{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T12:45:24Z","timestamp":1781527524435,"version":"3.54.1"},"reference-count":47,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2023,12,1]],"date-time":"2023-12-01T00:00:00Z","timestamp":1701388800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,12,1]],"date-time":"2023-12-01T00:00:00Z","timestamp":1701388800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,12,1]],"date-time":"2023-12-01T00:00:00Z","timestamp":1701388800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2023,12,1]],"date-time":"2023-12-01T00:00:00Z","timestamp":1701388800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2023,12,1]],"date-time":"2023-12-01T00:00:00Z","timestamp":1701388800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2023,12,1]],"date-time":"2023-12-01T00:00:00Z","timestamp":1701388800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2023,12,1]],"date-time":"2023-12-01T00:00:00Z","timestamp":1701388800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100008762","name":"Tamil Nadu State Council for Higher Education","doi-asserted-by":"publisher","award":["RGP\/2019-20\/ALU\/HECP-0049"],"award-info":[{"award-number":["RGP\/2019-20\/ALU\/HECP-0049"]}],"id":[{"id":"10.13039\/501100008762","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008762","name":"Tamil Nadu State Council for Higher Education","doi-asserted-by":"publisher","award":["27\/04\/2021"],"award-info":[{"award-number":["27\/04\/2021"]}],"id":[{"id":"10.13039\/501100008762","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001407","name":"Government of India Department of Biotechnology","doi-asserted-by":"publisher","award":["BT\/PR40156\/BTIS\/137\/54\/2023"],"award-info":[{"award-number":["BT\/PR40156\/BTIS\/137\/54\/2023"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001407","name":"Government of India Department of Biotechnology","doi-asserted-by":"publisher","award":["BT\/PR40154\/BTIS\/137\/34\/2021"],"award-info":[{"award-number":["BT\/PR40154\/BTIS\/137\/34\/2021"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001409","name":"Department of Science and Technology","doi-asserted-by":"publisher","award":["GITA\/DST\/TWN\/P-86\/2019"],"award-info":[{"award-number":["GITA\/DST\/TWN\/P-86\/2019"]}],"id":[{"id":"10.13039\/501100001409","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001409","name":"Department of Science and Technology","doi-asserted-by":"publisher","award":["SR\/FST\/LSI-667\/2016"],"award-info":[{"award-number":["SR\/FST\/LSI-667\/2016"]}],"id":[{"id":"10.13039\/501100001409","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100020970","name":"Rashtriya Uchchatar Shiksha Abhiyan","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100020970","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computational Biology and Chemistry"],"published-print":{"date-parts":[[2023,12]]},"DOI":"10.1016\/j.compbiolchem.2023.107942","type":"journal-article","created":{"date-parts":[[2023,8,23]],"date-time":"2023-08-23T19:57:06Z","timestamp":1692820626000},"page":"107942","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":12,"special_numbering":"C","title":["Multilayer precision-based screening of potential inhibitors targeting Mycobacterium tuberculosis acetate kinase using in silico approaches"],"prefix":"10.1016","volume":"107","author":[{"given":"Sneha","family":"Subramaniyan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hemavathy","family":"Nagarajan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Umashankar","family":"Vetrivel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeyakanthan","family":"Jeyaraman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"4","key":"10.1016\/j.compbiolchem.2023.107942_bib1","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1111\/cbdd.13446","article-title":"Suitability of MMGBSA for the selection of correct ligand binding modes from docking results","volume":"93","author":"Ahinko","year":"2019","journal-title":"Chem. Biol. Drug Des."