amino acids, peptides and proteins in organic chemistry (building blocks, catalysis and coupling...

13Chemoselective Peptide Ligation: A Privileged Toolfor Protein SynthesisChristian P.R. Hackenberger, Jeffrey W. Bode, and Dirk Schwarzer

13.1Introduction

The recognition that proteins are the machinery and mediators of living processesengendered the need to isolate, characterize, manipulate, and modify them forunderstanding and advancing biology and medicine. An era in which the onlymethod to obtain proteins was extraction from living sources gave way to the age ofgenetic engineering, whereby proteins could be expressed in foreign host organisms,making possible the production of significant quantities of protein targets forbiochemical studies, structural characterization, and even their use as pharmaceu-ticals. This recombinant approach to protein synthesis is limited by the restrictionthat the proteins thus prepared may contain only the 20 canonical amino acids. Theintroduction of unnatural amino acids or most post-translational modifications suchas glycosylations or phosphorylations can be accomplished only with great difficultyor time-consuming techniques [1]. It is with these goals in mind that scientists haverecently returned to the long-held dream of producing proteins by purely syntheticmethods. Remarkable advances in chemical methods over the last 15 years havemade chemical protein synthesis increasingly common, and emerging technologiespromise even more versatile and practical methods in the coming years.

Within this chapter, we seek to provide the reader with an overview of the state ofthe art of peptide and protein synthesis using the concept of �chemoselective peptideligation� – the selective coupling of two ormore peptide fragments by an amide-bond-forming reactionwithout theneed for chemical coupling reagents or the protection ofside-chain functionalities (Scheme 13.1). In general, this is accomplished by theplacement of uniquely reactive functional groups at the C-terminal end of onepeptide fragment and the N-terminal end of the other; these functional groups orauxiliaries react exclusively with one another give a native (i.e., backbone) amidebond [2]. This chapter includes a brief history and explanation of its various forms andtheir development, an overview of the prevailing methods as they are currentlypracticed, and a survey of emerging chemical reactions for chemoselective ligationthat will impact the field in the years to come. Additionally, we will limit ourselves

Amino Acids, Peptides and Proteins in Organic Chemistry.Vol.3 – Building Blocks, Catalysis and Coupling Chemistry. Edited by Andrew B. HughesCopyright � 2011 WILEY-VCH Verlag GmbH & Co. KGaA, WeinheimISBN: 978-3-527-32102-5

j445

exclusively to chemical methods that allow for the formation of polypeptide con-jugates in which the new linkage is an amide bond.

There are numerous aspects of chemical protein synthesis that cannot be coveredby this chapter and have been the subject of other reviews [3]. These include, forinstance, the synthesis of starting materials, namely thioesters and other activatedN-peptides, enzymatic ligations and other techniques from molecular biology, andligations which yield covalent linkages other than amide bonds and protein mod-ification strategies. The interested reader is kindly referred to other sources for theseissues [4].

It is important to distinguish chemoselective peptide ligations from the related andpowerful fragment condensation strategies (Scheme 13.2) [5], such as the valuableAg(I)-mediated coupling of C-terminal N-peptide thioesters with N-terminally unpro-tected C-peptides [6]. These methods have been essential to the history and devel-opment of chemical protein synthesis, including a starring role in the first chemicalsynthesis of intact proteins such as ribonuclease S [7] and the Green FluorescentProtein (GFP) [8]. Interest in these methods for the coupling of partially protectedglycopeptide fragments attest to the value of these approaches to chemical proteinsynthesis [9]. Despite the established utility of such methods, this general strategysuffers from several limitations that prevent its adoption as a unified approach to thepreparation of pure, homogeneous peptides and proteins. These include a highprobability of epimerization during the activation at the C-terminus of theN-peptidefragment, aggregation and poor solubility of the long, side-chain protected frag-ments, the usual need for an excess of one of the precious peptide fragments, and the

Scheme 13.1 Concept of chemoselective amide ligation for peptide and protein synthesis. Thecartoon elements represent unique functional groups that undergo a chemoselective reaction thatproduces a native (backbone) amide bond in the ligated product.

chemoselective ligation

CO2HHN CO2PGH2N+

coupling of protected peptides

NH

OPG

PG

PGremovalchemoselective

reaction partners

(A)

(B)

PG

N-peptid Ce -peptide

C-peptideN-peptide

HN CO2PG

PG

PG

PG

NH

OHN CO2PG

PG

CO2HHN CO2PGH2N+

PG

Scheme 13.2 Fragment-coupling strategies: (A) coupling of protected peptides and(B) chemoselective ligation of unprotected peptides.

446j 13 Chemoselective Peptide Ligation: A Privileged Tool for Protein Synthesis

requirement for a global deprotection step that compromises the purity and yield ofthe final peptide [10].

The chemoselective ligation reactions covered in this chapter are built on a longtradition of synthetic peptide chemistry that is outside the scope of this chapter.Muchof the chemistry discussed here relies on the powerful solid-phase methods forpeptide synthesis pioneered by Merrifield [11]. Fifty years of advances in couplingreagents, linkers, resins, and protecting group strategies have made the synthesis ofpeptide fragments in the range of 30–40 amino acids routine and commonplace. Thenecessary protected amino acids and other materials are widely available, andadvances in chromatographic purification render the synthesis of research quantitiesof linear peptides a reliable process. In fact, one of the major challenges in thedevelopment of new chemoselective ligation techniques is ensuring that the syn-thesis of the requisite peptide fragments containing orthogonally reactive functionalgroups or auxiliaries is compatiblewith the entrenched chemicalmethods for peptidesynthesis.

The motivation for the discovery and development of new chemoselective ligationreactions for peptide and protein synthesis stems therefore from needs that are notmet by the traditional methods of either linear peptide synthesis or protein produc-tion with recombinant expression techniques. These include (i) the large-scalemanufacture of therapeutic peptides in which hundreds of kilograms, rather thanthe usual milligram quantities, of large peptides must be produced in high purity,(ii) the chemical syntheses of peptides containing unnatural amino acids includingpost-translational modifications, glycosylations, isotopically labeled segments, orD-amino acids, and (iii) protein semisynthesis, in which an expressed proteinfragment is ligated to a synthetically produced peptide.

Each of these applications demands innovative chemical methods that allowselective backbone amide bond formation in the presence of the diverse, unprotectedfunctional groups common to proteogenic side-chains. All of these applications havein common the synthesis of longer peptides in homogeneous form – a goal that ismost effectively met by chemoselective ligation strategies that avoid the accumula-tion of difficult to remove addition or deletion sequences or impurities arising fromlate-stage global deprotection. Even for low-yielding ligation reactions it is usuallytrivial to separate the desired ligation product from unreacted starting materials(Scheme 13.3).

Intertwined in the clear need for chemical protein synthesis is the long history ofpeptide synthesis as a driving force for the development and discovery of newmethods and concepts for organic synthesis in general. From the earliest syntheses ofdipeptides [12] by Fischer to the modern implementation of native chemical ligation(NCL) for the synthesis of proteins by Kent and others, the overwhelming desire forchemical methods for protein and peptide synthesis has foreshadowed the devel-opment and direction of modern synthetic methods. Peptide chemists were amongthe first to demand and implement protecting groups for reactive functionalities – aconcept of enormous importance and impact on the field of organic chemistry.Likewise, the recognition that truly chemoselective reactions for amide bondformation were the only way that protein synthesis would become routine presaged

13.1 Introduction j447

23

me

r

24

me

r

25

me

r

CO

OH

H2N

H2N

CO

OH

CO

OH

H2N

OH

Co

nve

ntio

na

l

line

ar

SP

PS

23

me

r

24

me

r

25

me

r

H2N

H2N

H2N

OO

O

O

O

OD

esire

d pe

ptid

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othe

r tru

ncat

ed p

eptid

es

Mix

ture

of p

eptid

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ith s

imila

r pro

perti

es -

Ver

y di

fficu

lt to

sep

erat

e, lo

w p

urity

Aft

er

cle

ava

ge

fro

m

so

lid s

up

po

rt

O

O

OH

H2N

HO

HN

OH

O

12

me

r

ch

em

ose

lective

liga

tio

n-C

O2,

-H2O

25

me

rC

OO

HH

2N

Onl

y de

sire

d pr

oduc

t -

Eas

y to

sep

erat

e, h

igh

purit

y

NH

2

Fm

oc

SP

PS

the

n P

urifica

tio

n

NH

2

Fm

oc

SP

PS

the

n P

urifica

tio

n

13

me

r

Scheme13

.3Cartoon

illustratingtheadvantages

ofchem

oselectiveligationof

unprotectedpe

ptidefragmen

tsforthesynthesisof

difficultpe

ptidesequ

ences.

Thepu

rityof

thefin

alprod

uctisgreatly

enhanced

bytheuseof

chem

oselectiveligation.


the modern emphasis on bioorthogonal reactions for the synthesis, detection, andmodification of biological materials. These concepts have recently ignited a newdemand by the synthetic organic chemists for processes and strategic designs thatdispense with the waste and added steps required by protecting groups and oxidationstate adjustments [2]. It is within this spirit that we catalog, in Section 13.5, someof themost promising emerging methods for new chemoselective amide bond formation.

Before proceeding with our survey, it is useful to establish the graphical nomen-clature employed in this chapter as defined in Figure 13.1.

13.2Chemoselective Peptide Ligations Following a Capture/Rearrangement Strategy

13.2.1Basic Concepts and Early Experiments

Most ligation techniques applied today are based on a �capture/rearrangement�strategy. The basic concept relies on two reactions that in combination mediatechemoselective peptide bond formation. The first reaction (capture) forms a selectivebut reversible linkage of two ligation partners. The second reaction (rearrangement)converts this flexible linkage into a stabile peptide bond in an irreversible manner.Although the terms reversible and irreversible are not a precise description of thereaction processes, which are primarily driven by the reaction kinetics, they arecommonly used in this regard to illustrate the concept.

