In Silico Drug Design: Repurposing Techniques and Methodologies PDF
Preview In Silico Drug Design: Repurposing Techniques and Methodologies
IN SILICO DRUG DESIGN IN SILICO DRUG DESIGN Repurposing Techniques and Methodologies Edited by K R UNAL OY AcademicPressisanimprintofElsevier 125LondonWall,LondonEC2Y5AS,UnitedKingdom 525BStreet,Suite1650,SanDiego,CA92101,UnitedStates 50HampshireStreet,5thFloor,Cambridge,MA02139,UnitedStates TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UnitedKingdom #2019ElsevierInc.Allrightsreserved. Nopartofthispublicationmaybereproducedortransmittedinanyformorbyanymeans,electronicormechanical, includingphotocopying,recording,oranyinformationstorageandretrievalsystem,withoutpermissioninwriting fromthepublisher.Detailsonhowtoseekpermission,furtherinformationaboutthePublisher’spermissionspolicies andourarrangementswithorganizationssuchastheCopyrightClearanceCenterandtheCopyrightLicensing Agency,canbefoundatourwebsite:www.elsevier.com/permissions. ThisbookandtheindividualcontributionscontainedinitareprotectedundercopyrightbythePublisher(otherthan asmaybenotedherein). Notices Knowledgeandbestpracticeinthisfieldareconstantlychanging.Asnewresearchandexperiencebroadenour understanding,changesinresearchmethods,professionalpractices,ormedicaltreatmentmaybecomenecessary. Practitionersandresearchersmustalwaysrelyontheirownexperienceandknowledgeinevaluatingandusingany information,methods,compounds,orexperimentsdescribedherein.Inusingsuchinformationormethodsthey shouldbemindfuloftheirownsafetyandthesafetyofothers,includingpartiesforwhomtheyhaveaprofessional responsibility. Tothefullestextentofthelaw,neitherthePublishernortheauthors,contributors,oreditors,assumeanyliabilityfor anyinjuryand/ordamagetopersonsorpropertyasamatterofproductsliability,negligenceorotherwise,orfrom anyuseoroperationofanymethods,products,instructions,orideascontainedinthematerialherein. LibraryofCongressCataloging-in-PublicationData AcatalogrecordforthisbookisavailablefromtheLibraryofCongress BritishLibraryCataloguing-in-PublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary ISBN978-0-12-816125-8 ForinformationonallAcademicPresspublications visitourwebsiteathttps://www.elsevier.com/books-and-journals Publisher:AndreGerhardWolff AcquisitionEditor:ErinHill-Parks EditorialProjectManager:TracyTufaga ProductionProjectManager:SreejithViswanathan CoverDesigner:MilesHitchens TypesetbySPiGlobal,India Dedication For Aatreyi,Arpit, andChaitali. v Contributors BashirAkhlaqAkhoon DiscoveryInformatics AnshuBhardwaj CSIR-InstituteofMicrobial Division,CSIR—IndianInstituteofIntegrative Technology,Chandigarh;Councilof Medicine,Jammu,India ScientificandIndustrialResearch–Academyof MartaE.Alarco´n-Riquelme MedicalGenomics, ScientificandInnovativeResearch,Chennai, India GENYO:CentreforGenomicsandOncological Research,Pfizer/UniversityofGranada/ VijayaLakshmiBodiga Departmentof AndalusianRegionalGovernment,Granada; MolecularBiology,InstituteofGenetics& UnitofInflammatoryChronicDiseases, HospitalforGeneticDiseases,Begumpet, InstituteofEnvironmentalMedicine, OsmaniaUniversity,Hyderabad,India KarolinskaInstitutet,Solna,Sweden SreedharBodiga DepartmentofBiochemistry, LucasN.Alberca