PharmaceuticalChemistry

Prof.DanielO.Cicero

Introduction

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OutlineoftheCourse-  Introduction,OptimizingDrugBindingAffinity,Drug-like

Properties,Lead-to-DrugDesign(DanielCicero)-  Therapeutictargetidentificationfromhitcompounds(AlbertoBresciani)-  MedicinalChemistryandthediscoveryofleadcompounds

(VincenzoSumma,StevenHarper)-  Drugmetabolismandpharmacokinetics(EdithMonteagudo)-  Advancedanalyticaltools(FabioBonelli)-  Therapeuticpeptides:developmentandexamplesofnew

drugs(ElisabettaBianchi)

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TheDrugDiscoveryProcess

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TheDrugDiscoveryProcess

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Thephasesofdrugdevelopment

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TheDrugDiscoveryProcess

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Thedrugdiscoveryanddevelopmentprocess

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Thedrugdiscoveryanddevelopmentprocess

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Thedrugdiscoveryanddevelopmentprocess

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MedicinalchemistryTheprimaryobjectiveisthedesignanddiscoveryofnewcompoundsthataresuitableforuseasdrugs.Discoveryordesignofadrugrequires:ü Targetdiscoveryü synthesisofthedrugü methodofadministrationü  developmentoftestsandprocedurestoestablishhowit

operatesinthebodyü asafetyassessment

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Drugs

•  Drug is any substance presented for treating, curing or preventing disease in human beings or in animals. –  Activity: is its pharmaceutical effect on the subject –  Potency: is the quantitative nature of that effect

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Drugsideeffects•  Drugsactbyinterferingwithbiologicalprocesses,sonodrug

iscompletelysafe.

Overdosecancausecomaanddeath

Canalsocausegastricirritationandoccultbleeding

•  Sideeffectsarenotalwaysnon-beneficial;thetermalsoincludesbiologicaleffectsthatarebeneficialtothepatient.

Forexample:promethazine(antihistamine)isusedforthetreatmentofhayfeverbutalsoinducesdrowsiness,whichmayaidsleep.

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Drugresistance(tachyphylaxis)

Occurswhenadrugisnolongereffectiveincontrollingamedicalcondition.Reasons:•  Inductionofanenzymethatmetabolizesthedrug(barbiturates)

•  Downregulationofreceptors•  Appearanceofasignificantlyhighproportionofdrug-resistantstrainsofmicroorganisms(antimalarialandantiviraldrugs;antibiotics)

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DiscoveryofPenicillin

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Sincethen….

•  Inlatenineteenthcentury:searchforlesstoxicmedicinesthanthosebasedonnaturalsources

•  Introductionofsyntheticsubstances:useofknownpharmacologicallyactivecompoundsasleads

•  Synthesisoflead-relatedcompounds:analogues

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Thefirstrationaldevelopmentofsyntheticdrugs

•  Ehrlich-Hata(1910):bothbeneficialandtoxicpropertiesofadrugusedforitsevaluation.Moreeffectivedrugsaremoreselectiveforthetarget

•  Theysearchedforagentstotreatsyphilis,saferthanAtoxyl.600structurallyrelatedcompoundswerecataloguedusingthetherapeuticindex,leadingtothediscoveryofArsphenaminein1909(useduptothemid1940s)

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TheEhrlichindexrevisited•  Theindexusedtodaytakesintoaccountthevariabilityof

individuals:

LD50:lethaldoserequiredtokill50%ofthetestanimalsED50:doseproducinganeffectivetherapeuticresponsein50%ofthetestanimals.

•  Thelargeradrug’stherapeuticindex,thegreaterisitsmargin

ofsafety.

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Thetherapeuticwindowforadrug

Aproportionofthedrugiseither:•  Lostbyexcretion•  Convertedtootherproducts(metabolism)•  Boundtobiologicalsitesotherthanitstargetsite

Thedoseadministeredishigherthanthatwhichwouldbeneededifalldrugreachedtheappropriatesiteofbiologicalaction

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SARandQSAR•  Structure-activityrelationship(SAR)isnowusedtodescribe

Ehrlich’sapproachtodrugdiscovery:synthesizeandtestaseriesofstructurallyrelatedcompounds

•  HanschandFujita(1960s)incorporatedquantitativemeasurementsintoSAR:quantitativestructure-activityrelationship(QSAR)

•  OneofthemostsuccessfulusesofQSAR:developmentofantiulceragentscimetidineandranitidine.

