{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T05:51:11Z","timestamp":1784872271334,"version":"3.55.0"},"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T00:00:00Z","timestamp":1771286400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    Matrix metalloproteinase-9 (MMP-9) is a zinc-dependent enzyme that degrades the extracellular matrix and is involved in various diseases, including rheumatoid arthritis, atherosclerosis, tumor invasion, and metastasis. Despite the development of inhibitors, none have succeeded in trials. Our goal was to find potential inhibitors to regulate its proteolytic activity. Ligand- and structure-based drug design approaches were explored to identify inhibitors against wild-type (1GKC) and mutant (2OW1) MMP-9. A pharmacophore model was created, and drug-like molecules were prioritized to guide the development of benzamide and 1H-indole-2-carboxamide derivatives. These compounds were synthesized and characterized using \u00b9H NMR,\n                    <jats:sup>13<\/jats:sup>\n                    C NMR, and HRMS (ESI). An experimental evaluation assessed their inhibitory potential and IC\n                    <jats:sub>50<\/jats:sub>\n                    values against MMP-9. Most tested inhibitors fit the pharmacophore model, which consists of three aromatic\/hydrophobic spheres and two hydrogen-bond donors\/acceptors. Compounds\n                    <jats:bold>1<\/jats:bold>\n                    ,\n                    <jats:bold>2<\/jats:bold>\n                    ,\n                    <jats:bold>8<\/jats:bold>\n                    ,\n                    <jats:bold>10<\/jats:bold>\n                    ,\n                    <jats:bold>20<\/jats:bold>\n                    ,\n                    <jats:bold>21<\/jats:bold>\n                    ,\n                    <jats:bold>27<\/jats:bold>\n                    , and\n                    <jats:bold>29<\/jats:bold>\n                    exhibited significant inhibition (P\u2009&lt;\u20090.0001) of over 60%. Compounds\n                    <jats:bold>2<\/jats:bold>\n                    and\n                    <jats:bold>20<\/jats:bold>\n                    inhibited growth by over 70%, with IC\n                    <jats:sub>50<\/jats:sub>\n                    values of 28.59 \u03bcM and 30.82 \u03bcM, respectively. The IF docking showed strong binding for these, with scores of \u22129.179 and \u221210.739 kcal\/mol. The alignment between the computational approach and experimental validation reinforces the inhibitor\u2019s specificity and potency, confirms the docking model, and suggests that the predicted binding pose represents key biological interactions.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0337544","type":"journal-article","created":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T18:50:53Z","timestamp":1771354253000},"page":"e0337544","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Integrative computational, synthetic, experimental evaluation of targeted inhibitors against matrix metalloproteinase-9: Toward precision modulation of proteolytic activity"],"prefix":"10.1371","volume":"21","author":[{"given":"Zainab Ahmed","family":"Rashid","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1428-5097","authenticated-orcid":true,"given":"Dima A.","family":"Sabbah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kamal","family":"Sweidan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rima","family":"Hajjo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4823-0708","authenticated-orcid":true,"given":"Sanaa K.","family":"Bardaweel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,2,17]]},"reference":[{"issue":"4","key":"pone.0337544.ref001","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1007\/s000180050320","article-title":"Structural properties of matrix