Among the earliest capture/rearrangement ligation schemes is a strategy called�prior thiol capture,� which was developed by Kemp et al. [13, 14]. The procedurebegins with attaching the peptide that will end up in the N-terminal region ofthe ligation product (i.e., the N-peptide, see Figure 13.1) to an auxiliary template(6-hydroxy-4-mercaptodibenzofuran) through an ester bond in molecule 1(Scheme 13.4A) [15]. Alternatively, optimized solid-phase peptide synthesis (SPPS)protocols allow the direct assembly of the N-peptide on an immobilized template 1.The capture reaction is a disulfide exchange between a Cys residue located at theN-terminus of the C-peptide 2 and the free thiol of the template 1 (Scheme 13.4A).The following rearrangement reaction is an intramolecularO ! N transfer (3) to thepeptide bond between both ligation partners in 4, which is supported by the activatednature of the ester in 3. After ligation product 5 is formed it can be released bytreatment with reducing agents [16]. Although prior thiol capture has been opti-mized [16] and applied to polypeptides with up to 39 residues [17], nowadays thestrategy of NCL is more routinely used for peptide ligations.

Important early experiments towards the later development of NCL were pub-lished by Wieland et al. in 1953. They investigated the chemical properties of aminoacid thioesters [18] and reported that thiophenol-thioesters undergo an intermolec-ular aminolysis in the presence of amines. Most importantly, a glycine thioester ofcysteamine 6 could not be synthesized and isolated. Instead the thioester rearrangedrapidly through an intramolecular S ! N shift to the corresponding amide 7, which

13.2 Chemoselective Peptide Ligations Following a Capture/Rearrangement Strategy j449

N HC

O2H

H2N

O

SP

G

- B

ox inclu

din

g N

-term

inal am

ine a

nd C

-term

inal carb

oxylic

acid

- A

min

o a

cid

s o

r fu

nctionaliz

ed term

ini im

port

ant fo

r th

e s

chem

e

are

dra

wn p

recis

ely

Pro

tecte

d p

ep

tid

e:

- B

ox inclu

din

g a

PG

-labele

d, in

whic

h P

G s

tands for

com

monly

used

pro

tecting g

roups in F

moc-

or

Boc-b

ased S

PP

S (

PG

= p

rote

cting g

roup)

Un

pro

tecte

d p

ep

tid

e:

Part

ly p

rote

cte

d

pep

tid

e:

- O

nly

specifc p

rote

cte

d a

min

o a

cid

are

dra

wn w

ith P

G a

ttached

N-p

ep

tid

e-

Peptides w

hic

h p

art

icip

ate

in

a lig

ation r

eaction

- N

-peptide w

ill e

nd u

p in the N

-term

inal re

gio

n o

f th

e lig

atio

n p

roduct

- D

raw

n a

s w

hite b

oxes

C-p

ep

tid

e-

Peptides w

hic

h p

art

icip

ate

in

a lig

ation r

eaction

- C

-peptide w

ill e

nd u

p in the C

-term

inal re

gio

n o

f th

e lig

atio

n p

roduct

- D

raw

n a

s b

lack b

oxes

En

zym

e-

Enzym

es a

re d

raw

n a

s w

hite o

vals

Resin

- R

esin

s for

SP

PS

are

dra

wn a

s g

rey c

ircle

s

CO

2H

H2N

CO

2H

H2N

PG

CO

2H

H2N

CO

2H

H2N

En

zym

e

Figu

re13

.1Graph

ictoolbo

xforthedifferen

tpe

ptidefragmen

tsused

inthischap

ter.


OS

HO

O

OS

O

OS

H2N

NH

O

S

H2N

N H

O

S

OC

H3

O

S

O

RH

2N

OH

HS

O

O H2N

OH

S

ON H

OS

H

H2N

H2N

H2N

N H

OS

HE

t 3P

, H

2O

,

dio

xa

ne

(A)

(B)

H2N

H2N

H2N

CO

2H

CO

2H

CO

2H

O

H N

OH

O

OS

HO

S

HN

NH

OH

2N

CO

2H

O

810

911

1

2

35

4

S

O

H2N

NH

2

HN

O

HS

NH

2

67

ba

sic

an

dn

eu

tra

l p

H

HF

IP/H

2O

DM

SO

Earl

y e

xp

eri

men

ts

Pri

or

thio

l cap

ture

R =

Ph

, B

n

Scheme13

.4Aminolysisof

thioesters

byWieland

(A)an

dKem

p�spriorthiolcap

ture

strategy

(B).HFIP:

Hexafluoroisoprop

anol.


was attributed to the proximity of the additional amino group of cysteamine to thethioester. Since this rearrangement occurred under mild conditions the authorsconcluded that this reaction could be used for the formation of peptide bonds. Intoday�s nomenclature of a capture/rearrangement processess the latter reactionrepresents the rearrangement step. The preceding capture step is an intermolecularthiol–thioester exchange. Based on this observation, a Val-thiophenol thioester 8wassynthesized and treatedwithCys (9) (Scheme 13.4B). Due to the reactive nature of thearyl thioester a rapid exchange with the thiolmoiety of Cys occurred. The formedVal-S-Cys thioester 10 rearranged instantaneously to the Val–Cys dipeptide (11) linkedwith a native peptide bond [18].

13.2.2NCL

Today, NCL is the most widely used ligation technique. The key feature that makesNCL so successful is the chemoselectivity of this reaction, which was first fullyexploited by Kent et al. in 1994 [19]. In their contribution, which also introduced thename �native chemical ligation� for thefirst time, the authors ligated twounprotectedpeptides to synthesize the human interleukin (IL)-8 (Scheme 13.5A). This primarypublication has been cited nearly 1000 times, illustrating the importance of thisfinding for the chemical community. The capture step in NCL is mediated by areversible thiol–thioester exchange between an electrophilic (aryl) thioester 12 atthe C-terminus of theN-peptide and the nucleophilic thiol of a Cys residue located atthe N-terminus of theC-peptide 13 (Scheme 13.5A). In the rearrangement reaction, theCys-thioester 14 undergoes a rapid intramolecular S ! N transfer which proceedsthrough a favorable five-membered transition state and finally forms a native peptidebond between theC- and theN-peptide in 5 [20]. Full chemoselectivity is only achievedwhen all unprotected amino acids, including other Cys residues, are tolerated and donot interferewith the overall reactionpathway. This is indeed the case forNCLbecausethe irreversible intramolecular S ! N shift can only occur at the unique N-terminalCys residue.Therefore,Cys residueswithin theN- orC-peptide can form thioesters 15,but due to the lack of a nearby amino group 15 cannot undergo a rearrangementreaction and instead rapidly exchange backwards to 12 or 14 (Scheme 13.5B).

Several further examples of NCL-based peptide ligations for various purposes andapplications have followed the initial synthesis of human IL-8. These have beensummarized in various excellent overviews and will therefore not be furtherdiscussed here.

NCL reactions are generally performed in buffered aqueous solutions at neutralpH. These physiological conditions are important in many aspects. Strongly basicconditions would make other residues such as Lys amenable to reactions withthioesters and, furthermore, thioesters can hydrolyze under basic conditions. Acidicconditions would reduce the reactivity of the Cys thiol and the N-terminal amine ofthe C-peptide is reduced [9g,20].

Another key feature determining the efficiency of the NCL reaction is thechemical composition of the C-terminal thioester. Dawson et al. have conducted


S

O

RH

2N

H N

HS

O

O H2N

H N

S

ON H

OS

H

H2N

H2N

H2N

CO

2H

CO

2HC

O2H

irrev

ersi

ble

H N

O

1213

514

reve

rsib

le

(A)

Nat

ive

chem

ical

lig

atio

n

(B)

Eq

uili

bri

um

bet

wee

n t

hio

este

r p

epti

des re

vers

ible

+

nH

S

nH

S

nS

OH

2N

CO

2HN H

O

NH

2

SH

O H2N

H N

S

O

H2N

CO

2H

14

S

O

RH

2N

H N

HS

O

H2N

CO

2H

1213

n

+

HS

reve

rsib

le

N H

OS

H

H2N

CO

2HH N

O5

reve

rsib

le

irrev

ersi

ble

15

R =

Ph,

Bn

Scheme13

.5Nativechem

icalligation.

(A)Mechanisticpa

thway.(B)Eq

uilibrium

betweenthioesterpe

ptides.(C)Influ

ence

ofresidu

esat

theC-terminus

oftheN-

peptide.

(D)Th

ioesterexchan

gewith

arylthiols.


a detailed analysis by synthesizing a set ofmodel peptides containing each of the 20proteinogenic amino acids as the C-terminal thioester 16 [21]. The reaction with aC-peptide 17 yielded the product 18 and the progress of the reactions weremonitored over time by high-performance liquid chromatography (HPLC)(Scheme 13.5C). The fastest reaction rate was observed for the Gly-thioester, whichreacted quantitatively in less than 4 h. In contrast, thioesters containing b-branchedamino acids or Pro were not quantitatively converted into the ligation product 18after even 2 days [21].

Finally, the nature of the thioester is important for the ligation efficiency [22]. Ingeneral, alkyl thioesters are less reactive and easier to synthesize than their arylcounterparts. Therefore, a common modus operandi is the synthesis of alkyl deriva-tives 19, for example, with sodium-2-mercaptoethanesulfonate (MESNA), followedby an in situ conversion into the more reactive aryl thioesters 20 by the addition of anaccess of aryl thiols, like the water-soluble (4-carboxymethyl)thiophenol (MPAA,21, Scheme 13.5D) [23]. In addition to the mechanistic aspects, the addition of thiolsto the ligationmixtures also prohibits the oxidation of the Cys thiol, which is anotherimportant aspect of an efficient ligation reaction. (For a recent application inkinetically controlled segment ligations, see Chapter 13.6. Several NCL-basedligation protocols also include tris(2-carboxyethyl) phosphine hydrochloride (TCEP)as a thiol free reducing agent.).

