{"id":"https://openalex.org/W4285084873","doi":"https://doi.org/10.1080/08927022.2022.2097672","title":"Implication of Ab Initio, QM/MM, and molecular dynamics calculations on the prediction of the therapeutic potential of some selected HDAC inhibitors","display_name":"Implication of Ab Initio, QM/MM, and molecular dynamics calculations on the prediction of the therapeutic potential of some selected HDAC inhibitors","publication_year":2022,"publication_date":"2022-07-13","ids":{"openalex":"https://openalex.org/W4285084873","doi":"https://doi.org/10.1080/08927022.2022.2097672"},"language":"en","primary_location":{"id":"doi:10.1080/08927022.2022.2097672","doi":"https://doi.org/10.1080/08927022.2022.2097672","is_oa":false,"landing_page_url":"https://doi.org/10.1080/08927022.2022.2097672","pdf_url":null,"source":{"id":"https://openalex.org/S45504773","display_name":"Molecular Simulation","issn_l":"0892-7022","issn":["0892-7022","1026-7638","1029-0435"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","jufo-1","norway-1","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547","https://openalex.org/P4310320449"],"host_organization_lineage_names":["Taylor & Francis","Informa"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Molecular Simulation","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083727644","display_name":"Ramachandren Dushanan","orcid":"https://orcid.org/0000-0002-5975-5403","observed_orcids":["https://orcid.org/0000-0002-5975-5403"]},"institutions":[{"id":"https://openalex.org/I181714291","display_name":"Open University of Sri Lanka","ror":"https://ror.org/011rrqf91","country_code":"LK","type":"education","lineage":["https://openalex.org/I181714291"]}],"countries":["LK"],"is_corresponding":false,"raw_author_name":"Ramachandren Dushanan","raw_affiliation_strings":["Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka"],"raw_orcid":"https://orcid.org/0000-0002-5975-5403","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka","institution_ids":["https://openalex.org/I181714291"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039921506","display_name":"Samantha Weerasinghe","orcid":"https://orcid.org/0000-0003-4807-5784","observed_orcids":["https://orcid.org/0000-0003-4807-5784"]},"institutions":[{"id":"https://openalex.org/I90678064","display_name":"University of Colombo","ror":"https://ror.org/02phn5242","country_code":"LK","type":"education","lineage":["https://openalex.org/I90678064"]}],"countries":["LK"],"is_corresponding":false,"raw_author_name":"Samantha Weerasinghe","raw_affiliation_strings":["Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka"],"raw_orcid":"https://orcid.org/0000-0003-4807-5784","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka","institution_ids":["https://openalex.org/I90678064"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040806382","display_name":"D. P. Dissanayake","orcid":"https://orcid.org/0000-0002-6213-5782","observed_orcids":["https://orcid.org/0000-0002-6213-5782"]},"institutions":[{"id":"https://openalex.org/I90678064","display_name":"University of Colombo","ror":"https://ror.org/02phn5242","country_code":"LK","type":"education","lineage":["https://openalex.org/I90678064"]}],"countries":["LK"],"is_corresponding":false,"raw_author_name":"Dhammike P. Dissanayake","raw_affiliation_strings":["Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka"],"raw_orcid":"https://orcid.org/0000-0002-6213-5782","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka","institution_ids":["https://openalex.org/I90678064"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005084072","display_name":"Rajendram Senthilnithy","orcid":"https://orcid.org/0000-0001-9557-8750","observed_orcids":["https://orcid.org/0000-0001-9557-8750"]},"institutions":[{"id":"https://openalex.org/I181714291","display_name":"Open University of Sri Lanka","ror":"https://ror.org/011rrqf91","country_code":"LK","type":"education","lineage":["https://openalex.org/I181714291"]}],"countries":["LK"],"is_corresponding":true,"raw_author_name":"Rajendram Senthilinithy","raw_affiliation_strings":["Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka"],"raw_orcid":"https://orcid.org/0000-0001-9557-8750","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka","institution_ids":["https://openalex.org/I181714291"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5005084072"],"corresponding_institution_ids":["https://openalex.org/I181714291"],"apc_list":null,"apc_paid":null,"fwci":0.7301,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.61803529,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"48","issue":"16","first_page":"1464","last_page":"1475"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11736","display_name":"Histone