metalloproteinases","volume":"55","author":"W Bode","year":"1999","journal-title":"Cell Mol Life Sci"},{"key":"pone.0337544.ref002","doi-asserted-by":"crossref","first-page":"896099","DOI":"10.3389\/fmolb.2022.896099","article-title":"Insights into the role of matrix metalloproteinases in cancer and its various therapeutic aspects: a review","volume":"9","author":"S Mustafa","year":"2022","journal-title":"Front Mol Biosci"},{"issue":"4","key":"pone.0337544.ref003","doi-asserted-by":"crossref","DOI":"10.1111\/cpr.12649","article-title":"Matrix metalloproteinases: Expression, regulation and role in the immunopathology of tuberculosis","volume":"52","author":"N Sabir","year":"2019","journal-title":"Cell Prolif"},{"key":"pone.0337544.ref004","doi-asserted-by":"crossref","first-page":"116786","DOI":"10.1016\/j.lfs.2019.116786","article-title":"The role of matrix metalloproteinases in osteoarthritis pathogenesis: An updated review","volume":"234","author":"E-SE Mehana","year":"2019","journal-title":"Life Sci"},{"issue":"5","key":"pone.0337544.ref005","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1002\/path.5225","article-title":"Recent advances in understanding the roles of matrix metalloproteinases in tumour invasion and metastasis","volume":"247","author":"GA Conlon","year":"2019","journal-title":"J Pathol"},{"issue":"3","key":"pone.0337544.ref006","doi-asserted-by":"crossref","first-page":"2170","DOI":"10.3390\/cimb45030139","article-title":"In Vitro Evaluation of ALDH1A3-affinic compounds on breast and prostate cancer cell lines as single treatments and in combination with doxorubicin","volume":"45","author":"OH Abusara","year":"2023","journal-title":"Curr Issues Mol Biol"},{"issue":"20","key":"pone.0337544.ref007","doi-asserted-by":"crossref","DOI":"10.1016\/j.heliyon.2024.e39402","article-title":"Downregulation of aquaporins and PI3K\/AKT and upregulation of PTEN expression induced by the flavone scutellarein in human colon cancer cell lines","volume":"10","author":"N Tarawneh","year":"2024","journal-title":"Heliyon"},{"issue":"15","key":"pone.0337544.ref008","doi-asserted-by":"crossref","first-page":"12133","DOI":"10.3390\/ijms241512133","article-title":"Novel matrix metalloproteinase-9 (MMP-9) inhibitors in cancer treatment","volume":"24","author":"ZA Rashid","year":"2023","journal-title":"Int J Mol Sci"},{"issue":"5","key":"pone.0337544.ref009","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1002\/cmdc.200700290","article-title":"Zinc-binding groups modulate selective inhibition of MMPs","volume":"3","author":"A Agrawal","year":"2008","journal-title":"ChemMedChem"},{"issue":"4","key":"pone.0337544.ref010","doi-asserted-by":"crossref","first-page":"285","DOI":"10.2174\/1568009054064615","article-title":"Matrix metalloproteinase inhibitors as anticancer therapeutics","volume":"5","author":"F Mannello","year":"2005","journal-title":"Curr Cancer Drug Targets"},{"key":"pone.0337544.ref011","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.arr.2013.12.001","article-title":"Matrix metalloproteinase enzymes and their naturally derived inhibitors: novel targets in photocarcinoma therapy","volume":"13","author":"A Gupta","year":"2014","journal-title":"Ageing Res Rev"},{"issue":"9","key":"pone.0337544.ref012","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1038\/nrd2092","article-title":"Targeting proteases: successes, failures and future prospects","volume":"5","author":"B Turk","year":"2006","journal-title":"Nat Rev Drug Discov"},{"issue":"22","key":"pone.0337544.ref013","doi-asserted-by":"crossref","first-page":"5822","DOI":"10.1016\/j.bmcl.2006.08.066","article-title":"Potent, selective pyrimidinetrione-based inhibitors of MMP-13","volume":"16","author":"LA Reiter","year":"2006","journal-title":"Bioorg Med Chem Lett"},{"issue":"19","key":"pone.0337544.ref014","doi-asserted-by":"crossref","first-page":"13253","DOI":"10.1021\/acs.jmedchem.2c01088","article-title":"Discovery of highly potent and selective matrix metalloproteinase-7 inhibitors by hybridizing the s1\u2019 subsite binder with short peptides","volume":"65","author":"H Tabuse","year":"2022","journal-title":"J Med Chem"},{"key":"pone.0337544.ref015","unstructured":"Molecular Operating Environment (MOE) | MOEsaic | PSILO. https:\/\/www.chemcomp.com\/en\/Products.htm. Accessed 2024 September 20."