},{"issue":"3","key":"10.1016\/j.compbiolchem.2023.107942_bib2","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.compbiolchem.2023.107942_bib3","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gki070","article-title":"The universal protein resource (UniProt)","author":"Bairoch","year":"2004","journal-title":"Nucleic Acids Res."},{"issue":"11","key":"10.1016\/j.compbiolchem.2023.107942_bib4","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0277328","article-title":"Repositioning of anti-dengue compounds against SARS-CoV-2 as viral polyprotein processing inhibitor","volume":"17","author":"Bajrai","year":"2022","journal-title":"PLoS One"},{"issue":"2","key":"10.1016\/j.compbiolchem.2023.107942_bib5","doi-asserted-by":"crossref","first-page":"e00272","DOI":"10.1128\/mBio.00272-17","article-title":"Targeting energy metabolism in Mycobacterium tuberculosis, a new paradigm in antimycobacterial drug discovery","volume":"8","author":"Bald","year":"2017","journal-title":"MBio"},{"issue":"1","key":"10.1016\/j.compbiolchem.2023.107942_bib6","first-page":"E9","article-title":"The history of tuberculosis: from the first historical records to the isolation of Koch\u2019s bacillus","volume":"58","author":"Barberis","year":"2017","journal-title":"J. Prev. Med. Hyg."},{"issue":"2","key":"10.1016\/j.compbiolchem.2023.107942_bib7","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.tube.2014.12.003","article-title":"Increasing the structural coverage of tuberculosis drug targets","volume":"95","author":"Baugh","year":"2015","journal-title":"Tuberculosis"},{"issue":"1","key":"10.1016\/j.compbiolchem.2023.107942_bib8","doi-asserted-by":"crossref","first-page":"4639","DOI":"10.1038\/s41467-019-12614-7","article-title":"Acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2","volume":"10","author":"Bhusal","year":"2019","journal-title":"Nat. Commun."},{"issue":"1","key":"10.1016\/j.compbiolchem.2023.107942_bib9","doi-asserted-by":"crossref","first-page":"44826","DOI":"10.1038\/srep44826","article-title":"Modulation of central carbon metabolism by acetylation of isocitrate lyase in Mycobacterium tuberculosis","volume":"7","author":"Bi","year":"2017","journal-title":"Sci. Rep."},{"issue":"9","key":"10.1016\/j.compbiolchem.2023.107942_bib10","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1016\/j.tcb.2019.05.005","article-title":"Acetate metabolism in physiology, cancer, and beyond","volume":"29","author":"Bose","year":"2019","journal-title":"Trends Cell Biol."},{"key":"10.1016\/j.compbiolchem.2023.107942_bib11","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2022.878471","article-title":"Therapeutic vaccines for tuberculosis: an overview","volume":"13","author":"Bouzeyen","year":"2022","journal-title":"Front. Immunol."},{"issue":"Supplement 36","key":"10.1016\/j.compbiolchem.2023.107942_bib12","doi-asserted-by":"crossref","first-page":"54S","DOI":"10.1183\/09031936.02.00400702","article-title":"Molecular epidemiology of tuberculosis","volume":"20","author":"Burgos","year":"2002","journal-title":"Eur. Respir. J."},{"issue":"12","key":"10.1016\/j.compbiolchem.2023.107942_bib13","doi-asserted-by":"crossref","DOI":"10.1002\/pro.4482","article-title":"RCSB Protein Data bank: tools for visualizing and understanding biological macromolecules in 3D","volume":"31","author":"Burley","year":"2022","journal-title":"Protein Sci."},{"issue":"2","key":"10.1016\/j.compbiolchem.2023.107942_bib14","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1128\/JB.183.2.680-686.2001","article-title":"Urkinase: structure of acetate kinase, a member of the ASKHA superfamily of phosphotransferases","volume":"183","author":"Buss","year":"2001","journal-title":"J. Bacteriol."