Deacetylase Inhibitors Research","score":0.5185999870300293,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11736","display_name":"Histone Deacetylase Inhibitors Research","score":0.5185999870300293,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.47440001368522644,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.0012000000569969416,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/histone-deacetylase-inhibitors","display_name":"histone deacetylase inhibitors","score":0.9549999833106995},{"id":"https://openalex.org/keywords/hdac1","display_name":"HDAC1","score":0.5019999742507935},{"id":"https://openalex.org/keywords/panobinostat","display_name":"panobinostat","score":0.8519999980926514},{"id":"https://openalex.org/keywords/laq824","display_name":"LAQ824","score":0.9390000104904175},{"id":"https://openalex.org/keywords/vorinostat","display_name":"vorinostat","score":0.9340000152587891},{"id":"https://openalex.org/keywords/binding-energy","display_name":"binding energy","score":0.8140000104904175},{"id":"https://openalex.org/keywords/pka","display_name":"pKa","score":0.722000002861023},{"id":"https://openalex.org/keywords/epigenetics","display_name":"epigenetics","score":0.6819999814033508},{"id":"https://openalex.org/keywords/histone-deacetylation","display_name":"histone deacetylation","score":0.847000002861023},{"id":"https://openalex.org/keywords/molecular-docking","display_name":"molecular docking","score":0.5870000123977661},{"id":"https://openalex.org/keywords/molecular-dynamics-simulation","display_name":"molecular dynamics simulation","score":0.6179999709129333},{"id":"https://openalex.org/keywords/qm-mm","display_name":"QM/MM","score":0.9449999928474426}],"concepts":[{"id":"https://openalex.org/C25057246","wikidata":"https://www.wikidata.org/wiki/Q1344441","display_name":"Molecular mechanics","level":3,"score":0.7168549299240112},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.707128643989563},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.6436388492584229},{"id":"https://openalex.org/C20803032","wikidata":"https://www.wikidata.org/wiki/Q207900","display_name":"QM/MM","level":3,"score":0.6419102549552917},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.5958800315856934},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5884718298912048},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.5306017994880676},{"id":"https://openalex.org/C119157956","wikidata":"https://www.wikidata.org/wiki/Q796604","display_name":"Acetylation","level":3,"score":0.4672550857067108},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4362441599369049},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3708931803703308},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2933593988418579},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.25727564096450806},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1635282337665558},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.08350729942321777},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1080/08927022.2022.2097672","doi":"https://doi.org/10.1080/08927022.2022.2097672","is_oa":false,"landing_page_url":"https://doi.org/10.1080/08927022.2022.2097672","pdf_url":null,"source":{"id":"https://openalex.org/S45504773","display_name":"Molecular Simulation","issn_l":"0892-7022","issn":["0892-7022","1026-7638","1029-0435"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","jufo-1","norway-1","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547","https://openalex.org/P4310320449"],"host_organization_lineage_names":["Taylor & Francis","Informa"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Molecular Simulation","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.5683000087738037,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G3262792966","display_name":null,"funder_award_id":"RG/2018/BS/02","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"}],"funders":[{"id":"https://openalex.org/F4320335353","display_name":"National Science Foundation of Sri