},{"issue":"4","key":"pone.0337544.ref016","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 Arg424 side-chain to selectivity","volume":"371","author":"A Tochowicz","year":"2007","journal-title":"J Mol Biol"},{"key":"pone.0337544.ref017","unstructured":"NCI\/CADD Group Chemoinformatics Tools and User Services. https:\/\/cactus.nci.nih.gov\/. Accessed 2024 May 6."},{"issue":"1","key":"pone.0337544.ref018","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":"S Rowsell","year":"2002","journal-title":"J Mol Biol"},{"key":"pone.0337544.ref019","unstructured":"Maestro. Schr\u00f6dinger. https:\/\/www.schrodinger.com\/platform\/products\/maestro\/. Accessed 2025 February 1."},{"key":"pone.0337544.ref020","unstructured":"Glide. Schr\u00f6dinger. https:\/\/www.schrodinger.com\/platform\/products\/glide\/. Accessed 2024 September 28."},{"key":"pone.0337544.ref021","unstructured":"Synthesis of Amides. Chemistry LibreTexts. https:\/\/chem.libretexts.org\/Bookshelves\/Organic_Chemistry\/Basic_Principles_of_Organic_Chemistry_(Roberts_and_Caserio)\/24%3A_Organonitrogen_Compounds_II_-_Amides_Nitriles_and_Nitro_Compounds\/24.03%3A_Synthesis_of_Amides. 2014. Accessed 2025 February 16."},{"issue":"19","key":"pone.0337544.ref022","doi-asserted-by":"crossref","first-page":"6019","DOI":"10.3390\/molecules26196019","article-title":"Monoamine oxidase (MAO) as a potential target for anticancer drug design and development","volume":"26","author":"R Aljanabi","year":"2021","journal-title":"Molecules"},{"issue":"11","key":"pone.0337544.ref023","doi-asserted-by":"crossref","first-page":"2685","DOI":"10.1016\/j.bmcl.2016.04.011","article-title":"Computer-aided design, synthesis, and biological evaluation of new indole-2-carboxamide derivatives as PI3K\u03b1\/EGFR inhibitors","volume":"26","author":"K Sweidan","year":"2016","journal-title":"Bioorg Med Chem Lett"},{"issue":"4","key":"pone.0337544.ref024","doi-asserted-by":"crossref","first-page":"863","DOI":"10.3109\/14756366.2012.692085","article-title":"The pharmacological effects of novel 5-fluoro-N-(9,10-dihydro-9,10-dioxoanthracen-8-yl)-1H-indole-2-carboxamide derivatives on plasma lipid profile of Triton-WR-1339-induced Wistar rats","volume":"28","author":"G Shattat","year":"2013","journal-title":"J Enzyme Inhib Med Chem"},{"key":"pone.0337544.ref025","unstructured":"Cortellis Life Sciences Intelligence Solutions | Clarivate. https:\/\/clarivate.com\/life-sciences-healthcare\/cortellis\/. Accessed 2024 November 26."},{"key":"pone.0337544.ref026","unstructured":"RCSB PDB: Homepage. https:\/\/www.rcsb.org\/. Accessed 2024 May 6."},{"issue":"8","key":"pone.0337544.ref027","doi-asserted-by":"crossref","first-page":"2519","DOI":"10.1039\/C6MB00066E","article-title":"Identification of novel selective MMP-9 inhibitors as potential anti-metastatic lead using structure-based hierarchical virtual screening and molecular dynamics simulation","volume":"12","author":"S Kalva","year":"2016","journal-title":"Mol Biosyst"},{"issue":"1","key":"pone.0337544.ref028","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":"D Rathee","year":"2017","journal-title":"Biotechnology Research and Innovation"},{"issue":"4","key":"pone.0337544.ref029","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1080\/07391102.2018.1444510","article-title":"Identification of selective MMP-9 inhibitors through multiple e-pharmacophore, ligand-based