Protein-Ligand Interactions and Drug Design (Methods in Molecular Biology, 2266) PDF
Preview Protein-Ligand Interactions and Drug Design (Methods in Molecular Biology, 2266)
Methods in Molecular Biology 2266 Flavio Ballante Editor Protein-Ligand Interactions and Drug Design M M B ETHODS IN OLECULAR IO LO GY SeriesEditor JohnM.Walker School of Lifeand MedicalSciences University ofHertfordshire Hatfield, Hertfordshire, UK Forfurther volumes: http://www.springer.com/series/7651 For over 35 years, biological scientists have come to rely on the research protocols and methodologiesinthecriticallyacclaimedMethodsinMolecularBiologyseries.Theserieswas thefirsttointroducethestep-by-stepprotocolsapproachthathasbecomethestandardinall biomedicalprotocolpublishing.Eachprotocolisprovidedinreadily-reproduciblestep-by- step fashion, opening with an introductory overview, a list of the materials and reagents neededtocompletetheexperiment,andfollowedbyadetailedprocedurethatissupported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitutethekeyingredientineachandeveryvolumeoftheMethodsinMolecularBiology series. Tested and trusted, comprehensive and reliable, all protocols from the series are indexedinPubMed. Protein-Ligand Interactions and Drug Design Edited by Flavio Ballante Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden Editor FlavioBallante DepartmentofCellandMolecularBiology UppsalaUniversity Uppsala,Sweden ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-0716-1208-8 ISBN978-1-0716-1209-5 (eBook) https://doi.org/10.1007/978-1-0716-1209-5 ©SpringerScience+BusinessMedia,LLC,partofSpringerNature2021 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation, computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations andthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty, expressedorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeen made.Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. CoverIllustrationCaption:ImagecreatedbyFlavioBallante ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer Nature. Theregisteredcompanyaddressis:1NewYorkPlaza,NewYork,NY10004,U.S.A. Preface Drug discovery has profoundly changed in the past few decades. The ceaseless increase in structuraldataandthedevelopmentofcomputer technologyallowustosimulatecomplex biological systems and study protein–ligand interactions, at the atomic level, with a speed unthinkableuntilafewyearsago.Also,sincetheongoingexplosioninthesizeofaccessible chemicalspaceandcommerciallibrariesofcompounds,itisnowfeasibletosearchfor new ligandsindatabasesofseveralhundredmillionmolecules,withinafewweeks.Itissafetosay thatcomputer-aideddrugdesignisanessentialtooltoacceleratethedrugdiscoveryprocess and reduce failures and costs by avoiding the mere trial-and-error search practice. Protein- Ligand Interactions and Drug Design collects modern and established computer-based methods aimed at addressing the drug discovery challenge from disparate perspectives by exploitinginformationonligand–proteinrecognition.Duetotheinfluenceoftheexplored chemical space on finding new protein–ligand interaction patterns, techniques aimed to explore or design novel ligand chemotypes are also enclosed in this volume. Chapters are groupedaccordingtotheirunderlyingaimintothreemajorsectionswhichareorganizedin a logical order. In Section I: Chemical Space, methods that allow for the exploration of specific areas of chemical space and the designing of virtual libraries are presented. SectionII:HitIdentificationandHit-to-LeadOptimizationincludesaplethoraofdifferent