LaboratoryofBioactive KakatiyaUniversity,Warangal,India ResearchandDevelopment(LIDeB), MichalBrylinski DepartmentofBiological DepartmentofBiologicalSciences,Facultyof Sciences;CenterforComputation& ExactSciences,UniversityofLaPlata(UNLP); Technology,LouisianaStateUniversity,Baton ArgentineanNationalCouncilofScientificand Rouge,LA,UnitedStates TechnicalResearch(CONICET),BuenosAires, PedroCarmona-Sa´ez BioinformaticsUnit, Argentina GENYO:CentreforGenomicsandOncological JuanI.Alice LaboratoryofBioactiveResearch Research,Pfizer/UniversityofGranada/ andDevelopment(LIDeB),Departmentof AndalusianRegionalGovernment,Granada, BiologicalSciences,FacultyofExactSciences, Spain UniversityofLaPlata(UNLP),BuenosAires, SohiniChakraborti MolecularBiophysicsUnit, Argentina IndianInstituteofScience,Bangalore,India NuttapatAnuwongcharoen CenterofData VaishaliChaudhry Departmentof MiningandBiomedicalInformatics,Facultyof Biotechnology,GraphicEra(deemedtobe MedicalTechnology,MahidolUniversity, University),Dehradun,India Bangkok,Thailand LixiaChen WuyaCollegeofInnovation, KazimYalcinArga Departmentof SchoolofTraditionalChineseMateriaMedica, Bioengineering,MarmaraUniversity,Istanbul, KeyLaboratoryofStructure-BasedDrug Turkey Design&Discovery,MinistryofEducation, CarolinaL.Belllera LaboratoryofBioactive ShenyangPharmaceuticalUniversity, ResearchandDevelopment(LIDeB), Shenyang,China DepartmentofBiologicalSciences,Facultyof MohaneSelvarajCoumar Centrefor ExactSciences,UniversityofLaPlata(UNLP); Bioinformatics,SchoolofLifeSciences, ArgentineanNationalCouncilofScientificand PondicherryUniversity,Puducherry,India TechnicalResearch(CONICET),BuenosAires, Argentina DanielToro-Domı´nguez BioinformaticsUnit; MedicalGenomics,GENYO:Centrefor VladimirP.Berishvili Departmentof GenomicsandOncologicalResearch,Pfizer/ Chemistry,LomonosovMoscowState UniversityofGranada/AndalusianRegional University,Moscow,Russia Government,Granada,Spain xiii xiv CONTRIBUTORS NikolasDietis MedicalSchool,Universityof BaniJolly CSIR-InstituteofMicrobial Cyprus,Nicosia,Cyprus Technology,Chandigarh,India NoelieDouanne PathologyandMicrobiology PrashantS.Kharkar ShobhabenPratapbhai Department,UniversityofMontreal,Saint- PatelSchoolofPharmacyandTechnology Hyacinthe,QC,Canada Management,SVKM’sNMIMS,Mumbai, DmitryDruzhilovskiy InstituteofBiomedical India Chemistry,Moscow,Russia Se-MinKim DepartmentofMedicine,Mount K.Eur´ıdiceJua´rez-Mercado Departmentof SinaiSchoolofMedicine,NewYork,NY, UnitedStates Pharmacy,SchoolofChemistry,National AutonomousUniversityofMexico,Mexico ShivaniKumar UniversitySchoolof City,Mexico Biotechnology,GGSIndraprasthaUniversity, ChristopherFerna´ndez-Prada Pathologyand Dwarka,NewDelhi,India MicrobiologyDepartment,Universityof SureshKumar UniversitySchoolof Montreal,Saint-Hyacinthe,QC,Canada Biotechnology,GGSIndraprasthaUniversity, PankajGautam DepartmentofLifeSciences, Dwarka,NewDelhi,India GraphicEra(deemedtobeUniversity), PawanKumar SchoolofComputationaland Dehradun,India IntegrativeSciences,JawaharlalNehru IndiraGhosh SchoolofComputationaland University,NewDelhi,India IntegrativeSciences,JawaharlalNehru LukaszKurgan DepartmentofComputer University,NewDelhi,India