 Example 1 a pharmaceutical composition , that can include an effective

amount of one or more compounds described herein ( e . g . , a Preparation of Compound la compound of Formula ( I ) , a compound of Formula ( II ) and / or a compound of Formula ( III ) , or a pharmaceutically acceptable salt of the foregoing ) and a pharmaceutically 55 acceptable carrier , diluent , excipient or combination thereof .

The term “ pharmaceutical composition ” refers to a mix ture of one or more compounds disclosed herein with other chemical components , such as diluents or carriers . The pharmaceutical composition facilitates administration of the 60 compound to an organism . Pharmaceutical compositions can HO also be obtained by reacting compounds with inorganic or organic acids such as hydrochloric acid , hydrobromic acid , sulfuric acid , nitric acid , phosphoric acid , methanesulfonic acid , ethanesulfonic acid , p - toluenesulfonic acid , and sali - 65 cylic acid . Pharmaceutical compositions will generally be tailored to the specific intended route of administration .

NH2

P1 - 1

* * 1111 MMTro

HO HOM ºv HO - THORIT

?

* * 1111

US 9 , 815 , 864 B2 149 150

- continued and sym - collidine ( 17 . 9 g , 149 . 2 mmol ) , AgNO3 ( 25 g , NHMMTr 149 . 2 mmol ) and MMTrCl ( 45 g , 149 . 2 mmol ) were added .

The mixture was stirred at R . T . for 16 hours . The mixture was quenched with water , and the organic layer was sepa rated and concentrated . The residue purified on a silica gel column ( 30 % PE in EA ) to give the crude product . The crude product was dissolved in 1M TBAF ( 50 mL ) in THF . The mixture was stirred at R . T . for 2 hours . The solvent was removed , and the residue was purified on a silica gel column

10 ( 50 % PE in EA ) to give P1 - 2 as a white solid ( 21 . 4 g , 66 % for three steps ) . P1 - 2 To a solution of pyridine ( 521 mg , 6 . 59 mmol ) in anhy NHMMTr drous DMSO ( 5 mL ) was added TFA ( 636 mg , 5 . 58 mmol ) dropwise at 10° C . under nitrogen . The reaction mixture was stirred until the solution became clear . The solution was then added into a mixture of P1 - 2 ( 4 . 0 g , 5 . 07 mmol ) and DCC ( 3 . 86 g , 18 . 76 mmol ) in anhydrous DMSO ( 18 mL ) at R . T . under nitrogen . The reaction mixture was stirred at 30° C . overnight . Water ( 80 mL ) was added into the mixture ,

20 diluted with EtoAc ( 100 mL ) and filtered . The filtrate was MMTIÓ extracted with DCM ( 100 mLx6 ) . The organic layer was

P1 - 3 washed with saturated aq . NaHCO3 , dried over Na2SO4 and NHMMTr concentrated in vacuo . The residue was purified on a silica

gel column eluted with 1 % MeOH in DCM to give the 25 intermediate ( 3 . 5 g , 87 . 7 % ) as a yellow solid . The interme

diate ( 3 . 5 g , 4 . 45 mmol ) was dissolved in dioxane ( 25 mL ) and aq . HCHO ( 668 mg , 22 . 25 mmol ) was added at R . T . 2N

MMTIO NaOH ( 4 . 5 mL , 8 . 9 mmol ) was then added . The reaction H0 — 111 mixture was stirred at 30° C . overnight . NaBHA ( 593 mg ,

30 15 . 6 mmol ) was added in by portions at 5° C . , and the mixture was stirred at R . T . for 15 min . The reaction was MMTIO MMTIOS quenched with water , and the mixture was extracted with

P1 - 4 P1 - 4 EtOAc ( 100 mLx3 ) . The organic layer was dried over NHMMTr Na2SO4 and concentrated in vacuo . The residue was purified 35 on a silica gel column eluted with 1 % MeOH in DCM to

give P1 - 3 as a yellow solid ( 2 . 5 g , 67 % ) . ' H NMR ( CDC13 , 400 MHz ) 8 6 . 82 - 7 . 50 ( m , 29H ) , 5 . 40 ( d , J = 23 . 2 Hz , 1H ) , 4 . 99 ( d , J = 7 . 6 Hz , 1H ) , 4 . 46 ( dd , J , = 6 . 0 Hz , Jz = 54 . 4 Hz , MMTIO 1H ) , 3 . 94 ( dd , J , = 4 . 4 Hz , J = 12 . 4 Hz , 1H ) , 3 . 78 ( s , 6H ) ,

40 3 . 42 - 3 . 69 ( m , 2H ) , 2 . 71 - 3 . 05 ( m , 2H ) , 2 . 45 ( m , 1H ) . To an ice cooled solution of P1 - 3 ( 4 . 0 g , 4 . 9 mmol ) in dry

pyridine ( 20 mL ) was added dropwise TBSC1 in pyridine P1 - 5 ( 1M , 5 . 88 mL ) . The reaction mixture was stirred at R . T . for

NH 16 hours . The reaction mixture was then quenched with 45 water , concentrated to give a residue . The residue was

separated in EA and saturated aq . NaHCO2 . The organic layer was separated and dried , and then concentrated . The residue was purified on a silica gel column ( 1 % MeOH in

HO HOMO DCM ) to give the intermediate as a yellow solid ( 3 . 2 g , 50 70 % ) . ' H NMR ( CDC12 , 400 MHz ) 8 7 . 53 - 6 . 83 ( m , 29H ) ,

5 . 51 ( d , J = 21 . 2 Hz , 1H ) , 4 . 98 ( d , J = 7 . 6 Hz , 1H ) , 4 . 67 ( dd , J , = 5 . 6 Hz , Jo = 22 . 4 Hz , 1H ) , 4 . 22 ( dd , J , = 5 . 6 Hz , Ju = 53 . 2 Hz , 1H ) , 4 . 07 ( m , 1H ) , 3 . 89 ( m , 1H ) , 3 . 80 ( s , 6H ) , 3 . 70 - 3 . 67

1a ( m , 1H ) , 3 . 03 - 2 . 98 ( m , 1H ) , 2 . 26 ( m , 1H ) , 0 . 93 ( s , 9H ) , 0 . 10 55 ( s , 6H ) .

The obtained intermediate was dissolved in anhydrous To an ice cooled solution of P1 - 1 ( 10 . 0 g , 40 . 8 mmol ) in DCM ( 20 mL ) and collidine ( 360 mg , 3 mmol ) , and AgNO3 dry pyridine ( 100 mL ) was added TBSC1 in pyridine ( 1M , 53 ( 500 mg , 3 mmol ) and MMTrC1 ( 606 mg , 2 mmol ) were mL ) dropwise at room temperature ( R . T . ) . The reaction added . The mixture was stirred at R . T . for 16 hours . The mixture was stirred at R . T . for 16 hours . The reaction 60 reaction mixture was quenched with water , and the organic mixture was then quenched with water , concentrated to give layer was separated and concentrated . The residue was a residue . The residue was separated by ethyl acetate ( EA ) purified on a silica gel column ( 0 . 5 % MeOH in DCM ) to and saturated NaHCO3 aq . solution . The organic phase was give the fully protected intermediate as a yellow solid ( 3 . 3 dried and concentrated . The residue was purified on a silica g , 80 % ) . The intermediate was dissolved in 1M TBAF in gel column ( 5 % MeOH in DCM ) to give a crude 5 ' - 0 - TBS 65 THF ( 5 mL ) and was stirred at R . T . for 2 hours . The solution protected intermediate as a white solid ( 13 . 4 g , 91 % ) . The was concentrated , and the residue was purified on a silica gel intermediate was dissolved in anhydrous DCM ( 100 mL ) column ( 1 % MeOH in DCM ) to give a mixture of P1 - 3 and

MMTre * 11011 MMTIOMED

. . . =

1111

151 US 9 , 815 , 864 B2

152 P1 - 4 , which was separated by HPLC separation ( MeCN and rochloridate ( 104 mg , 0 . 4 mmol ) in THF ( 0 . 5 mL ) was added 0 . 1 % HCOOH in water ) to give P1 - 4 as a white solid ( 1 . 5 dropwise . After addition , the mixture was stirred at 25° C . g , 25 % ) . for 16 hours . The reaction was quenched with HCOOH Compound P1 - 4 ( 1 . 5 g , 1 . 22 mmol ) was suspended in ( 80 % aq . ) at 0° C . The solvent was removed , and the residue

anhydrous DCM ( 50 mL ) . and Dess Martin periodinane ( 1 . 2 5 was purified on silica gel ( DCM : MOH = 50 : 1 to 10 : 1 ) to g , 2 . 73 mmol ) was added at 0° C . The reaction mixture was give 2a as a white solid ( a mixture of two Pisomers , 8 . 0 mg ,

7 . 9 % ) . ESI - LCMS : m / z 539 . 0 [ M + H ] * . stirred at R . T . for 3 hours . The reaction mixture was then quenched with saturated aq . Na 8 , 02 and Na2CO3 . The Example 3 organic layer was separated and dried , and then concentrated to give the aldehyde intermediate as a white solid . 10 Preparation of Compound 3a A solution of CICH PPh Br ( 2 . 19 g , 5 . 6 mmol ) in anhy drous THF ( 40 mL ) was cooled to - 78° C . n - BuLi ( 2 . 5 M , 2 . 3 mL ) was added in dropwise . After the addition , the mixture was stirred at 0° C . for 2 hours . A solution of the aldehyde in anhydrous THF ( 10 mL ) was then added . The 15 mixture was stirred at R . T . for 16 hours . The reaction was quenched with saturated NH4Cl aq . and extracted by EA . The organic layer was separated , dried and concentrated . The residue was purified on a silica gel column ( 1 % MeOH in DCM ) to give the intermediate as a yellow solid ( 1 . 1 g , 20 73 % ) . To a solution of the intermediate ( 1 . 1 g , 0 . 98 mmol ) in anhydrous THF ( 40 mL ) was added n - BuLi ( 2 . 5M , 6 HO mL ) - 78° C . dropwise . The mixture was stirred at - 78° C . for 5 hours and then quenched with a saturated NH4Cl aq . P3 - 1

solution . The mixture was extracted with EA . The organic 25 layer was separated , dried and concentrated . The residue was purified on a silica gel column ( 2 % MeOH in DCM ) to give P1 - 5 as a yellow solid ( 910 mg , 86 % ) . Compound P1 - 5 ( 910 mg , 0 . 84 mmol ) was suspended in

80 % CH3COOH ( 50 mL ) , and the reaction mixture was 30 stirred at 40° C . for 15 hours . The solvents were evaporated , and the residue was co - evaporated with toluene to remove traces of acid and water . The residue was purified by HPLC separation ( MeCN and 0 . 1 % HCOOH in water ) to give pure P3 - 2 la as a white solid ( 101 mg , 45 % ) . ESI - TOF - MS : m / z 35 270 . 09 [ M + H ] " , 539 . 17 [ 2M + H ] * .

HO

* 11111

HO HOM

* * 1111 TBSOS

Example 2

Preparation of Compound 2a # HOM HO 111111 )

1111 TBSO

NH HO HOT PLNH2 P3 - 3

NH H? ? TBDPSO TBDPOVO

HIRD HO -

TBSÓ TBSON O 0 - P - 0 TNH2 55 P3 - 4

??

# 111 NH

60 2a TBDPSO

0 = * * 1111

TBSC

To a stirred solution of la ( 50 mg , 0 . 186 mmol ) in anhydrous THF ( 3 mL ) was added dropwise a solution of t - BuMgCl ( 0 . 37 mL , 1M in THF ) at - 78° C . The mixture 65 was then stirred at 0° C . for 30 min and re - cooled to - 78° C . A solution of phenyl ( isopropoxy - L - alaninyl ) phospho

P3 - 5

NH

TBDPSO

1111 *

* 11111 TBSO

135 .

111

NH

1111111

•1111

US 9 , 815 , 864 B2 153 154

- continued at R . T . The reaction mixture was refluxed for 3 hours and then cooled to 0° C . The precipitate was filtered - off , and the filtrate was concentrated to give the crude aldehyde ( 121 . 3 g ) as a yellow solid . The aldehyde was dissolved in 1 , 4

5 dioxane ( 1000 mL ) . 37 % CHO ( 81 . 1 mL , 1 . 3536 mol ) and 2M NaOH aq . solution ( 253 . 8 mL , 507 . 6 mmol ) were added . The mixture was stirred at R . T . for 2 hours and then neutralized with AcOH to pH = 7 . To the solution were added EtOH ( 400 mL ) and NaBH . ( 51 . 2 g , 1 . 354 mol ) . The mixture was stirred at R . T . for 30 minutes . The mixture was

P3 - 6 quenched with saturated aq . NH _ C1 and extracted with EA . NH2 The organic layer was dried over Na SO4 and concentrated .

The residue was purified by silica gel column chromatog 15 raphy ( 1 - 3 % MeOH in DCM ) to give P3 - 3 ( 51 . 4 g , 38 . 9 % )

as a white solid . To a solution of P3 - 3 ( 51 . 4 g , 131 . 6 mmol ) in anhydrous

TBDPSO DCM ( 400 mL ) were added pyridine ( 80 mL ) and DMTrC1 ( 49 . 1 g , 144 . 7 mmol ) at 0° C . The reaction was stirred at R . T .

20 for 14 hours , and then treated with MeOH ( 30 mL ) . The TBSO solvent was removed , and the residue was purified by silica

P3 - 7 P3 - 7 gel column chromatography ( 1 - 3 % MeOH in DCM ) to give a mono - DMTr protected intermediate as a yellow foam ( 57 . 4 g , 62 . 9 % ) . To the intermediate ( 57 . 4 g , 82 . 8 mmol ) in

25 CH2C12 ( 400 mL ) was added imidazole ( 8 . 4 g , 124 . 2 mmol ) and TBDPSC1 ( 34 . 1 g , 124 . 2 mmol ) . The mixture was stirred at R . T . for 14 hours . The precipitate was filtered off ,

TBDPSO and the filtrate was washed with brine and dried over Na , SO4 . The solvent was removed to give the residue ( 72 . 45

30 g ) as a white solid . The solid was dissolved in 80 % HOA TBSO aq . solution ( 400 mL ) . The mixture was stirred at R . T . for 15

hours . The mixture was diluted with EtoAc and washed P3 - 8 with NaHCO , solution and brine . The organic layer was

dried over Na , SO , and purified by silica gel column chro matography ( 1 - 2 % MeOH in DCM ) to give P3 - 4 ( 37 . 6 g , 84 . 2 % ) as a white solid . ' H NMR ( CD , OD , 400 MHz ) 8 7 . 76 ( d , J = 4 . 0 Hz , 1H ) , 7 . 70 ( dd , J = 1 . 6 Hz , Jn = 8 . 0 Hz , 2H ) , 7 . 66 ~ 7 . 64 ( m , 2H ) , 7 . 48 ~ 7 . 37 ( m , 6H ) , 6 . 12 ( dd , J2 = 2 . 8 Hz , Jy = 16 . 8 Hz , 1H ) , 5 . 22 ( d , J = 8 . 0 Hz , 1H ) . 5 . 20 - 5 . 05 ( m , 1H ) ,

40 4 . 74 ( dd , J , = 5 . 6 Hz , Ju = 17 . 6 Hz , 1H ) , 4 . 16 ( d , J = 12 . 0 Hz , 1H ) , 3 . 87 – 3 . 80 ( m , 2H ) , 3 . 56 ( d , J = 12 . 0 Hz , 1H ) , 1 . 16 ( s , 9H ) , 0 . 92 ( s , 9H ) , 0 . 14 ( s , 6H ) .