approaches,basedonprotein–ligandinteractions,forliganddiscoveryanddesign.Finally,in Section III: Drug Repurposing, Polypharmacology, and Target Identification are reported methods aimed at drug repositioning or exploiting an ensemble of protein struc- turesfortheidentificationofligandswithtailoredpolypharmacologicalprofilesornovelpro- teintargets. The main goal of this volume is to provide detailed practical procedures of solid computer-aideddrugdesignmethodologiesemployedtorationalizeandoptimizeprotein–- ligandinteractions.Thisbookisaimednotonlyatscientistswithexperienceindrugdesign butalsoatthosewhoarenewtothefield. Uppsala,Sweden FlavioBallante v Acknowledgments Iwouldliketothankalltheauthorsthatcontributedtotherealizationofthisvolume,aswell as the Series Editor Prof. John Walker, Mr. David C. Casey, Ms. Anna Rakovsky, and the teamatHumanaPressfortheirpreciousguidanceduringtherealizationofthisbook.Many thanksalsotoallthegreatscientistsandcollaboratorsIhavemetsofarwhogreatlyinspired andenrichedmyresearchjourney,inparticulartoProf.JensCarlsson(UppsalaUniversity), Prof. Gilbert Kirsch (University of Lorraine), Prof. Garland R. Marshall (Washington UniversityinSt.Louis),andDr.ChrisM.Ho(DrugDesignMethodologies,LLC). This volume is dedicated to Prof. Garland R. Marshall on the occasion of his 81stbirthday. vii Contents Preface ..................................................................... v Acknowledgments............................................................. vii Contributors................................................................. xi AbouttheEditor ............................................................. xv PART I CHEMICAL SPACE 1 InvestigationoftheClick-ChemicalSpaceforDrugDesignUsing ZINClick .............................................................. 3 AlbertoMassarotti 2 MolecularScaffoldHoppingviaHolisticMolecularRepresentation........... 11 FrancescaGrisoniandGisbertSchneider PART II HIT IDENTIFICATION AND HIT-TO-LEAD OPTIMIZATION 3 BiasedDockingforProtein–LigandPosePrediction......................... 39 JuanPabloArcon,Adria´nG.Turjanski,MarceloA.Martı´, andStefanoForli 4 BindingModePredictionandVirtualScreeningApplications byCovalentDocking.................................................... 73 AndreaScarpino,Gy¨orgyG.Ferenczy,andGy¨orgyM.Keseru˝ 5 Ligand–ReceptorInteractionsandDrugDesign............................ 89 AggelikiSyriopoulou,IoannisMarkopoulos,AndreasG.Tzakos, andThomasMavromoustakos 6 SimulationofLigandTransportinReceptorsUsingCaverDock .............. 105 JanaHozzova´,OndrˇejVa´vra,DavidBedna´rˇ,andJirˇı´ Filipovicˇ 7 NegativeImage-BasedScreening:RigidDockingUsingCavity Information............................................................ 125 PekkaA.Postila,SamiT.Kurkinen,andOlliT.Pentika€inen 8 NegativeImage-BasedRescoring:UsingCavityInformation toImproveDockingScreening ........................................... 141 OlliT.Pentika€inenandPekkaA.Postila 9 Fragment-BasedDrugDesignofSelectiveHDAC6Inhibitors................ 155 DusanRuzic,NemanjaDjokovic,andKatarinaNikolic 10 AProtocoltoUseComparativeBindingEnergyAnalysis toEstimateDrug-TargetResidenceTime.................................. 171 GauravK.Ganotra,ArianeNunes-Alves, andRebeccaC.Wade 11 DynamicDockingUsingMulticanonicalMolecularDynamics: SimulatingComplexFormationattheAtomisticLevel ...................... 187 Gert-JanBekkerandNarutoshiKamiya ix x Contents 12 FreeEnergyCalculationsforProtein–LigandBindingPrediction............. 