{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T05:09:16Z","timestamp":1777698556440,"version":"3.51.4"},"reference-count":52,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100009589","name":"Jadavpur University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009589","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Molecular Graphics and Modelling"],"published-print":{"date-parts":[[2024,1]]},"DOI":"10.1016\/j.jmgm.2023.108671","type":"journal-article","created":{"date-parts":[[2023,11,11]],"date-time":"2023-11-11T02:25:46Z","timestamp":1699669546000},"page":"108671","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":3,"special_numbering":"C","title":["A fragment-based exploration of diverse MMP-9 inhibitors through classification-dependent structural assessment"],"prefix":"10.1016","volume":"126","author":[{"given":"Sandip Kumar","family":"Baidya","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suvankar","family":"Banerjee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Balaram","family":"Ghosh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tarun","family":"Jha","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5523-7716","authenticated-orcid":false,"given":"Nilanjan","family":"Adhikari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.jmgm.2023.108671_bib1","doi-asserted-by":"crossref","DOI":"10.1016\/j.jnutbio.2020.108576","article-title":"The response of zinc transporter gene expression of selected tissues in a pig model of subclinical zinc deficiency","volume":"90","author":"Brugger","year":"2021","journal-title":"J. Nutr. Biochem."},{"key":"10.1016\/j.jmgm.2023.108671_bib2","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.3390\/cells9051313","article-title":"Metalloproteinases and their inhibitors: potential for the development of new therapeutics","volume":"9","author":"Raeeszadeh-Sarmazdeh","year":"2020","journal-title":"Cells"},{"key":"10.1016\/j.jmgm.2023.108671_bib3","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/j.avsg.2018.07.043","article-title":"The relationship between the concentration of cathepsin A, D, and E and the concentration of copper and zinc, and the size of the aneurysmal enlargement in the wall of the abdominal aortic aneurysm","volume":"55","author":"Kurianiuk","year":"2019","journal-title":"Ann. Vasc. Surg."},{"key":"10.1016\/j.jmgm.2023.108671_bib4","doi-asserted-by":"crossref","DOI":"10.1128\/MCB.00128-19","article-title":"Translocating a high-affinity designer TIMP-1 to the cell membrane for total renal carcinoma inhibition: putting the prion protein to good use","volume":"39","author":"Jiang","year":"2019","journal-title":"Mol. Cell Biol."},{"key":"10.1016\/j.jmgm.2023.108671_bib5","doi-asserted-by":"crossref","DOI":"10.1016\/j.prp.2019.04.002","article-title":"The metalloprotease ADAM17 in inflammation and cancer","volume":"215","author":"D\u00fcsterh\u00f6ft","year":"2019","journal-title":"Pathol. Res. Pract."},{"key":"10.1016\/j.jmgm.2023.108671_bib6","doi-asserted-by":"crossref","DOI":"10.1016\/j.lfs.2019.117181","article-title":"Angiotensin-converting enzyme inhibitors and angiotensin receptor blockers as therapeutic options in the treatment of renal cancer: a meta-analysis","volume":"242","author":"Asgharzadeh","year":"2020","journal-title":"Life Sci."},{"key":"10.1016\/j.jmgm.2023.108671_bib7","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1038\/s41416-019-0642-z","article-title":"Carbonic anhydrase IX and acid transport in cancer","volume":"122","author":"Becker","year":"2020","journal-title":"Br. J. Cancer"},{"key":"10.1016\/j.jmgm.2023.108671_bib8","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1016\/j.semcancer.2019.09.004","article-title":"Emerging roles of ECM remodeling processes in cancer","volume":"62","author":"Mohan","year":"2020","journal-title":"Semin. Cancer Biol."},{"key":"10.1016\/j.jmgm.2023.108671_bib9","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1038\/nrm3904","article-title":"Remodelling the extracellular matrix in development and disease","volume":"15","author":"Bonnans","year":"2014","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.jmgm.2023.108671_bib10","series-title":"The Role of Matrix Metalloproteinase in Human Body Pathologies","author":"Djuric","year":"2017"},{"key":"10.1016\/j.jmgm.2023.108671_bib11","doi-asserted-by":"crossref","first-page":"5578","DOI":"10.1073\/pnas.87.14.5578","article-title":"The cysteine switch: a principle of regulation of metalloproteinase activity with potential applicability to the entire matrix metalloproteinase gene family","volume":"87","author":"Van Wart","year":"1990","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.jmgm.2023.108671_bib12","doi-asserted-by":"crossref","DOI":"10.1016\/j.ejmech.2020.112260","article-title":"Matrix metalloproteinase-9 (MMP-9) and its inhibitors in cancer: a minireview","volume":"194","author":"Mondal","year":"2020","journal-title":"Eur. J. Med. Chem."