3a To a solution of P3 - 4 ( 11 . 8 g , 18 . 8 mmol ) in anhydrous DCM ( 100 mL ) was added Dess - Martin periodinane ( 16 . 3 g ,

45 37 . 6 mmol ) at 0° C . under nitrogen . The reaction was stirred To a solution of P3 - 1 ( 100 . 0 g , 406 . 5 mmol ) in pyridine R . T . for 2 . 5 hours . Water ( 100 mL ) was added , and the

( 750 mL ) was added DMTRC1 ( 164 . 9 g , 487 . 8 mmol ) . The mixture was then filtered . The filtrate was washed with solution was stirred at R . T . for 15 hours . MeOH ( 300 mL ) saturated aq . NaHCO , and concentrated . The crude residue was added , and the mixture was concentrated to dryness was purified by silica gel column chromatography ( 20 % under reduced pressure . The residue was dissolved in EtOAC 50 EtoAc in hexane ) to give P3 - 5 as a white solid ( 10 . 1 g , and washed with water . The organic layer was dried over 86 . 0 % ) . Na SO , and concentrated . The residue was dissolved in To a mixture of methyltriphenylphosphonium bromide DCM ( 500 mL ) . Imidazole ( 44 . 3 g , 650 . 4 mmol ) and TBSC1 ( 15 . 7 g , 48 . 5 mmol ) in anhydrous THF ( 100 mL ) was added ( 91 . 9 g , 609 . 8 mmol ) was added . The reaction mixture was n - BuLi ( 19 . 4 mL , 48 . 48 mmol ) at - 78° C . under nitrogen . stirred at R . T . for 14 hours . The reaction solution was 55 The reaction was stirred at 0° C . for 30 minutes . A solution washed with NaHCO3 and brine . The organic layer was of P3 - 5 ( 10 . 1 g , 16 . 2 mmol ) in anhydrous THF ( 70 mL ) was dried over Na S04 , and concentrated to give the crude as a added dropwise at 0° C . under nitrogen . The reaction was light yellow solid . The crude ( 236 . 4 g , 356 . 6 mmol ) was stirred at R . T . for 1 . 5 hours . The reaction was quenched by dissolved in 80 % HOAc aq . solution ( 500 mL ) . The mixture NHCl and extracted with EtoAc . The crude product was was stirred at R . T . for 15 hours . The mixture was diluted 60 purified by silica gel column chromatography ( 20 % EtOAC with EtoAc and washed with a NaHCO3 solution and brine . in hexane ) to give P3 - 6 as a white solid ( 8 . 3 g , 82 . 2 % ) . ' H The organic layer was dried over Na , so , and purified by NMR ( CDC12 , 400 MHz ) 88 . 16 ( s , 1H ) , 8 . 81 ( d , J = 8 . 0 Hz , silica gel column chromatography ( 1 - 2 % MeOH in DCM ) to 1H ) , 7 . 58 - 7 . 67 ( m , 4H ) , 7 . 37 - 7 . 46 ( m , 6H ) , 6 . 17 ( d , J = 16 . 0 give P3 - 2 ( 131 . 2 g , 89 . 6 % ) as a light yellow solid . ESI - MS : Hz , 1H ) , 5 . 91 ( dd , J = 10 . 8 Hz , J2 = 17 . 6 Hz , 1H ) , 5 . 42 ( d , m / z 802 IM + H ] * . 65 J = 17 . 6 Hz , 1H ) , 5 . 22 - 5 . 30 ( m , 2H ) , 4 . 60 - 4 . 84 ( m , 2H ) , 3 . 69

To a solution of P3 - 2 ( 131 . 2 g , 364 . 0 mmol ) in anhydrous ( dd , J = 11 . 6 Hz , J2 = 21 . 2 Hz , 2H ) , 1 . 10 ( s , 9H ) , 0 . 91 ( s , 1H ) , CH3CN ( 1200 mL ) was added IBX ( 121 . 2 g , 432 . 8 mmol ) 0 . 12 ( d , J = 8 . 0 Hz , 6H ) .

NH2

HO * * 1

.

11

156 Example 5

Preparation of Compound 5a

10

US 9 , 815 , 864 B2 155

To a solution of P3 - 6 ( 6 . 3 g , 10 . 09 mmol ) in anhydrous CH3CN ( 50 mL ) were added TPSCI ( 6 . 1 g , 20 . 2 mmol ) , DMAP ( 2 . 5 g , 20 . 2 mmol ) and NEtz ( 3 mL ) at R . T . The reaction was stirred at R . T . for 2 hours . NH4OH ( 25 mL ) was added , and the reaction was stirred for 1 hour . The mixture 5 was diluted with DCM ( 150 mL ) and washed with water , 0 . 1 M HCl and saturated aq . NaHCO3 . The solvent was removed , and the crude product was purified by silica gel column chromatography ( 2 % MeOH in DCM ) to give P3 - 7 as a yellow solid ( 5 . 9 g , 93 . 6 % ) .

To a solution of P3 - 7 ( 5 . 9 g , 9 . 5 mmol ) in MeOH ( 10 mL ) TBDPSO was added Pd / C ( 1 . 5 g ) at R . T . The reaction was stirred at = R . T . for 2 hours under H , ( balloon ) . The mixture was filtered , and the filtrate was concentrated in vacuo to give 15 P3 - 8 as a white solid ( 5 . 4 g , 91 . 3 % ) .

To a solution of P3 - 8 ( 5 . 4 g , 8 . 6 mmol ) in MeOH ( 60 mL ) was added NH4F ( 10 . 0 g ) , and the reaction mixture was refluxed overnight . After cooling to R . T . , the mixture was filtered , and the filtrate was concentrated . The crude product was purified by silica gel column chromatography ( 10 % MeOH in DCM ) to give compound 3a as a white solid ( 1 . 6 g , 67 . 8 % ) . ESI - MS : m / z 274 [ M + H ] * , 547 [ 2M + H ] * .

171 1111 TBSO

P3 - 6

TBDPSO

20 11n

TBSO 1111 TBS

P5 - 1

25 HO Example 4 * * NH

Preparation of Compound 4a 11

30

NH2

TBDPSO

1111 TBSO

To a solution of P3 - 6 ( 600 mg , 0 . 96 mmol ) in MeOH ( 30 mL ) was added 10 % Pd / C ( 320 mg ) at R . T . The mixture was

35 stirred under H , balloon at R . T . for 3 hours . The reaction mixture was filtered , and the filtrate was concentrated to give P5 - 1 ( 540 mg , 89 . 8 % ) as a colorless solid . The crude product was used directly for the next step without purification .

To a solution of P5 - 1 ( 540 mg , 0 . 86 mmol ) in MeOH ( 8 40 mL ) was added NH F ( 1 . 2 g , 32 . 4 mmol ) R . T . The mixture

was refluxed for 30 hours . The solid was removed by filtration , and the filtrate was concentrated . The residue was purification by silica gel column chromatography ( 2 . 5 % - 9 % MeOH in DCM ) to give 5a ( 190 mg , 80 . 6 % ) as a colorless solid . ' H NMR ( CD , OD , 400 MHz ) 8 8 . 05 ( d , J = 8 . 0 Hz , 1H ) , 6 . 09 ( dd , J2 = 4 . 0 Hz , J2 = 14 . 8 Hz , 1H ) , 5 . 04 - 5 . 20 ( m , 1H ) , 4 . 42 ( dd , J , = 5 . 2 Hz , Jo = 13 . 6 Hz , 1H ) , 3 . 71 ( d , J = 11 . 6 Hz , 1H ) , 3 . 57 ( d , J = 12 . 0 Hz , 1H ) , 1 . 61 - 1 . 82 ( m , 2H ) , 0 . 94 ( t , J = 7 . 2 Hz , 3H ) .

50 Example 6

P3 - 7

NH

N 50

Hoyv HO Preparation of Compound 6a 111111

1111 55

4a

NH

HO To a solution of P3 - 7 ( 280 mg , 0 . 45 mmol ) in MeOH ( 10 6

mL ) was added NH4F ( 1 . 0 g ) at R . T . The reaction mixture was refluxed for 5 hours . After cooling to R . T . , the mixture was filtered , and the filtrate was concentrated . The crude product was purified by silica gel column chromatography ( 10 % MeOH in DCM ) to give 4a as a white solid ( 82 mg , 65 67 . 2 % 1 . 6 g , 67 . 8 % ) . ESI - MS : m / z 272 [ M + H ] * , 543 [ 2M +

HO - HERCE

TBSO P3 - 3

H ] * .

US 9 , 815 , 864 B2 157

- continued 158

- continued

NH NH

TBSOS TBDPSO TBDPOVO TBSO II . . . SO

01 — C1 — 111

TBSO * 11111 10 1111 TBS? P6 - 1 P7 - 1

NH

' N 15 NH

HOT

HO

11 . 20 TBDPSO

6a ba 01 - 11 /

01111 TBSO

5

NH2

01 .

11 Home 7a 7a

To a solution of P3 - 3 ( 800 mg , 2 . 05 mmol ) in anhydrous DCM ( 15 mL ) were added imidazole ( 558 mg , 8 . 2 mmol ) , P7 - 2

TBSCI ( 1 . 2 g , 8 . 2 mmol ) and AgNO3 ( 700 mg , 4 . 1 mmol ) at R . T . The reaction mixture was stirred at R . T . overnight . The mixture was filtered , and the filtrate was washed with brine and concentrated in vacuo . The residue was purified by 30 column chromatography on silica gel to give P6 - 1 as a white solid ( 950 mg , 79 . 2 % ) .

To a solution of P6 - 1 ( 600 mg , 0 . 97 mmol ) in anhydrous CH2CN ( 18 mL ) was added DMAP ( 239 mg , 2 . 91 mmol ) , NEtz ( 294 mg , 2 . 91 mmol ) and TPSC1 ( 879 mg , 2 . 91 mmol ) 25 HO at R . T . The reaction was stirred at R . T . for 1 hour . NH OH ( 9 mL ) was added , and the reaction was stirred for 3 hours . The mixture was diluted with EtoAc ( 200 mL ) and washed with water , 0 . 1 M HCl and saturated aq . NaHCO3 . The organic layer was separated , dried and concentrated to give 10 a crude residue . The crude residue was purified by column chromatography on silica gel to give the product as a white solid ( 500 mg , 83 . 3 % ) . The solid was treated with NH4F ( 1 . 0 g ) in MeOH ( 20 mL ) at refluxed temperature for 5

A mixture of P3 - 4 ( 1 . 60 g , 2 . 5 mmol ) , PPhz ( 1 . 3 g , 5 . 0 hours . The mixture was filtered , and the filtrate was con - 15 centrated in vacuo . The residue was purified by column mmol ) and CCl4 ( 0 . 16 g , 2 . 0 mmol ) in DCE ( 20 mL ) was chromatography on silica gel ( 15 % MeOH in DCM ) to give ( 15 % MeOH in DCM ) to give heated to 130° C . under microwave irradiation under N , for 6a as a white solid ( 132 mg , 59 . 3 % ) . ESI - MS : m / z 276 40 mins . After cooled to R . T . , the solvent was removed , and [ M + H ] * , 551 [ 2M + H ] * . the residue was purified on a silica gel column ( PE / EA = 50 / 1

to 10 / 1 ) to give P7 - 1 ( 1 . 1 g , 68 . 8 % ) as a white solid . Example 7 Compound P7 - 1 ( 0 . 80 g , 1 . 3 mmol ) , DMAP ( 0 . 3 g , 2 . 6 mmol ) , TPSC1 ( 0 . 8 g , 2 . 6 mmol ) and EtZN ( 0 . 3 g , 2 . 6 mmol ) Preparation of Compound 7a were dissolved in MeCN ( 30 mL ) . The mixture was stirred at R . T . for 14 hours . NH , in THF ( saturated at 0° C . , 100

55 mL ) was added to the mixture , and the mixture was stirred at R . T . for 2 hours . The solvent was removed , and the residue was purified by column ( DCM / MeOH = 100 : 1 to 50 : 1 ) to give P7 - 2 ( 0 . 63 g , 78 . 8 % ) as a white solid .

To a solution of P7 - 2 ( 0 . 63 g , 0 . 98 mmol ) in MeOH ( 10 mL ) was added NH F ( 0 . 3 g ) , and the reaction was refluxed for 12 hours . The reaction was cooled to R . T . , and the

HO — precipitate was filtered off . The filtrate was concentrated in vacuo . The residue was purified by silica gel column chro

65 matography ( 10 % MeOH in DCM ) to give 7a as a white solid ( 153 mg , 53 . 5 % ) . ESI - MS : m / z 294 [ M + H ] * , 587 [ 2M + H ] *

NH

TBDPSO

HO

* 1111 TBSO

P3 - 4

US 9 , 815 , 864 B2 159

Example 8 160

- continued

Preparation of Compound 8a

TBDPSO

111

1111 * NH TBSOS

P9 - 2

TBDPSOLO

+ 1111 TBSÓW TBSO P7 - 1 TBDPSO

1111111 1111

NH TBSO P9 - 3

NH2 HOS

0 — 15 ) , HO 116

HO sa

1111111 30 * 11111

9a

To a solution of P7 - 1 ( 630 mg , 0 . 5 mmol ) in MeOH ( 10 30 mL ) was added NH F ( 0 . 1 g ) , and the reaction was refluxed for 12 hours . The mixture was filtered , and the filtrate was concentrated in vacuo . The crude product was purified by silica gel column chromatography ( 10 % MeOH in DCM ) to 35 A mixture of P3 - 4 ( 3 . 2 g , 5 . 0 mmol ) , PhzP ( 5 . 2 g , 20 give 8a as a white solid ( 153 mg , 53 . 5 % ) . Negative - ESI - MS : mmol ) , iodine ( 2 . 60 g , 10 . 2 mmol ) and imidazole ( 1 . 4 g , 20 m / z 293 [ M - H ] " mmol ) in anhydrous THF ( 40 mL ) was stirred at 80° C . for

14 hours . The reaction was cooled to R . T . and quenched with Example 9 saturated aq . Na2S2O3 . The solution was extracted with EA .

40 The organic layer was dried over Na2SO4 and concentrated . The residue was purified by silica gel column chromatog

Preparation of Compound 9a raphy ( 20 - 50 % EA in PE ) to give P9 - 1 ( 1 . 6 g , 68 . 2 % ) as a white solid .