13.2.3Protein Semisynthesis with NCL

The term �protein semisynthesis� describes ligation reactions between both syn-thetic and recombinantly-produced starting materials. Chemoselective ligationtechniques are ideally suited for such approaches because polypeptides frombiological sources are unprotected. Protein semisynthesis combines the advantagesof organic chemistry with biochemical techniques and allows incorporation of

-Xaa-SR Cys- -Xaa-Cys-+

Xaa = Gly,Cys,His > Xaa = Phe,Met,Tyr,Ala,Trp > Xaa = Asn,Asp,Gln,Glu,Ser,Arg,Lys > Xaa = Leu, Thr,Var,Ile,Pro < 2h < 9h < 12h < 48h

H2N CO2H H2N CO2HH2N

16 17 18

(C) Influence of the C-terminal thioester on the NCL reaction

(D) Thioester exchange

S

OH2N S

O

OOH

HOO

SH

excess

S

OH2N OH

O

19 20

21

Scheme 13.5 (Continued )


various unnatural functionalities into biopolymers without the size limitations ofSPPS. The groundwork formodern protein semisynthesis was laid in the early 1970sby Offord et al. [24, 25]. However, these early semisynthesis schemes relied on theinstallation of protection groups into the isolated peptides and were therefore notchemoselective. Today, chemoselective ligation techniques that do not requirecomplex protecting group strategies are used preferentially to link recombinant andsynthetic peptides.

NCL has proven to be especially useful for protein semisynthesis because thecapture/rearrangement process is mediated by Cys, which is genetically encoded(Scheme 13.6) [3, 19, 26]. Still, some manipulations of the starting material arerequired as all recombinant peptides and proteins are initially produced with anN-terminal Met. The essential N-terminal Cys in the C-peptide can be installed bygenetic methods like site-directed mutagenesis and controlled cleavage with pro-teases. With this approach, a Cys residue can be introduced into the recognition sitefor a specific protease 23, such as factor Xa [26, 27] or the TEV protease [28, 29] in afusion protein 22 on the genetic level [65–67]. When the expressed protein is treatedwith the corresponding protease the N-terminal Cys is released in the recombinantpeptide 12 which can be ligated with a synthetic peptide thioester 13 (Scheme 13.7).Alternative approaches use intein fusion proteins [30] or cyanogen bromide (CNBr)-

S

O

R H2N

HN

HS

O

O

H2N

HN

S

O

H2N

H2N

CO2H

CO2H

12 13

14

reversible

irreversible

synthetic recombinant

NH

OSH

H2N CO2H

HN

O

5

R = alkyl or aryl

Scheme 13.6 Concept of protein semisynthesis.


mediated cleavage between aMet–Cysmotif in a protein [31]. A construct containinga Cys following the initial Met can sometimes be obtained from bacteria with anN-terminal Cys without further manipulations. In these cases the endogenousmethionine aminopeptidase of the host organism removes the initial Met residueand liberates the downstream Cys moiety [32].

13.2.4Protein Semisynthesis with Expressed Protein Ligation

The semisynthetic scheme described above is suitable for ligating syntheticpeptides to the N-terminus of recombinant proteins. However, several biologicallyinteresting proteins require a ligation method in which the C-terminus of arecombinant protein can be synthetically manipulated. In these cases a recombi-nant protein thioester is required, which cannot be synthesized with chemicaltools. To address this problem, Muir and Cole introduced �expressed proteinligation� (EPL) [33]. EPL is based on an enzymatic approach to generate proteinthioesters. The exploited process is referred to as �protein splicing� – a naturallyoccurring reaction where an internal protein domain excises itself out of aprecursor polypeptide 24 and links the flanking N- and C-fragments with a nativepeptide bond [34–37]. The internal protein domain is called the �intein� and the

S

O

R

NH

HN

HS

O

H2N

CO2H

Protease cleavage site

cleavage

H2N

HN

HS

O

CO2H

NH

OSH

H2N CO2H

synthetic recombinant

H2NO

HN

R

HN

O

O

22

13

12

5

23Protease

R = alkyl or aryl

Scheme 13.7 Generating recombinant peptides with an N-terminal Cys.


flanking regions (N- and C-) �exteins�. The intein is the sole catalyst possessing allenzymatic activities for the splicing process which is illustrated in Scheme 13.8A.Protein splicing is initiated by a reversibleN ! S acyl shift of the peptide backboneonto the side-chain of a catalytic Cys to form the thioester 25 at the N-terminus ofthe intein [38]. In the following step, the Cys-thioester migrates to a downstreamCys in 26, which is the first amino acid of the C-extein. The final rearrangementinvolves a catalytic Asn residue at the C-terminus of the intein and releases theintein with a C-terminal succinimide 27 and the splice product 28 linked with anative peptide bond [39].

EPL uses a mutated intein that can only catalyze the initial N ! S acyl shift. Aprotein of interest (POI) is fused N-terminally to this mutated intein on the geneticlevel representing the N-extein in 29 (Scheme 13.8B). The intein is usually extendedby an affinity tag like a chitin-binding domain (CBD), which remains covalentlyattached to the intein and can be used for purification purposes. A reversibleN ! Sshift yields the thioester 30, which is intercepted by the addition of access thiols likeMESNA 31 through a thiol–thioester exchange. The POI is delivered as a C-terminalthioester 32 that can be isolated by simple elution off the resin and used for asubsequent NCL with a synthetic C-peptide 13. Alternatively, the synthetic peptidecan be added directly to the thiol cleavage reaction and the ligation product 33 isformed in situ (Scheme 13.8B).

13.2.5Protein Trans-Splicing

Protein splicing can also be employed directly for protein semisynthesis. Thisprocess, �semisynthetic protein trans-splicing,� requires a special kind of inteinwhich is split into two fragments. These so-called �split inteins� occur in nature andreassociate spontaneously to a noncovalent, but fully functional complex that linksthe N- and C-exteins by the splicing process described above (Scheme 13.9A).

Split inteins were first discovered in the cyanobacterium Synechocystis sp. strainPCC6803. In this organism the catalytic subunit of the DNA polymerase III isexpressed as two separate DnaE fragments (Scheme 13.9A), which are extended byN- and C-terminal parts of the intein. These intein pieces later rejoin and deliver thefull-length DnaE [40].

For a semisynthetic application of protein trans-splicing a synthetic peptideincluding the short IntC fragment can be extended by an ExC sequence and usedfor trans-splicingwith a recombinant ExN–IntN fusion protein. Thismethodhas beenapplied successfully for ligating a synthetic FLAG epitope to a recombinant GFP(Scheme 13.9B) [41]. This method was also performed in live cells, as demonstratedfor the ligation of construct 34 and the synthetic IntC-FLAG peptide 35, in which thecellular import of the synthetic peptide 35 was achieved by adding a proteintransduction domain (PTD) for shuttling into the cell.

Split inteins can be also generated artificially [42–45] as, for example, reported byMootz et al. [46]. Their artificially split Ssp DnaB intein system is split only 11 aminoacids downstream of the N-terminus of the intein and was capable of ligating a


N H

N H

H N

OS

N H

NN H

O

NH

2

OS

O

HH

H

H NN H

OH

S

O

H2N

HS

NH

N H

O O

Inte

in

Inte

in+

H2N

CO

2H

H N

OS H

H2N S

O

Inte

in

Inte

in

H2N

H2N

-C

BD

PO

I

-C

BD

SS

O

OH

S

O

H2N

S O

O

CO

2H

H2N

HS

H N

OH

S

O

H2N

H2N S

O

H2N

O

CO

2H CO

2H

(A)

(B)

N-e

xte

in

CO

2H

H2N

O

N H

O

H2N S

N H

NN H

O

NH

2

OS

O

HHIn

tein

CO

2H

O

N H

O

O

H2N

O

HS

N HN H

O

NH

2

O

O

Inte

in

H2N

CO

2H

O

N H

O

H2N

S

NH

N H

OO

N H

O

N H

O

O

N H

ME

SN

a

24 25

26

28

27

29

31

30

32

13

33

O

O

C-e

xte

in

C-e

xte

in

N-e

xte

in

C-e

xte

in

N-e

xte

in

C-e

xte

inN

-ex

tein

PO

I

PO

I

PO

I PO

I

sy

nth

eti

c

sy

nth

eti

c

sy

nth

eti

c

= C

-peptide

= N

-peptide

Scheme13

.8Proteinsplicing(A)an

dEP

L(B).


fluorescein (Fl)-conjugated peptide 36 to recombinant thioredoxin (Trx) 37. Thelocation of the split side decreased the length of the synthetic intein sequence, whichwill not end up in the ligation product, to one third of that of the naturally split SspDnaE intein. In addition, this system can be used to ligate synthetic peptides to theN-terminus of recombinant proteins, rather than the C-terminus as in the case of theSsp DnaE intein. In a recently reported artificially split intein system a newC-terminal split site was identified and used for semisynthetic protein trans-splicing.This site is located only six amino acids upstream of C-terminus of the Ssp GyrBintein and is therefore very promising for ligating synthetic peptides to theC-terminus of recombinant proteins [47].

