2.2 L...1 ilodltlcation: Drug D$lgn .

nd Devtopnenr

75

TABLE 2.11 > lvplcalMombers Clusters of Based r,z, r, R.MR. on andMW lwith permi$lonfromMartin,Y (1979). C, Reprintd from DrugD$ign,Vol.Vlll,E, ArlEn6, "Advanc$In the Methodotogy J. ed., ol Ouantllallve Dlgn",pp 2-72,Copyright Drug @1979,with permEslon lromElsevier.l
Clusier nunbef Typical rnenbes
Me, H,3,4-(OCH2O), CHTCHTCOOH, CH=CH2,Et. CH2OH CH=CHCOOH cN, NOr. CHO, COOH, COMe c + cH, cHrcl, Cl, NNN, SH, sne, CH:NOH. CHTCN, OCoMe, SCOMe, cooMe, SCN CO\Hr. CONHMe.SOTNH.:, SOrMe,SOMe NHCHo, NHCOMe, NHCONHT,NHCSNH2.NHSOTMe 4 OMq NH2, NHNHT, OH, NHMe, NHEI, NMe2 Br OCF3,CF3. NCS,I. SF5,SO2F cHrBr. SeMe.NHCOTEI,SO2Ph.OSOTMe NHcOPh, NHSO2Ph.OsorPh, COPh,N=NPh. oCOPh, PorPh 9 l0 3,4-(CH)!,3,4-(CH2)4, i-Pr.3,4,(CH)r, Pr. NHBu,Ph,CH2Ph, r-Bu.oPh Fenocenyl,adammtyl

a Cluste 3 ard 4 conhh mmy of thcommoD substituents in medicinal used chenistryr hence, 6eseclusreB furthersubdivided de according theircluster io membership 20closteB when have been made. to tbeind, n, n2, Es, F (field constant, R (rcsonance constant),MR (molar refractivity), andMW (molecularweight) values.Someof rhe clustersarc shownin Table2.11.12221 Otre memberof eachcluster would be selected substitutioninto th leadcomDound. the for and compoundc wouldbe sln$e\i7edandresred. iubslituent tfa showed dominanl Dokncv. rhen ot-her sublriruenls tromrharclu\rer \4ould selecred funler invesligation. irnpon*r be for fn. ad!antage oflhe balch selecrion merhods Ihattheinioalbatch i\ prepared ofanalogs is;eri!ed from the widestrangeof parameters possibleso that rhedominantphysicochimicalproperty canbe revealedearly in dle leadmodificationprocess. The initial pronise of thesecomputationalmethodshasyer to be realized.They seemto be just additional examplesof potenrially exciting new approaches which linle success for hasbeenfonhcoming.Theseearly computationat merhodshavelargely beensupplanted by what is known as 3D-QSAR andmolecularmodelingapFoaches. G,4 ComputeFBasedMethodsot OSAR Retatedto ReceptorBlnding: 3D.OSAR Thre-dimensional quantitative structure-acrivily relationships(3D-eSAR) pemit cofielations btweena seriesof djverse molcular structuresand thei biological functions at a particulartarget.The generalapproach 3D-QSARis io selecta group of motecules, of each