A mixture of P9 - 1 ( 1 . 4 g , 0 . 2 mmol ) , EtzN ( 40 mg , 0 . 4 45 mmol ) and Pd / C in EtOH ( 20 mL ) was stirred at R . T . under

H , ( balloon ) overnight . The precipitate was filtered off , and the filtrate was concentrated . The residue was purified on a silica gel column ( 20 % - 50 % EtoAc in PE ) to give P9 - 2 as a white solid ( 1 . 1 g , 78 % ) . ' H NMR ( CDC13 , 400 MHz ) d

50 8 . 11 ( br s , 1H ) , 7 . 76 ( d , J = 8 . 0 Hz , 1H ) , 7 . 39 - 7 . 67 ( m , 10H ) , 6 . 18 ( dd , J = 3 . 2 Hz , J2 = 14 . 4 Hz , 1H ) , 5 . 26 - 5 . 30 ( m , 1H ) ,

H0 — 11577 4 . 86 ( m , 1H ) , 4 . 42 ( dd , J , = 5 . 2 Hz , Jo = 15 . 2 Hz , 1H ) , 3 . 81 ( d , J = 11 . 2 Hz , 1H ) , 3 . 58 ( d , J = 11 . 2 Hz , 1H ) , 1 . 16 ( s , 3H ) , 1 . 11

TBSON ( s , 9H ) , 0 . 91 ( s , 9H ) , 0 . 13 ( s , 3H ) , 0 . 08 ( s , 3H ) . 55 Compound P9 - 2 ( 650 mg , 1 . 1 mmol ) , DMAP ( 270 mg , P3 - 4 2 . 2 mmol ) , TPSCI ( 664 mg , 2 . 2 mol ) and EtzN ( 222 mg , 2 . 2 mmol ) were dissolved in MeCN ( 20 mL ) . The mixture was stirred at R . T . for 14 hours . The reaction was added NHz in THF ( saturated at 0° C . ) , and the mixture was stirred at R . T .

60 for 2 hours . The solvent was removed , and the residue was purified on a silica gel column ( 1 - 10 % MeOH in DCM ) to give P9 - 3 ( 430 mg , crude ) as a light yellow syrup .

A mixture of P9 - 3 ( 430 mg , 0 . 7 mmol ) and NH F ( 97 mg , 2 . 1 mmol ) in MeOH ( 10 mL ) was refluxed for 14 hours . The TBSONO TBSO 65 solvent was removed , and the residue was purified on a silica gel column ( 5 % - 10 % MeOH in DCM ) to give 9a as a white solid ( 64 . 8 mg , 35 . 4 % ) . ' H NMR ( CD , OD , 400 MHz ) 88 . 10

NH

TBDPSO

HO

O

TBDPSO

111111

11111 * P9 - 1

US 9 , 815 , 864 B2 161 162

- continued ( d , J = 7 . 6 Hz , 1H ) , 6 . 03 ( dd , J2 = 2 . 0 Hz , J2 = 16 . 8 Hz , 1H ) , 5 . 87 ( d , J = 7 . 6 Hz , 1H ) , 4 . 98 ( m , 1H ) , 4 . 37 ( dd , J , = 5 . 2 Hz , Jz = 21 . 6 Hz , 1H ) , 3 . 59 ( dd , J , = 12 . 0 Hz , J2 = 28 . 4 Hz , 2H ) , 1 . 23 ( d , J = 0 . 8 Hz , 3H ) .

Example 10 TBDPSO

Preparation of Compound 10a H2C = CCHI tis .

10 TBSON TBSO P11 - 2

NH2

TBDPSO TBDPSOLO H2C = CEHO

20 TBSO 1111 * * * 1115

TBSO P9 - 2 P11 - 3

NH2

| NH 25

07 HO HOM H2C = C HILLE 11111111

30 HOME * 11111 HO

" 111

10a 11a

To a stirred solution of P9 - 2 ( 400 mg , 0 . 65 mmol ) in za To a solution of P3 - 5 ( 2 . 1 g , 3 . 5 mmol ) in anhydrous THF MeOH ( 20 mL ) was added NH4F ( 52 mg , 1 . 5 mmol ) . The ( 25 mL ) was added ethynylmagnesium bromide ( 5 . 1 mmol ) mixture was refluxed overnight . The solvent was removed , at – 78° C . The reaction was stirred at 0° C . for 3 hours . The and the residue was purified on a silica gel column ( 5 - 10 % reaction was quenched with saturated aq . NH4Cl ( 10 mL ) . MeOH in DCM ) to give 10a ( 140 mg , 82 . 4 % ) as a white The mixture was diluted with EtOAC ( 200 mL ) and washed solid . ESI - TOF - MS : m / z 283 [ M + Na ] * . 40 with water and brine . The organic layer was dried and

concentrated to give a residue . The residue was purified by Example 11 column chromatography on silica gel ( eluting with DCM : MeOH = 60 : 1 ) to give P11 - 1 as a white solid ( 870 mg ,

Preparation of Compound 11a 83 . 3 % ) . 45 Compound P11 - 1 ( 870 mg , 1 . 34 mmol ) was dissolved in

anhydrous DCM ( 12 mL ) , and methyl chloroformate ( 2 . 3 mL ) and pyridine ( 2 . 5 mL ) were added at R . T . The reaction mixture was stirred at R . T . for 1 hour . The mixture was diluted with DCM and washed with saturated aq . NaHCOZ .

50 The organic layer was separated , dried and concentrated to give a residue . The residue was purified by column chro matography on silica gel ( eluting with PE : EtOAc = 8 : 1 ) to

TBDPSO give a crude product as a white solid ( 830 mg , 88 . 4 % ) . To 0 = AUDIO a mixture of Pd ( dba ) , ( 55 mg , 0 . 06 mmol ) in anhydrous

DMF ( 12 mL ) was added P ( nBu ) ( 35 mg , 0 . 17 mmol ) and TBSOM HCOONH4 ( 108 mg , 1 . 7 mmol ) at R . T . under nitrogen . The

reaction mixture was stirred at R . T . for 30 min . A solution of P3 - 5 the crude product ( 830 mg , 1 . 16 mmol ) in anhydrous DMF ( 16 mL ) was added , and the reaction mixture was stirred at

60 70° C . for 3 hours . The reaction was diluted with EtoAc and N . NH NH washed with brine . The organic layer was separated , dried and concentrated to give a residue . The residue was purified by column chromatography on silica gel ( eluting with PE : EtOAc = 9 : 1 ) to give P11 - 2 as a white solid ( 510 mg , 67 . 6 % ) .

65 H NMR ( CD , OD , 400 M Hz ) 87 . 61 - 7 . 75 ( m , 5H ) , 7 . 36 P11 - 1 7 . 47 ( m , 6H ) , 6 . 04 ( d , J = 18 . 8 Hz , 1H ) , 5 . 34 ( t , J = 6 . 8 Hz ,

1H ) , 5 . 21 ( dd , J2 = 1 . 2 Hz , J2 = 7 . 2 Hz , 1H ) , 5 . 10 ( 9 , J1 = 5 . 2 Hz ,

NH

TBDPSO HO .

* 11111

US 9 , 815 , 864 B2 163 164

J2 = 53 . 6 Hz , 1H ) , 4 . 80 - 4 . 92 ( m , 1H ) , 4 . 59 - 4 . 79 ( m , 2H ) , 3 . 86 elution . The corresponding fractions were combined , con ( d , J = 12 . 0 Hz , 1H ) , 3 . 75 ( d , J = 12 . 0 Hz , 1H ) , 1 . 09 ( s , 9H ) , centrated and lyophilized 3 times to remove excess of buffer . 0 . 92 ( d , J = 4 . 4 Hz , 9H ) , 0 . 15 ( t , J = 4 . 0 Hz , 6H ) . MS : m / z 517 . 2 [ M – 1 ] .

To a solution of P11 - 2 ( 490 mg , 0 . 77 mmol ) in anhydrous MeCN ( 15 mL ) was added TPSC1 ( 700 mg , 2 . 31 mmol ) , 5 Example 13 DMAP ( 282 mg , 2 . 31 mmol ) and TEA ( 234 mg , 2 . 31 mmol ) at R . T . The reaction mixture was stirred at room temperature Preparation of Compound 13a for 1 hour . Then NH OH ( 8 mL ) was added and the reaction mixture was stirred for another 4 hours . The mixture was diluted with EtoAc and washed with water , 1 . 0 M aq . HC11 NH , and saturated aq . NaHCO3 . The organic layer was separated and dried , concentrated to give the residue which was purified by HPLC separation ( MeCN and 0 . 1 % HCOOH in water ) to give P11 - 3 as a white solid ( 190 mg , 38 . 8 % ) . ' H 15 NMR ( CD2OD , 400 MHz ) 87 . 88 ( d , J = 7 . 2 Hz , 1H ) , 7 . 63 7 . 70 ( m , 4H ) , 7 . 37 - 7 . 48 ( m , 6H ) , 6 . 12 ( d , = 18 . 4 Hz , 1H ) , 5 . 49 ( d , J = 7 . 6 Hz , 1H ) , 5 . 34 ( t , J = 6 . 8 Hz , 1H ) , 4 . 84 - 5 . 01 ( m , 2H ) , 4 . 66 - 4 . 78 ( m , 2H ) , 3 . 89 ( d , J = 11 . 6 Hz , 1H ) , 3 . 75 ( d , J = 11 . 6 Hz , 1H ) , 1 . 10 ( s , 9H ) , 0 . 91 ( d , J = 3 . 2 Hz , 9H ) , 0 . 13 20 HOW TO ( t , J = 5 . 2 Hz , 6H ) . 3a

To a solution of P11 - 3 ( 130 mg , 0 . 21 mmol ) in MeOH ( 8 mL ) was added NH F ( 1 g ) , and the reaction mixture was refluxed for 6 hours . The mixture was filtered , and the filtrate was concentrated in vacuo . The residue was purified by 25 column chromatography on silica gel ( eluting with DCM : MeOH = 13 : 1 ) to give 11a as a white solid ( 47 mg , 79 . 1 % ) . ESI - MS : m / z 284 . 02 [ M + H ] * , 567 . 08 [ 2M + H ] * .

- 15

HO

3a NHMMTr

Example 12 30 MMTrC 11115 P13 - 1 Preparation of Compound 111a NH

O 0 - P - 0 NH

NH *

HO — P - TIL 0 - 2 - 0 - 2 - 0 No

HO HO HO 13a

F * 1111

HO 45 To a solution of 3a ( 700 mg , 2 . 56 mmol ) in anhydrous pyridine ( 5 mL ) were added TBDPSCI ( 2 . 8 g , 10 . 24 mmol ) ,

The dry nucleoside ( 0 . 05 mmol ) was dissolved in a imidazole ( 522 mg , 7 . 68 mmol ) and AgNO3 ( 870 mg , 5 . 12 mixture of PO ( OMe ) 3 ( 0 . 7 mL ) and pyridine ( 0 . 3 mL ) . The mmol ) at R . T . under N2 . The reaction mixture was stirred at mixture was evaporated in vacuum for 15 mins at bath R . T . for 3 hours . The mixture was diluted with MeOH and temperature ( 42° C . ) , than cooled down to R . T . N - Methyl - 50 filtered . The mixture was concentrated , and the residue was imidazole ( 0 . 009 mL , 0 . 11 mmol ) was added followed by purified by column chromatography on silica gel ( eluting POC1z ( 9 ul , 0 . 11 mmol ) , and the mixture was kept at R . T . with DCM : MOH = 80 : 1 ~ 40 : 1 ) to give the crude interme for 40 mins . The reaction was controlled by LCMS and diate as a yellow solid ( 1 . 05 g , 80 . 8 % ) . ' H NMR ( DMSO monitored by the appearance of corresponding nucleoside d6 , 400 MHz ) 87 . 75 ( d , J = 7 . 6 Hz , 1H ) , 7 . 61 - 7 . 65 ( m , 4H ) , 5 ' - monophosphate . After more than 50 % of the transforma - 55 7 . 41 - 7 . 50 ( m , 7H ) , 6 . 02 ( dd , J = 2 . 8 Hz , J2 = 17 . 2 Hz , 1H ) , tion was achieved , tetrabutylammonium salt of pyrophos - 5 . 69 ( d , J = 6 . 0 Hz , 1H ) , 5 . 56 ( d , J = 7 . 6 Hz , 1H ) , 4 . 96 - 5 . 11 ( m , phate ( 150 mg ) was added , followed by DMF ( 0 . 5 mL ) to 1H ) , 4 . 37 - 4 . 46 ( m , 1H ) , 3 . 82 ( d , J = 10 . 8 Hz , 1H ) , 3 . 62 ( d , get a homogeneous solution . After 1 . 5 hours at ambient J = 10 . 8 Hz , 1H ) , 1 . 70 - 1 . 78 ( m , 1H ) , 1 . 53 - 1 . 59 ( m , 1H ) , 1 . 02 temperature , the reaction was diluted with water ( 10 mL ) ( s , 9H ) , 0 . 79 ( t , J = 7 . 6 Hz , 3H ) . To a solution of the crude and loaded on a column HiLoad 16 / 10 with Q Sepharose 60 intermediate ( 1 . 0 g , 1 . 96 mmol ) in anhydrous DCM ( 15 mL ) High Performance . Separation was done in a linear gradient were added sym - collidine ( 1 . 4 g , 11 . 76 mmol ) , AgNO3 ( 1 . 0 of NaCl from 0 to 1N in 50 mM TRIS - buffer ( pH7 . 5 ) . g , 5 . 88 mmol ) and MMTrCl ( 4 . 8 g , 15 . 6 mmol ) at R . T . under Triphosphate was eluted at 75 - 80 % B . Corresponding frac N2 . The reaction mixture was stirred at R . T . overnight . The tions were concentrated . Desalting was achieved by RP mixture was filtered and concentrated . The residue was HPLC on Synergy 4 micron Hydro - RP column ( Phenom - 65 purified by column chromatography on silica gel ( eluting inex ) . A linear gradient of methanol from 0 to 30 % in 50 mM with PE : ETOAc = 2 : 1 ) to give crude full protected interme triethylammonium acetate buffer ( pH 7 . 5 ) was used for diates as a white solid ( 1 . 1 g , 53 . 1 % ) . To a solution of the

US 9 , 815 , 864 B2 165 166

crude intermediate ( 600 mg , 0 . 57 mmol ) in THF ( 5 mL ) was mixture was stirred for 30 mins . The reaction was quenched added TBAF ( 446 mg , 1 . 71 mmol ) ) at R . T . The reaction was with Nas , 02 solution and extracted with EA . The organic stirred at 4050° C . overnight . The crude product was purified layer was dried over Na2SO4 and concentrated . The residue by column chromatography on silica gel eluted with PE : E - was purified by column on silica gel ( PE : EA = 1 : 1 to 1 : 2 ) to TOAc = 3 : 2 to give crude P13 - 1 ( 350 mg , 75 . 1 % ) as a yellow 5 give P14 - 1 ( 205 mg , 37 % ) as a white solid . solid . Compound P14 - 1 ( 205 mg , 0 . 21 mmol ) was dissolved in

To a solution of P13 - 1 ( 300 mg . 0 . 37 mmol ) in CH . CN 80 % HCOOH aq . solution , and the mixture was stirred at ( 2 . 5 mL ) were added NMI ( 2 . 5 mL ) and a solution of R . T . for 16 hours . The solvent was removed , and the residue phenyl ( isopropoxy - L - alaninyl ) phosphorochloridate ( 2 . 55 was purified by RP HPLC ( HCOOH system ) to give 14a as g . 7 . 4 mmol ) in CH , CN ( 2 . 5 mL ) at R . T . under N . The 10 a mixture of 2 P - isomers ( 24 mg , 18 % ) . ESI - LCMS : m / z 456 reaction mixture was stirred at R . T . for 3 hours . The mixture [ M + H ] " . was concentrated in vacuo . The residue was purified by column chromatography on silica gel ( PE : ETOAc = 1 : 1 ) to Example 15 give crude product as a yellow oil ( 500 mg , 81 % ) . The crude product was further treated with 80 % HCOOH ( 70 mL ) at 15 Preparation of Compound 15a R . T . overnight . The mixture was concentrated in vacuo , and the crude product was purified by RP HPLC ( MeCN and 0 . 1 % HCOOH in water ) to give 13a as a white solid ( a mixture of two P isomers , 86 mg , 40 . 3 % two steps ) . ESI MS : m / z 582 . 93 [ M + H ] * . 20

Example 14

Preparation of Compound 14a TBDPSO .

