Protein Allostery in Drug Discovery PDF
Preview Protein Allostery in Drug Discovery
Advances in Experimental Medicine and Biology 1163 Jian Zhang Ruth Nussinov Editors Protein Allostery in Drug Discovery Advances in Experimental Medicine and Biology Volume 1163 EditorialBoard IRUNR.COHEN,TheWeizmannInstituteofScience,Rehovot,Israel ABELLAJTHA,N.S.KlineInstituteforPsychiatricResearch,Orangeburg,NY,USA JOHND.LAMBRIS,UniversityofPennsylvania,Philadelphia,PA,USA RODOLFOPAOLETTI,UniversityofMilan,Milan,Italy NIMAREZAEI,Children’sMedicalCenterHospital,TehranUniversityofMedical Sciences,Tehran,Iran Advances in Experimental Medicine and Biology presents multidisciplinary and dynamic findings in the broad fields of experimental medicine and biology. The widevarietyintopicsitpresentsoffersreadersmultipleperspectivesonavarietyof disciplines including neuroscience, microbiology, immunology, biochemistry, biomedicalengineeringandcancerresearch. Advances in Experimental Medicine and Biology has been publishing excep- tional works in the field for over 30 years and is indexed in Medline, Scopus, EMBASE, BIOSIS, Biological Abstracts, CSA, Biological Sciences and Living Resources (ASFA-1), and Biological Sciences. The series also provides scientists withuptodateinformationonemergingtopicsandtechniques.2018ImpactFactor: 2.126 Contentpublishedinthisbookseriesispeerreviewed. Moreinformationaboutthisseriesathttp://www.springer.com/series/5584 (cid:129) Jian Zhang Ruth Nussinov Editors Protein Allostery in Drug Discovery Editors JianZhang RuthNussinov DepartmentofPathophysiology,Key CancerandInflammationProgram,Leidos LaboratoryofCellDifferentiation BiomedicalResearch,Inc.,FrederickNational andApoptosisofChinese LaboratoryforCancerResearch MinistryofEducation NationalCancerInstitute ShanghaiJiaoTongUniversity, Frederick,MD,USA SchoolofMedicine SacklerInstituteofMolecularMedicine, Shanghai,China DepartmentofHumanGeneticsandMolecular Medicine,SacklerSchoolofMedicine TelAvivUniversity TelAviv,Israel ISSN0065-2598 ISSN2214-8019 (electronic) AdvancesinExperimentalMedicineandBiology ISBN978-981-13-8718-0 ISBN978-981-13-8719-7 (eBook) https://doi.org/10.1007/978-981-13-8719-7 ©SpringerNatureSingaporePteLtd.2019 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe materialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. The publisher, the authors, and the editorsare safeto assume that the adviceand informationin this bookarebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsor theeditorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinorforany errorsoromissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictional claimsinpublishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSingaporePteLtd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore Preface Thebookseriesfocusesonproteinallosteryindrugdiscovery.Allostericregulation, “the second secret of life,” fine-tunes virtually most biological processes and con- trolsphysiologicalactivities.Allosterycanbothcausehumandiseasesandcontrib- ute to the development of new therapeutics. Allosteric drugs exhibit unparalleled advantagescomparedtoconventionalorthostericdrugs,renderingthedevelopment ofallostericmodulatorsasanappealingstrategytoimproveselectivityandpharma- codynamicpropertiesindrugleads.Theseriesdelineatestheimmensesignificance of protein allostery—as demonstrated by recent advances in the repertoires of the concept, its mechanistic mechanisms, and networks; characteristics of allosteric proteins, modulators, and sites; development of computational and experimental methods to predict allosteric sites; small-molecule allosteric modulators of protein kinasesandG-protein-coupled receptors; engineering allostery;andthe underlying role of allostery in precise medicine. A comprehensive understanding of protein allosteryisexpectedtoguidetherationaldesignofallostericdrugsforthetreatment ofhumandiseases. SchoolofMedicine JianZhang ShanghaiJiaoTongUniversity Shanghai,China v Contents 1 AllosteryinDrugDevelopment. . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 XiChengandHualiangJiang 2 DynamicProteinAllostericRegulationandDisease. . . . . . . . . . . . 25 RuthNussinov,Chung-JungTsai,andHyunbumJang 3 ProteinAllosteryinRationalDrugDesign. . . . . . . . . . . . . . . . . . . 45 TakayoshiKinoshita 4 ProgressinAllostericDatabase. . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 KunSong,JianZhang,andShaoyongLu 5 CorrelationBetweenAllostericandOrthostericSites. . . . . . . . . . . 89 WeilinZhang,JuanXie,andLuhuaLai 6 CharacteristicsofAllostericProteins,Sites,andModulators. . . . . . 