Chaptr2 OrugObcdery Dsslgn,and t ovdoprent

of which hasbeen assayed a particular activityi align the moleculesaccordingto some for predetermined orientationrules; calculatea set of spatially dependent paramete$for each moleuledeterminedin the receptorspacesurounding the aligned series;derivea function that relateseach molecule'sspatial parameters their respectivebiological propefiy; and to establishself-consistency predictability of the derivedfunction. A variety of computer, and basedrnethodshavebeen usedto correlatemolecular stluctule with receptorbinding, and, thercfore,activity. Somearementioned here;manymorearelisted in the GeneralRefercnces at the endof the chapter Crippen and coworkerst22124deviseda linear fiee-energymodel,termedthe dirranc" aryrcafh, for czlculatingQSARfrom rcceptorbinding data.The distances between Eeometry variousatons in the molecule,compiled into a table called the distancenmtrc, define the conformationof fte nolecule. Rotationsaboutsinglebondschange molecularconformathe tion and,tlerefore, ahese distances; consequendy, upperandlower distancelimit is seton an eachdistance. Experimentallydeterrnined hee energies bindiry of a seriesof compounds of to the receptorareusedwith the distancematdx of eachmole.ule in a computerized method to deducepossiblebinding sites in terms of geometryand chemical characterof the site, phamacophoie.Although this approach therebydefining a three-dimensional requies more computationaleffon and adjustableparaneten than Hanschanalysis,it is thought to give good resultson morediffrcult datasets. geomery appoach wasextended Sheri<lan al. t22sl treattwo or more The distance by er to rnoleculesas a single ensemble. The ensernble approachto distancegeometrycan b used to find a commonphamacophorefor a rcceptorwith unknownstruture from a small setof biologically activemolecules. Oncethephamacophorehasbeen,at least,pa{ially identified, new molecular scaffoldscan be revealedwhich contain that phamacophoreembedded in their sfucture by t/rrcs-dimensional database(or similanry')searching.I226l this tnettod In you startftom a receptorligand,enzymesubstftte,or othermoleculewhosepharmacophoric groupsareknown for a particulartarget.Thena database compounds (e.g.,the company's of [bmry of compounds, CMC database, anydatabase compounds) searched deterthe or of is to mine which oneshavea similar tbree-dimensional structureas lhe pharmacophore. top The virtual "hiis" are visually inspected.o determinewhich onesrnight be the best candidates, andthenthey aretested.This wasthe approach lalcn to identify iniibitors of humanimmunodeficiencyvirus type I integase (Hry-l IN) as potential anti-AIDS drugs.l22?l HtV"l n{ mediatesthe idegration of HIV-1 DNA into host cbromosomal targetsand is essential for effectiveviral replication.From a lcrown inhibitor of HIV- I IN, a phannacophore hypothesis was proposed. Basedon this hypothesis, thre-dimensional a searchof the National Cancer Institute (NCI) database compounds of was performed,which produced26? structures that matqhedthe phamHcophore; of thosewere testedagainstHry-l IN, and 19 were found 60 to be active.The relevance the Foposed pharmacophorc testedusing a small threewas of dirnensionalvatidationdatabase known HIV-I IN inhibitors, which had no overlapwith of found in the initial search. This ne\r three-dimensional the group of compounds searchsuppo{ed the existence the postulatedpharmacophore also suggested possiblesecond and of a pharmacophore. pharmacophore anoth$ thre-dimnsional in Using the second search the of NCI database, novel, stmctually diverseHIV-I IN inhibiton were found. l0 prccedves tal:.trted olecular shape Hopfingerl223l developed setof computational has a andl)rir for the determinationof the active confomations and, ihereby,molecular shapes duringreceptor binding.Commonpairwiseovedapstericvolumes calculated from low-energy