25 V

TBSO NHMMTr P3 - 8

NHMMTr

HO

HO * 11111 11111

MMTrO * * 1111 P13 - 1

NHMMTr P15 - 1

NH2 $

II OGO Vu | HN _ P _ o * 11111

MMTIO NH

HOW 1111 P14 - 1

NH2

15a dology -

is .

14a

To a mixture of P3 - 8 ( 2 . 2 g , 2 . 5 mmol ) , AgNO3 ( 844 mg , 55 5 . 0 mmol ) and collidine ( 907 mg , 7 . 5 mmol ) in anhydrous

DCM ( 10 mL ) was added MMTrCl ( 1 . 54 g , 5 . 0 mmol ) under Ny . The reaction mixture was stirred at R . T . overnight . The reaction mixture was filtered through a Buchner Funnel . The filtrate was washed with saturated NaHCO , solution and

60 brine . The organic layer was separated , dried over anhydrous To a stirred solution of P13 - 1 ( 451 mg , 0 . 55 mmol ) and Na2SO4 and filtered . The filtrate was concentrated to dry

NMI ( 1 mL ) in anhydrous acetonitrile ( 2 mL ) was added ness . The residue was purified by column on silica gel dropwise a solution of 2 - chloro - 8 - methyl - 4H - benzo [ d ] [ 1 , 3 , ( PE : EA = 10 : 1 to 1 : 2 ) to give the intermediate ( 2 . 3 g , 84 % ) , 2 ] dioxaphosphinine ( 855 mg , 4 . 2 mmol ) in acetonitrile ( 0 . 2 which was dissolved in a solution of TBAF in THF ( 1M , 2 . 6 mL ) at 0° C . under Ny . The mixture was stirred at R . T . for 65 mL ) under N2 . The reaction mixture was stirred at R . T . 2 hours . Solution of I , ( 3 . 2 g , 12 . 6 mmol ) , pyridine ( 9 mL ) , overnight . The residue was dissolved in EA ( 200 mL ) and H , O ( 3 mL ) and DCM ( 3 mL ) was added . The reaction washed with water and brine . The organic layer was sepa

US 9 , 815 , 864 B2 167 168

Example 17

Preparation of Compound 17a

TBDPSO TBDPSO $ 0 Tam NH

TBSO P3 - 7 P3 - 7

rated , dried over anhydrous Na2SO4 and filtered . The filtrate was concentrated to dryness , and the residue was purified by column on silica gel ( DCM / MeOH = 100 : 1 to 30 : 1 ) to give P15 - 1 as a white foam ( 1 . 3 g , 94 % ) .

To a stirred solution of P15 - 1 ( 300 mg , 0 . 55 mmol ) and proton sponge ( 235 mg , 1 . 1 mmol ) in anhydrous MeCN ( 9 mL ) was added with a solution of POC13 ( 169 mg , 1 . 1 mmol ) in MeCN ( 1 mL ) via syringe at 0° C . The mixture was stirred at R . T . for 40 mins . A mixture of ( S ) - cyclohexyl 2 - amino - 10 propanoate hydrochloride ( 525 mg , 2 . 55 mmol ) and TEA ( 0 . 1 mL ) was added at 0° C . The mixture was warmed to R . T . and stirred for 3 hours . The reaction mixture was quenched with saturated NaHCO3 , and extracted with EA ( 100 mLx2 ) . The combined organic layers was dried over 15 Na , SO , , concentrated and purified by silica gel column ( 1 ~ 4 % MeOH in DCM ) to give the crude product ( 400 mg , 78 . 15 % ) as a yellow solid . The crude product was treated with 80 % HCOOH ( 50 mL ) at R . T . for 16 hours . The solvent was removed , and the residue was purified by RP HPLC to 20 give 15a as a white solid ( 40 mg , 14 % ) . ESI - LCMS : m / z 660 [ M + H ] + .

HO

HOS? P17 - 1 P17 - 1

O

O = = O — P - 0

NH 1114 ?? Example 16 25

HO 1116 Preparation of Compound 16a 17a

- NH2 HO

11

ylin A

To a solution of P3 - 7 ( 1 . 4 g , 2 . 3 mmol ) in MeOH ( 50 mL ) 30 was added NH4F ( 8 . 0 g ) at R . T . The reaction mixture was

refluxed overnight . After cooling to R . T . , the mixture was filtered , and the filtrate was concentrated . The crude product was purified by silica gel column chromatography ( 10 % MeOH in DCM ) to give P17 - 1 as a white solid ( 410 mg , 77 . 8 % ) .

To a stirred solution of P17 - 1 ( 60 mg , 0 . 19 mmol ) in anhydrous THF ( 3 mL ) was added dropwise a solution of t - BuMgCl ( 0 . 38 mL , 1M in THF ) at - 78° C . The mixture

40 was stirred at 0° C . for 30 min and re - cooled to - 78° C . A solution of phenyl ( isopropoxy - L - alaninyl ) phosphorochlo ridate ( 104 mg , 0 . 4 mmol ) in THF ( 0 . 5 mL ) was added dropwise . After addition , the mixture was stirred at 25° C . for 16 hours . The reaction was quenched with HCOOH

45 ( 80 % aq . ) at 0° C . The solvent was removed , and the residue was purified on silica gel ( DCM : MeOH = 50 : 1 to 10 : 1 ) to give 17a as a white solid ( a mixture of two P isomers , 11 . 0 mg , 11 % ) . ESI - LCMS : m / z 542 . 0 [ M + H ] * .

OO - P - 0 o = - - NH

ill 50 1116 Example 18

16a Preparation of Compound 18a

NH

To a stirred solution of 4a ( 150 mg , 0 . 56 mmol ) in anhydrous THF ( 3 mL ) was added dropwise a solution of t - BuMgCl ( 1 . 2 mL , 1M in THF ) at - 78° C . The mixture was stirred at 0° C . for 30 min and re - cooled to - 78° C . A solution of phenyl ( isopropoxy - L - alaninyl ) phosphorochlo ridate ( 312 mg , 1 . 2 mmol ) in THF ( 1 . 0 mL ) was added 60 dropwise . After addition , the mixture was stirred at 25° C . for 16 hours . The reaction was quenched with HCOOH ( 80 % aq . ) at 0° C . The solvent was removed , and the residue was purified on silica gel ( DCM : MeOH = 50 : 1 to 10 : 1 ) to 65 give 16a as a white solid ( 24 . 0 mg , 15 % ) . ESI - LCMS : m / z 541 . 0 [ M + H ] *

TBDPSO

= ! TBSO 11111 TBSO

P3 - 5

169 - continued

5

TBDPSO w l . .

r .

US 9 , 815 , 864 B2 170

refluxed for 3 hours . After cooling R . T . , the mixture was filtered , and the filtrate was concentrated in vacuo . The residue was purified by column chromatography on silica gel ( eluting with DCM : MeOH = 50 : 1 - 30 : 1 ) to give P18 - 3 as a white solid ( 135 mg , 78 . 1 % ) . ' H NMR ( CD , OD , 400 MHz ) 87 . 84 ( d , J = 8 . 0 Hz , 1H ) , 6 . 06 ( dd , J = 1 . 6 Hz , Ju = 19 . 6 Hz , 1H ) , 5 . 67 ( d , J = 8 . 4 Hz , 1H ) , 5 . 18 - 5 . 03 ( m , 1H ) , 4 . 50 ( dd , J1 = 5 . 2 Hz , J2 = 21 . 6 Hz , 1H ) , 3 . 85 ( d , J = 12 . 4 Hz , 1H ) , 3 . 72 ( d , J = 12 . 4 Hz , 1H ) , 3 . 09 ( s , 1H ) .

To a solution of P18 - 3 ( 130 mg , 0 . 5 mmol ) in anhydrous THF ( 4 mL ) was added dropwise t - BuMgCl ( 1 . 0 mL , 1 . 0 mmol ) at – 70° C . under nitrogen . The reaction was stirred at R . T . for 30 mins . A solution of phenyl ( isopropoxy - L - alani nyl ) phosphorochloridate in anhydrous THF ( 1M , 0 . 8 mL ,

15 0 . 78 mmol ) was added at - 70° C . , and the reaction mixture was stirred at R . T . for 5 hours . The reaction was quenched by HCOOH , and the mixture was concentrated in vacuo . The residue was purified by column chromatography on silica gel ( DCM : MOH = 60 : 1 ) to give 18a as a white solid ( a

20 mixture of two Pisomers , 25 mg , 7 . 7 % ) . ESI - MS : m / z 540 . 2 [ M + H ] * .

TBSON 10

P18 - 1

TBDPSO

11 TBSO

P18 - 2

Example 19 25

NH

Preparation of Compound 19a

HO ' 30 NHMMTr * * 1111

P18 - 3

35 . . HO

00 - P - 0 NH NH E .

NH 1105 = 40 40 P15 - 1 P15 - 1 * 1111

NHMMTr

18a

+ 1111

Net P19 - 1

NHMMTr

O = P 111r .

To a solution of ( chloromethyl ) triphenylphosphonium 45 chloride ( 2 . 1 g , 6 . 0 mmol ) in anhydrous THF ( 10 mL ) was added dropwise n - BuLi ( 4 . 6 mL , 6 . 0 mmol ) at - 70° C . under nitrogen . The reaction was stirred at - 70° C . for 50 mins . A solution of compound P3 - 5 ( 950 mg , 1 . 5 mmol ) in anhy drous THF ( 5 mL ) was added at - 70° C . , and the reaction 50 was stirred at 0° C . for 3 hours . The reaction was quenched by saturated aq . NH _ C1 and extracted with EtoAc . The organic layer was separated , dried and concentrated to give a residue . The residue was purified by column chromatog raphy on silica gel ( eluting with PE : EtOAc = 6 : 1 ) to give 55 P18 - 1 as a yellow gum ( 900 mg , 91 . 2 % ) .

To a solution of compound P18 - 1 ( 600 mg , 0 . 91 mmol ) in anhydrous THF ( 18 mL ) was added dropwise n - BuLi ( 4 . 7 mL , 10 . 9 mmol ) at - 70° C . under nitrogen . The reaction was stirred at - 70° C . for 3 hours . The reaction was quenched by 60 saturated aq . NH _ Cl and extracted with EtoAc . The organic layer was separated , dried and concentrated to give a resi due . The residue was purified by column chromatography on silica gel ( eluting with PE : EtOAc = 8 : 1 – 5 : 1 ) to give P18 - 2 as a white solid ( 300 mg , 53 . 0 % ) . 65

To a solution of P18 - 2 ( 300 mg , 0 . 44 mmol ) in MeOH ( 10 mL ) was added NH F ( 1 . 0 g ) at R . T . The reaction was

P19 - 2

NHMMTr

O = P

P19 - 3

US 9 , 815 , 864 B2 171

- continued 172

- continued NH

a NH - -

O = P 111110 1111

?

Ho * # 1111

19a P20 - 1 P2012 -

and 20 till P20 - 2

-

30

Compound P15 - 1 ( 1 . 2 g , 2 . 2 mmol ) was dissolved in dry acetonitrile ( 20 mL ) , and 0 . 45 M tetrazole ( 24 . 0 mL , 11 . 0 13 mmol ) and 3 - ( bis ( diisopropylamino ) phosphinooxy ) pro panenitrile ( 1 . 13 g , 3 . 74 mmol ) was added . The reaction mixture was stirred for 1 hour under N , at R . T . TBDPH ( 2 . 7 mL , 15 mmol ) was added , and the mixture was stirred for 1 hour . The reaction was quenched by Na2S2O3 solution and extracted with EA . The organic layer was dried over Na2SO4 and concentrated . The residue was purified by column on silica gel ( DCM : MeOH = 100 : 1 to 40 : 1 ) to give P19 - 1 as a white solid ( 759 mg , 52 % ) . 25

Compound P19 - 1 ( 750 mg , 1 . 14 mmol ) was dissolved in saturated NHz in MeOH solution . The mixture was stirred for 2 hours at R . T . The solution was concentrated to dryness to give crude P19 - 2 as a yellow solid ( 662 mg , 100 % ) . Negative - ESI - LCMS : m / z 606 [ M - H ] .

Compound P19 - 2 ( 292 mg , 0 . 47 mmol ) was co - evapo rated with pyridine twice and dissolved in anhydrous DMF ( 0 . 5 mL ) . DIPEA ( 1 . 2 mL ) was added and followed by 2 , 2 - dimethyl - propionic acid iodomethyl ester ( 680 mg , 2 . 8 35 mmol ) . The reaction mixture was stirred at R . T . under N2 for 16 hours . The reaction was quenched by Na , s , o , solution and extracted with EA . The organic layer was dried over Na2SO4 and concentrated . The residue was purified by column on silica gel ( DCM : MeOH = 100 : 1 to 30 : 1 ) to give 40 P19 - 3 as a white solid ( 95 mg , 30 % ) .

Compound P19 - 3 ( 95 mg , 0 . 13 mmol ) was dissolved in a 80 % HCOOH aq . solution , and the mixture was stirred at R . T . for 16 hours . The solvent was removed , and the residue 46 was purified by RP HPLC ( MeCN and 0 . 1 % HCOOH in water ) to give 19a as a white solid ( 10 mg , 17 % ) . ESI LCMS : m / z 450 [ M + H ] * .

itil TBSO P20 - 3

??