Science,VirginiaCommonwealthUniversity, C.GopiMohan Bioinformaticsand Richmond,VA,UnitedStates ComputationalBiologyLab,Centerfor Yu-ChenLo DepartmentofBioengineering, NanosciencesandMolecularMedicine,Amrita StanfordUniversity,Stanford,CA,United InstituteofMedicalSciencesandResearch States Centre,AmritaVishwaVidyapeetham,Kochi, EdgarLo´pez-Lo´pez MedicinalChemistry India Laboratory,UniversityofVeracruz,Veracruz, ShozebHaider SchoolofPharmacy,University Mexico College,London,UnitedKingdom JanvhiS.Machhar ShobhabenPratapbhaiPatel LiHua HubeiKeyLaboratoryofNatural SchoolofPharmacyandTechnology MedicinalChemistryandResourceEvaluation, Management,SVKM’sNMIMS,Mumbai, SchoolofPharmacy,TongjiMedicalCollege, India HuazhongUniversityofScienceand K.Manzoor BioinformaticsandComputational Technology,Wuhan;WuyaCollegeof BiologyLab,CenterforNanosciencesand Innovation,SchoolofTraditionalChinese MolecularMedicine,AmritaInstituteof MateriaMedica,KeyLaboratoryofStructure- MedicalSciencesandResearchCentre,Amrita BasedDrugDesign&Discovery,Ministryof VishwaVidyapeetham,Kochi,India Education,ShenyangPharmaceutical Jos(cid:1)eL.Medina-Franco Departmentof University,Shenyang,China Pharmacy,SchoolofChemistry,National JameelIqbal DepartmentofMedicine,Mount AutonomousUniversityofMexico,Mexico SinaiSchoolofMedicine;Departmentof City,Mexico Pathology,JamesJ.PetersVAMedicalCenter, AnuR.Melge Bioinformaticsand NewYork,NY,UnitedStates ComputationalBiologyLab,Centerfor NivyaJames DepartmentofBiotechnology, NanosciencesandMolecularMedicine,Amrita SchoolofBioSciencesandTechnology, InstituteofMedicalSciencesandResearch VelloreInstituteofTechnology,Vellore, Centre,AmritaVishwaVidyapeetham,Kochi, India India xv CONTRIBUTORS GeorgeMinadakis BioinformaticsERAChair, DmitryI.Osolodkin DepartmentofChemistry, TheCyprusInstituteofNeurologyand LomonosovMoscowStateUniversity;Institute Genetics,Nicosia,Cyprus ofPoliomyelitisandViralEncephalitides, AidaMinguez-Menendez Pathologyand FSBSIChumakovFSCR&DIBPRAS,Moscow, Russia MicrobiologyDepartment,Universityof Montreal,Saint-Hyacinthe,QC, AnastasisOulas BioinformaticsERAChair,The Canada CyprusInstituteofNeurologyandGenetics, MakedonkaMitreva McDonnellGenome Nicosia,Cyprus Institute,WashingtonUniversityinSt.Louis; ManojKumarPal DepartmentofLifeSciences, DepartmentofMedicine,DivisionofInfectious GraphicEra(deemedtobeUniversity), Diseases,WashingtonUniversitySchoolof Dehradun,India Medicine,St.Louis,MO,UnitedStates VladimirA.Palyulin Departmentof RubensL.Monte-Neto ReneRachouInstitute, Chemistry,LomonosovMoscowState BeloHorizonte,Brazil University,Moscow,Russia GurusamyMuneeswaran CentreforMolecular AshmaPandya DelhiPublicSchool,NewDelhi, Modeling,CSIR-IndianInstituteofChemical India Technology,Hyderabad,India AnuragPassi CSIR-InstituteofMicrobial SelvaramanNagamani CentreforMolecular Technology,Chandigarh;Councilof Modeling,CSIR-IndianInstituteofChemical ScientificandIndustrialResearch–Academyof Technology,Hyderabad,India ScientificandInnovativeResearch,Chennai, ShantikumarV.Nair Bioinformaticsand India ComputationalBiologyLab,Centerfor JoanPena PathologyandMicrobiology NanosciencesandMolecularMedicine,Amrita