},{"key":"10.1016\/j.jmgm.2023.108671_bib13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40199-015-0111-z","article-title":"A study on quantitative structure\u2013activity relationship and molecular docking of metalloproteinase inhibitors based on L-tyrosine scaffold","volume":"23","author":"Abbasi","year":"2015","journal-title":"DARU J. Pharm. Sci."},{"key":"10.1016\/j.jmgm.2023.108671_bib14","article-title":"Outline of gelatinase inhibitors as anti-cancer agents: a patent mini-review for 2010-present","volume":"24","author":"Baidya","year":"2020","journal-title":"Eur. J. Med. Chem."},{"key":"10.1016\/j.jmgm.2023.108671_bib15","doi-asserted-by":"crossref","first-page":"2171","DOI":"10.18632\/oncotarget.1426","article-title":"Chemokines in tumor progression and metastasis","volume":"4","author":"Sarvaiya","year":"2013","journal-title":"Oncotarget"},{"key":"10.1016\/j.jmgm.2023.108671_bib16","doi-asserted-by":"crossref","first-page":"e6","DOI":"10.1016\/j.pbj.0000000000000006","article-title":"Prediction of MMP-9 inhibitory activity of N-hydroxy-\u03b1-phenylsulfonylacetamide derivatives by pharmacophore based modeling and 3D-QSAR studies","volume":"3","author":"Rathee","year":"2018","journal-title":"Porto. Biomed. J."},{"key":"10.1016\/j.jmgm.2023.108671_bib17","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/S0022-2836(02)00262-0","article-title":"Crystal structure of human MMP9 in complex with a reverse hydroxamate inhibitor","volume":"319","author":"Rowsell","year":"2002","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmgm.2023.108671_bib18","doi-asserted-by":"crossref","first-page":"310","DOI":"10.6026\/97320630005310","article-title":"Structural insights into the binding of MMP9 inhibitors","volume":"5","author":"Tandon","year":"2011","journal-title":"Bioinformation"},{"key":"10.1016\/j.jmgm.2023.108671_bib19","doi-asserted-by":"crossref","DOI":"10.1016\/j.ejmech.2019.111875","article-title":"Battle tactics against MMP-9; discovery of novel non-hydroxamate MMP-9 inhibitors endowed with PI3K\/AKT signaling attenuation and caspase 3\/7 activation via Ugi bis-amide synthesis","volume":"186","author":"Ayoup","year":"2020","journal-title":"Eur. J. Med. Chem."},{"key":"10.1016\/j.jmgm.2023.108671_bib20","doi-asserted-by":"crossref","first-page":"933","DOI":"10.3892\/or.2013.2487","article-title":"Withaferin A inhibits matrix metalloproteinase-9 activity by suppressing the AKT signaling pathway","volume":"30","author":"Lee","year":"2013","journal-title":"Oncol. Rep."},{"key":"10.1016\/j.jmgm.2023.108671_bib21","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/sj.cdd.4400476","article-title":"Emerging roles of caspase-3 in apoptosis","volume":"6","author":"Porter","year":"1999","journal-title":"Cell Death Differ."},{"key":"10.1016\/j.jmgm.2023.108671_bib22","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1002\/(SICI)1097-4652(200002)182:2<290::AID-JCP18>3.0.CO;2-8","article-title":"Cleavage and inactivation of antiapoptotic Akt\/PKB by caspases during apoptosis","volume":"182","author":"Rokudai","year":"2000","journal-title":"J. Cell. Physiol."},{"key":"10.1016\/j.jmgm.2023.108671_bib24","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0169-409X(96)00423-1","article-title":"Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings","volume":"23","author":"Lipinski","year":"1997","journal-title":"Adv. Drug Deliv. Rev."},{"key":"10.1016\/j.jmgm.2023.108671_bib25","doi-asserted-by":"crossref","first-page":"2615","DOI":"10.1021\/jm020017n","article-title":"Molecular properties that influence the oral bioavailability of drug candidates","volume":"45","author":"Veber","year":"2002","journal-title":"J. Med. Chem."