Sclion 2.2 Lead Modlflcarbn: Orug o$ign 6nd Devetopmenr

conibnnations molecules usedto obtainrhree-dimensional of are motecutar shape descriptors thatcanbe teated quantitatjvelyandusedwith oiher physicochemicat parameter descriptors. Two orhrdescriptors subsiructure for representation, atompairt22el theropotogical the and to ion,t230l havebeendescribed Ventataraghavan coworkers. by and Thesedesapiors ct'aracierizemoleculesin fundamental waysthai ale useful for the selectionbf potentialtyactive compounds from hundreds thousands structures a database. atompair methodcan of of in The selectcompounds from diversestructuralclasses thar havearomswithin the entire mole.ule similar to thoseof a parricularactivestructure. The topologicaltorsiondescriptoris complementaryto the atom pair descriptor,and focuseson a local environmenr a moleculefor of comparison wiih activestructures. One of the most widely usedcomputer-based 3D-QSAR methodologies. developedby Cramerandcoworkers.t23tt terltned is Comparuth,e MotecutarFieM Analysis (Covtl;1.1.t23at In thls methodthe molecule receptorinteracrionis represented rhestericandelecrrostatic by lields exertedby each nole'cule. A series of adive cornpoundsis identified, and threedimensionalstructuralmodels are constructed. Thesestnrcturesare supedmposed one on anotherandplacedwithin a regularthree-dirnensional grid. A probeatom,wirh irs own energetic values,is placed at lattice points on the grid, where it is used to calculatethe steric andelectostatic poteniialsbetweenitself and eachof rhe superimposed srructures. each At Iatticepoint one steric value,one electrostaticvalue.and one inhibition value are savedfor eachinhibitor in the series. The resultsarerepresented a ttreedimensional conrourmapin as which contoursof variouscolors represent locationson the structue wherelower or higher steric or electrostaticinteractionswould iftIease binding. Howevet because simple steric dndelecrro\tatic field\ are unlilel) ro repre,ent complere d de,cnprion a drug-recepror of inleracrion. alrem ive ]nd modihed form. ha\e beenpropo,edArrlBecau.e j. dssumed rr that the moleculesbind with similar orientationsin the recepr-or, {rhich may not necessarily be the case,correct alignmentsare almost impossjble,particularly for compoundswith a l,rge numberof rotatablebonds,which limits the applicability of CoMFA. Otherapproaches havebeendeveloped that do not dependon a commonalignmenrof the molecules,suchas Conparati|e Molecular Mo,"enr A,abrir (CoMMA),lral EVA,t23sl WHIN{.12361 and these provide3D desoiptorsthat areindepedent of the orienrationof the molecules approaches in space. they do not haveto be aligned.However it is not possiblero give a 3D display of so the rcsuliing modet.Goodford'spro$am calledcRlD usesa grid force field that includesa very gooddesc ption of hlclrogenbonding.t23z] S6cause energerics, well asrhe shape rhe as complementarity, a dnrg receptorcomplexarevital ro its stabiliry this methodsimultaneof ouslydisplaysthe energycontoursurfaces the macromolecular and srrucrweon the compurer graphicssystem. This allowsboth the energyandshape be considered to togetherwhen consideringthe designof rnoleculesthat have an optimal fit to the rcceprot and it determines probableinteractionsitesbetweenvariousfunctional groupson rhe ligand and the enzyrne \urface. The p'9gramH/,NT Hydrophobic INTerrc'ionsr map. po'enlialhydrophobic and ' dr p^larinreraclion. berwen mblecule d receplorrz a and Anotherusefulmethodolo is he hrpotheticalacti.resik laftice( HASL) technique,whjch Ey creates QSAR modelftom a composit a lattice generated from a seriesofrcgutar orthogonal pointsarcrestrictedto locarions 3D grids established eachmolecule.l23el for These embeddeal in thevanderWaalsradii of a moleculeandarekepi in the analysis dependenr somefeature on of a proximal atom (for example, hydrophobiciry).Eachmolcule'sbiological activiry value is then averaged over all points on its respective lattice. A compositelanice is consrructed from thesepartial activity valuesby averaging overall moleculesthat sharecommonpoinrs.

7A

Chaplor 2 DrugOl.covry ttsdgn,.nd D4lopm{t

the Using an iterativeoptimization scheme, partial activity valuesarc gradualy adjustedro yield a compositelatticebestfitting the molecularseries. Otherpharmacophore-based design Ahddin,l2all ard SpacerSkeletons.t2a2l algorithmsincludeCaveat,l24ol (2.92,Aricept) wasdiscovered The anti'Alzheime/s drug donepezilhydrohloride using a variety of 3D-QSARmethods.Iu3l