Department,UniversityofMontreal,Saint- InstituteofMedicalSciencesandResearch Hyacinthe,QC,Canada Centre,AmritaVishwaVidyapeetham,Kochi, ChuleepornPhanus-umporn CenterofData India MiningandBiomedicalInformatics,Facultyof ChaninNantasenamat CenterofDataMining MedicalTechnology,MahidolUniversity, andBiomedicalInformatics,FacultyofMedical Bangkok,Thailand Technology,MahidolUniversity,Bangkok, DouglasE.V.Pires ReneRachouInstitute,Belo Thailand Horizonte,Brazil G.NarahariSastry CentreforMolecular VladimirPoroikov InstituteofBiomedical Modeling,CSIR-IndianInstituteofChemical Chemistry,Moscow,Russia Technology,Hyderabad,India FernandoD.Prieto-Martı´nez Departmentof AmitNargotra DiscoveryInformaticsDivision, Pharmacy,SchoolofChemistry,National CSIR—IndianInstituteofIntegrativeMedicine, AutonomousUniversityofMexico,Mexico Jammu,India City,Mexico AnastasiaA.Nikitina Departmentof EugeneV.Radchenko Departmentof Chemistry,LomonosovMoscowState Chemistry,LomonosovMoscowState University;InstituteofPoliomyelitisandViral University,Moscow,Russia Encephalitides,FSBSIChumakovFSCR&DIBP GayatriRamakrishnan MolecularBiophysics RAS,Moscow,Russia Unit;IndianInstituteofScienceMathematics AlexeyA.Orlov DepartmentofChemistry, Initiative,IndianInstituteofScience, LomonosovMoscowStateUniversity;Institute Bangalore,IndiaDivisionofGenetics, ofPoliomyelitisandViralEncephalitides, DepartmentofMedicine,Brighamand FSBSIChumakovFSCR&DIBPRAS,Moscow, Women’sHospitalandHarvardMedical Russia School,Boston,MA,UnitedStates xvi CONTRIBUTORS K.Ramanathan DepartmentofBiotechnology, KleitosSokratous BioinformaticsERAChair, SchoolofBioSciencesandTechnology,Vellore TheCyprusInstituteofNeurologyand InstituteofTechnology,Vellore,India Genetics,Nicosia,Cyprus BruceA.Rosa McDonnellGenomeInstitute, GeorgeM.Spyrou BioinformaticsERAChair, WashingtonUniversityinSt.Louis,St.Louis, TheCyprusInstituteofNeurologyand MO,UnitedStates Genetics,Nicosia,Cyprus RosaleenSahoo CentreforMolecular NarayanaswamySrinivasan Molecular Modeling,CSIR-IndianInstituteofChemical BiophysicsUnit,IndianInstituteofScience, Technology,Hyderabad,India Bangalore,India NiteshkumarU.Sahu ShobhabenPratapbhai NagayaSriwanichpoom CenterofDataMining PatelSchoolofPharmacyandTechnology andBiomedicalInformatics,FacultyofMedical Management,SVKM’sNMIMS,Mumbai, Technology,MahidolUniversity,Bangkok; India MahidolUniversityInternationalCollege, PemraOzbekSarica Departmentof NakhonPathom,Thailand Bioengineering,FacultyofEngineering, LiSun DepartmentofMedicine,MountSinai MarmaraUniversity,I˙stanbul,Turkey SchoolofMedicine,NewYork,NY,United SailuSarvagalla CentreforBioinformatics, States SchoolofLifeSciences,PondicherryUniversity, SafiullaBashaSyed CentreforBioinformatics, Puducherry,India SchoolofLifeSciences,PondicherryUniversity, KyriakiSavva BioinformaticsERAChair,The Puducherry,India CyprusInstituteofNeurologyandGenetics, AlanTalevi LaboratoryofBioactiveResearch Nicosia,Cyprus andDevelopment(LIDeB),Departmentof Marı´aL.Sbaraglini LaboratoryofBioactive BiologicalSciences,FacultyofExactSciences, UniversityofLaPlata(UNLP);Argentinean ResearchandDevelopment(LIDeB), NationalCouncilofScientificand DepartmentofBiologicalSciences,Facultyof