},{"key":"10.1016\/j.jmgm.2023.108671_bib26","series-title":"Discovery Studio 3.0 (DS 3.0)","year":"2015"},{"key":"10.1016\/j.jmgm.2023.108671_bib27","doi-asserted-by":"crossref","first-page":"1392","DOI":"10.1016\/j.tiv.2015.05.017","article-title":"Structural findings of phenylindoles as cytotoxic antimitotic agents in human breast cancer cell lines through multiple validated QSAR studies","volume":"29","author":"Adhikari","year":"2015","journal-title":"Toxicol. Vitro"},{"key":"10.1016\/j.jmgm.2023.108671_bib28","doi-asserted-by":"crossref","first-page":"2538","DOI":"10.1021\/acs.jcim.9b00295","article-title":"QSAR-Co: an open source software for developing robust multitasking or multitarget classification-based QSAR models","volume":"59","author":"Ambure","year":"2019","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/j.jmgm.2023.108671_bib29","series-title":"DRAGON 6.0","year":"2001"},{"key":"10.1016\/j.jmgm.2023.108671_bib30","doi-asserted-by":"crossref","first-page":"1282","DOI":"10.1080\/07391102.2018.1456975","article-title":"Identifying natural compounds as multi-target-directed ligands against Alzheimer's disease: an in silico approach","volume":"37","author":"Ambure","year":"2019","journal-title":"J. Biomol. Struct. Dyn."},{"key":"10.1016\/j.jmgm.2023.108671_bib32","doi-asserted-by":"crossref","first-page":"1128","DOI":"10.1021\/acs.chemrestox.8b00162","article-title":"Prediction of farnesoid X receptor disruptors with machine learning methods","volume":"31","author":"Chen","year":"2018","journal-title":"Chem. Res. Toxicol."},{"key":"10.1016\/j.jmgm.2023.108671_bib33","article-title":"A new QSAR model for acute fish toxicity based on mined structural alerts","volume":"5","author":"Gini","year":"2019","journal-title":"J. Toxicol. Risk Assess."},{"key":"10.1016\/j.jmgm.2023.108671_bib34","series-title":"Bayesian Inference in Statistical Analysis","author":"Box","year":"2011"},{"key":"10.1016\/j.jmgm.2023.108671_bib35","doi-asserted-by":"crossref","first-page":"742","DOI":"10.1021\/ci100050t","article-title":"Extended-connectivity fingerprints","volume":"50","author":"Rogers","year":"2010","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/j.jmgm.2023.108671_bib36","first-page":"1","article-title":"Comparing structural fingerprints using a literature-based similarity benchmark","volume":"8","author":"O'Boyle","year":"2016","journal-title":"J. Cheminf."},{"key":"10.1016\/j.jmgm.2023.108671_bib37","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1021\/mp100465q","article-title":"ADME evaluation in drug discovery. 10. Predictions of P-glycoprotein inhibitors using recursive partitioning and naive Bayesian classification techniques","volume":"8","author":"Chen","year":"2011","journal-title":"Mol. Pharm."},{"key":"10.1016\/j.jmgm.2023.108671_bib38","first-page":"1","article-title":"Structural analysis of arylsulfonamide-based carboxylic acid derivatives: a QSAR study to identify the structural contributors toward their MMP-9 inhibition","volume":"17","author":"Mondal","year":"2020","journal-title":"Struct. Chem."},{"key":"10.1016\/j.jmgm.2023.108671_bib39","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/07391102.2019.1661876","article-title":"Development of decision trees to discriminate HDAC8 inhibitors and non-inhibitors using recursive partitioning","volume":"39","author":"Amin","year":"2021","journal-title":"J. Biomol. Struct. Dyn."},{"key":"10.1016\/j.jmgm.2023.108671_bib40","doi-asserted-by":"crossref","first-page":"2746","DOI":"10.1021\/ci2003076","article-title":"Two new parameters based on distances in a receiver operating characteristic chart for the selection of classification models","volume":"51","author":"P\u00e9rez-Garrido","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/j.jmgm.2023.108671_bib41","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/j.patrec.2005.10.010","article-title":"An introduction to ROC analysis","volume":"27","author":"Fawcett","year":"2006","journal-title":"Pattern Recogn. Lett."},{"key":"10.1016\/j.jmgm.2023.108671_bib42","series-title":"Understanding the Basics of QSAR for Applications in Pharmaceutical Sciences and Risk Assessment","author":"Roy","year":"2015"},{"key":"10.1016\/j.jmgm.2023.108671_bib43","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1016\/j.tiv.2012.10.015","article-title":"First report on predictive chemometric modeling, 3D-toxicophore mapping and in silico screening of in vitro basal cytotoxicity of diverse organic chemicals","volume":"27","author":"Kar","year":"2013","journal-title":"Toxicol. Vitro"},{"key":"10.1016\/j.jmgm.2023.108671_bib44","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1080\/1062936X.2021.1914721","article-title":"Robust classification-based molecular modelling of diverse chemical entities as potential SARS-CoV-2 3CLpro inhibitors: theoretical justification in light of experimental evidences","volume":"32","author":"Adhikari","year":"2021","journal-title":"SAR QSAR Environ. Res."