;cd..o^D
domp.rl hydrcchlorl.b 252

DrugDesign 2.2.H Molecular Graphiqs-Based

QSAR studieshave relied heavily on the use of computersfrom the beginning for statistical calculationsinvolving multipadmeter equations.Researchers soon realized that &ug designcould be aided significandyif structues of recepton and drugs could be displayed on a computerterminal, and molecularprocesses could be obseryed. Mole&lar eraphicsis the visualization and nanipulation of 3D teprcsentations moleculeson a graphicsdisof play device.The origins of moleculargraphicshavebentracdby Hassalt4l to the project which Foducedmoleculargraphics MAC (Multiple AccessComputer),t2asl modelsofmacromolecules the first time. The potentialto apply this technologyto proteincrystallogaphy for wasquickly rcalized,andby theearly 1970s electrondensitydataftom X-ray diffraction studies could be presented manipulated stick or space-fillingmulticoloredrepresniations and in on a computerterminal.l26l The numberof X-my crystal stuctues availablein the Fotein databant (PDB)l2a?l went ftom about200 in 1990to morc than20,000by 2003. Medicinal.chemistssaw the potential of dis approachin dnrg design as well. These approaches knownasrtructure-bateddtug design(SBDD),compukr-assisted are bug design (CADD), ot conputerassiskd mokcular design(CAMD). A variety of commercialsoftware pakages availablefor structure-based are drug design,for example,Sybyl (Tripos),Insight (Molecular SimulationsInc.), and Gold (CambridgeCrystallographicData Centre).lt is II now possiblefor a syntheticchemistto carry out his or her own molecularmodelingwthout havingto beome computerscientist. a Stick (Dreiding) and space-filling(CPK) molecularmodelshavebeenusedextensively by organic chemistsfor yearsfor small molcules,but thesehandheldmodels havemajor the disadvantages.l!3] Space-fillingmodelsoften obscure stiuctureofthe molecule,andwire or plastic modelscan give falseimpressions molecularflexibility and tendto changeinto of unfavorable confomations at inopportunemoments. Plasticmodelsof proteinsaremuchtoo cunbersome work with. A three-dimensional to computergraphicsrepresentarion a Fotein of thatcanbe rnanipulated threedimensions in allowstheoperator visualizethe interactions to of smallmolecules with biologically importantmacromolecules. Superimposition structurcs, of which is cumbe$omeat best with manual models,can be performedeasily by molecular gmphics.Also, somesystems havethe capabilityto synlhesize graphicallynew structures by the assemblage appropriate of molecularfragments Iiom a ftagment6le.

Sclion 2.2 Lerd Modiffcatlon: prug Dlgn and DMlopnenl

Numercusmoleculargraphicssystemsare available,l2ael the typical systern,which but muchoverthe years.utilized by everymajor pharnaceuiicalcompanyin the hasnot changed WestemEuope, and Japan,consistsof a mainframeor superminicomputer United States, linked to a high-rcsolutiongraphicsterminal wift local intejligence.The graphicsterminal may b equippedwith a variety of peripheraldevicessuchasgraphictablets,light pens,tunction keys,anddials to effect the moleculardisplay andthree-dimensional manipulations. The all mainframeor minicomputerexcutes of the molecularcalculations,suchas calculations of bond lengths,bond angles,andquantumchemicalor force field calculations. A variety of apFoachescan be taken to utilize molecular modeling for &ug design; arc direct deign appro^ches usedwhen the structureof the target receptoris known, and are indirect design approaches used when the rcceptor structureis not known. The basic premisein the utilization of molculargraphicsis ftat the betterthe complementary of the fit drug to the receptor, morepotentthe drug will be. This is the lock-and-keyhypothesis the of Fischert25ol which the receptoris ihe lock into whlch the key (i.e., the drug) fits. To apply in this conceptmost effectively,the structureof the receptor(either X-ray crystal structureor NMR solution structure)shouldbe known; then, different drug analogscan be dockedinto the receptor Drc,tjrg is a moleculargraphicsterm for the computer-assisted movementof moleculeinto its receptor It cannotbe assumed the lowest energy that a terminal-displayed structue of the moleculebinds to the receptor;the bioactiveconformationcan be a higher energyconformationof the mol.ule.t25ll The most effectiveuseof nolecular modelingis when a high-resolutioncrystal structure (or NMR solutionstructue) of a recptorwith a ligandboundis available. Molecular graphics visualizationof the electrondensily map of this complex may revealempty pocketsin the modification of a lead compound.An imponant complexthat coirld be filled by appropriate drug design is the discovery of zanamivir (2.93, Relenza),an exampleof structue-based 'Ihe A antiviralagentusedagainst influenza andB infections.tz52l hemagglutinin the surface at (2,94)residues receptors the host cell surface.The virus on al of the virus bindsto sialic acid entersthe cell and replicatesin the nucleus.The progenyvirus padcles escape cell and the stick to the sialic acid residueson the cell surfaceas well as to eachother Nerrdnfu,i/rre (alsoknown asgdlrddre) is a key viral surface th enzymethat catalyzes cleavage terminal of the sialic acid residuesfrom the cell surface,which releases virus particlesto sFead into the respiratorytract and infect new cells. The importantfeatureof this enzymethat madeit an attractivetarget for drug designis that its active site is lined with arnino acids that are invariantin neunminidasesof all known strainsof influenzaA andB. Therefore.inhibition of this enzymeshouldbe effectiveagainbt strainsof influenzaA andB. Randomscreening all did not Foduce any potentinhibitors of the enzyme,altbougha nonselective neuraminidase inhibitor (2.95,R : OH) wasidentified.The breakthrough camewhenthecrystalstructures of wereobtained. theinfluenzaA neuaminidasetsll with inhibitors boundt2sal The activesiteof the enzymewith 2,95 (R : OH) boundwasprobedcomputationallyusingGoodford'scRlD program(seeSection2.2.G.4).Predictionsby CRID of energeticallyfavorablesubstitutions suggested rplacemenof the4-hydroxylgroupof 2.95(R: OH) by anaminogroup(2.95,R = NH2), which whenprotonatedwould form a favorableelectrostaticinteractionwith clu,119 (Figure 2.18a).It was apparent ftom the crystal structurethat extensionof the 4-ammonium group with a 4'guanidinium group (2.93) would producean eventighter affinity because of the inffease in basicityof the guanidiniumgroup andalsobecause could interactwith both it Glu-l19 andClu-227(Figure 2.18b).