},{"issue":"2","key":"10.1016\/j.compbiolchem.2023.107942_bib15","doi-asserted-by":"crossref","first-page":"88","DOI":"10.3390\/metabo11020088","article-title":"Metabolic versatility of mycobacterium tuberculosis during infection and dormancy","volume":"11","author":"Chang","year":"2021","journal-title":"Metabolites"},{"key":"10.1016\/j.compbiolchem.2023.107942_bib16","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/j.molstruc.2016.06.082","article-title":"Identification of novel histone deacetylase 1 inhibitors by combined pharmacophore modeling, 3D-QSAR analysis, in silico screening and Density Functional Theory (DFT) approaches","volume":"1125","author":"Choubey","year":"2016","journal-title":"J. Mol. Struct."},{"issue":"2","key":"10.1016\/j.compbiolchem.2023.107942_bib17","doi-asserted-by":"crossref","first-page":"1454","DOI":"10.3390\/life5021454","article-title":"Acetate metabolism in anaerobes from the domain archaea","volume":"5","author":"Ferry","year":"2015","journal-title":"Life"},{"issue":"7","key":"10.1016\/j.compbiolchem.2023.107942_bib18","doi-asserted-by":"crossref","first-page":"2105","DOI":"10.3390\/molecules27072105","article-title":"Molecular dynamics simulations: advances and applications","volume":"27","author":"Filipe","year":"2022","journal-title":"Molecules"},{"issue":"7","key":"10.1016\/j.compbiolchem.2023.107942_bib19","doi-asserted-by":"crossref","first-page":"3965","DOI":"10.1128\/IAI.70.7.3965-3968.2002","article-title":"Mycobacterium tuberculosis CDC1551 is resistant to reactive nitrogen and oxygen intermediates in vitro","volume":"70","author":"Firmani","year":"2002","journal-title":"Infect. Immun."},{"key":"10.1016\/j.compbiolchem.2023.107942_bib20","first-page":"461","article-title":"Modeller: Generation and Refinement of Homology-Based Protein Structure Models","volume":"Vol. 374","author":"Fiser","year":"2003"},{"key":"10.1016\/j.compbiolchem.2023.107942_bib21","first-page":"3474","article-title":"Direct detection of the acetate-forming activity of the enzyme acetate kinase","volume":"58","author":"Fowler","year":"2011","journal-title":"J. Vis. Exp."},{"issue":"6","key":"10.1016\/j.compbiolchem.2023.107942_bib22","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1093\/bioinformatics\/11.6.681","article-title":"SOPMA: Significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments","volume":"11","author":"Geourjon","year":"1995","journal-title":"Bioinformatics"},{"issue":"11","key":"10.1016\/j.compbiolchem.2023.107942_bib23","doi-asserted-by":"crossref","first-page":"10731","DOI":"10.1074\/jbc.M412118200","article-title":"Structural and kinetic analyses of arginine residues in the active site of the acetate kinase from Methanosarcina thermophila","volume":"280","author":"Gorrell","year":"2005","journal-title":"J. Biol. Chem."},{"issue":"3","key":"10.1016\/j.compbiolchem.2023.107942_bib24","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1093\/femsre\/fux011","article-title":"Antimicrobial resistance in Mycobacterium tuberculosis: Mechanistic and evolutionary perspectives","volume":"41","author":"Gygli","year":"2017","journal-title":"FEMS Microbiol. Rev."},{"key":"10.1016\/j.compbiolchem.2023.107942_bib25","doi-asserted-by":"crossref","first-page":"434","DOI":"10.3389\/fphar.2019.00434","article-title":"In silico ADME and toxicity prediction of ceftazidime and its impurities","volume":"10","author":"Han","year":"2019","journal-title":"Front. Pharmacol."},{"issue":"2","key":"10.1016\/j.compbiolchem.2023.107942_bib26","doi-asserted-by":"crossref","first-page":"156","DOI":"10.4103\/ijmy.ijmy_33_18","article-title":"Mycobacterium tuberculosis Strains H37ra and H37rv have equivalent minimum inhibitory concentrations to most antituberculosis drugs","volume":"7","author":"Heinrichs","year":"2018","journal-title":"Int. J. Mycobacteriol."