TechnicalResearch(CONICET),BuenosAires, ExactSciences,UniversityofLaPlata(UNLP), Argentina BuenosAires,Argentina NaliniSchaduangrat CenterofDataMining HarshitaTiwari DiscoveryInformatics Division,CSIR—IndianInstituteofIntegrative andBiomedicalInformatics,FacultyofMedical Medicine,Jammu,India Technology,MahidolUniversity,Bangkok, Thailand JorgeZ.Torres DepartmentofChemistryand OnurSerc¸inog˘lu Departmentof Biochemistry,UniversityofCalifornia-Los Angeles,LosAngeles,CA,UnitedStates Bioengineering,FacultyofEngineering, MarmaraUniversity,I˙stanbul,Turkey LuizaG.Tunes ReneRachouInstitute,Belo ChetanP.Shah ShobhabenPratapbhaiPatel Horizonte,Brazil SchoolofPharmacyandTechnology BesteTuranli DepartmentofBioengineering, Management,SVKM’sNMIMS,Mumbai, IstanbulMedeniyetUniversity;Departmentof India Bioengineering,MarmaraUniversity,Istanbul, V.Shanthi DepartmentofBiotechnology, Turkey SchoolofBioSciencesandTechnology,Vellore RahulTyagi McDonnellGenomeInstitute, InstituteofTechnology,Vellore,India WashingtonUniversityinSt.Louis,St.Louis, TinaSharma CSIR-InstituteofMicrobial MO,UnitedStates Technology,Chandigarh;CouncilofScientific ChenWang DepartmentofComputerScience, andIndustrialResearch–AcademyofScientific VirginiaCommonwealthUniversity, andInnovativeResearch,Chennai,India Richmond,VA,UnitedStates xvii CONTRIBUTORS JarlE.S.Wikberg Departmentof SamirZaidi DepartmentofMedicine, PharmaceuticalBiosciences,BMC,Uppsala MassachusettsGeneralHospital,Harvard University,Uppsala,Sweden MedicalSchool,Boston,MA,UnitedStates XuhuaXia DepartmentofBiology,Universityof MoneZaidi DepartmentofMedicine,Mount Ottawa;OttawaInstituteofSystemsBiology, SinaiSchoolofMedicine,NewYork,NY, Ottawa,ON,Canada UnitedStates TonyYuen DepartmentofMedicine,Mount AlbertaZallone DepartmentofMedicine, SinaiSchoolofMedicine,NewYork,NY, MountSinaiSchoolofMedicine,NewYork, UnitedStates NY,UnitedStates MargaritaZachariou BioinformaticsERA MengzhuZheng HubeiKeyLaboratoryof Chair,TheCyprusInstituteofNeurologyand NaturalMedicinalChemistryandResource Genetics,Nicosia,Cyprus Evaluation,SchoolofPharmacy,Tongji NeehaZaidi KimmelComprehensiveCancer MedicalCollege,HuazhongUniversityof ScienceandTechnology,Wuhan, Center,JohnsHopkinsUniversity,Baltimore, China MD,UnitedStates About the Editor Dr.KunalRoyisaprofessorintheDepartmentofPharma- ceuticalTechnology,JadavpurUniversity,Kolkata,India.He has been a recipient of the Commonwealth Academic Staff Fellowship (University of Manchester, 2007) and the Marie CurieInternationalIncomingFellowship(UniversityofMan- chester,2013).HisresearchinterestslieinthefieldsofQSAR and molecular modeling with applications in drug design and ecotoxicological modeling. Dr. Roy has published more than 280 research articles in refereed journals (current SCOPUS h index 38). He has also coauthored two QSAR- relatedbooks,editedthreeQSARbooks,andpublishedmore than 10 book chapters. He is Co-Editor-in-Chief of Molecular Diversity (Springer Nature) and Editor-in-Chief of Interna- tional Journal of Quantitative Structure-Property Relationships (IJQSPR) (IGI Global). He also serves as a member on editorial boards of several interna- tional journals. xix
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