80

O.siEn,and Developmeni Chaptor 2 Drug Olscovory,

HN

HN

NH. l NH

*-./ f'J *o" o1*/--__,

no

oHo tH

.t,Au

ut

2.93

(a) of actile of slructure neuraDinidase siGwnh inhibilo$bound. Intenction Figure 2.18 > Crystal of aninosrcup 2.95(R = NHi) withGlu I 19.(b)Interaclion theProlonaled of theprcronated sumidiniun ir] wnh from grcup 2.93 of sith Glu I I 9 ed clu 227lReprinred petnission Ndtu..363, 8 Copynehr 1993 O pages asd173 in 172 Ltd.l.Reproducedcolo.belween MacMillan Magazines

Scrion2.2 Ldd Modttica{on: OrugDtgn and Devetopment

is rypically, the idealcompound not realizdso quicHy.Rather anideafor teadmodificarion manifestsflom the crystal srructure the leadboundto the receprorThis modifiedlead of is synthesized tesrd; and maybeonty a minor imFovementin potencyis.produced maybe (or lower potency).ff thereis someimptovement,a new crystal structureis obtained.aalditional noleular nodeling is carrid out for fu(her refinementof ideas,and new compoundsare synthesized tested. and This Focessis ritemtedwith ftrrtherroundsof design,syn;hesis, tesring, and crysral structureuntil higher potencyanalogsare obtained.A be;udful examDle of howtheileraLive combinarion otmotecutar modeling. crlsrdlography. combinarori;t and and traditional medicinalchemistrysynthesis was usedto modiry a bad neuraminidase inhibitor andenhance potency72,500-foldwas described the group at Abbon Laboratories.t2s5l its by Sometimeseven a crystal structure with the ligand bound is not sufficienr. A hish_ resoluhon crysralstructure rh)midylate of synriase $irfi a tigandbounddjd notproperty 'dnl; lisand-'nduced enllme conformarionat change during ,rructure_b;ed i..:,"1,1:r i oesrgn.i*a Ac a resutL structur imparred improper rhe an bia! inlo the designof novel ligands. Eadier in the chapter the SAR ofpaclitaxel was describd(2.36, Serion2.2.C.D. 23). By o\erlaling rhe molecular graphics depicdon the crlsrdl sructureof Dactirax;t of wilh rhose four olher natural of producllalsofoundro promoLe stabitiTarjon mjcrotubutes of in comperition \4ith paclila\el{Figure2.t9. Th\otr. a common phd-crnacophore proposed wa5 (rrgure.z.lu).'.-'Ihrsgrve5ane$perspec[!etoleadmodificanon.rDdpermihrheconsnuc_ tion of new s),nrhetic analogs havinghyb.id structures eachof the fo; umelatedscaffolds. of Basedon fiis pharmacophore model,2,96wassynthesized wasshownto stabilizemicro_ and tubules well.Orher3D compurer as modets pactira\el ot bindingto microrubules been have promored well rz)dr a\ Wirhour motecu graph capdbililie.. woutdbe verydimcutr the I3r ic, il to makethis sort of comparison designa new hybrid scaffold. and