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TaxonomyofBiologicalMechanisms

Receptors – agonists antagonists partial agonists inverse agonists

Enzymes – inhibitors Ion Channels –openers

blockers

Protein-Protein – inhibitors

In vivo Effectors

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BiologicalMechanisms2014 Top 50 drugs by Worldwide sales

Enzyme Inhibitor 38%

Ion Channel Modulator

8% Biological

10%

Receptor Agonist

12%

Misc 8%

Receptor Antagonist

24%

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BlockbusterDrugs

NF

NH

O

OH

OH

OOH

CholesterolPfizer

$12.0billion

LipitorHMGCoAinhibitor

PlavixAnti-platelet

S

N

Cl COOMe

ThrombosisBMS/Sanofi-Aventis

$5.0billion

NH

O

O O

O

ONH2

Cl

NorvascCalciumchannelblockerHyper-tension

Pfizer$4.8billion

N

N

OS

N

OO

NexiumProtonpumpinhibitor

Anti-ulcerAstraZeneca$4.8billion

Enzyme

Enzyme

Receptor

Ion-channel

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Enzymefunction

Active Site is tailored to bind the transition state for S P Usually, the substrate & inhibitors bind at the active site Allosteric (non-competitive) binding occurs remotely to the active site

E + S ES E + P #

E Free

Ene

rgy

Progress of Reaction

TS

S

P

S

P

TS

Progress of Reaction

Free

Ene

rgy

NH2

NHNH2NH

OOH

NH2

NHNH2O

OOH

O2iNOS

+ NO+

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Enzymeinhibition–Fourmechanisticcategories

1. Competitive inhibition. Inhibitor competes reversibly with substrate for the active site.

2. Uncompetitive inhibition. Inhibitor binds only to the ES complex, leading to EIS intermediates. This is very rare.

3. Non-competitive inhibition. Inhibitor binds non-covalently to sites other than the active site (Allosteric inhibition). Kinetics are complex and partially inhibited enzymes can still turn over substrate.

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Enzymeinhibition–Fourmechanisticcategories

N

S

O

NH

p-OH-Ph

O

CO2H

NH2

NH

SOH

NH

p-OH-PhO

CO2H

O

NH2

N

O

O

OH

CO2H

OH

OH

O O

Scys

turnover

irreversibleinhibition

4. Irreversible inhibition. Inhibitor binds covalently, usually to the active site machinery. Also known as Suicide inhibitors. Examples include MAO inhibitors and β-lactamase inhibitors:

Amoxycillin

Clavulanic acid

β

β

β

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Proteases(proteinases,peptidases)

Endopeptidases cleavage site may be anywhere in the substrate Exopeptidases terminal residue (carboxypeptidase, aminopeptidase)

Hydrolytically cleave peptidic amide bonds

Four Mechanistic Classes

Serine

Cysteine (thiol)

Aspartic

Zinc (metallo)

Nucleophile pH preference Endo/Exo

R-CH2OH

R-CH2SH

~7

~7

endo

endo/exo ~7

3-6

endo

endo

H2O

H2O

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ProteaseSpecificity

S3’ S1’ S2

Specificity-Pocket nomenclature (Schechter & Berger, Biochem Biophys Res Com, 1967, 27, 157-162)

prime side non-prime side

S3 S1 S2’

..

substrate N-terminus

Substrate C-terminus

P3'

NH

NH

NH

NH

NH

NH

O

O

O

O

O

P1P3 P2'

P2 P1'

E-XH

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SerineProteasesThrombin, Tryptase , β-Lactamase, Elastase, Chymotrypsin, HCV-NS3

Catalytic triad boosts serine nucleophilicity

enzyme

substrate

O Ser195

NH

NH

O

P1

P1'

H

P1 is the primary specificity site

Inhibitors create or mimic stable tetrahedral

intermediates

β-lactams

trifluoromethyl ketones

saccharins

NO

O

CF3

ONHCOR

SN

O

O OX

NN

HO

O

Asp102

His57

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Thereceptivesubstances•  In1905Langleyproposedthatso-calledreceptivesubstancesinthebodycouldaccepteitherastimulatingcompound(causingabiologicalresponse)oranon-stimulatingcompound(preventingaresponse)