107 XinhengHe,DuanNi,ShaoyongLu,andJianZhang 7 AdvancesintheComputationalIdentificationofAllosteric SitesandPathwaysinProteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . 141 XavierDaura 8 AdvancesinNMRMethodstoIdentifyAllostericSites andAllostericLigands. . .. . . .. . . . .. . . .. . . .. . . . .. . . .. . . . .. 171 HazemAbdelkarim,BenHitchinson,AvikBanerjee, andVadimGaponenko 9 InterrogatingRegulatoryMechanismsinSignaling ProteinsbyAllostericInhibitorsandActivators:ADynamic ViewThroughtheLensofResidueInteractionNetworks. . . . . . . . 187 LindyAstl,AmandaTse,andGennadyM.Verkhivker 10 GPCRAllostericModulatorDiscovery. . . . . . . . . . . . . . . . . . . . . . 225 YiranWu,JiahuiTong,KangDing,QingtongZhou,andSuwenZhao vii viii Contents 11 AllostericSmall-MoleculeSerine/ThreonineKinaseInhibitors. . . . 253 ResmiC.Panicker,SouvikChattopadhaya,AnthonyG.Coyne, andRajavelSrinivasan 12 AllostericRegulationofProteinKinasesDownstream ofPI3-KinaseSignalling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279 AlejandroE.Leroux,LissyZ.F.Gross,MarianaSacerdoti, andRicardoM.Biondi 13 AllostericModulatorsofProtein–ProteinInteractions(PPIs). . . . . 313 DuanNi,NaLiu,andChunquanSheng 14 AllostericModulationofIntrinsicallyDisorderedProteins. . . . . . . 335 AshfaqUrRehman,MueedUrRahman,TaahaArshad, andHai-FengChen 15 EngineeringAllosteryintoProteins. . . . . . . . . . . . . . . . . . . . . . . . . 359 ScottD.Gorman,RebeccaN.D’Amico,DennisS.Winston, andDavidD.Boehr Contributors HazemAbdelkarim DepartmentofBiochemistryandMolecularGenetics,College ofMedicine,UniversityofIllinoisatChicago,Chicago,IL,USA Taaha Arshad State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life SciencesandBiotechnology,SchoolofLifeSciencesandBiotechnology,Shanghai JiaoTongUniversity,Shanghai,China Lindy Astl Graduate Program in Computational and Data Sciences, Schmid Col- legeofScienceandTechnology,ChapmanUniversity,Orange,CA,USA Avik Banerjee Department of Chemistry, University of Illinois at Chicago, Chi- cago,IL,USA David D. Boehr Department of Chemistry, The Pennsylvania State University, UniversityPark,PA,USA Souvik Chattopadhaya School of Applied Sciences, Republic Polytechnic, Sin- gapore,Singapore Xi Cheng State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai,China Hai-Feng Chen State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life SciencesandBiotechnology,SchoolofLifeSciencesandBiotechnology,Shanghai JiaoTongUniversity,Shanghai,China ShanghaiCenterforBioinformationTechnology,Shanghai,China Anthony G. Coyne University Chemical Laboratory, University of Cambridge, Cambridge,UK Rebecca N. D’Amico Department of Chemistry, The Pennsylvania State Univer- sity,UniversityPark,PA,USA ix x Contributors Xavier Daura Catalan Institution for Research and Advanced Studies (ICREA) and Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barce- lona,CerdanyoladelVallès,Spain KangDing iHumanInstitute,ShanghaiTechUniversity,Shanghai,China VadimGaponenko DepartmentofBiochemistryandMolecularGenetics,College ofMedicine,UniversityofIllinoisatChicago,Chicago,IL,USA Scott D. Gorman Department of Chemistry, The Pennsylvania State University, UniversityPark,PA,USA XinhengHe DepartmentofPathophysiology,KeyLaboratoryofCellDifferentia- tionandApoptosisofChineseMinistryofEducation,Shanghai JiaoTongUniver- sity,SchoolofMedicine,Shanghai,China Ben Hitchinson Department of Biochemistry and Molecular Genetics, College of Medicine,UniversityofIllinoisatChicago,Chicago,IL,USA HyunbumJang CancerandInflammationProgram,LeidosBiomedicalResearch, Inc.,FrederickNationalLaboratoryforCancerResearch,NationalCancerInstitute, Frederick,MD,USA Hualiang Jiang State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sci- ences,Shanghai,China Takayoshi Kinoshita Graduate School of Science, Osaka Prefecture University, Sakai,Osaka,Japan Luhua Lai BNLMS, Peking-Tsinghua Center for Life Sciences at the College of ChemistryandMolecularEngineering,PekingUniversity,Beijing,China CenterforQuantitativeBiology,AAIS,PekingUniversity,Beijing,China NaLiu SchoolofPharmacy,SecondMilitaryMedicalUniversity,Shanghai,China ShaoyongLu DepartmentofPathophysiology,KeyLaboratoryofCellDifferenti- ationandApoptosisofChineseMinistryofEducation,ShanghaiJiaoTongUniver- sity,SchoolofMedicine,Shanghai,China Duan Ni Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, SchoolofMedicine,Shanghai,China Ruth Nussinov Cancer and Inflammation Program, Leidos Biomedical Research, Inc.,FrederickNationalLaboratoryforCancerResearch,NationalCancerInstitute, Frederick,MD,USA Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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