Fi9ur6 2Js Five naturat prcducbfo;d to prcmotestabilization ofmicrcilbules. Tbeborcd sections ' wqe usedro identify a comon phmeophoft. Iwith peDissioDfrom I. Ojin. ReDrinE;;i; pemi$ion ftom PNaS96.4256.Coprnshl 1999NalionarAcadenyof Science.0999). O U.S.Aj

a2

oev.lopment Deslgn,and chaprer2 oruq Dlscovery

setionsid Figue2.19. of based theconposite boxed o. fwith Figure2.20 > Connonphmacophore National 96,4256copvrightO 1999 Rep.inted pcmision fromPN,4S vilh pemissionfromL ojina ( 1999). pages ed 173 172 in colorbetween ReProduced U,S.A,]. Academy sciences, of

ta;:

r' "c

Kuntz at al.l25elreportedon an atSorithmcalled DOCK that \\'as designedto fit snall 1t;5 receBtors leaddiscovery'12601 tltape-matching for moleculesinto their macromolecular molecule93ndrecepto restricted rigid ligands(receptor-bound method.which wasoriginally as tors. was modifiedi26llfor flexlble ligands wherea ligand is approximated a small set of high-resolutionsiructure(X ray crystal structu.eor NMR spectal rigid fragnents.Ideally. a ld structure)of the receptorwith a lieand bound sho\t be available.The ligand is removed of graphic thenDOCK Rllsthe bindingsitewith sets display, from the bindingsitein the as image ofthe binding centers serves thenegative a setof sphere where overlapping spheres, DOCK is but of site.Wlen a crystalstrucnne a receptor available, withouta ligandbound, that with regard grooves couldpotentially to receptor ofthe the characcrizes entiresurface spheres. NextDOCKmatches whichare6lledwith theoverlapping bindings;tes, fo|m targer to ofthe recepbron the ofpuiativeligands the image structures X-ray or computer-derived

end Dcvelopmenl Sclion 2.2 Lead Modlllc.rbnr Drug [t619n

83

of Thenthe programsearches databases small 3D of basisof a comparison intemal distances. that on molecules rankseachcandidate thebasisof thebestorientations canbefound for a and are suchasthe various databases availableto search, particularmolecularconfomation.t262l (CSD), a compendiuniof >200,000small moleculeswhose CambridgeStnctural Database are crystal structures known andthe Fine ChemicalsDhectory (FCD) disributed by Molecular Design Limited, but the best onesto use are thosecontainingcomrnerciallyavailable Directory (ACD), so that anyvirtual hits catrbe compounds, suchasthe AvailableChemials of quickly the effectiveness ihe searchThe drawbacks of purchased assayed determine to and pdmadly by shape complementhat are this approach the assumptions binding is determined in tarity and that only small changes the shapeof the receptoroccur on ligand binding. An though,is that this methodis not limited to docking of known ligands importantadvantage, to bestfit a particular can A library of molecularshapes be scanned determinewhich shapes reeptorbinding site. In fact, DOCK was usedto ident8 fullerenesas potentialifibitors antibiotic The ofHIV-1 protease.l263l high-resolutionNMR stru'rtureofthe aminoglycoside paromomycin(2.97,Humatin)boundto the A site of the bacterialribosomalRNA wasused (a to pedorm a DOCK searchof tlle CSD and the National CancerInstitute 3D database formedthe that from this search total of 273.000compounds).l2alThe cornpounds emerged basisfor the designof sevencompositestluctuleswith additionalfeaturesaddedto suppress activity As resistance. a result, sevenl of thesecompoundswere found to have enhanced yitro at:din'rivo agai(tst vmiety of pathogenic bactriaresistantto aminoglycosidesa in