HN

OS

NH

N

O

NH2

OS

O

H

H

H

HN

NH

OS

O

H

H2N

HS

NH

NH

O

O+ IntN IntC

IntN IntC

recombinant

36 aa123 aa

IntN IntC

143 aa11 aa

(A)

(B)

(C)

DnaE-N

GFP

Fl

H2NCO2H

H2N CO2H

H2N CO2H

H2N CO2H

123 aa774 aa 423 aa

36 aa123 aa1197 aa

N-fusion protein C-fusion protein

IntN

O

NH

O

NH

O O

34 35

36 37

36 aa

IntC

Split Intein

synthetic

recombinantsynthetic

DnaE-C

DnaE-CDnaE-N

FLAG

Trx= C-peptide

= N-peptide

Scheme 13.9 Protein trans-splicing. (A) Trans-splicing reaction of the split DnaE intein.(B) C-terminal semisynthetic protein trans-splicing, (C) N-terminal semisynthetic proteintrans-splicing.


13.3Chemical Transformations for Cys-Free Ligations in Peptides and Proteins

NCL has emerged as themost powerful technique for the ligation of two unprotectedpeptide or protein fragments to yield a native amide bond. Nevertheless, therequirement of a Cys residue at the ligation site still motivates researchers to searchfor alternative ligation methods, because Cys residues are incorporated in proteinsonly to an extent of 1.7% [48]. This often excludes a direct retrosynthetic discon-nection for peptide ligation via NCL. Additionally, Cys residues cannot necessarily beregarded as small �non-native� building blocks for the replacement of the naturallyoccurring residue at the ligation site, as they can oxidize to disulfide bonds andthereby influence the overall folding pathway.

As a possible solution to this problem, several methods have been developed toallow a chemoselective connection of amide bonds at non-Cys containing peptidejunctions (38). All methods described in this chapter rely on a two-step protocol, inwhich eitherNCL (Chapter 13.3.1) or an auxiliarymediated capture/rearrangementstrategy (Chapter 13.3.2) is followed by a final chemical transformation(Scheme 13.10). These approaches yield native peptide bonds with non-Cys orfurnish amino acid analogs at the ligation site while maintaining the a-amino acidbackbone.

In this context it is important to note that ligation procedures have been reported inwhich nucleophilic amino acids other than Cys participate in the previouslydiscussed capture/rearrangement steps when located at the N-terminus of theC-peptide. Examples include peptide ligations at a His residue [49] or ligationsinvolving a -SeH nucleophile, thus leading to a ligation product with the rare aminoacid selenocysteine (Sec) [50]. In particular the latter approach has been used in thesynthesis of various peptides [51] and also proteins by EPL [52], which allowedimportant mechanistic investigations of proteins [53].

13.3.1Chemical Modification of NCL Products

The protein ligation strategies in this section employ a selective chemical transfor-mation of a Cys (Scheme 13.11) [54, 55]. The advantage of a chemical modificationstrategy in combination with NCL stems from the fact that these transformationscan address the unique chemical properties of Cys at the ligation site. Never-theless, additional Cys residues in the ligation product limit the generality of thisstrategy, as selective transformations are often impossible to perform withoutfurther protecting group manipulations.

A critical aspect of this approach is the fact that chemical transformations have tobe performed onproteinmaterial. Apart fromchemoselectivity considerations, harshreaction conditions could harm the valuable protein and thus significantly decreasethe overall ligation yield or, even worse, influence the overall protein architecture byaggregation.


H NH

2N

O

HS

NC

L

H NN H

O

HS

O

H2N

Cys

at l

igat

ion

site

ch

em

ica

l m

od

ific

ati

on

O

HN

R2

HS

Aux

H N

O

N

R2

HS

Aux

H N

O

H2N

au

xil

iary

re

mo

va

lo

r tr

an

sfo

rma

tio

Au

xil

iary

me

dia

ted

NC

L

CO

2H

CO

2H

CO

2H

CO

2H

R1 =

Ph

, A

lk

R1 =

Ph

, A

lk

SR

1

O

H2N

12

H NN H

O

R2

O

H2N

nativ

e am

ino

acid

or

ana

logu

e

n

CO

2H

38

Scheme13

.10

Synthetic

pathwaysforno

n-Cys-con

tainingpe

ptides

andproteins.

13.3 Chemical Transformations for Cys-Free Ligations in Peptides and Proteins j461

Raney N

i

CO

2H

H NN H

O

O

H2N

Ala

at l

igat

ion

site

MeS

O2S

R2

CO

2H

H NN H

O

SO

H2N

Met

-ana

logu

eG

lyco

prot

ein

anal

ogue

SR

2

CO

2H

H NN H

O

SO

H2N

R1

O

Br

O

R1

CO

2H

H NN H

O

SO

H2N

NH

2

Gln

- or G

lu-a

nalo

gue

Lys-

anal

ogue

or

Pd/A

l 2O

3

H2

CO

2H

H NN H

O

O

H2N

Ala

at l

igat

ion

site

TC

EP

tBuS

H

radic

al

sta

rter

Acm

-Cys

resi

dues

tole

rate

d

Met

and

Thz

tole

rate

d

Br

NH

2

R2 =

Me, A

lk

45

44

39 39

50

49

OH

O

CO

2H

H NN H

O

SO

H2N

CN

Br

80%

HC

O2H

O

O

H2N

CO

2H

H NH

2N

O

CO

2H

H NN H

O

HO

O

H2N

pH

7-8

Ser a

t lig

atio

n si

te

MeS

O2A

r

46

51

R1 =

NH

2 4

7

O

H 48

CO

2H

H NN H

O

HS

O

H2N

Cys

at l

igat

ion

site

5

Scheme13

.11

Chemicalmod

ificatio

nof

NCLprod

ucts:a

lkylationan

ddesulfu

rizatio

nstrategies.


13.3.1.1 Desulfurization

Ala Ligation: Desulfurization of Cys Most frequently, Cys-containing ligation pro-ducts are converted into other polypeptides by desulfurization techniques usingRaney-Nickel or Ni-boride (Scheme 13.11). This strategy, which delivers ligationproducts with Ala (39) residues at the ligation site, was introduced by Perlstein [56]and has been applied in various challenging polypeptide systems [57, 58]. (For thedesulfurization in the glycopeptide assisted ligation as introduced byWong et al., seeChapter 13.3.2.4.) Furthermore, it was extended to the selective desulfurization ofunprotected Cys over acetamidomethyl (Acm)-protected Cys residues [59], thusallowing the ligation of Cys-containing polypeptides at Ala junctions after a finalAcm-deprotection step. However, the heterogeneous nature of the nickel catalyst canlead to protein aggregation [60] and other side reactions including desulfurization ofthioethers of Met or thiazolidines and the epimerization of secondary alcohols [61].This disadvantage has been addressed by Danishefsky, who reported a metal-freeradical based desulfurization to convert Cys residues in the presence of residues likeMet, Acm-protected Cys and thiazolidines in high yields (Scheme 13.11) [62]. Thisprotocol was recently applied to the desulfurization of phosphorylated and acetylatedhistone H2B proteins that were obtained by NCL (Scheme 13.12). The radicaldesulfurization conditions gave considerably higher yields than the heterogeneousRaney-Nickel catalyst (68–71 versus 30–35%) [63].

S

O

HN

H2N

O

HS

NCL

HN

NH

O

HSO

SO3

HNAc

OP

O

O

O

H2N1-16

HNAc

OP

O

O

O

H2N

E.coli expression

posttranslationalmodifications

HN

NH

O

O

HNAc

OP

O

O

O

H2N

Desulfurization

CO2H

CO2H

CO2H

Histone H2B

18-125

18-1251-16

18-1251-16

Raney nickel radical-initiated

30-35%68-71%

Desulfurization conditions

Scheme 13.12 Desulfurization of histone H2B proteins.


Phe Ligation and Val Ligation: Desulfurization of b-Mercapto -Building Blocks Inrecent publications, NCL reactions were performed with b-branched Cys derivativesinstead of Cys. Subsequent desulfurization of these unnatural thiol-containingamino acids introduced the natural residues at the ligation site. (For a previousdiscussion on the use of thiol-containing analogs of natural amino acids at ligationjunctions see [58]). Although these protocols have not been used in the ligation ofproteins they represent impressive examples in modern ligation techniques.

In the first example, b-mercaptophenylalanine was used as a template for ligationsat Phe junctions (Scheme 13.13, top) [64]. This derivative can be attached to theN-terminus of the C-peptide as a disulfide building block 40, which, under NCLconditions, generates 41in situ. The benzylic thiol in the decapeptide 42was removedby heterogeneous desulfurization in good overall yields.

In a related approach Val derivatives with an added thiol are used for the ligation ata hydrophobic ligation site. For example, a penicillamine building block 43a isemployed, in which the b,b-dimethylcysteine functionality reacted surprisingly fastand in high yields with an N-peptide thioester to penicillamine-containing modelpeptides with up to 22 amino acids (Scheme 13.13, bottom) [65]. These weretransformed into the corresponding Val peptides by applying an optimized versionof Danishefsky�s homogeneous desulfurization technique.

Another system for the ligation at Val residues employs a primary thiol group at thec-position of theVal building block 43b. This auxiliary delivered, in an analogous two-step protocol, ligated peptides in very good yields. These two procedures have allowedligations at junctions between various sterically demanding amino acids includingLeu–Val and Thr–Val.

13.3.1.2 Alkylation and Thioalkylation ProtocolsThe nucleophilic properties of Cys at the NCL site can also be employed in alkylationor thioalkylation reactions. Although the examples mentioned here have beenapplied mostly to expressed proteins and not to NCL products, they will be brieflydiscussed here because they demonstrate the scope of this concept. For example, Cysresidues in proteins can be transformed via thioalkylation withmethyl methanethio-sulfonate 44 to Met analogs 45 [66, 67] or other important proteins carrying post-translation modification mimics such as disulfide-linked glycoconjugates [68]. Thelatter bioconjugates can be converted into stable derivatives with glycosyl thioetherlinkages by a chemoselective reaction with P(III) reagents [69]. Other alkylationprotocols give Gln or Glu derivatives 46 by reaction with a-iodoacetamide (47) [70] ora-iodoacetic acid (48) [71]. Lys analogs 49 can be derived by reactionwith aziridines orbromoethylamines (50) (Scheme 13.11) [72]. Although all of these transformationsyield analogs of natural occurring amino acids, several studies have shown compa-rable protein function in comparison to their natural analogs [71].