.

TBSO P20 - 4

NH

Example 20

Preparation of Compound 20a TBSO

P20 - 5

NH TBSO N

?? 11 .

TBSC 111 to P20 - 6

P3 - 1 P3 - ?

NH2

-

TBSO

* * 1111 10 TBSO

NHMMTr

TBSO

20 11111 )

NH

HO

US 9 , 815 , 864 B2 173 174

- continued To a stirred solution of P20 - 2 ( 3 . 2 g , 14 . 0 mmol ) in anhydrous pyridine ( 10 mL ) and DCM ( 100 mL ) was added dropwise a solution of TBSCI ( 4 . 2 g , 28 . 0 mmol ) at 0° C . Stirring was continued at R . T . for 18 hours . The mixture was

5 diluted with DCM . The organic layer was washed with brine and dried over Na , SO2 . The solvent was removed , and the residue was purified on a silica gel column ( 10 % MeOH in DCM ) to afford P20 - 3 as a white solid ( 3 . 4 g , 70 . 8 % ) .

To a stirred solution of NaHCO3 in H2O ( 250 mL ) and acetone ( 200 mL ) was added oxone ( 30 . 0x4 g ) at 0° C . The

P20 - 7 mixture was warmed to R . T . , and the distillate was collected at - 78° C . ( 120 mL ) under slightly reduced pressure to give a solution of DMDO in acetone . To a stirred solution of

15 P20 - 3 ( 250 . 0 mg , 0 . 7 mmol ) in DCM ( 20 mL ) were added a DMDO ( 120 mL ) solution at - 40° C . and MgSO4 . The mixture was warmed to R . T . and then stirred for 2 hours . The solution was filtrated , and the filtrate was used for the next - step directly .

To a stirred solution of P20 - 4 ( 500 . 0 mg , 1 . 4 mmol ) in anhydrous DCM ( 50 mL ) was added allyl - trimethyl - silane

TBSO ( 760 . 0 mg , 6 . 7 mmol ) and SnC14 ( 1 . 2 g , 4 . 5 mmol ) at - 40° P20 - 8 C . The mixture was warmed and stirred at 0° C . for 1 hour .

The reaction was quenched with saturated NaHCO , and extracted with DCM . The organic layer was dried over Na SO , and concentrated . The residue was purified on a silica gel column ( 2050 % EA in PE ) to give P20 - 5 as a white foam ( 120 mg , 41 % ) . ESI - LCMS : m / z = 422 [ M + Na ] * .

30 To a stirred solution of P20 - 5 ( 270 . 0 mg , 0 . 7 mmol ) in dry DCM were added imidazole ( 400 . 0 mg , 5 . 9 mmol ) and TBSC1 ( 390 . 0 mg , 2 . 6 mmol ) at R . T . The mixture was stirred at R . T . for 18 hours . The solution was diluted with EA . The solvent was washed with brine and dried over Na S04 . The 35 solvent was removed , and the residue was purified on a silica gel column ( 2040 % EA in PE ) to afford compound P20 - 6 as a white foam ( 280 mg , 80 . 7 % ) . ESI - LCMS : m / z 537 To a stirred suspension of P3 - 1 ( 20 . 0 g , 81 . 3 mmol ) , [ M + Na ] * . imidazole ( 15 . 9 g , 234 . 0 mmol ) , PPhz ( 53 . 5 g , 203 . 3 mmol )

and pyridine ( 90 mL ) in anhydrous THF ( 360 mL ) was 40 To a stirred solution of P20 - 6 ( 280 . 0 mg , 0 . 5 mmol ) in dry added dropwise a solution of I . ( 41 . 3 g . 162 . 6 mmol ) in THF MeCN were added TPSC1 ( 350 . 0 mg , 1 . 2 mmol ) , NEt ( 350 mL ) at 0° C . After addition , the mixture was warmed ( 400 . 0 mg , 4 . 0 mmol ) and DMAP ( 270 . 0 mg , 2 . 2 mmol ) at to R . T . and stirred for 14 hours . The solution was quenched R . T . The mixture was stirred at R . T . for 18 hours . The with ag . Na , s , o , ( 150 mL ) and extracted with EA . The solution was quenched with ammonium . The organic layer organic layer was dried over Na2SO4 and concentrated . The residue was purified on a silica gel column ( DCM : was removed , and the residue was purified by TLC ( using MeOH = 100 : 1 to 10 : 1 ) to afford P20 - 1 as a white solid ( 22 . 1 EA ) to afford compound P20 - 7 as a white foam ( 240 . 0 mg , g , 76 . 4 % ) . ' H NMR ( CD , OD , 400 MHz ) 87 . 70 ( d , J = 8 . 0 Hz , 85 . 7 % ) . ESI - LCMS : m / z 514 [ M + H ] * . 1H ) , 5 . 88 ( dd , J , = 1 . 6 Hz , J , = 20 . 8 Hz , 1H ) , 5 . 71 ( d , J = 8 . 4 50 To a stirred solution of P20 - 7 ( 270 . 0 mg , 0 . 5 mmol ) in dry Hz , 1H ) , 5 . 24 ( dd , = 2 . 0 Hz , J2 = 5 . 2 Hz , 1H ) , 5 . 10 ( dd , = 2 . 0 DCM were added AgNO3 ( 1 . 5 g , 8 . 8 mmol ) , MMTrCl Hz , J2 = 5 . 2 Hz 1H ) , 3 . 78 - 3 . 83 ( m , 1H ) , 3 . 61 - 3 . 65 ( m , 1H ) , ( 450 . 0 mg , 1 . 5 mmol ) and collidine ( 500 . 0 mg , 4 . 1 mmol ) at 3 . 44 ( dd , = J2 = 6 . 0 Hz , 1H ) . R . T . The mixture was stirred at R . T . for 18 hours . The

To a stirred solution of P20 - 1 ( 22 . 1 g , 62 . 1 mmol ) in solution was diluted with DCM . The organic layer was anhydrous THF ( 200 mL ) was added dropwise DBU ( 14 . 2 55 washed with brine and dried over Na SO4 . The solvent was g , 93 . 1 mmol ) in THF ( 50 mL ) at 0° C . over 10 mins . The removed , and the residue was purified on a silica gel column mixture was stirred at 60° C . for 6 hours . The reaction was ( 2040 % EA in PE ) to afford compound P20 - 8 as a white quenched with ag . NaHCO , ( 200 mL ) and extracted with foam ( 300 mg , 81 . 6 % ) . ESI - LCMS : m / z 786 ( M + H ] * : EA . The organic layer was washed with brine and dried over To a stirred solution of P20 - 8 ( 170 . 0 mg , 0 . 3 mmol ) in dry Na2SO4 . The solvent was removed , and the residue was 60 MeOH was added NH F ( 300 . 0 mg , 8 . 1 mmol ) , and the purified on a silica gel column ( MeOH : DCM = 1 / 100 to 1 / 30 ) mixture was refluxed for 24 hours . The solvent was removed to afford P20 - 2 as a white solid ( 8 . 7 g , 61 . 5 % ) . ' H NMR under reduced pressure , and the residue was purified on a ( CD , OD , 400 MHz ) 8 7 . 51 ( d , J = 8 . 0 Hz , 1H ) , 6 . 05 ( dd , silica gel column ( 2 - 5 % MeOH in DCM ) to give the crude Jq = 1 . 2 Hz , Jz = 17 . 2 Hz , 1H ) , 5 . 73 ( d , J = 8 . 0 Hz , 1H ) , 5 . 26 product . The crude product was further purified by RP ( dd , = 1 . 2 Hz , Jo = 4 . 8 Hz , 1H ) , 5 . 13 ( dd , = 1 . 2 Hz , Jo = 4 . 8 Hz , 65 HPLC ( water and 0 . 1 % HCOOH in MeCN ) to afford 20a as 1H ) , 4 . 63 ( dd , Jy = 2 . 0 Hz , J2 = 3 . 2 Hz , 1H ) , 4 . 41 ( dd , a white solid ( 47 . 0 mg , 49 . 8 % ) . ESI - LCMS : m / z 286 J = J2 = 2 . 0 Hz , 1H ) . [ M + H ] * .

20a

was

175 Example 21 neurone

US 9 , 815 , 864 B2 176

was dissolved in methanol with a drop of concentrated aqueous ammonia and concentrated . The residue was puri fied on silica gel with 5 - 12 % methanol in DCM to give 21a ( 27 mg ) as a white solid ; MS : m / z 417 [ M + 2 - methylhep

5 tylamine ] *

Preparation of Compound 21a B NHMMTr

Example 22

= Preparation of Compound 22a TBSO

TBSÒ =

P20 - 8 NHMMTr NH

=

TBSO1 101

P20 - 2 = 10 TBSO

P21 - 1 NHMMTr NH

N

- Oh . . ilo * 1111

??

P22 - 1 * 1111

P21 - 2 NH2 NH

?

HO * * * 1115

0 L110 / ? P22 - 2 015

21a NH

Bz0

* 11116

P22 - 3 NHBz

To a stirred solution of P20 - 8 ( 250 . 0 mg , 0 . 3 mmol ) in 50 MeOH was added Pd / C ( 500 . 0 mg ) , and the mixture was stirred under H , ( balloon ) for 18 hours at R . T . The reaction was filtered , and the solvent removed under reduced pres sure . The residue was purified by prep . TLC ( 30 % EtoAc in PE ) to afford P21 - 1 as a white foam ( 210 . 0 mg , 84 . 0 % ) . 55

To a stirred solution of P21 - 1 ( 210 . 0 mg , 0 . 3 mmol ) in dry THF was added TBAF ( 1 mL , 1 mmol ) , and the mixture was stirred at R . T . for 18 hours . The solvent was removed under reduced pressure , and the residue was purified by prep . TLC ( 30 % EtoAc in PE ) to give P21 - 2 as a white foam ( 111 . 2 60 mg , 74 . 6 % ) . ESI - MS : m / z 560 [ M + H ] * . Compound P21 - 2 ( 81 mg ) was dissolved in a mixture ( 5

mL ) of formic acid ( 80 % ) and water ( 20 % ) . The resulting solution was stirred at R . T . for 3 hours and then concen trated . The residue was co - evaporated with methanol / tolu - 65 ene three times . Chromatography on silica gel with 5 - 12 % methanol in DCM gave a mixture of two compounds , which

BzO

INDE . Bzo

P22 - 4

US 9 , 815 , 864 B2 177

- continued 178

Example 23 NH2

Preparation of Compound 23a 5

HO 011 . )

* 11115 10 NH

22a

TBDPSO

DMTro

TBSON TBSO 11111 P23 - 1

NPMB

Bn0 HO

Bnos * 01011

P23 - 2

NPMB

Bn0

* + 1111 Bno

To a solution of P20 - 2 ( 5 . 23 g , 23 . 1 mmol ) in anhydrous MeOH ( 50 mL ) was added PbCO3 ( 12 . 7 g , 46 . 3 mmol ) at 15 R . T . A solution of 12 ( 11 . 7 g , 46 . 3 mmol ) in MeOH ( 10 mL ) was then added dropwise at 0° C . The reaction mixture was stirred at R . T . for overnight . The reaction was quenched with Na , s , o , and dissolved in EA . The organic layer was dried over Na , SO and concentrated . The residue was purified by 20 column ( DCM / M OH = 100 / 1 to 20 / 1 ) to give P22 - 1 as a white solid ( 5 . 6 g , 71 . 8 % ) . ' H NMR ( CD , OD , 400 MHz ) 87 . 67 ( d , J = 8 . 0 Hz , 1H ) , 5 . 88 ( dd , Ji = J2 = 7 . 6 Hz , 1H ) , 5 . 73 ( d , J = 8 . 0 Hz , 1H ) , 5 . 24 ( dd , Ji = 4 . 4 Hz , J2 = 6 . 4 Hz , 1H ) , 5 . 11 ( dd , = 6 . 4 Hz , J = 6 . 0 Hz , 1H ) ; 4 . 65 ( dd , J , = 20 . 0 Hz , Ja = 20 . 4 Hz , 1H ) , 3 . 67 ( d , J = 11 . 6 Hz , 1H ) , 3 . 54 ( d , J = 11 . 6 Hz , 1H ) , 3 . 43 ( s , 3H ) .

To a stirred solution of P22 - 1 ( 5 . 6 g , 14 . 5 mmol ) in anhydrous pyridine ( 20 mL ) was added dropwise BzCl ( 2 . 9 30 g , 20 . 9 mmol ) at 0° C . The mixture was stirred at R . T . for 10 hours . The reaction was quenched with H , O , and the solution was concentrated . The residue was dissolved in EA and washed with saturated NaHCO3 . The organic layer was dried over Na SO , and concentrated . The residue was puri - 35 fied on a silica gel column ( 20 - 40 % EA in PE ) to give P22 - 2 as a white foam ( 4 . 9 g , 74 . 2 % ) . Compound P22 - 2 ( 4 . 9 g , 10 . 0 mmol ) , BZONa ( 14 . 4 g , 100

mmol ) and 15 - crown - 5 ( 22 . 0 g , 100 mmol ) were suspended in DMF ( 200 mL ) . The mixture was stirred at 60 - 70° C . for 40 3 days . The precipitate was removed by filtration , and the filtrate was diluted with EA . The solvent was washed with brine and dried over Na2SO4 . The solvent was removed , and the residue was purified on a silica gel column ( 2060 % EA in PE ) to afford P22 - 3 as a white foam ( 2 . 3 g , 47 . 9 % ) . Compound P22 - 3 ( 2 . 3 g , 4 . 8 mmol ) , DMAP ( 1 . 2 g , 9 . 6

mmol ) , TPSC1 ( 2 . 9 g , 9 . 6 mmol ) and EtzN ( 0 . 97 g , 9 . 6 mmol ) were suspended in MeCN ( 10 mL ) . The mixture was stirred at R . T . for 14 hours . NHz in THF ( saturated at 0° C . , 100 mL ) was added to the mixture , and the mixture stirred at R . T . for 2 hours . The solvent was removed , and the residue was purified by column ( DCM / MeOH = 100 : 1 to 50 : 1 ) to give the crude product ( 1 . 2 g ) . The crude product was dissolved in pyridine , and BzCl ( 0 . 42 g , 3 . 0 mmol ) was 55 added . The mixture was stirred at R . T . for 16 hours and quenched with water . The solvent was removed , and the residue was purified on a silica gel column ( PE : EA = 2 : 1 to 1 : 1 ) to give P22 - 4 as a white foam ( 460 mg , 31 % ) . Compound P22 - 4 ( 0 . 46 g , 0 . 8 mmol ) was dissolved in 60

saturated methanolic ammonia ( 100 mL ) , and the mixture was stirred at R . T . for 14 hours . The solvent was removed , and the residue was dissolved in H , and washed with DCM . The aqueous phase was lyophilized and further purified by prep . HPLC ( 0 . 1 % formic acid in water / acetoni - 65 trile ) to give 22a as a white solid ( 145 mg , 78 . 9 % ) . ESI - MS : m / z 276 [ M + H ] * .