*1Vo,

"..,--r_l_+\__1
HiN (

^* ^(")? * * ' Ho.\-,-",

n,N Lo__J Ju ,." _/
2.97
pol.--^-j \-

contactsin crystal packings of The programIUDI usesstatisticatanalyses nonbonded nonbonded conlacts a to of orsanicmolecules establish .et o[ rule\ thatdefinethepossible 2651 lo rule"it alsocansearch databa\es fiDdstrucproteins lrgands. t singLhe.e and berw;en tures thai fit a particular binding site in a protein basednot on shape,as in DOCK, but on and hydrophobic propsties, suchashydrogenbonding,ionic interactions, physicochemical (called Allecrcwl26?l in Another programfor d nov, moleculd design,GrowMolt266l the latest version),approaches problem of recPtorbinding from a different direction the moleculeswith steric Insteadof dockingknown moleculesinto the binding site, it generates to Complementarity the tkee-dimensional structureof the receptorbinding and chemical to site by evaluatingeachnew atom accordingto its chemicalcomPlementarity the nearby a atoms.The programalsoconnects newly grown atom to a previouslygro*n atom receptor The in the growing structureto makering systems. princiPal"liability" to this methodis that to generates many diversestructures,and it is necessary evaluateeach one visually too it which onesare best to try first Often the de.ision comesfrom a synthetic and determine perspective a knowledgeof Potentialoral bioavailability. Having too many choices'of or course.also can be an asset,and a variety of other cdteria could be set up to searchthe for compounds specificbeneficialproprtles database newly generated of

a=Chaplor2 OruqDlscovery Design,and Develophent

In the modified methodfor docking flexible ligandsinto a receptordescrjbedabove,an the of to is of X-ray structure thereceptor not necessary characterize shape thereceplorbinding from the shapes activeligands-This of site. Rather,the receptorbinding site canbe deduced geometry, calledrcceptot is which is usefulfor identificationof ihe pharmacophore technique. is to naplrjrg.t263lIt too is foundedon the Femise that receptortopography complementary from the shapeof the keys rhat of drugs,bot in this casethe structureof the lock is deduced termed havebeendescribedAn approach mappingtechniques that fit it. A vaiety of receptor known to graphicsto combinethevolumesof compounds $es stericmappingl26el molecular volume an This compositevolume generates enzyme-excluded bind to the desiredreceptor. map. which definesthat regionof the binding site availablefor binding by drug analogsand, therefore,not occupiedby the receptoritself. The sameprocedureis, then, caffied out for for volumeis inspected regionsof volume similar moleculesthat areiractive. The composite regions' sites Thesearethe enzymeessential overlapcommonto all of the inaciive analogs. for by requiredby the receptoritself andunavailable occupancy ligands.Any othermolecule that overlapswith theseregions shouldbe inactive Drug design, then. would involve the phamacophorethat filled the enzyme-excluded with the appropriate of synthesis compounds regions.AnotherapFoachthat doesnot requre regionsandthatavoidedtheenzyme-essential of deducec lhe.topography receplor. knowna. ,omolo8)flrdel1ns. ot lhe.lrucrure rherurger \lrucrure: !l receplor receplor from thatol a kno\tnrelated rire rheunknown cryscame whenhigh throughput in A majoriinprovenent theuseofnolecularmodeling t2Tll structurechemistry approaches Because with combinatorial wai tallography coupled baseddrug designusually invotvestargetswhose strucluresare alreadyknown, but which havedifferent ligandsbound.only the part of the structurewherethe ligand bindsneedsto be analyzes interprets and eleclron Software suchas Autosolve(AstexTechnology) resolved. data automaticallywi$out $e needfor an expen crystallogapher, so hundredsof density synthetic in With crystals be analyzed just a few days.t272l solidphase can receptor complex produce largenumbers of npidly, the two processes to makemanyanalogs methodology ligands boundveryrapidly with various crystal structures would receptor binders drug for Theinidalxpectation structure-based design-thatpotent a of leading thediscovery manynewdrugs-hasnotyet become realto be designed rapidly may contributeto its lessthanoptimal effectiveness. problemswith this approach ity. Several and modelitgapproaches its many to 2.12lists vaious advantagestheuseof molecular Table are is the of visualization appealing, mainproblens (1)ihatthe Although ease the limitations. structureof the molecularmodelmay be complelelydifferent from the actualstructurein t}le living organism;(2) evenif the structurewerecorrect.theresolutionof the structureis insufand conformalion ofligandbinding; (3) thebioactive assessment ficientto makean accurate appropriate small moleculesmay not be usedin docking of the ligandsis not known. so the in why therehasnot beena largeincrease ihe number xperiments. Anotherimponantreason modelingtechniques derivesfrom ihe lact thai by of new dlugs being developed molecular interactingwith a phamacoknetics are ignoredby this method.Prior io lhe dmg candidate ic reachthereceptorwithout metabol or chemiit .eceptot it mustbe properly absorbed, must rate, (unlessit is a prodrug;seeChapter8), excredon mustbe at an appropriate ca1 degradation toxic or lead1oundesirable sideeffects must not be and andthe drug candidate metabotites ofmolecular nodeling. with thisnethod,theprocess involved Because theuncertainty of to manyiterations.Slructuretesting,andmolecularmodelingagainneeds undergo synthesis, tool to chemist;itis as drugdesign to be taken yet another available themedicinal has based panofthe process. but to not theanswer drugdiscovery, it canbe animportanl