In a recent publication the Cys residue was converted into a Ser in peptides 51 inhigh yields by a sophisticated procedure. First, theCyswasmethylatedwithmethyl-4-nitrobenzenesulfonate, which was followed by an intramolecular rearrangementwith CNBr in formic acid and a subsequent O ! N acyl shift under slightly basicconditions (pH 7–8) [73, 74]. This protocol has great potential in the synthesis of


OH

N HO

Boc

SP

hE

tS

40

H2N

1. S

PP

S2. R

eagent K

H NH

2N

O

SP

hE

tS

CO

2H

O

H2N

SB

n

TC

EP

, M

ES

NA

pH

8

O

H2N

S

Dis

ulf

ide r

ed

ucti

on

to p

rom

ote

NC

L

H NH

2N

O

CO

2H

CO

2H

H NN H

O

O

H2N

N S

shift

HS

Ph

CO

2H

H NN H

O

O

H2N

R2

NiC

l 2, N

aB

H4

pH

7

Phe

at li

gatio

n si

te (R

1 =

H, R

2 =

Ph)

Val a

t lig

atio

n si

te (R

1 , R

2 =

CH

3)

57-6

0 %

72-7

4 %

41

42

OH

N HO

Boc

ST

rt

H NH

2N

O

HS

CO

2H

SP

PSR

1 R2

via

:

O

H2N

SB

n

TC

EP

, P

hS

HpH

8.5

65-8

7 %

CO

2H

H NN H

O

O

H2N

HS

radic

al sta

rter

TC

EP

, glu

tath

ione

pH

6.5

, 65 °

C72-9

8 %

R1

43a

H NH

2N

O

CO

2H

SH

43b

Scheme13

.13

Nativechem

icalligationat

aPh

e(top

)or

Valjunctio

n(bottom)viaatwo-step

ligationan

ddesulfu

rizatio

nprotocol.


N-linked glycopeptides as they contain an Asn–Xaa–Ser or Asn–Xaa–Thr consensussequence in which Xaa resembles any amino acid except proline [75].

13.3.2Auxiliary Methods

Since the above discussedmethods affect all Cys residues, auxiliary groups have beendeveloped which facilitate the ligation reaction and can be removed without mod-ifying any other amino acid residue of the ligation product [76].

Here, a thiol-containing auxiliary 52 is placed in a peptide, which subsequentlyreacts with an N-peptide thioester 12 in a rearrangement similar to the NCL(Scheme 13.14). The auxiliary is removed in a final synthetic transformation tofurnish the desired native peptide or protein sequence 53. Obviously, these chemicaltransformations have to meet the same requirements concerning mild reactionconditions and chemoselectivity as discussed previously.

SR2

O

H2N

HN

NH

O

R1O

H2N

O

HN

R1

HSAux

HN

O

N

R1

HSAux

HN

O

H2N

CO2H

CO2H

CO2H

S

O

H2N O

HN

R1

Aux

HN CO2H

N S shift

auxiliary removal

52

12

53

Scheme 13.14 Mechanism and scope of the auxiliary mediated ligation.


13.3.2.1 (Oxy-)Ethanethiol AuxiliaryA very simple auxiliary system employed an ethanethiol (X¼CH2,54) or oxyetha-nethiol (X¼OCH2, 55) substituent (Table 13.1, entry 1), in which the ethanethiol

Table 13.1 Auxiliary systems with possible ligation junctions and auxiliary removal conditions.

O

HN

R1

HSAux

Ligation junction Auxiliary removal conditions

1O

HN

R1

XHS

X = CH2 54

X = OCH2 55

Gly–Gly (for 54) None (for 54)Gly–Gly Zn, acetic acid (for 55)Phe–GlyAla–Gly (for 55)

2O

HN

R1

HS

R2 R2

R2 = H, OMe 56

Gly–Gly HF (for R2¼H)Ala–Gly TFA (for R2¼OMe)His–GlyLys–Gly

3O

HN

R1

HS

O2N R2

R2

R2 = H, OMe 57

Gly–Gly hn (310–365 nm)Ala–Gly

4

OHN

R1

SH

OMeMeO

R2

R2 = H 58a (Dmb)

OMe 58b (Tmb)

Gly–Gly HF (for 58a (Dmb))Ala–Gly TFA (Hg2þ ) (for 58b (Tmb))Lys–Gly

Dmb: 4,6-dimethoxy-2-mercaptobenzylamine, Tmb: 4,5,6-trimethoxy-2-mercaptobenzylamine.


auxiliary delivered better ligation yields at Gly junctions (up to 90%) in comparison tothe oxyethanethiol analog. However, in contrast to the ethanethiol auxiliary, theoxyethanethiol analog can be removed from the protein material by reductivecleavage of theN�Obondwith zinc [77]. Both systems have been applied to advancedpeptide and protein synthesis, including peptide cyclization as well as the acquisitionof disulfide-bridged protein analogs [78, 79].

13.3.2.2 Photoremovable Na-1-Aryl-2-Mercaptoethyl AuxiliaryIn auxiliary system 56 the N-terminus of the C-peptide is converted into a secondaryamine with an aryl in the 1-position and a thiol functionality in the 2-position(Table 13.1, entry 2) [80]. This auxiliary can be incorporated into the peptide either byreaction of the parent aminewith ana-bromopeptide or by a building block approachof theBoc- or Fmoc-protectedNa-(1-aryl-2-mercaptoethyl) amino acid derivatives [81].The auxiliary system enables sterically nondemanding peptide ligations at Gly andAla junctions in good overall yields in peptides; however, the auxiliary has to beremoved under strong acidic conditions with HF or trifluoroacetic acid (TFA)/bromotrimethylsilane (TMSBr), which limits its applicability in advanced proteinexamples.

Therefore, the development of a mild light-induced removal procedure for thisauxiliary by the groups ofAimoto [82] andDawson [83] is particularly important. Theyhave identified light-sensitive auxiliary 57 with an o-nitrobenzene function, whichefficiently ligated two nonapeptides, again at sterically nondemanding peptideligations at Gly–Gly or Ala–Gly junctions, in high yields prior to photolytic removal(Table 13.1, entry 3). This improvement has recently found an important applicationin the semisynthesis of ubiquitylated histone peptides and proteins, which repre-sented the first entry of an EPL at a non-Cys ligation site [81]. The combination with asecond EPLwill be discussed further in the final part of this chapter, since it involvesan impressive example of a three-segment ligation approach of a biologically mostrelevant post-translationally modified histone protein [85].

13.3.2.3 4,5,6-Trimethoxy-2-Mercaptobenzylamine AuxiliaryA 2-mercaptobenzyl based auxiliary system 58with an electron-rich arylthiol can alsoundergo the thioester exchange with a C-terminal peptide thioester (Table 13.1, entry4). After the subsequent S ! N shift of the secondary amine, a tertiary amide isformed, which can be removed with TFA [86]. The most potent auxiliary is the 4,5,6-trimethoxy-2-mercaptobenzylamine (Tmb) 58b with increased nucleophilicity of thearylthiol and increased acid lability of the tertiary amide. This auxiliary has beenemployed in peptide ligations that contained at least one Gly at the ligation site, withshort coupling times of 0.5 (Gly–Gly), 2 (Lys–Gly) and 5 h (Ala–Gly) [87]. Further-more, it has beenused in the synthesis of cytochrome b562– a 106-residueprotein [88].In another study, the Tmb auxiliary was combined with a C-terminal peptide phenolester 59 with an o-disulfide for sterically demanding ligations of two glycopeptidefragments 59 and 60, in which each contained an N-linked chitobiose residue at aGly–Gln junction [89]. In this investigation it was found that the acidic conditionsapplied for the auxiliary removal lead to an accumulation of the thioester


intermediate 61 via protonation of the secondary amine, thereby resulting in anN ! S shift [90]. Methylation of the arylthiol increased the removal efficiency to giveglycopeptide 62 (Scheme 13.15).

13.3.2.4 Sugar-Assisted Glycopeptide LigationsRecently, a ligation strategywas published byWong et al. inwhich the auxiliary for thecapture step is incorporated into the glycan called �sugar-assisted glycopeptide

O

O

H2N

SH

S

O

H2N

OH

HNO CO2H

O

O

HO

HO

OHO

O

N

HN

O

H2NCO2H

Tmb

OHOO

HO

1. Capture2. S N shift

1. p-NO2-Ph-SO2-Me

2. TFA

O

NH

HN

O

H2NCO2H

OHOO

HO

O

H2N

OHO

H2NS

R

TFA

glycopeptide

O

O

H2N

SSEt

OHO

TCEPpH 8.0

pH 7.4

HNR

SHR

Tmb

R

59

60

61

62

R = OMe

Scheme 13.15 Cys-free glycopeptide couplings using the Tmb auxiliary approach.


ligation� (SAL, Scheme 13.16A) [91]. The thiol function can be introduced as ab-thioacetamido substituent at the C-2 position, either in a GalNAc forO-linked [92]or in a GlcNAc residue for N-linked glycopeptides 63 [93]. The thiol is assumed toinitially form a macrocyclic thioester with a C-terminal peptide thioester before thefree amine at the N-terminus of the glycopeptide fragment performs the S ! N shiftto generate the native amide bond in 64 under slightly basic conditions. Finaldesulfurization conditions (see Section 13.3.3.1) yield the native glycopeptide 65. Itwas demonstrated that glycopeptides with up to six additional amino acidsN-terminal to the glycosylation site were able to undergo SAL [94]. In further studies,a b-thioacetic ester in the C-3 position of a GalNAc residue as the auxiliary 66can be used as well, which allows a final auxiliary removal with hydrazine(Scheme 13.16B) [95]. Additionally, a cyclohexyl-based auxiliary 67 was introduced[96a] and applied to the ligation of the HIV-1 Tat protein (Scheme 13.16C) [96b]. Thissystem delivers, after auxiliary removal, Ser at the ligations junction; however, theauxiliary cleavage under basic conditions (pH 10–11) only proceeded well with apeptide, whereas attempts for the corresponding protein failed.