},{"issue":"4","key":"10.1016\/j.compbiolchem.2023.107942_bib27","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1002\/jcc.10402","article-title":"Partial rigid-body dynamics in NPT, NPAT and NP?T ensembles for proteins and membranes","volume":"25","author":"Ikeguchi","year":"2004","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.compbiolchem.2023.107942_bib28","doi-asserted-by":"crossref","DOI":"10.1016\/j.gene.2019.144082","article-title":"Structural insight into conformational dynamics of non-active site mutations in KasA: a Mycobacterium tuberculosis target protein","volume":"720","author":"Jayaraman","year":"2019","journal-title":"Gene"},{"issue":"7","key":"10.1016\/j.compbiolchem.2023.107942_bib29","doi-asserted-by":"crossref","first-page":"4047","DOI":"10.1021\/acs.jctc.1c01214","article-title":"Accelerators for classical molecular dynamics simulations of biomolecules","volume":"18","author":"Jones","year":"2022","journal-title":"J. Chem. Theory Comput."},{"issue":"8","key":"10.1016\/j.compbiolchem.2023.107942_bib30","doi-asserted-by":"crossref","first-page":"1689","DOI":"10.1021\/acs.jpca.8b09082","article-title":"New method for constant- NPT molecular dynamics","volume":"123","author":"Kim","year":"2019","journal-title":"J. Phys. Chem. A"},{"issue":"23","key":"10.1016\/j.compbiolchem.2023.107942_bib31","doi-asserted-by":"crossref","first-page":"e00402","DOI":"10.1128\/JB.00402-21","article-title":"Regulation of the icl1 Gene Encoding the Major Isocitrate Lyase in Mycobacterium smegmatis","volume":"203","author":"Ko","year":"2021","journal-title":"J. Bacteriol."},{"issue":"7","key":"10.1016\/j.compbiolchem.2023.107942_bib32","doi-asserted-by":"crossref","first-page":"1951","DOI":"10.1021\/ci500020m","article-title":"g_mmpbsa\u2014a GROMACS tool for high-throughput MM-PBSA calculations","volume":"54","author":"Kumari","year":"2014","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/j.compbiolchem.2023.107942_bib33","doi-asserted-by":"crossref","DOI":"10.1016\/j.cellsig.2021.110031","article-title":"Characterization of putative transcriptional regulator (PH0140) and its distal homologue","volume":"84","author":"Mariadasse","year":"2021","journal-title":"Cell. Signal."},{"issue":"6","key":"10.1016\/j.compbiolchem.2023.107942_bib34","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1007\/s10822-022-00459-0","article-title":"Deciphering the conformational transitions of LIMK2 active and inactive states to ponder specific druggable states through microsecond scale molecular dynamics simulation","volume":"36","author":"Nagarajan","year":"2022","journal-title":"J. Comput. -Aided Mol. Des."},{"issue":"8","key":"10.1016\/j.compbiolchem.2023.107942_bib35","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1016\/j.jmgm.2009.01.006","article-title":"Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case","volume":"27","author":"Papaleo","year":"2009","journal-title":"J. Mol. Graph. Model."},{"issue":"22","key":"10.1016\/j.compbiolchem.2023.107942_bib36","doi-asserted-by":"crossref","first-page":"6889","DOI":"10.1128\/JB.181.22.6889-6897.1999","article-title":"Catabolite regulation of the pta Gene as Part of carbon flow pathways in Bacillus subtilis","volume":"181","author":"Presecan-Siedel","year":"1999","journal-title":"J. Bacteriol."},{"issue":"3","key":"10.1016\/j.compbiolchem.2023.107942_bib37","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1007\/s002030050626","article-title":"Acetyl phosphate and the phosphorylation of OmpR are involved in the regulation of the cell division rate in Escherichia coli","volume":"170","author":"Pr\u00fc\u00df","year":"1998","journal-title":"Arch. Microbiol."},{"issue":"1","key":"10.1016\/j.compbiolchem.2023.107942_bib38","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s13721-017-0147-8","article-title":"In silico characterization of hypothetical proteins obtained from Mycobacterium tuberculosis H37Rv","volume":"6","author":"Raj","year":"2017","journal-title":"Netw. Model. Anal. Health Inform. Bioinforma."