P23 - 3

45

Bn0 50

F F Bn0

P23 - 4

NH2

Bn0

11111 P23 - 5

- continued HMMTI

Bn01

111 10 Bno

NHMMTr

HO

F 11

NH ,

30

US 9 , 815 , 864 B2 179 180

The third intermediate ( 2 . 5 g , 2 . 84 mmol ) was dissolved in 80 % HOAC ( 25 mL ) at R . T . , and the mixture was stirred at R . T . for overnight . The reaction was quenched with MeOH , and the solvent was removed . The crude was puri

5 fied on a silica gel column ( PE : EA = 5 : 1 to 1 : 1 ) to give P23 - 2 as a white solid ( 1 . 2 g , 73 % ) .

To a stirred solution of DAST ( 1 . 39 g , 8 . 68 mmol ) in anhydrous toluene ( 15 mL ) was added dropwise a solution of P23 - 2 ( 1 . 0 g , 1 . 73 mmol ) at - 78° C . The mixture was stirred at - 78° C . for 30 mins . The solution was heated to 60°

P23 - 6 C . gradually and then stirred overnight . The mixture was poured into saturated Na2CO3 solution . The concentrated organic phase was purified on a silica gel column ( PE : EA = 10 : 1 to 4 : 1 ) to give P23 - 3 as a white solid ( 449 mg , 45 % ) . ' H NMR ( CD , OD , 400 MHz ) 8 7 . 87 ( d , J = 8 . 4 Hz , 1H ) , 7 . 27 - 7 . 37 ( m , 12H ) , 6 . 82 - 6 . 84 ( m , 2H ) , 6 . 14 ( dd , J = 16 . 8 , 2 . 0 Hz , 1H ) , 5 . 18 - 5 . 50 ( m , 4H ) , 4 . 96 ( s , 2H ) , 4 . 45 - 4 . 88 ( m , 7H ) , 3 . 67 - 3 . 89 ( m , 5H ) .

20 A mixture of P23 - 3 ( 1 . 20 g , 2 . 07 mmol ) and CAN ( 3 . 41 g , 6 . 23 mmol ) in a solution of MeCN : Water ( 3 : 1 , 10 mL ) was stirred at R . T . overnight . Brine ( 10 mL ) was added , and the mixture was extracted with EA . The combined organic HOW extracts were dried and evaporated under reduced pressure .

P23 - 7 25 The residue was purification by chromatography on silica gel ( PE : EA = 10 : 1 to 2 : 1 ) to give P23 - 4 as a yellow solid ( 475 mg , 49 . 8 % ) .

To a stirred solution of P23 - 4 ( 550 mg , 210 mmol ) in anhydrous MeCN ( 10 mL ) were added TPSC1 ( 725 mg , 2 . 40

30 mmol ) , DMAP ( 293 mg , 2 . 40 mmol ) and TEA ( 242 mg , 2 . 40 mmol ) at R . T . , and the mixture was stirred at R . T . overnight . NH , OH ( 25 mL ) was added , and the mixture was stirred for 2 hours . The solvent was removed , and the residue was HO purified on a silica gel column ( PE : EA = 8 : 1 to 2 : 1 ) to give P23 - 5 as a white solid ( 700 mg crude ) . ? H NMR ( CD , OD , 400 MHz ) 87 . 86 ( d , J = 8 . 4 Hz , 1H ) , 7 . 27 - 7 . 36 ( m , 10H ) , 6 . 13 ( dd , = 17 . 2 Hz , J2 = 2 . 0 Hz , 1H ) , 5 . 48 - 5 . 53 ( m , 1H ) , 5 . 11 - 5 . 26 ( m , 1H ) , 4 . 44 - 4 . 74 ( m , 7H ) , 3 . 89 ( dd , J = 10 . 4 Hz , J2 = 2 . 0

40 Hz , 1H ) , 3 . 69 ( dd , J = 10 . 8 Hz , J2 = 1 . 6 Hz , 1H ) . To a solution of P23 - 1 ( 3 . 1 g , 4 . 5 mmol ) in DMF ( 30 mL ) To a stirred solution of P23 - 5 ( 1 . 0 g , 2 . 18 mmol ) in was added anhydrous K , CO , ( 1 . 24 g , 9 . 03 mmol ) and anhydrous DCM ( 15 mL ) was added MMTrCl ( 2 . 02 g , 6 . 56 PMBC1 ( 1 . 40 g , 9 . 03 mmol ) . The mixture was stirred at mmol ) and AgNO3 ( 1 . 11 g , 6 . 56 mmol ) at R . T . , and the ambient temperature overnight . The reaction was quenched mixture was stirred at R . T . overnight . The solid was filtered with water and extracted with EA . The organic layer was 45 off and washed with DCM . The filtrate was washed with concentrated , and the residue was purified on a silica gel brine and dried over Na SO . . The organic phase was con column ( PE : EA = 10 : 1 to 4 : 1 ) to give the intermediate as a centrated , and the residue was purified on a silica gel column white solid ( 2 . 36 g , 74 . 8 % ) . ' H NMR ( CDC13 , 400 MHz ) ( PE : EA = 8 : 1 to 2 : 1 ) to give P23 - 6 as a white solid ( 520 mg , 87 . 29 - 7 . 88 ( m , 23H ) , 6 . 83 - 6 . 98 ( m , 6H ) , 6 . 35 - 6 . 45 ( m , 1H ) , 41 % ) . 4 . 51 - 5 . 50 ( m , 6H ) , 3 . 89 - 3 . 95 ( m , 9H ) , 3 . 66 - 3 . 71 ( m , 2H ) , 50 To a stirred solution of P23 - 6 ( 520 mg , 0 . 713 mmol ) in 3 . 03 ( d , J = 11 . 2 Hz , 1H ) , 1 . 21 ( s , 9H ) , 0 . 89 ( m , 9H ) , acetone were added ammonium formate ( 2 . 0 g , 31 . 7 mmol , 0 . 01 - 0 . 11 ( m , 6H ) . The intermediate was used in the next in portions ) and 10 % palladium on carbon ( 1 . 0 g ) . The step . mixture was refluxed for 12 hours . The catalyst was filtered

To a stirred solution of the intermediate ( 11 . 0 g , 10 . 47 off and washed with solvent . The filtrate was added EA and mmol ) in anhydrous THF ( 100 mL ) was added TBAF ( 8 . 20 55 washed with brine . The concentrated organic phase was g , 31 . 42 mmol ) at R . T . , and the mixture was stirred at R . T . purified by column chromatography ( DCM : MeOH = 100 : 1 to for 5 hours . The solution was removed , and the residue was 15 : 1 ) and prep . TLC to give P23 - 7 as a white solid ( 270 mg , purified on a silica gel column ( PE : EA = 5 : 1 to 1 : 1 ) to give 69 . 0 % ) . ESI - MS : m / z 549 . 6 [ M + H ] * . a second intermediate as a white solid ( 5 . 99 g , 82 % ) . Compound P23 - 7 ( 130 mg , 0 . 236 mmol ) was dissolved in

To a stirred solution of the second intermediate ( 500 mg , 60 80 % HCOOH ( 20 mL ) at R . T . , and the mixture was stirred 0 . 716 mmol ) in anhydrous DMF ( 10 mL ) was added NaH at 50° C . for 12 hours . The solvent was removed , and the ( 51 . 5 mg , 2 . 14 mmol ) and BnBr ( 365 mg , 2 . 14 mmol ) residue was co - evaporated with toluene twice . The residue dropwise at 0° C . The mixture was stirred at R . T . for was re - dissolved in MeOH ( 20 mL ) at 60° C . and stirring overnight . The solution was quenched with water and was continued for 48 hours . The solvent was removed , and extracted with EA . The concentrated organic phase was 65 the residue was purified by column chromatography ( DCM : purified on a silica gel column ( PE : EA = 10 : 1 to 4 : 1 ) to give MeOH = 100 : 1 to 10 : 1 ) to give 23a as a white solid ( 45 mg , a third intermediate as a white solid ( 496 mg , 79 % ) . 69 . 0 % ) . ESI - MS : m / z 277 . 8 [ M + H ] * , 554 . 8 [ 2M + H ] * .

35 F * * 111

HO 23a

US 9 , 815 , 864 B2 181

Example 24 182

- continued

Preparation of Compound 24a a

HO NHz . HCI HO - HO — HIRST L aat

10 TBSO TBSO P24 - 6

NH 11111 P24 - 1 TBDPSO

NHBZ HO - 11 . 2009

20 1111 TBSO P24 - 7

Bzo

25 NH

Bzo P24 - 2 TBDPSO

co OS SUU

30 4F 1111 TBSO

P24 - 8 NH o

35 Bz0

NH

TBDPSO 111111 Bz F 11111111 40 P24 - 3

1111 TBSO P24 - 9

45

NH

HO TBDPSO

50 1111111

HOM . 1111

HO 211111 TBSON P24 - 4 824 - 4 P24 - 10

55

NHMMTr

NH 60

HO TBDPSO .

11

ount 11 TBSO 65 TBSO P24 - 5 P24 - 11

183

HO HOM

* 1111

NH al

HO :

1

1111

US 9 , 815 , 864 B2 184

- continued 2 hours and then neutralized with AcOH to pH = 7 . To the NHMMTr reaction were added EtOH ( 50 mL ) and NaBH , ( 12 . 7 g ,

333 . 6 mmol ) . The mixture was stirred at R . T . for 30 mins . The reaction was quenched with saturated aq . NH _ C1 . extracted with EA . The organic layer was dried over Na , SO4 and concentrated . The residue was purified by silica gel column chromatography ( 1 - 3 % MeOH in DCM ) to give P24 - 6 as a white solid ( 13 . 5 g , 59 . 5 % ) .

To a solution of P24 - 6 ( 13 . 5 g , 33 . 1 mmol ) in DCM ( 100 10 mL ) were added pyridine ( 20 mL ) and DMTC1 ( 11 . 2 g , 33 . 1 mmol ) at 0° C . The solution was stirred at 25° C . for 3 hours , P24 - 12 and then treated with MeOH ( 30 mL ) . The solvent was removed , and the residue was purified by silica gel column chromatography ( DCM : MeOH = 300 : 1 to 100 : 1 ) to give a

15 residue . The residue was dissolved in anhydrous pyridine ( 150 mL ) and TBDPSCI ( 16 . 5 g , 60 mmol ) and AgNO3 ( 10 . 2 g , 60 mmol ) were added . The mixture was stirred at 25° C . for 15 hours , and then filtered and concentrated . The mixture was dissolved in EtoAc and washed with brine . The

20 organic layer was dried over Na2SO4 . Purified by silica gel column chromatography ( DCM : MeOH = 300 : 1 to 100 : 1 )

24a gave the product as a yellow solid ( 16 . 2 g , 85 . 3 % ) . The solid was dissolved in 80 % HOAc aq . solution ( 400 mL ) . The

To a solution of P24 - 1 ( 30 . 0 g , 100 . 0 mmol ) in pyridine mixture was stirred at R . T . for 15 hours . The mixture was ( 300 mL ) was added BzCl ( 56 . 0 g , 400 mmol ) at 25° C . The 25 diluted with EtoAc and washed with NaHCO , solution and mixture was stirred at 25° C . for 15 hours . The mixture was brine . The organic layer was dried over Na2SO4 and purified concentrated and purified by column chromatography ( PE : by silica gel column chromatography ( DCM : MeOH = 200 : 1 EA = 20 : 1 to 2 : 1 ) to give crude P24 - 2 ( 55 . 0 g , 81 % ) . to 50 : 1 ) to give P24 - 7 as a white solid ( 9 . 5 g , 86 . 5 % ) . ' H

Compound P24 - 2 ( 55 . 0 g , 92 mmol ) was dissolved in NMR ( CD2OD , 400 MHz ) 8 7 . 39 - 7 . 70 ( m , 11H ) , 6 . 34 - 6 . 38 80 % HOAc aq . solution , and the mixture was refluxed for 14 30 ( m , 1H ) , 5 . 12 ( d , J = 8 . 0 Hz , 1H ) , 4 . 79 ( dd , J , = 10 . 0 Hz , hours . The solvent was removed under reduced pressure , J2 = 16 . 0 Hz , 1H ) , 4 . 14 ( dd , Ji = 1 . 6 Hz , Jz = 11 . 6 Hz , 1H ) , and the residue was co - evaporated with toluene . The residue 3 . 48 - 3 . 84 ( m , 2H ) , 3 . 49 ( dd , = 1 . 6 Hz , Jo = 11 . 6 Hz , 1H ) , 1 . 12 was purified on a silica gel column ( PE / EA = 4 : 1 to 2 : 1 ) to ( s , 9H ) , 0 . 92 ( s , 9H ) , 0 . 16 ( s , 6H ) . give P24 - 3 as a white solid ( 39 . 2 g , 83 % ) . To a solution of P24 - 7 ( 6 . 0 g , 9 . 3 mmol ) in anhydrous

Compound P24 - 3 ( 39 . 2 g , 83 mmol ) was dissolved in 35 DCM ( 80 mL ) was added Dess - Martin periodinane ( 7 . 9 g , saturated methanolic ammonia , and the resulting solution 18 . 6 mmol ) at 0° C . under nitrogen . The reaction was stirred was stirred at R . T . for 15 hours . The solvent was removed , at R . T . for 1 hour . The solvent was removed in vacuo , and and the residue was purified on a silica gel column ( DCM the residue was triturated with diethyl ether ( 50 mL ) . The MeOH = 50 : 1 to 20 : 1 ) to give P24 - 4 ( 21 . 0 g , 95 . 8 % ) . mixture was filtered through a pad of MgSO4 , and the