(A)

OH

O

H2N

O

NH

O

HS

HOHO

HO

SR

O

H2N

2.

1.

1. Capture (thioester equilibrium)2. S N shift

OH

O

NH

O

NH

O

HS

HOHO

HO

O

H2N

Desulfurization

OH

O

NH

O

NH

O

HOHO

HO

O

H2N

O- or N-linkage

(C)

OH

O

H2N

O

NH

OHO

HO

O

HSAc

auxiliary removalunder basic conditions

12

63

64

65

66

6 M Gn:HCl, 37°C,pH 8.5, 2% Ph-SH

(D)

OH

O

H2N

auxiliary removalunder basic conditions

67

NH

O

HS

O

O

(B)

OH

O

SR

O

H2N

2.

1.

HS

H2N

1-5 amino acidsbefore Cys

Scheme 13.16 SAL.


Based on these findings another investigation probed whether internal Cysresidues within theN-peptide can accelerate the aminolysis of the N-terminal aminevia the formation ofmacrocyclic thioester intermediates (Scheme 13.16D) [97]. It wasfound that appropriately positionedCys residues can induce rate enhancements of upto 25-fold in comparison to a Cys-lacking control peptide.

In light of these investigations, another report from the Wong group wasparticularly important, because it demonstrated the fine balance between a directaminolysis reaction and the macrocyclic thioester participation. In this report, a(glyco-)peptide thioester and another (glyco-)peptide at a non-Cys or sugar auxiliaryjunction were coupled [98]. In this nonchemoselective conjugation strategy, which isbased upon early observations by Wieland, a carefully optimized N-methylpyrroli-done (NMP)/HEPES buffer at neutral to slightly basic pH makes the N-terminus ofthe C-peptide sufficiently nucleophilic to perform an aminolysis with the N-peptidethioester and simultaneously suppresses thioester hydrolysis. However, this methodcannot be employed as a general chemoselective ligation technique, since additionalamino groups in Lys side-chains have to be protected.

13.4Other Chemoselective Capture Strategies

As discussed in Section 13.2, NCL is based on a thioester equilibrium resembling thecapture step before the amide bond is formed via an S ! N shift. The following twomethods utilize different chemoselective capture steps before a rearrangement to anamide bond occurs.

13.4.1Traceless Staudinger Ligation

This ligation reactionwas introduced in 2000 and represents a traceless variant of the(nontraceless) Staudinger ligation for the synthesis of amide bonds [99, 100]. Bothreactions originate from the classical Staudinger reaction, in which an azide reactswith a phosphine to forman iminophosphorane [101]. This reactionwas identified byBertozzi as chemoselective and further extended to a chemoselective functionaliza-tion ofmetabolically engineered azido-glycans in cellular environment. This could beachieved by placing an electrophilic ester in proximity to the iminophosphorane toprevent undesired hydrolysis to the phosphine oxide and amine [102]. The tracelessStaudinger ligation utilizes this concept; however, the electrophilic ester moiety ischanged.Here, the iminophosphorane 70, formed between ana-azido-amino acid or-peptide 68 and a phosphinothioester 69, reacts with an internal thioester to yield anative amide bond in high yields even in dipeptides at an Ala–Ala junction (71)(Scheme 13.17A) [103]. In this regard the formation of 70 in principle resembles thechemoselective capture step.

The traceless Staudinger ligation has received considerable attention as a verypotent, universal strategy for peptide ligations, since it does not, like NCL, require a

13.4 Other Chemoselective Capture Strategies j471

Cys residue at the ligation site. In recent years considerable improvements andmechanistic investigations [104] have been performed to reach this goal. Theseincluded various applications in the area of bioorganic chemistry, such as the site-specific immobilization of peptides on surfaces [105], the ligation of protected (glyco-)peptide fragments [106], the conjugation of unprotected sugar derivatives on proteincarriers [107], or the cyclization of unfunctionalized lactams [108]. Recently, thechemoselectivity of the traceless Staudinger ligation was probed in the cyclization ofunprotected peptide sequences. This was realized by the finding that borane-protected peptide azidophosphinothioesters 73 can be deprotected under acidicconditions, which simultaneously removed the protecting groups of the peptide side-chains aswell as the borane protecting group to yield phosphonium salts 74. After theaddition of a base the cyclization to medium sized peptides 72 with up to 11 aminoacids proceeded in good yields (Scheme 13.17B) [109]. Another important and verypromising study for future intermolecular peptide ligationswas the development of awater-soluble version of the traceless Staudinger ligation. Here, water soluble

N

S

O

PPh2

S

O

PPh2

N3

HN

R

+

O

R

NH

OHN

R O

R(A)

aza ylide

Staudinger reaction

S N shift

(B)

O

S PPh2HN

NHCH2

O

O O

N3

O

S

BH3

PPh2

O

N3

1. TFA

2. Baseno protecting groups

PG

PGPG

PG

Staudinger cyclization

O

Peptide

PG

O

N3O

trityl-resin

1. 0.5 % TFA

HS

BH3

PPh22.

DIC, DMAP

> 90 %

up 36 % over four steps

69

68

70

71

73

74

72

- N2

(C)

NH

O

S

O

P

N 2

N3

C

O

NH2

0.4 M phosphate

buffer

CH3

NH

O

O

RHN

C NH2

O

59%

13

13

Peptide

PG

PeptidePeptide

75

76

Peptide = GAGHVEPYFVG

R = H, CH3

Scheme 13.17 (A) Scope and mechanism of the traceless Staudinger ligation. (B) Staudingercyclization after acidic deprotection of borane-protected phosphinothiols. DIC:diisopropylcarbodiimide. (C) Water-soluble Staudinger ligation.


phosphinothiol linkers 75 with a tertiary amine were utilized, which resulted in theformation of an amide bond between a dipeptide 76 at pH 8 in good yields(Scheme 13.17C) [110].

13.4.1.1 Imine Ligations with Subsequent Pseudo-Pro FormationIn another ligation the formation of an imine is used as the capture step. Thisprocedure by Tam et al. delivers a pseudo-Pro by reaction of a C-terminal glycolalde-hyde peptide 77 with another peptide 78 containing a hydroxyl or thiol function in aCys, Thr or Ser residue at the N-terminus (Scheme 13.18) [111]. After iminecondensation to 79 the nucleophile of the N-terminal amino acid can react withthe imine to form an oxazolidine (Oxz, 80a) or thiazolidine (Thz, 80b). Then anirreversible O ! N shift via a bicyclic five-membered intermediate delivers ahydroxylmethylene substituted pseudo-Pro 81 at the ligation junction with a newstereogenic center at the C-2 position [112]. In this process, the thiazolidine can beformed in aqueous solution whereas the oxazolidine synthesis requires anhydrousconditions.

This reaction was applied in the assembly of proline-rich analogs of the 59-residuehelical antibacterial peptide bactenecin 7, which showed comparable biologicalactivities to the natural product [113]. In this aspect it is important to note that athree-segment condensationwas used, in which the first junctionwas constructed by

H2NO

O

O

H

glycolaldehyde

HN

OH

O

O

H2N

RHX

imine formation(capture)

HN

OH

O

O

N

RHX

O

O

H2N

HN

OH

O

ONH

RX

O

OH2N

O N shiftHN

OH

O

ON

RX

**

OH2N

HO

77

78

79

8081

(rearrangement)

Thiaproline-ligation: X = S, R = H (Cys)

80a

Oxaproline-ligation: X = O, R = CH3 (Thr)

80b X = O, R = H (Ser)

Scheme 13.18 Pseudo-Pro ligation of unprotected N-peptides with C-terminal glycoaldehydeC-peptides.

13.4 Other Chemoselective Capture Strategies j473

the formation of a thiazolidine of the Cys peptide – a faster step than the formation ofthe corresponding oxazolidine of the Thr peptide. Simultaneously, an oxidativeconversion of a C-terminal glycerol ester of a peptide dimer into the correspondingglycolaldehyde and subsequent formation of the second pseudo-Pro was reported asanother segment ligation protocol.

13.5Peptide Ligations by Chemoselective Amide-Bond-Forming Reactions

The development of chemoselective ligation strategies allows the selective formationof a covalent bond between highly complex biological molecules without therequirement of protecting group transformations. Apart from the two-step�capture/rearrangement� strategy presented in the previous two sections, severalorganic reactions have been recently identified that allow a �direct� chemoselectivebond formation in 84 (Scheme 13.19A). In an ideal scenario, these chemoselectivereactions proceed under physiologically benign conditions (neutral pH in aqueousmedia and at room temperature) to yield a native amide bond. This bond isconstructed from two �bioorthogonal� [114] functionalities in 82 and 83 that do notshow any cross-reactivity with other functional groups present in a biologicalenvironment.

Within this section we will give an overview of examples of alternative amide bondforming strategies with the potential for impact as chemoselective reactions inpeptide and protein synthesis. A distinguishing feature of these reactions is their

Scheme 13.19 Chemoselective reaction for a native or non-native conjugation of polypeptides andselective transformation of natural amino acids.


departure from the canonical mechanistic paradigm of acyl substitution in theformation of the amide bond. A hallmark of all of these processes is the use of twounnatural functional groups as the amide precursors. This has the advantage ofoffering outstanding chemoselectivity, but brings with it the disadvantage of requir-ing modifications of the C- and N-termini of the ligation partners that must be madeeither synthetically or by challenging site-specificmodifications of expressed proteinfragments.