•  Thisidealeadtothetheoryofreceptors

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Receptors•  Receptors are membrane-bound proteins that bind endogenous ligands (usually extracellular) to induce a physiological effect (usually intracellular)

•  A receptor is often the first step in a long intracellular signalling cascade leading to physiological effects

•  G-Protein Coupled, Seven-Transmembrane Spanning Receptors comprise the majority of known examples

intracellular

extracellular

7TM GPCR

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BindingtoReceptors

R R*

ground-state receptor

no signal

Excited-state receptor

signal

Agonist a ligand that binds to, and provokes a signal from a receptor via conformational changes in the excited state

Antagonist a ligand that binds to a receptor and induces no signal.

Blocks agonist binding. Little conformational change overall

ligands can be proteins, peptides or small molecules

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Typesofreceptors

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TypesofReceptors

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Typesofreceptors

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IonChannelsAll of life exists within an electric potential window of less than one volt

The membrane potential of most cells is 60-70mV

Ion channels regulate passive ion flow through membranes in an electric or concentration gradient

Channels are ion selective and comprise groups of glycoprotein subunits in homo- or heteropolymer arrays. Almost no channels have an open rest state

Channels are involved in cardiac, neuronal and psychiatric disorders

Which ions? Na+ K+ Ca++ ( Cl- )

hERG (IKr) channel: blockade causes prolongation of cardiac Q-T interval

“Long QT syndrome” can lead to sudden death

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hERGChannel

•  Thehumanether-a-go-gorelatedgene(hERG)encodestheinwardrectifyingvoltagegatedpotassiumchannelintheheart(IKr)whichisinvolvedincardiacrepolarization.

•  InhibitionofthehERGcurrentcausesQTintervalprolongationresultinginpotentiallyfatalventriculartachyarrhythmiacalledTorsadedePointes.

•  Anumberofdrugshavebeenwithdrawnfromlatestageclinicaltrialsduetothesecardiotoxiceffects,thereforeitisimportanttoidentifyinhibitorsearlyindrugdiscovery.

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IonChannels

Channel families are complex, but all channels are either

Voltage-gated

or

Ligand-gated

Ligands can be other ions, small molecules or toxins & venoms such as tetrodotoxin, pumiliotoxin, margatoxin & charybdotoxin

Blockbuster antihypertensive drugs have emerged from calcium-channel antagonist programmes – Nifedipine, Nimodipine, Isradipine, Amlodipine

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Theα-adrenoceptor

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Gprotein

•  Guaninenucleotide-bindingproteins

•  Actasmolecularswitchesinsidecells,andareinvolvedintransmittingsignalsfromavarietyofstimulioutsideacelltoitsinterior

•  TheiractivityisregulatedbyfactorsthatcontroltheirabilitytobindtoandhydrolyzeGTPtoGDP.

•  WhentheyareboundtoGTP,theyare‘on’,andwhentheyareboundtoGDPtheyare‘off’

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Mechanismofadrenergicreceptorα1couplestoGq,whichresultsinincreasedintracellularCa2+α2couplestoGi,whichcausesadecreaseinneurotransmitterrelease,aswellasadecreaseofcAMPactivityβreceptorscoupletoGs,andincreasesintracellularcAMPactivity

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Drugsactingonareceptor•  adrugismosteffectivewhenitsstructureorasignificantpartofits

structure,bothasregardsmolecularshapeandelectrondistribution(stereoelectronicstructure),iscomplementarywiththestereoelectronicstructureofthereceptorresponsibleforthedesiredbiologicalaction

Sincemostdrugsareabletoassumeanumberofdifferentconformations,theconformationadoptedwhenthedrugbindstothereceptorisknownasitsactiveconformation

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Pharmacophore

•  Thesectionofthestructureofaligandthatbindstoareceptorisknownasitspharmacophore.

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Newtoolsfordrugdiscovery

Molecularmodelling–  allowstheresearchertopredictthe3Dshapesofmoleculesandtarget

–  Enablestocheckwhethertheshapeofapotentialleadiscomplementarytotheshapeofitstarget

–  Allowstocalculatethebindingenergyliberatedwhenamoleculebindstoitstarget

–  Reducedtheneedtosynthesizeeveryanalogueofaleadcompound