In Silico Drug Design: Repurposing Techniques and Methodologies

856 Pages·2019·21.456 MB·English

by  Kunal Roy (editor)

IN SILICO DRUG DESIGN
IN SILICO DRUG
DESIGN
Repurposing Techniques
and Methodologies
Edited by
K R
UNAL OY
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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
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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.
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