In addition to the examples in this chapter it is important to note that the emerginggeneration of chemoselective peptide ligation reactions has grown in concert with therecognition that highly chemoselective reactions enable researchers to (site-)selec-tively functionalize ormodify complex biomolecules even in cells or living organisms(Scheme 13.19B) [115]. These applications have significantly advanced study ofthe function of post- and cotranslationallymodified proteins, such as by site-selectiveincorporation of biophysical probes into a biopolymer, commonly referred to as the�(bioorthogonal) chemical reporter strategy� [116], or by chemoselective transforma-tions that resemble natural protein modifications, such as a chemoselective phos-phorylation strategy [117].

13.5.1Thio Acid/Azide Amidation

The coupling of thio acids with azides, first reported by Rosen in 1988 [118], providesthe basis for a promising new approach for amide ligation. In 2003, Williams et al.explored this reaction for the synthesis of simple peptides and N-linked carbohy-drates from glycosyl azides 85 [119]. These authors postulated that the reaction doesnot occur via an azide conversion to amine 86 but via the formation of a thiatriazolinederivative 87 as a result of [3 þ 2] cycloaddition (Scheme 13.20) [120]. Additionally, aRuCl3-promoted variant of the reaction was demonstrated to be high-yielding, evenwith sterically hindered azides [121]. Although not applied to the ligation of longerpeptide substrates yet, this reaction is a promising new approach to chemoselectiveamide formation, and may have other important applications in the synthesis andmodification of peptides and glycoproteins [122].

13.5.2Thio Acid/N-Arylsulfonamide Ligations

A variant of the former reaction, first reported by Tomkinson [123], employingN-arylsulfonamides as the electrophilic amidation partner has been advanced as anexciting route to the synthesis of peptides (Scheme 13.21). Crich et al. exploited thisprocess, which proceeds via nucleophilic addition of the thio acid to the highlyelectrophilic sulfonamide to give Meisenheimer complex 88, to the synthesis ofsmall peptide fragments including the couplings of sterically demanding sub-strates [124]. Alternatively, the amide component can be activated by theMukaiyama or Sanger reagents or as an isocyanate [125]. More recently, the abilityof these reactions to be sequenced for the formation of triblock peptides by iterative

13.5 Peptide Ligations by Chemoselective Amide-Bond-Forming Reactions j475

N3Ph

HS R

O

NH2Ph

Base

S R

O

S R

O

NNN

S RO

Ph

[3+2]

H+

NH

Ph

O

R

up to 94%

ON3

HOHO

OH

HOHS R

Base

OHOHO

HO

HO

80%

RCOSH

86

not via

87

85

- N2S

O

HN

R

O

R = Ph, Me

Scheme 13.20 Mechanism of the thio acid/azide amidation.

O

SHpeptideAcHN

O

NH2peptideN

H

SO O

NO2O2N

SSNH

O O

NOO

O2N

O

peptide

Cs2CO3, DMF

+

O

NH

O

NH2peptide

–SO2

PGPG

O

NH2

peptideAcHN

peptideAcHN

88

HS

O2N

NO2

-

Scheme 13.21 Amide-forming ligation of peptide thio acids with electron-deficient sulfonamides.


couplings has been demonstrated [126]. If it can be established these reactionsproceed in the presence of unprotected peptide side-chains containing amine andcarboxylic acid functional groups, this process has the potential to be a generalsolution to peptide ligation.

13.5.3Chemoselective Decarboxylative Amide Ligation

In 2006, Bode et al. reported the decarboxylative condensation of N-alkylhydrox-ylamines 89 with a-ketoacids 90 to yield chemoselectively amide bonds 91(Scheme 13.22) [127]. This reaction does not involve, in contrast to almost allother amide bond forming strategies, an addition/elimination reaction of anactivated carboxylic acid derivative but the decarboxylation and elimination ofwater from a hemiaminal. In preliminary studies of this amide ligation, Bodeestablished that the reaction proceeds without additional reagents or catalysts inpolar solvents at 37–60 �C. The reaction is highly chemoselective, and readilytolerates the presence of unprotected amines, acids, alcohols, thiols, and nitrogen-based functional groups without any observed cross reactivity. The more conve-nient salts of the hydroxylamines can be employed directly in the reaction. There ispotential for epimerization at the C-terminal a-ketoacid fragment but the stereo-chemical integrity ismaintained throughout the ligation reaction, although caremustbe taken in the preparation of the a-ketoacid. Preliminary investigations establishedthe potential utility of this process as a general approach to peptide ligation, withligation reactions at sites including Phe–Ala, Pro–Ala, Val–Gly, Ala–Ala, and manyothers already demonstrated.

The Bode group has recently reported novel linkers and reagents for preparing therequisite C-terminal a-ketoacids [128] and N-terminal hydroxylamines [129] byFmoc-based SPPS. As these methods continue to improve and develop, they shouldmake access to the requisite C- and N-terminal-modified peptides a robust andstraightforward process.

O

O

OHR1

NH

R2HO+

O

R1

NH

R2

O

OHR1N OH

OHR2

R1

N

OH

R2

–CO2

DMF, 40 °C

no reagents

8990 91

92

Scheme 13.22 Decarboxylative amide ligation (R1, R2¼ alkyl, aryl, heteroatoms, heteroaryl).

13.5 Peptide Ligations by Chemoselective Amide-Bond-Forming Reactions j477

His

–A

la-G

lu-G

ly-T

hr–

Phe–T

hr–

Ser–

Asp–V

al–

Ser–

Ser–

Tyr–

Leu–G

lu—

Gly

–G

ln–A

la–A

la–Lys–G

lu–P

he–Ile–A

la–T

rp–Leu–V

al–

Lys–G

ly–A

rg–N

H2

H-A-E-G-T-F-T-S-D-V-S-S-Y-L

H2NHN N

OH

HO

Me

HO

Me

OH

O

O

OH

OH

H N

O

O

OH

OH

O

NH

2

OH N

O

NH

2 NH

2

HO

O

NH

HN

NH

2H

N

O

N H

HO

1 G

lucagon L

ike P

eptide-1

(G

LP

-1 7

–36)

(1.0

equiv

)(1

.05 e

quiv

)

711

23

136

1

HO

HO

Q-A-A-K-E-F-I-A-W-L-V-K-G-R

NH

2α-

keto

acid

–h

yd

roxyla

min

ep

ep

tid

e lig

ati

on

95

93

94

Scheme13

.23

Synthesisof

human

GLP

-1(7–36

)by

chem

oselectiveligationof

unprotectedpe

ptidefragmen

ts.


While the application of this reaction to the chemical synthesis of proteins is yetto be demonstrated, recent work on its application to the synthesis of humanglucagon-like peptide (GLP)-1 [7–35] 93 reveals the remarkable chemoselectivityand potential of this reaction (Scheme 13.23). The 15mer N-terminal fragment 94was prepared by Fmoc-based solid-phase synthesis from a side-chain linked sulfurylide. Following resin cleavage and deprotection, this fully unprotected sulfur ylidewas converted, in the presence of Oxone, to a-ketoacid 94. The hydroxylaminefragment (C-terminus of the assembled peptide) 95 was prepared by displacementof a commercially synthesized N-terminal bromoacetate with a protected hydrox-ylamine. For solubility reasons, the key ligation reaction was performed in a 3 : 1mixture of dimethylacetamide (DMA)/dimethylsulfoxide (DMSO) at 60 �C for12 h, leading to a 70% isolated yield of the ligated peptide. Importantly, thereaction was conducted using a 1 : 1 stoichiometry of the ligation partners at only10mM.

A promising feature of this ligation reaction for the future development of newprotocols for peptide synthesis is the still unexplored scope of the reaction partnersfor chemoselective amide formation. For example, the reaction is not limited tohydroxylamines of the structure RNHOH. O-Alkyl substituted hydroxylamines canundergo the ligation reaction, a finding exploited in an elegant approach to theiterative coupling of enantiopure isoxazolidine monomers for an iterative synthesisof b3-oligopeptides [130]. For these later reactions, the preferred solvent is water ormixtures of water and tBuOH. Acylated hydroxylamines (e.g., RNH–OBz) are alsoexcellent substrates for ligations in either N,N-dimethylformamide (DMF) or water,but their use for a-peptides is currently limited by the propensity of these groups toundergo elimination.

13.6Strategies for the Ligation of Multiple Fragments

The size limitation of SPPShas for a long timeprohibited the total chemical synthesisof proteins. Chemoselective ligation techniques represent an important contributionto extending this limit. However, the size of ligation products that can be obtainedfrom two synthetic peptides is still smaller than most natural proteins [131, 132].Therefore, multiple segment ligation schemes must be developed to access fullysynthetic proteins, in which ligation procedures can be used iteratively to constructlarger structures. For NCL-type ligation schemes an additional protection groupmanipulation is required to assemble the fragments in the desiredmanner, since thecentral segment in ligations with three (or more) ligation partners has to contain anN-terminal Cys and a C-terminal thioester. To prohibit undesired polymerizationand/or cyclization, either theN-terminal Cys or theC-terminal thioester of the centralsegment must be protected. In contrast to thioesters, orthogonal protecting groupsare available for Cys moieties, which can be installed during the synthesis andremoved after a ligation reaction.