Seclion 2.2 L@d Modlflc.rbn:

Drug DBign and Development

85

2.12 > Advantag and Limitations lhe Usof Molecular lo ^-"4ABLE In LeadModificalion Modellng
Advantages cu > ProreiDs be visualizdin 3D andeveryarninoacid can be located. The structurecfl be maDipulated that it can b observed so from any dietion in 3D. Particule regions,e.9..the binding site, canbe enbiged for betr viewing. ' The physicochemicalprcperties.e.9.. hy.lrophobic, lolar. p$inve or negative charge,etc.,of eachpait of the receptorce be viewed. Distances bet\teeneroupscan be detemined. Small nolecules can be docked into various regiom to detemine their fir and cd Residues aremostsuitableto mutatefor m&hanism studies be determined. tha! Limittli.n. , > The coordinatesfrom m X-ray crystal ltructuie or NMR solution structur@ > by condiCryslalsa obtained crystallizationof proteinsundernonphysiological tions, sncha at low or high !H. wel below 37'C, andin lhe prsenc additives, of suchasbuffersor detergents. fte protinsrenlly in tle samecoDforution as Are tu the living cell? Crysral structuresrepFsent th ftermodynamically most stable conJomtiotr of the lrotein utrde! ihese tronphysiologicalconditions. Therefore, $e crystal srruclw may depict the protein in a confomariotr very diflerent from that in a living cell. often crystalstructures with ligandsboundareobtained scking the ligandinto by theprfmed crystal.Ifbinding ofthe ligandin solutionresultsin aconformational chmge. it is higuy utrlikely that it will oc.ur in the crystalline slatebe.auseth confomtiotr. crystal peking forceswill favor the preexistinS The prctein structureis considered be rigid, bul small codfomational changes ro of sid chainscd induclargechanges the size,sr'ape,md interactionpatte$ in of binding pocke$. Typically, when a small moleculebinds to a lrotein, thereis ,one novenent of side chains. Resolutionsof crystal structuresare gene.ally in lhe rangeof 2 2.5 Ai someat 1.5 2.0 A; raEly moreresolved(although< 1.0A basb@nre?cted).' Therefore. ftere is nr.n uDcertainty to lhe exacl position of eacbatom.A rule of tbumb as is that $e Dositionalenor of aiom is abou. one{ixth of th Esolution," so a structureat 2.4 A resolutionhasd urcertainty of evdy atom of 0.4 A. Small molecUles tbe ground statede geDe.allyenergyminimized to give the in lowestenergyconfomd prioi to dockingtheminto thestftclure, buta ligmd does not haveto bind in the lowest energyconfomation, and it can be quire diLtrerent from the grqund stateconformtion. Also, solventeffecb generallyde trot taken For higHy nexible moleculeswith severaltoBional angles.ther may be many different geohetries having fte sDe confornational energy,but significutly You lendto beliwe whatyou se in your molcularmodelandthink it is accuateI This leadsto manywrctrg assumpliotrs.

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' For example. Betzel, c.: couinath. S.i Kumm, P.i Kaur, P.: PerbraDdt M.r EschenbDrS, Singh.T. P Biochenistt! 2001,4. 3080. S.; , Bijbm,H.-J.;Klebe,d. dneN. chen. L E L En8L1996, 2588. J5,

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