To a solution of P24 - 4 ( 21 . 0 g , 79 . 5 mmol ) in pyridine 40 organic solvent was stirred with an equal volume of ( 250 mL ) was added DMTrCl ( 28 . 2 g , 83 . 5 mmol ) at 0° C . Na2S2O3 . 5H2O in saturated NaHCO3 ( 50 mL ) until the The solution was stirred at R . T . for 15 hours . The reaction organic layer became clear ( approx . 10 min ) . The organic was quenched with MeOH and concentrated to dryness layer was separated , washed with brine , and dried over under reduced pressure . The residue was dissolved in EtOAC M gSO4 . After concentration in vacuo , P24 - 8 was obtained and washed with water . The organic layer was dried over 45 as a red solid ( 5 . 8 g . 98 % ) . Na , so , and concentrated . The residue was dissolved in To a mixture of methyltriphenylphosphonium bromide DCM ( 300 mL ) . Imidazole ( 13 . 6 g , 200 mmol ) and TBSC1 ( 9 . 6 g , 27 . 0 mmol ) in anhydrous THF ( 60 mL ) was added ( 30 . 0 g , 200 mmol ) were added . The reaction mixture was n - BuLi ( 10 . 8 mL , 27 . 0 mmol ) at - 70° C . under nitrogen . stirred at R . T . for 12 hours . The reaction mixture was The reaction was stirred at 0° C . for 30 mins . A solution of washed with NaHCO , and brine . The organic layer was 50 P24 - 8 ( 5 . 8 g , 9 . 0 mmol ) in anhydrous THF ( 20 mL ) was dried over Na SO , and concentrated . The residue ( 48 . 5 g , added dropwise at 0° C . under nitrogen . The reaction was 79 . 5 mmol ) was dissolved in 80 % HOAc aq . solution ( 400 stirred at R . T . for 12 hours . The reaction was quenched with mL ) . The mixture was stirred at R . T . for 20 hours . The NH4Cl and extracted with EtOAc . The organic layer was mixture was diluted with EtoAc and washed with NaHCO? separated , dried and concentrated , and the residue was solution and brine . The organic layer was dried over Na S04 55 purified by silica gel column chromatography ( DCM : and purified by silica gel column chromatography ( 1 - 2 % MeOH = 300 : 1 to 100 : 1 ) to give P24 - 9 as a white solid ( 3 . 0 MeOH in DCM ) to give P24 - 5 as a white solid ( 21 . 0 g , g , 51 % ) . 70 % ) . ESI - MS : m / z 379 . 1 [ M + H ] * . To a solution of P24 - 9 ( 2 . 9 g , 4 . 5 mmol ) in anhydrous

To a solution of P24 - 5 ( 21 . 0 g , 55 . 6 mmol ) in anhydrous MeOH ( 20 mL ) was added Pd / C ( 1 . 4 g ) at 25° C . under CH , CN ( 200 mL ) was added IBX ( 17 . 1 g , 61 . 1 mmol ) at 60 hydrogen atmosphere . The mixture was stirred at 25° C . for R . T . The reaction mixture was refluxed for 1 hour and then 1 hour . The solution was filtered , evaporated to dryness and cooled to 0° C . The precipitate was filtered off , and the purified on a silica gel column ( DCM : MeOH = 300 : 1 to filtrate was concentrated to give the aldehyde as a yellow 100 : 1 ) to give P24 - 10 as a white solid ( 2 . 3 g , 79 . 3 % ) . solid ( 21 . 0 g , 55 . 6 mmol ) . To a solution of the aldehyde To a solution of P24 - 10 ( 1 . 0 g , 1 . 55 mmol ) in anhydrous ( 21 . 0 g , 55 . 6 mmol ) in dioxane ( 200 mL ) were added 37 % 65 CH2CN ( 20 mL ) were added TPSC1 ( 940 mg , 3 . 1 mmol ) , CH2O ( 22 . 2 mL , 222 . 4 mmol ) and 2N NaOH aq . solution DMAP ( 380 mg , 3 . 1 mmol ) and NEtz ( 470 mg , 4 . 6 mmol ) ( 55 . 6 mL , 111 . 2 mmol ) . The mixture was stirred at R . T . for at R . T . The reaction was stirred at R . T . for 5 hours . NH OH

186 - continued

TBDPSO NH

HO TBSON " 1115 NHMMTr

P25 - 5

US 9 , 815 , 864 B2 185

( 8 mL ) was added , and the reaction was stirred for 1 hour . The mixture was diluted with DCM ( 150 mL ) and washed with water , 0 . 1 M HCl and saturated aq . NaHCO3 . The solvent was removed , and the residue was purified by silica gel column chromatography ( PE : EA = 10 : 1 to 1 : 1 ) to give the 5 crude product as a yellow solid ( 900 mg , 90 % ) . To a solution of the crude product in DCM ( 10 mL ) were added MMTrC1 ( 930 mg , 3 . 0 mmol ) , AgNO3 ( 510 mg , 3 . 0 mmol ) and colliding ( 720 mg , 6 . 0 mmol ) at R . T . The reaction was stirred for 12 hours at R . T . The reaction was filtered , 10 concentrated and purified by silica gel column chromatog raphy ( DCM : MeOH = 200 : 1 to 50 : 1 ) to give P24 - 11 as a TBDPSO

yellow solid ( 1 . 1 g , 77 . 6 % ) . To a solution of P24 - 11 ( 1 . 1 g , 1 . 2 mmol ) in MeOH ( 40

mL ) was added NH F ( 1 . 0 g , 30 mmol ) at 25° C . and stirred at 70° C . for 15 hours . The solution was filtered and evaporated to dryness , and the residue was purified by silica gel column ( DCM : MeOH = 200 : 1 to 20 : 1 ) to give P24 - 12 as a white solid ( 450 mg , 66 . 6 % ) . ESI - LCMS : m / z 563 . 6 au 20 [ M + H ] * . Compound P24 - 12 ( 250 mg , 0 . 44 mmol ) was dissolved in

80 % HCOOH in H2O ( 6 . 0 g ) at 25° C . The mixture was stirred at 35° C . for 15 hours . The solution was evaporated to dryness , dissolved in MeOH ( 30 mL ) and stirred at 60° C . for 12 hours . The solution was evaporated to dryness and purified by silica gel column chromatography methylene chloride : methanol to give 24a as a white solid ( 125 . 6 mg , 97 % ) . ESI - LCMS : m / z 291 . 9 [ M + H ] * .

* 11111 TESO NHMMTr

P25 - 6

TBDPSO NH

TBSO NHMMTr

P25 - 1

HO ?? NA

30 Example 25 NHMMTr

P25 - 8 Preparation of Compound 25a

HO

will HOS

y ! ! ! ! NH2 HO 25a El N

line

P25 - 1 N

HO

1113 TBSÓF TBSO P25 - 2

OK NZ HO1 NH NH .

To a solution of P25 - 1 ( 20 . 0 g , 70 . 16 mmol ) in anhydrous pyridine ( 200 mL ) was added imidazole ( 19 . 08 g , 280 . 7 mmol ) and TBSCI ( 42 . 10 g , 280 . 7 mmol ) at 25° C . The

45 solution was stirred at 25° C . for 15 hours , and then concentrated to dryness under reduced pressure . The residue was washed with EtoAc to give the crude product as a white solid ( 36 . 4 g ) . The crude product was dissolved in THF ( 150 mL ) and H , O ( 100 mL ) , and then HOAC ( 300 mL ) was

50 added . The solution was stirred at 80° C . for 13 hours . The reaction was cooled to R . T . , and the mixture was concen trated to dryness under reduced pressure . The residue was dissolved washed with EtoAc and dried to give P25 - 2 as a white solid ( 31 . 2 g , 60 . 9 % ) .

To a stirred solution of P25 - 2 ( 31 . 2 g , 78 . 2 mmol ) in anhydrous pyridine ( 300 mL ) was added AcZO ( 11 . 96 g , 117 . 3 mmol ) . The mixture was stirred at 25° C . for 18 hours . MMTrCi ( 72 . 3 g , 234 . 6 mmol ) and AgNO3 ( 39 . 9 g , 234 . 6 mmol ) were then added . The solution was stirred at 25° C .

60 for 15 hours . And H0 was added to quench the reaction . The solution was concentrated to dryness under reduced pressure . The residue was dissolved in EtoAc and washed with water . The organic layer was dried over Na2SO4 and filtered . The filtrate was concentrated in vacuo to give a

65 residue . The residue was purified by silica gel ( DCM : MeOH = 200 : 1 to 50 : 1 ) to give the product . The product was dissolved in NH / MeOH ( 300 mL ) , and the mixture was

SS

TBSOF * 11111 TBSO NHMMTr

P25 - 3

HO NH

HO 110 * *

TBS NHMMTr

P25 - 4

NH

US 9 , 815 , 864 B2 187 188

stirred at 25° C . for 20 hours . The solvent was removed , and and then stirred at 25° C . for 15 hours . The reaction was the residue was purified on a silica gel column ( DCM : quenched with saturated NH C1 ( 50 mL ) . The mixture was MeOH = 100 : 1 to 50 : 1 ) to give P25 - 3 as a yellow solid ( 28 . 6 extracted with EtOAc . The combined organic phase was g , 86 . 5 % ) . H NMR ( 400 MHz , MeOD ) 88 . 01 ( s , 1H ) , dried with Na2SO4 , filtered and evaporated to dryness to 7 . 23 - 7 . 35 ( m , 12H ) , 6 . 85 - 6 . 87 ( m , 2H ) , 5 . 60 ( dd , J , = 11 . 2 5 give a light yellow oil . The oil was purified by column Hz , J2 = 5 . 6 Hz , 1H ) , 4 . 78 - 4 . 94 ( m , 1H ) , 4 . 44 ( dd , J = 8 . 0 Hz , chromatography ( DCM : MeOH = 200 : 1 to 50 : 1 ) to give Jo = 4 . 8 Hz . 1H ) . 3 . 78 ( s . 3H ) , 3 . 60 - 3 . 63 ( m . 11 ) . 3 . 50 ( dd . P25 - 7 as a white solid ( 1 . 6 g , 76 % ) .

To a solution of P25 - 7 ( 1 . 6 g , 1 . 7 mmol ) in MeOH ( 50 J1 = 32 . 0 Hz , Jz = 12 . 0 Hz , 2H ) , 3 . 32 ( s , 3H ) , 0 . 94 ( s , 9H ) , mL ) was added NH F ( 1 . 5 g , 40 mmol ) , and the mixture was 0 . 12 - 0 . 14 ( m , 6H ) . stirred at 70° C . for 15 hours . The solution was filtered and To a solution of P25 - 3 ( 7 . 24 g , 10 . 79 mmol ) in anhydrous 10 evaporated to dryness . The residue was purified by silica gel CH3CN ( 100 mL ) was added IBX ( 3 . 93 g , 14 . 03 mmol ) at column ( DCM : MOH = 200 : 1 to 20 : 1 ) to give P25 - 8 as a 20° C . The reaction mixture was refluxed at 90° C . for 1 white solid ( 450 mg , 49 % ) . ESI - LCMS : m / z 584 . 1 [ M + H ] * . hour . The reaction was filtered , and the filtrate was concen Compound P25 - 8 ( 130 mg , 0 . 22 mmol ) was dissolved in trated to give the aldehyde as a yellow solid ( 7 . 1 g ) . To a 80 % HCOOH and the mixture was stirred at 25° C . for 1 solution of the aldehyde ( 7 . 1 g , 10 . 6 mmol ) in dioxane ( 80 15 hour . Then the solution was evaporated to dryness . The mL ) was added 37 % CH2O ( 4 . 2 mL , 42 . 4 mmol ) and 2N residue was dissolved in MeOH ( 30 mL ) and stirred at 60° NaOH aq . solution ( 8 . 0 mL , 15 . 9 mmol ) . The mixture was stirred at 25° C . for 2 hours and then neutralized with AcOH C . for 12 hours . Then the solution was evaporated to

dryness , and the residue was washed by EtoAc to give 25a to pH = 7 . To reaction was added EtOH ( 30 mL ) and NaBH . as a white solid ( 52 . 3 mg , 76 % ) . ESI - MS : m / z 334 . 1 ( 2 . 4 g , 63 . 6 mmol ) , the reaction was then stirred for 30 mins . 20 [ M + Na ] * The mixture was quenched with saturated aq . NH _ C1 . The mixture was extracted with EA , and the organic layer was Example 26 dried over Na2SO4 . The solvent was removed , and the residue was purified by silica gel column chromatography Preparation of Compound 26a ( DCM : MeOH = 200 : 1 to 50 : 1 ) to give P25 - 4 as a yellow 25 solid ( 4 . 86 g , 65 . 4 % ) .

To a solution of P25 - 4 ( 3 . 8 g , 5 . 4 mmol ) in DCM ( 40 mL ) were added pyridine ( 10 mL ) and DMTrC1 ( 1 . 8 g , 5 . 4 mmol ) at 0° C . The solution was stirred at 25° C . for 1 hour . The reaction mixture was treated with MeOH ( 15 mL ) and 30 concentrated . The residue was purified by silica gel column TBDPSO1 chromatography ( DCM : MeOH = 200 : 1 to 50 : 1 ) to give the mono - DMTr protected intermediate as a yellow solid ( 3 . 6 g , 66 . 4 % ) . To a solution of the intermediate in anhydrous NHMMTr

pyridine ( 30 mL ) were added TBDPSC1 ( 2 . 96 g , 10 . 8 mmol ) 35 P25 - 6

and AgNO3 ( 1 . 84 g , 10 . 8 mmol ) . The mixture was stirred at 25° C . for 15 hours . The mixture was filtered and concen trated , and then dissolved in EtoAc and washed with brine . The organic layer was dried over Na , SO2 , and then con TBDPSO

centrated . The residue was purified by silica gel column 40 N

chromatography ( DCM : MeOH = 200 : 1 to 50 : 1 ) to give the HO HÓTBSOAS NHMMTr pure intermediate as a white solid ( 3 . 8 g , 85 . 1 % ) . To a solution of the intermediate ( 3 . 6 g , 2 . 9 mmol ) in anhydrous P26 - 1

DCM ( 50 mL ) was added C1 , CHCOOH ( 1 . 8 mL ) in anhy drous DCM ( 18 mL ) at - 78° C . The mixture was stirred at 45 - 10° C . for 30 mins . The mixture was quenched with TBDPSO saturated aq . NaHCO3 and extracted with DCM . The organic layer was dried over Na2SO4 , and then purified by silica gel NC column chromatography ( DCM : MeOH = 200 : 1 to 50 : 1 ) to TBSO NHMMTr give P25 - 5 as a white solid ( 2 . 2 g , 80 . 7 % ) . 50

P26 - 2 Compound P25 - 5 ( 2 . 2 g , 2 . 3 mol ) was added to a sus pension of Dess - Martin periodinane ( 2 . 5 g , 5 . 8 mol ) in anhydrous CH C12 ( 30 mL ) at 25° C . The mixture was stirred at 25° C . for 4 hours . The solvent was removed in vacuo , and the residue triturated with diethyl ether ( 30 mL ) . 55 The mixture was filtered through a pad of MgSO4 . The organic solvent was stirred with an equal volume of HO NHMMTr

Na2S2O3 . 5H20 in saturated NaHCO3 ( 30 mL ) until the P26 - 3

organic layer became clear ( approx . 10 min ) . The organic layer was separated , washed with brine , and dried over 60 MgSO4 . The solvent was removed in vacuo to give P25 - 6 as a yellow solid ( 2 . 1 g , 95 % ) .

To a stirred solution of methyl - triphenyl - phosphonium bromide ( 2 . 3 g , 6 . 6 mmol ) in anhydrous THF ( 30 mL ) was added dropwise n - BuLi ( 2 . 6 mL , 6 . 6 mmol , 2 . 5 M in THF ) 65 at - 78° C . over 1 minute . Stirring was continued at 0° C . for 1 hour . P25 - 6 ( 2 . 1 g , 2 . 2 mmol ) was added to the mixture ,

TBSC 11115 TBSON

NH

* * 111

NH

* 11116 50

HO NH

* * 1111

HO NH

linea NH2 MO ! ! ! ! !

na

HO ??