13.6 Strategies for the Ligation of Multiple Fragments j479

13.6.1Synthetic Erythropoietin

A prominent example for such a ligation strategy is the four-segment ligation ofthe glycoprotein hormone erythropoietin (EPO), which stimulates the prolifera-tion of erythroid cells (Scheme 13.24) [133, 134]. In order to mimic the naturalglycosylation patterns of EPO, branched, negatively charged precision-lengthpolymers were installed in the protein by oxime ligation. The N-terminal Cysresidues of both central fragments were orthogonally protected by an Acm group,which can be removed by treatment with Hg(II) [135]. The process started withthe ligation of the polymer modified C-terminal fragment 96 with the first centralfragment followed by removal of the Acm group. Repetition of this process withthe two remaining fragments yielded synthetic full-length EPO 97. Since two ofthe three Cys residues installed at ligation sites represented mutations, theywere masked by alkylation with bromoacetic acid (48), thus reinstalling analogs ofthe naturally occurring glutamic acids (see Section 13.3.1.2). The biologicalactivity of the synthetic EPO 97 was similar to wild-type EPO; however, thesynthetic hormone maintained a 2- to 3-fold higher plasma level for severalhours when injected into rats, which could be contributed by the stabilizingpolymers.

13.6.2Convergent Strategies for Multiple Fragment Ligations

The example mentioned above requires the stepwise assembly of individualfragments from the C- to N-terminus. In these, the N-terminus of one peptidesegment has to be protected to avoid undesired cyclization by an intramolecularNCL. A kinetically controlled ligation strategy was introduced by Kent et al., whichis convergent and does not require the strict C ! N assembly [136]. In principle,this approach exploits the different reactivities of aryl and alkyl thioesters in aconvergent protein syntheses [137]. Alkyl thioesters are sufficiently unreactiveand do not participate in ligation reactions when competing aryl thioestersare present nor do they undergo an intramolecular NCL with an unprotectedN-terminal Cys residue. Nevertheless, they can be converted into reactive arylthioesters by thiol–thioester exchange upon adding an excess of aryl thiols. Thesefeatures are employed in kinetically controlled ligation procedures: A centralpeptide fragment 99 containing an N-terminal Cys residue and a C-terminal alkylthioester is ligated at the N-terminal Cys residue with an aryl thioester 98. Theligation product 100 is then converted into an aryl thioester by thioester exchangefor a ligation reaction (Scheme 13.25), thereby allowing the ligation of multiplefragments in parallel. This approach was applied to the convergent synthesis ofcrambin and lysozyme (Scheme 13.25) [138]. For lysozyme, the 130-amino-acidenzyme was synthesized from four fragments, resulting into a protein with fullenzymatic activity and an identical X-ray structure as compared to biologicallyproduced lysozyme.


cen

tral

pe

ptid

es

= N

-pep

tide

=S

O

RH

2NHS

O

CO

2HH

2N

H N

S

O

Acm

1.)

Liga

tion

2.)

Cys

alk

ylat

ion

with

48

+

Pol

ymer

H2N

H N

S

O

Acm

H N

S

O

RH

2NHS

O

1.)

Liga

tion

2.)

Cys

alk

ylat

ion

with

48

+H N

1.)

Cys

dep

rote

ctio

n

Acm

= A

ceta

mid

omet

hyl

Pol

ymer

= p

olym

er a

ttach

ed

by

oxi

me

ligat

ion

R

= a

ryl

EP

O(3

3-88

)H

2N

H N

S

O

Acm

CO

2H

Pol

ymer

N H

OS

H N

O

OH

O

EP

O(8

9-11

6)E

PO

(117

-166

)

CO

2H

Pol

ymer

N H

OS

H N

O

OH

O

EP

O(8

9-11

6)E

PO

(117

-166

)

EP

O(8

9-11

6)E

PO

(117

-166

)

96=

C-p

eptid

e

Scheme13

.24

Totalchemicalsynthesisof

synthetic

EPO.


syn

thet

ic E

PO

Cys

dep

rote

ctio

n

S

O

RH

2NHS

O

+H N

H2N

CO

2H

Pol

ymer

N H

OS

H N

O

OH

O

N H

OS

H N

O

OH

O

EP

O(1

-32)

H2N

Pol

ymer

Liga

tion

N H

OS

H H N

O

EP

O(3

3-88

)E

PO

(89-

116)

EP

O(1

17-1

66)

CO

2H

Pol

ymer

N H

OS

H N

O

OH

O

N H

OS

H N

O

OH

O

EP

O(1

-32)

Pol

ymer

EP

O(3

3-88

)E

PO

(89-

116)

EP

O(1

17-1

66)

CO

2H

Pol

ymer

N H

OS

H N

O

OH

O

N H

OS

H N

O

OH

O

EP

O(3

3-88

)E

PO

(89-

116)

EP

O(1

17-1

66)

H2N

H N

S

O

Acm

97

Scheme13

.24

(Contin

ued)


S

O

H2N

HS

O

+

sy

nth

eti

c p

rote

inH2N

H N

S

O

PG

SR

O

H2N

S

O

H2N

HS

O

+C

O2H

N H

OS

H

N H

OS

H

SR

O

H2N

N H

OS

H

CO

2H

H2NS

O

PG

Cys d

ep

rote

ctio

nH

S+

N H

OS

H

H2N

CO

2H

R =

alk

yl

H N

H N

O

H N

O

H NH N

H N

O

H N

O

N H

OS

H

H N

O

99

98

10

0

= C

-pe

ptid

e

ce

ntr

al

pe

ptid

es

= N

-pe

ptid

e

=

Scheme13

.25

Con

vergen

tmultip

lefragmen

tligations

viakine

ticallycontrolledligation.


13.6.2.1 Ubiquitylated Histone ProteinsAnother impressive three-segment ligation strategy was developed by Muir et al. forthe synthesis of ubiquitylated proteins [139–142]. The universal 76-amino-acidprotein ubiquitin is attached to the e-NH2 groups of lysine residues via an isopeptidebond. The functions of this post-translational modification are manifold, includingthe triggering of proteosomal degradation or regulation of gene activity. In the lattercase histone proteins are of particular interest, since they are essential for alleukaryotic organisms; they form a complex with DNA called chromatin, whichpacksDNAmolecules of enormous size into the limited space of the cellular nuclei.The basic structural unit of chromatin is called nucleosome and consists of fourpairs of the core histones H2A, H2B, H3, and H4, which form the protein scaffoldaroundwhich theDNA iswrapped. In addition, histones also play an important rolein the regulation of adjacent genes. These regulatory effects are mediated by post-translation modifications, including acetylation, methylation, and ubiquitylation,which can dynamically interact with each other. One example is the ubiquitylationof Lys120 of histone H2B, which triggers the methylation of Lys79 on histone H3.To uncover the mechanistic aspects for this modification cross-talk an EPL-basedscheme for the synthesis of ubiquitylated peptides was developed which waslater extended to homogeneously ubiquitylated recombinant histones proteins[139–141].

The first step in this process is the ligation of ubiquitin to the e-NH2 group ofLys120 in a syntheticC-terminal peptide of histoneH2B (H2B-C,101, Scheme13.26).Since Lys lacks a thiol adjacent to the e-NH2,which could perform the capture step, anauxiliary based strategy was employed. Therefore, a retrosynthetic cut was madebetween Gly76 and Gly75 of ubiquitin. The synthesis starts with the C-terminal H2Bwith an orthogonally trityl-protected K120. After selective deprotection, the K120e-NH2 group was coupled with bromoacetic acid 48 to afford 102 before the disulfideprotected auxiliary 103 (see Section 13.3.2.2)was reactedwith the protected peptide toyield an auxiliary peptide 104. After cleavage, peptide 105was ligated to the ubiquitinthioester 106, which was generated by EPL and contained all native ubiquitinresidues except the C-terminal Gly76. This ligation yielded the ubiquitylated peptide107, inwhich the ligation auxiliary and theCys protection groupwere simultaneouslyremoved by UV irradiation. Afterwards, the resulting H2B-C peptide 108 canparticipate in a second ligation with a recombinant H2B-N thioester 109, whichwas generated by thiolysis of an intein fusion protein. The ligated semisyntheticH2B110was desulfurized (see Section 13.3.1.1) to render the native Ala at the ligation sitein the homogeneously ubiquitylated uH2B 111.

In the following uH2B 111 was used with the other core histones to reconstitutenucleosomes and probe the cross-talk between the ubiquitylation of H2B at K120and the methylation of H3 at K79. The authors could show that the methyltransferase Dot1, which is responsible for catalyzing the H3 K79 methylation, isactively stimulated by the ubiquitin moiety attached to the neighboring uH2B.These and further observations lead to the intriguing conclusion that all nucleo-somes methylated at H3 K79 must at some point have been ubiquitylated on K120of H2B.


R1

=M

eR

2=

CH

2CH

2CH

2C(O

)N(C

H3)

HR

3=

CH

2C

H2S

O3-

H2N

H N

S

O

O

O

NH

Br

OH

2NN

O2

R2

R1

SS

tBu

O2N

H2N

H N

S

O

O

O

NH

HN

O

O2N

R2

R1

SS

tBu

PG

PG

H2N

H N

S

O

O

O

NH

2

PG

H2N

H N

S

O

CO

2H

NH

HN

O

O2N

R2

R1

SS

tBu

NH

OO

H2N

H N

S

O

CO

2H

NH

ON

O2

NO

2N

R1

R2

SH

NH

OO

H2N

H N

HS

O

CO

2H

NH

ON H

H2N

N H

OS

H H N

O

101

NH

OO C

O2H

NH

ON H

H2N

S

O

R3

h*

ν

NH

OO

R3

S

O2N

O2N

O2N

Gly

76G

ly75

cle

ave

DIC

/DM

F

102

105

104

103

107

108

109

110

Br

OH

O

H2B

-N

48

H2N

N H

OS

H H N

O

NH

OO C

O2H

NH

ON H

111

Ra

Ni

106

+

EP

L

K12

0

H2B

-CH

2B

-CH

2B

-CH

2B-C

H2

B-C

H2B

-CH

2B-C

H2B

-CH

2B-N

H2B

-N

Scheme13

.26

Semisynthesisof

homog

enou

slyub

iquitylatedhiston

eH2B

.


References

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amino acids, peptides and proteins in organic chemistry (building blocks, catalysis and coupling...

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