203 WillemJespers,JohanÅqvist,andHugoGutie´rrez-de-Tera´n 13 ExploitingWaterDynamicsforPharmacophoreScreening................... 227 DavidSchaller,SzymonPach,MarcelBermudez,andGerhardWolber 14 MarkovStateModelstoElucidateLigandBindingMechanism............... 239 YunhuiGeandVincentA.Voelz PART III DRUG REPURPOSING, POLYPHARMACOLOGY, AND TARGET IDENTIFICATION 15 FromHomologyModelingtotheHitIdentificationandDrug Repurposing:AStructure-BasedApproachintheDiscovery ofNovelPotentialAnti-ObesityCompounds............................... 263 Giosue` Costa,AnnaArtese,FrancescoOrtuso,andStefanoAlcaro 16 MultipleTargetDrugDesignUsingLigBuilder3 .......................... 279 XiaoyuQing,ShiweiWang,YaxiaYuan,JianfengPei, andLuhuaLai 17 Bionoi:AVoronoiDiagram-BasedRepresentationofLigand-Binding SitesinProteinsforMachineLearningApplications......................... 299 JosephFeinstein,WentaoShi,J.Ramanujam,andMichalBrylinski 18 MDock:ASuiteforMolecularInverseDockingandTargetPrediction........ 313 ZhiweiMaandXiaoqinZou Index ...................................................................... 323 Contributors STEFANO ALCARO • DipartimentodiScienzedellaSalute,Universit`adegliStudi“Magna Græcia”diCatanzaro,Campus“S.Venuta”,Catanzaro,Italy;Net4ScienceAcademic Spin-Off,Universit`adegliStudi“MagnaGræcia”diCatanzaro,Campus“S.Venuta”, Catanzaro,Italy JOHANÅQVIST • DepartmentofCellandMolecularBiology,BiomedicalCenter, UppsalaUniversity,Uppsala,Sweden JUANPABLO ARCON • DepartamentodeQuı´micaBiol(cid:2)ogicaeIQUIBICEN-UBA/ CONICET,FacultaddeCienciasExactasyNaturales,UniversidaddeBuenosAires, CiudadUniversitaria,BuenosAires,Argentina;InstituteforResearchinBiomedicine (IRBBarcelona),TheBarcelonaInstituteofScienceandTechnology,Barcelona,Spain ANNAARTESE • DipartimentodiScienzedellaSalute,Universit`adegliStudi“Magna Græcia”diCatanzaro,Campus“S.Venuta”,Catanzaro,Italy;Net4ScienceAcademic Spin-Off,Universit`adegliStudi“MagnaGræcia”diCatanzaro,Campus“S.Venuta”, Catanzaro,Italy DAVIDBEDNA´Rˇ • DepartmentofExperimentalBiologyandRECETOX,FacultyofScience, MasarykUniversity,Brno,CzechRepublic GERT-JANBEKKER • InstituteforProteinResearch,OsakaUniversity,Suita,Osaka,Japan MARCELBERMUDEZ • PharmaceuticalandMedicinalChemistry,FreieUniversita€tBerlin, Berlin,Germany MICHAL BRYLINSKI • Center forComputationandTechnology,LouisianaStateUniversity, BatonRouge,LA,USA;DepartmentofBiologicalSciences,LouisianaStateUniversity, BatonRouge,LA,USA GIOSUE` COSTA • DipartimentodiScienzedellaSalute,Universit`adegliStudi“Magna Græcia”diCatanzaro,Campus“S.Venuta”,Catanzaro,Italy;Net4ScienceAcademic Spin-Off,Universit`adegliStudi“MagnaGræcia”diCatanzaro,Campus“S.Venuta”, Catanzaro,Italy NEMANJA DJOKOVIC • DepartmentofPharmaceuticalChemistry,FacultyofPharmacy, UniversityofBelgrade,Belgrade,Serbia JOSEPH FEINSTEIN • Center forComputationandTechnology,LouisianaStateUniversity, BatonRouge,LA,USA GYO¨RGYG.FERENCZY • MedicinalChemistryResearchGroup,ResearchCentreforNatural Sciences,Budapest,Hungary JIRˇI´ FILIPOVICˇ • InstituteofComputerScience,MasarykUniversity,Brno,CzechRepublic STEFANOFORLI • DepartmentofIntegrativeStructuralandComputationalBiology,Scripps Research,LaJolla,CA,USA GAURAVK.GANOTRA • MolecularandCellularModelingGroup,HeidelbergInstitutefor TheoreticalStudies,Heidelberg,Germany YUNHUIGE • DepartmentofChemistry,TempleUniversity,Philadelphia,PA,USA FRANCESCAGRISONI • DepartmentofChemistryandAppliedBiosciences,RETHINK,ETH Zurich,Zurich,Switzerland HUGOGUTIE´RREZ-DE-TERA´N • DepartmentofCellandMolecularBiology,Biomedical Center,UppsalaUniversity,Uppsala,Sweden xi
The list of books you might like