Lanka","ror":"https://ror.org/010xaa060"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W79079033","https://openalex.org/W1497672106","https://openalex.org/W1930265233","https://openalex.org/W1964830748","https://openalex.org/W1966248219","https://openalex.org/W1976210387","https://openalex.org/W1982619775","https://openalex.org/W1988092130","https://openalex.org/W1990794028","https://openalex.org/W1991193196","https://openalex.org/W1997836228","https://openalex.org/W1998749998","https://openalex.org/W2003110754","https://openalex.org/W2005065816","https://openalex.org/W2015539456","https://openalex.org/W2015645056","https://openalex.org/W2028046413","https://openalex.org/W2032860541","https://openalex.org/W2035687084","https://openalex.org/W2036017196","https://openalex.org/W2039879670","https://openalex.org/W2040506727","https://openalex.org/W2046789414","https://openalex.org/W2047280630","https://openalex.org/W2048722552","https://openalex.org/W2051933643","https://openalex.org/W2068609125","https://openalex.org/W2068934093","https://openalex.org/W2071370392","https://openalex.org/W2078277930","https://openalex.org/W2080057665","https://openalex.org/W2086799752","https://openalex.org/W2096083625","https://openalex.org/W2099030380","https://openalex.org/W2101402339","https://openalex.org/W2102376919","https://openalex.org/W2102458112","https://openalex.org/W2103434802","https://openalex.org/W2120944595","https://openalex.org/W2127587233","https://openalex.org/W2128951011","https://openalex.org/W2132629607","https://openalex.org/W2133338317","https://openalex.org/W2145438015","https://openalex.org/W2158890625","https://openalex.org/W2160451368","https://openalex.org/W2160544821","https://openalex.org/W2171268876","https://openalex.org/W2171799021","https://openalex.org/W2404368222","https://openalex.org/W2609038578","https://openalex.org/W2737914125","https://openalex.org/W2756929056","https://openalex.org/W2760016018","https://openalex.org/W2766148353","https://openalex.org/W2785797480","https://openalex.org/W2916113589","https://openalex.org/W3095138998","https://openalex.org/W3097452398","https://openalex.org/W3131919058","https://openalex.org/W3135541636","https://openalex.org/W3159780747","https://openalex.org/W3181281182","https://openalex.org/W3198240016","https://openalex.org/W3199592749","https://openalex.org/W3217141529","https://openalex.org/W4210850449"],"related_works":["https://openalex.org/W4310898525","https://openalex.org/W3097452398","https://openalex.org/W3199592749","https://openalex.org/W7202073358","https://openalex.org/W4293799461","https://openalex.org/W4393357084","https://openalex.org/W4292677918","https://openalex.org/W2887347998","https://openalex.org/W2930805850","https://openalex.org/W2139829289"],"abstract_inverted_index":{"Epigenetics":[0],"regulates":[1],"gene":[2],"expression":[3],"through":[4],"post-translational":[5],"modification":[6,15],"of":[7,90,135,154,172],"protein":[8,18],"complexes":[9,171],"accompanying":[10],"DNA.":[11],"The":[12,87,125],"most":[13],"significant":[14],"in":[16,60],"histone":[17],"is":[19,185],"deacetylation,":[20],"regulated":[21],"by":[22],"HDAC":[23,30],"enzyme.":[24],"This":[25],"study":[26],"focuses":[27],"on":[28,33],"the":[29,34,56,61,91,97,102,116,133,142,151,155,164,170],"inhibitors'":[31],"effect":[32],"HDLP":[35,62,92,173,198],"enzyme's":[36],"stability.":[37],"Ab":[38],"initio":[39],"quantum":[40],"mechanics":[41,45],"(QM),":[42],"Quantum":[43],"mechanics/molecular":[44],"(QM/MM),":[46],"and":[47,73,79,101,115,137,177,189],"Molecular":[48],"dynamics":[49],"(MD)":[50],"analyses":[51],"were":[52,75,105],"executed":[53],"to":[54,65,112,121,194],"investigate":[55],"changes":[57],"that":[58,132,150,169,187],"occur":[59],"enzyme":[63,93],"due":[64],"inhibitor":[66,103],"binding.":[67],"LBH589,":[68,175],"PCI24781,":[69,176],"PXD101,":[70],"LAQ824,":[71],"SB939,":[72],"RAS2410":[74],"selected":[76],"as":[77,83,197],"inhibitors,":[78],"SAHA":[80,178],"was":[81,94,110,119,148],"used":[82,111,120],"a":[84],"reference":[85],"inhibitor.":[86],"crystal":[88],"structure":[89],"obtained":[95],"from":[96],"Protein":[98],"Data":[99],"Bank,":[100],"structures":[104],"optimized":[106],"using":[107],"G09W.":[108],"AutoDock-Vina":[109],"perform":[113,122],"docking,":[114],"resultant":[117],"complex":[118],"MD":[123],"simulation.":[124],"QM/MM":[126],"two-layer":[127],"binding":[128,161],"energy":[129],"studies":[130],"revealed":[131],"stabilities":[134],"HDLP-LBH589":[136],"HDLP-PCI24781":[138],"are":[139,157,179,191],"higher":[140],"than":[141],"other":[143],"studied":[144,196],"complexes.":[145],"Also,":[146],"it":[147,184],"found":[149],"pKa":[152],"values":[153],"inhibitors":[156],"correlated":[158],"with":[159,174],"their":[160],"energy.":[162],"Further,":[163],"trajectory":[165],"analysis":[166],"results":[167],"showed":[168],"comparatively":[180],"more":[181],"stable.":[182],"Therefore,":[183],"concluded":[186],"LBH589":[188],"PCI24781":[190],"excellent":[192],"candidates":[193],"be":[195],"inhibitors.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2022-07-14T00:00:00"}