NH ,

27 a

US 9 , 815 , 864 B2 189 190

To a stirred solution of P25 - 6 ( 2 . 1 g , 2 . 2 mmol ) in - continued pyridine was added HONH , HC1 ( 0 . 61 g , 8 . 8 mmol ) at 25° C . The mixture was stirred at 25° C . for 2 hours . The mixture was concentrated , and the residue was purified by column chromatography ( DCM : MeOH = 200 : 1 to 50 : 1 ) to give 5 P26 - 1 as a white solid ( 1 . 8 g , 83 % ) .

To a stirred solution of P26 - 1 ( 1 . 4 g , 1 . 47 mmol ) in DCM were added TEA ( 0 . 44 g , 4 . 4 mmol ) and methanesulfonyl HOE chloride ( 0 . 34 g , 2 . 9 mmol ) at 0° C . The mixture was stirred at 25° C . for 1 hour . The mixture was quenched with 10 saturated aq . NaHCO , and extracted with DCM . The organic phase was dried with Na2SO4 , filtered and evaporated . The To a stirred solution of chloromethyl - triphenyl - phospho residue was purified by column chromatography ( DCM : nium chloride ( 1 . 9 g , 5 . 4 mmol ) in anhydrous THF ( 30 mL ) MeOH = 200 : 1 to 50 : 1 ) to give P26 - 2 as a white solid ( 1 . 1 g , was added dropwise n - BuLi ( 2 . 16 mL , 5 . 4 mmol , 2 . 5 M in 79 % ) . 15 THF ) at - 78° C . over 10 mins . Stirring was continued at

To a solution of P26 - 2 ( 1 . 1 g , 1 . 18 mmol ) in MeOH ( 50 - 78° C . for 2 hours . P25 - 6 ( 1 . 7 g , 1 . 8 mmol ) was added , and mL ) was added NH F ( 1 . 5 g , 40 mmol ) , and the mixture was the mixture and stirred at 25° C . for 15 hours . The reaction stirred at 70° C . for 15 hours . The solution was filtered and was quenched with saturated NH _ C1 ( 50 mL ) . The mixture evaporated to dryness . The residue was purified by silica gel was extracted with EtoAc . The combined organic phase was column ( DCM : MeOH = 200 : 1 to 20 : 1 ) to give P26 - 3 as a 20 dried with Na2SO4 , filtered and evaporated to dryness to white solid ( 400 mg , 71 % ) . ESI - LCMS : m / z 583 . 1 [ M + H ] * . give a light yellow oil . The oil was purified by column

Compound P26 - 3 ( 200 mg , 0 . 34 mmol ) was dissolved in chromatography ( DCM : MeOH = 200 : 1 to 50 : 1 ) to give 80 % HCOOH aq . solution . The mixture was stirred at 25° C . P27 - 1 as a white solid ( 1 . 2 g , 70 % ) . for 1 hour . The solution was evaporated to dryness , dis 25 To a stirred solution of P27 - 1 ( 1 . 2 g , 1 . 3 mmol ) in solved in MeOH ( 30 mL ) and stirred at 60° C . for 12 hours . anhydrous THF ( 20 mL ) was added dropwise n - BuLi ( 8 . 0 The solvent was removed , and the residue was washed by EtoAc to give 26a as a white solid ( 100 . 4 mg , 95 % ) . mL , 20 mmol , 2 . 5 M in THF ) at - 78° C . over 10 minutes . ESI - MS : m / z 311 . 1 [ M + H ] * . Stirring was continued at - 78° C . for 4 hours . The reaction

was quenched with saturated NH4Cl ( 50 mL ) . The mixture Example 27 30 was extracted with EtoAc ( 50x2 mL ) . The combined

organic phase was dried over Na S04 , filtered and evapo Preparation of Compound 27a rated to dryness . The residue was purified by column chro

matography ( DCM : MeOH = 200 : 1 to 50 : 1 ) to give P27 - 2 as a white solid ( 1 . 0 g , 83 % ) .

To a solution of P27 - 2 ( 1 . 0 g , 1 . 1 mmol ) in MeOH ( 40 mL ) was added NH F ( 1 . 5 g , 40 mmol ) , and the mixture was stirred at 70° C . for 25 hours . The solution was filtered , and

TBDPOXY the filtrate was evaporated to dryness . The residue was 40 purified on a silica gel column ( DCM : MeOH = 200 : 1 to 20 : 1 )

to give P27 - 3 as a white solid ( 240 mg , 38 % ) . ESI - LCMS : m / z 582 . 1 [ M + H ] * .

P25 - 6 Compound P27 - 3 ( 130 mg , 0 . 22 mmol ) was dissolved in 80 % HCOOH aq . solution . The mixture was stirred at 25° C . for 1 hour . The solution was evaporated to dryness . The

TBDPSO residue was dissolved in MeOH ( 30 mL ) and stirred at 60° C . for 12 hours . The solvent was removed , and the residue was washed with EtoAc to give 27a as a white solid ( 43 . 0

CI TBSO NHMMTr somg , 63 % ) . ESI - MS : m / z 310 . 1 [ M + H ] * . P27 - 1

35 35

TBDPSO NH

NHMMTr TBSO 45

N

NS

11111

Example 28

TBDPSO 55 Preparation of Compound 28a

11111 TBSO NHMMTr

P27 - 2

60

HO NH ?? NH

NS

1111 NHMMTr 65 HØS F NH2 P27 - 2 P25 - 1

HO NH

NS

11101

NH

* * 1111 NHMMTr

NH

NS

11111 NHMMTr

EN NH

111 30 NHMMTr Bzo

US 9 , 815 , 864 B2 191 192

- continued hours . The solvent was removed , and the residue was purified by silica gel column chromatography ( DCM / MeOH = 80 : 1 to 30 : 1 ) to afford P28 - 1 as a white solid ( 9 . 2 g , 87 . 5 % ) .

To a stirred solution of P28 - 1 ( 9 . 2 g , 16 . 5 mmol ) in dry THF ( 300 mL ) were added imidazole ( 9 . 0 g , 132 mmol ) and

NHMMTr PPhz ( 34 . 8 g , 132 mmol ) . A solution of 12 ( 26 . 0 g , 103 mmol ) P28 - 1 in THF ( 100 mL ) was added dropwise under Ny at 0° C . The

10 mixture was stirred at R . T . for 18 hours . The reaction was quenched with Na S , Oz solution , and the mixture was extracted with EtoAc . The organic layer was dried over Na SO , and concentrated . The residue was purified by silica gel column chromatography ( DCM / MeOH = 80 : 1 to 30 : 1 ) to

15 give P28 - 2 as a light yellow solid ( 10 . 3 g , 93 . 4 % ) . P28 - 2 To a stirred solution of P28 - 2 ( 10 . 2 g , 15 . 3 mmol ) in dry

THF ( 300 mL ) was added DBU ( 4 . 7 g , 30 . 1 mmol ) . The mixture was stirred at 60° C . for 8 hours . The solution was diluted with NaHCO3 solution and extracted with EtOAc . The organic layer was dried over Na SO , and concentrated . The residue was purified by silica gel column chromatog raphy ( PE / EtOAc = 3 : 1 to 1 : 3 ) to afford P28 - 3 as a light yellow foam ( 6 . 2 g , 75 . 6 % ) . ESI - MS : m / z 540 [ M + H ] * . P28 - 3

25 To a stirred solution of P28 - 3 ( 5 . 42 g , 10 mmol ) in anhydrous CH2OH ( 100 mL ) were added PbCOz ( 13 . 7 g ,

N 53 . 1 mmol ) followed by a solution of I , ( 12 . 3 g , 48 . 9 mmol ) in CH2OH ( 300 mL ) at 0° C . The mixture was stirred at R . T . for 10 hours . The solution was quenched with a Na S203 solution and extracted with DCM . The organic layer was

P28 - 4 washed with NaHCO3 solution , dried over Na SO4 and concentrated . The residue was purified by pre - HPLC ( MeCN and 0 . 1 % HCOOH in water ) to give the pure

35 product as a white foam ( 2 . 4 g , 34 % ) . The product was NY dissolved in dry pyridine ( 20 mL ) and BzCl ( 723 mg , 5 . 2

mmol ) was added dropwise at 0° C . The mixture was stirred at 0° C . for 1 hour . The solution was quenched with

P28 - 5 NaHCO3 solution , and extracted with EtoAc . The organic layer was dried over Na S04 and concentrated . The residue was purified by silica gel column chromatography using

NH petroleum ether : ethyl acetate to afford P28 - 4 as a white solid ( 2 . 1 g , 77 . 1 % ) .

Compound P28 - 4 ( 2 . 0 g , 2 . 5 mmol ) , BzONA ( 3 . 6 g , 25 mmol ) and 15 - crown - 5 ( 5 . 5 g , 25 mmol ) were suspended in DMF ( 50 mL ) . The mixture was stirred at 110 - 125° C . for 5 days . The precipitate was removed by filtration , and the filtrate was diluted with EA . The solution was washed with

NH brine and dried over Na SO4 . The solvent was removed , and the residue was purified on a silica gel column ( PE / EA = 10 / 1 to 2 / 1 ) to afford crude P28 - 5 as a light yellow foam ( 1 . 6 g ,

NH2 80 % ) . Compound P28 - 5 ( 1 . 6 g , 2 . 0 mmol ) was dissolved in

methanolic ammonia ( 100 mL , saturated ) , and the mixture To a stirred solution of P25 - 1 ( 5 . 7 g . 20 mmol ) in was stirred at R . T . for 20 hours . The solvent was removed ,

anhydrous pyridine ( 20 mL ) was added dropwise Ac , O ( 5 . 8 and the residue was purified on a silica gel column ( DCM / mL , 60 mmol ) at 0° C . The mixture was stirred at R . T . for MeOH = 100 : 1 to 20 : 1 ) to give P28 - 6 as a white solid ( 410 10 hours . AgNO3 ( 8 . 5 g , 50 mmol ) and MMTrC1 ( 15 . 5 g . 50 60 mg , 34 . 9 % ) . ESI - LCMS : m / z 588 . 1 [ M + H ] + . mmol ) were added . The mixture was stirred at R . T . for 10 Compound P28 - 6 ( 200 mg , 0 . 34 mmol ) was dissolved in hours . The solution was quenched with saturated NaHCO , 80 % HCOOH and the mixture was stirred at 25° C . for 1 and extracted with EA . The organic layer was dried over hour . The solution was evaporated to dryness , and the Na2SO4 and concentrated . The residue was purified on a residue was dissolved in MeOH ( 30 mL ) and stirred at 60° silica gel column ( DCM / MeOH = 100 : 1 to 50 : 1 ) to afford the 65 C . for 12 hours . The solvent was removed , and the residue intermediate as a light yellow solid ( 12 . 1 g , 93 . 4 % ) . The washed with EtoAc to give 28a as a white solid ( 46 . 1 mg , solid was treated with saturated NHZ in MeOH at R . T . for 14 43 % ) . ESI - MS : m / z 316 . 1 [ M + H ] * .

Bzo NH

Monument NHMMTr

40

. ?? NH N

11111 NHMMT

P28 - 6

50

HO NH

HO 282

US 9 , 815 , 864 B2 193

Example 29 194

- continued NH2 Preparation of Compound 29a

DEAS 0 - 0 - 0

NH 10

1111 0 - P — 0

11111 * * *

11111 30a

DEAD ( 40 % in toluene , 0 . 15 mL , 0 . 33 mmol ) was added 20 to a stirred solution of triphenylphosphine ( 78 mg , 0 . 3 To a solution of 1 - 1 ( 313 mg ; 0 . 55 mmol ) in THF ( 8 mL ) mmol ) in anhydrous 1 , 4 - dioxane ( 0 . 5 mL ) at 0° C . under argon . The mixture was warmed up to R . T . and 10a ( 26 mg , under Ar was added a solution of triethylammonium bis 0 . 1 mmol ) and bis ( pivalovloxymethyl ) phosphate ( 98 mg . ( POM ) phosphate in THF ( prepared from bis ( POM ) phos 0 . 3 mmol ) were added . The resulting mixture was stirred at 25 phate ( 215 mg ; 1 . 2 equiv ) , THF ( 2 mL ) and Et N ( 0 . 1 mL ; 65° C . for 3 days . Diisopropylethylamine ( 50 UL ) was 1 . 3 equiv ) ) . The resulting mixture cooled in an ice - bath . added , and the mixture was stirred at 70° C . for 3 days . Diisopropylethyl amine ( 0 . 38 mL ; 4 equiv ) was added . Another reaction of the same scale was conducted sepa - BOP _ C1 ( 280 mg ; 2 equiv ) and 3 - nitro - 1 , 2 , 4 - triazole ( 125 rately . The two reaction mixtures were combined and con mg ; 2 equiv ) was then added . The reaction mixture was centrated . Chromatography on silica gel with 5 - 10 % metha - 30 , 10 - 30 stirred at 0° C . for 90 mins . The mixture was diluted with nol in DCM gave the desired product ( 20 mg ) with a minor CH C12 ( 60 mL ) and washed with saturated aq . NaHCO3 impurity . A second chromatography on silica gel , followed by RP HPLC with acetonitrile / water , gave 29a ( 2 . 8 mg ) as ( 2x10 mL ) and brine . The combined aqueous layers were a colorless residue . MS : m / z 698 [ M + 2 - methylheptylam back extracted with CH , C1 , ( ~ 20 mL ) . The combined ine ] * . organic extract was dried ( Na , SO ) and evaporated . The

35 residue purified on silica ( 25 g column ) with CH , C12 / i - PrOH Example 30 solvent system ( 2 - 10 % gradient ) . Yield : 140 mg ( 27 % ) .

A solution of 1 - 2 ( 110 mg ; 0 . 13 mmol ) in 80 % aq . formic Preparation of Compound 30a acid was heated at 35 - 37° C . for 3 hours . The mixture was 40 evaporated to give an oily residue . The residue was co

evaporated 2 times with toluene . Purification on a silica gel column ( 10 g ) with CH , C1 , / MeOH solvent system ( 4 - 10 % gradient ) to afford 30a ( 46 mg , 59 % yield ) . 31P - NMR

10 - P - OH ( DMSO - do ) : 8 - 4 . 45 . MS : m / z 646 [ M + 46 – 1 ] . a 6 - 0 - - OH

NMMT

Example 31

HO HOS H0 VOY N 0 Preparation of Compound 31a Et2N 50

CI - HIRA BOP - Cl , DIPEA , NT THF ; 0° C . ; 90 min HOME

1 - 1 O

NHMMT =

55 0 - P - OH -

SN O

O NHDMT =

0 - P - 07 80 % aq . - O

60 11111 Cl — " u HOW

HCOOH 35 - 37° C . ,

3 h HO Hovo N

- 2 Et3N

BOP - CI , DIPEA , NT THF ; 0° C . ; 90 min

65 HOME 1 - 2 2 - 1