},{"issue":"19","key":"10.1016\/j.compbiolchem.2023.107942_bib39","doi-asserted-by":"crossref","first-page":"3182","DOI":"10.1128\/JB.00259-15","article-title":"Acetate dissimilation and assimilation in mycobacterium tuberculosis depend on carbon availability","volume":"197","author":"R\u00fccker","year":"2015","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.compbiolchem.2023.107942_bib40","doi-asserted-by":"crossref","first-page":"233","DOI":"10.3389\/fmicb.2020.00233","article-title":"The Impact of ackA, pta, and ackA-pta mutations on growth, gene expression and protein acetylation in Escherichia coli K-12","volume":"11","author":"Sch\u00fctze","year":"2020","journal-title":"Front. Microbiol."},{"issue":"5","key":"10.1016\/j.compbiolchem.2023.107942_bib41","doi-asserted-by":"crossref","first-page":"1182","DOI":"10.1111\/mmi.14196","article-title":"Cognate sensor kinase\u2010independent activation of Mycobacterium tuberculosis response regulator DevR (DosR) by acetyl phosphate: Implications in anti\u2010mycobacterial drug design","volume":"111","author":"Sharma","year":"2019","journal-title":"Mol. Microbiol."},{"issue":"1","key":"10.1016\/j.compbiolchem.2023.107942_bib42","doi-asserted-by":"crossref","DOI":"10.1063\/1.4885338","article-title":"Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates","volume":"141","author":"Sittel","year":"2014","journal-title":"J. Chem. Phys."},{"key":"10.1016\/j.compbiolchem.2023.107942_bib43","doi-asserted-by":"crossref","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: the universal protein knowledgebase in 2023","author":"The UniProt Consortium","year":"2023","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"10.1016\/j.compbiolchem.2023.107942_bib44","article-title":"Multiple sequence alignment using clustalW and ClustalX","volume":"00","author":"Thompson","year":"2003","journal-title":"Curr. Protoc. Bioinforma."},{"issue":"4","key":"10.1016\/j.compbiolchem.2023.107942_bib45","doi-asserted-by":"crossref","first-page":"a021121","DOI":"10.1101\/cshperspect.a021121","article-title":"Mycobacterium tuberculosis metabolism","volume":"5","author":"Warner","year":"2015","journal-title":"Cold Spring Harb. Perspect. Med."},{"issue":"1","key":"10.1016\/j.compbiolchem.2023.107942_bib46","article-title":"Comparative protein structure modeling using MODELLER","volume":"54","author":"Webb","year":"2016","journal-title":"Curr. Protoc. Bioinforma."},{"key":"10.1016\/j.compbiolchem.2023.107942_bib47","doi-asserted-by":"crossref","DOI":"10.1042\/BSR20211215","article-title":"Mycobacterium tuberculosis carbon and nitrogen metabolic fluxes","author":"Xu","year":"2022","journal-title":"Biosci. Rep."}],"container-title":["Computational Biology and Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927123001330?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927123001330?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T20:01:05Z","timestamp":1778616065000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476927123001330"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12]]},"references-count":47,"alternative-id":["S1476927123001330"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2023.107942","relation":{},"ISSN":["1476-9271"],"issn-type":[{"value":"1476-9271","type":"print"}],"subject":[],"published":{"date-parts":[[2023,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Multilayer precision-based screening of potential inhibitors targeting Mycobacterium tuberculosis acetate kinase using in silico approaches","name":"articletitle","label":"Article Title"},{"value":"Computational Biology and Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2023.107942","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"107942"}}