},{"key":"10.1016\/j.jmgm.2023.108671_bib45","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1080\/1062936X.2021.1976831","article-title":"A robust classification-dependent multi-molecular modelling study on some biphenyl sulphonamide based MMP-8 inhibitors","volume":"32","author":"Guti","year":"2021","journal-title":"SAR QSAR Environ. Res."},{"key":"10.1016\/j.jmgm.2023.108671_bib46","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1016\/j.molstruc.2017.12.005","article-title":"Structural exploration for the refinement of anticancer matrix metalloproteinase-2 inhibitor designing approaches through robust validated multi-QSARs","volume":"1156","author":"Adhikari","year":"2018","journal-title":"J. Mol. Struct."},{"key":"10.1016\/j.jmgm.2023.108671_bib47","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1016\/j.jmb.2007.05.068","article-title":"Crystal structures of MMP-9 complexes with five inhibitors: contribution of the flexible Arg 424 sidechain to selectivity","volume":"371","author":"Tochowicz","year":"2007","journal-title":"J. Mol."},{"key":"10.1016\/j.jmgm.2023.108671_bib48","doi-asserted-by":"crossref","first-page":"7224","DOI":"10.1021\/acs.jmedchem.5b00367","article-title":"N-O-Isopropyl sulfonamido-based hydroxamates as matrix metalloproteinase inhibitors: hit selection and in vivo antiangiogenic activity","volume":"58","author":"Nuti","year":"2015","journal-title":"J. Med. Chem."},{"key":"10.1016\/j.jmgm.2023.108671_bib49","doi-asserted-by":"crossref","first-page":"10709","DOI":"10.1021\/acs.jmedchem.1c01855","article-title":"Selective inhibitors of medium-size S1' pocket matrix metalloproteinases: a stepping stone of future drug discovery","volume":"65","author":"Baidya","year":"2022","journal-title":"J. Med. Chem."},{"key":"10.1016\/j.jmgm.2023.108671_bib50","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1016\/S0968-0896(02)00438-8","article-title":"A quantitative structure-activity relationship study on some matrix metalloproteinase and collagenase inhibitors","volume":"11","author":"Kumar","year":"2003","journal-title":"Bioorg. Med. Chem."},{"issue":"12","key":"10.1016\/j.jmgm.2023.108671_bib51","doi-asserted-by":"crossref","first-page":"4137","DOI":"10.1016\/j.bmc.2006.01.072","article-title":"Linear and nonlinear QSAR study of N-hydroxy-2-[(phenylsulfonyl) amino] acetamide derivatives as matrix metalloproteinase inhibitors","volume":"14","author":"Fern\u00e1ndez","year":"2006","journal-title":"Bioorg. Med. Chem."},{"key":"10.1016\/j.jmgm.2023.108671_bib52","doi-asserted-by":"crossref","first-page":"6298","DOI":"10.1016\/j.bmc.2007.06.014","article-title":"QSAR modeling of matrix metalloproteinase inhibition by N-hydroxy-alpha-phenylsulfonylacetamide derivatives","volume":"15","author":"Fern\u00e1ndez","year":"2007","journal-title":"Bioorg. Med. Chem."},{"key":"10.1016\/j.jmgm.2023.108671_bib53","doi-asserted-by":"crossref","first-page":"243","DOI":"10.2174\/157340606776930790","article-title":"Quantitative structure-activity relationship studies on matrix metalloproteinase inhibitors: hydroxamic acid analogs","volume":"2","author":"Gupta","year":"2006","journal-title":"Med. Chem."},{"key":"10.1016\/j.jmgm.2023.108671_bib54","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.biori.2017.10.002","article-title":"Pharmacophore modeling and 3D QSAR studies for prediction of matrix metalloproteinases inhibitory activity of hydroxamate derivatives","volume":"1","author":"Rathee","year":"2017","journal-title":"Biotech. Res. Innov."}],"container-title":["Journal of Molecular Graphics and Modelling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1093326323002693?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1093326323002693?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T21:18:24Z","timestamp":1761081504000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1093326323002693"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1]]},"references-count":52,"alternative-id":["S1093326323002693"],"URL":"https:\/\/doi.org\/10.1016\/j.jmgm.2023.108671","relation":{},"ISSN":["1093-3263"],"issn-type":[{"value":"1093-3263","type":"print"}],"subject":[],"published":{"date-parts":[[2024,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A fragment-based exploration of diverse MMP-9 inhibitors through classification-dependent structural assessment","name":"articletitle","label":"Article Title"},{"value":"Journal of Molecular Graphics and Modelling","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jmgm.2023.108671","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 Elsevier Inc. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"108671"}}