pharmacophore, molecular docking, and density functional theory approaches","volume":"37","author":"S Jana","year":"2019","journal-title":"J Biomol Struct Dyn"},{"issue":"43","key":"pone.0337544.ref030","doi-asserted-by":"crossref","first-page":"26820","DOI":"10.1039\/D1RA03891E","article-title":"Ligand-based pharmacophore modeling and molecular dynamic simulation approaches to identify putative MMP-9 inhibitors","volume":"11","author":"BKR Sanapalli","year":"2021","journal-title":"RSC Adv"},{"key":"pone.0337544.ref031","unstructured":"NCI Data Catalog | CBIIT. https:\/\/datascience.cancer.gov\/resources\/nci-data-catalog. Accessed 2024 September 28."},{"issue":"4","key":"pone.0337544.ref032","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.ddtec.2004.11.007","article-title":"Lead- and drug-like compounds: the rule-of-five revolution","volume":"1","author":"CA Lipinski","year":"2004","journal-title":"Drug Discov Today Technol"},{"issue":"21","key":"pone.0337544.ref033","doi-asserted-by":"crossref","first-page":"6177","DOI":"10.1021\/jm051256o","article-title":"Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes","volume":"49","author":"RA Friesner","year":"2006","journal-title":"J Med Chem"},{"issue":"7","key":"pone.0337544.ref034","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1021\/jm0306430","article-title":"Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy","volume":"47","author":"RA Friesner","year":"2004","journal-title":"J Med Chem"},{"issue":"4","key":"pone.0337544.ref035","doi-asserted-by":"crossref","first-page":"2630","DOI":"10.1021\/acs.jctc.1c00136","article-title":"Reliable and accurate solution to the induced fit docking problem for protein-ligand binding","volume":"17","author":"EB Miller","year":"2021","journal-title":"J Chem Theory Comput"},{"issue":"9","key":"pone.0337544.ref036","doi-asserted-by":"crossref","first-page":"5710","DOI":"10.1021\/acs.jctc.2c00371","article-title":"Induced-fit docking enables accurate free energy perturbation calculations in homology models","volume":"18","author":"T Xu","year":"2022","journal-title":"J Chem Theory Comput"},{"key":"pone.0337544.ref037","unstructured":"PyMOL. https:\/\/www.pymol.org\/. Accessed 2025 January 18."},{"key":"pone.0337544.ref038","doi-asserted-by":"crossref","first-page":"111875","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":"MS Ayoup","year":"2020","journal-title":"Eur J Med Chem"},{"issue":"24","key":"pone.0337544.ref039","doi-asserted-by":"crossref","first-page":"21131","DOI":"10.1021\/acsomega.2c01949","article-title":"First-in-class star-shaped triazine dendrimers endowed with MMP-9 inhibition and VEGF suppression capacity: design, synthesis, and anticancer evaluation","volume":"7","author":"NS Haiba","year":"2022","journal-title":"ACS Omega"},{"issue":"7","key":"pone.0337544.ref040","doi-asserted-by":"crossref","first-page":"3042","DOI":"10.1021\/cr030448t","article-title":"Quantitative structure-activity relationship studies on zinc-containing metalloproteinase inhibitors","volume":"107","author":"SP Gupta","year":"2007","journal-title":"Chem Rev"},{"issue":"3","key":"pone.0337544.ref041","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1006\/bbrc.2000.3212","article-title":"New thiol and sulfodiimine metalloproteinase inhibitors and their effect on human microvascular endothelial cell growth","volume":"274","author":"QX Sang","year":"2000","journal-title":"Biochem Biophys Res Commun"},{"issue":"8","key":"pone.0337544.ref042","doi-asserted-by":"crossref","first-page":"310","DOI":"10.6026\/97320630005310","article-title":"Structural insights into the binding of MMP9 inhibitors","volume":"5","author":"A Tandon","year":"2011","journal-title":"Bioinformation"},{"issue":"38","key":"pone.0337544.ref043","doi-asserted-by":"crossref","first-page":"6515","DOI":"10.1016\/j.tetlet.2005.07.078","article-title":"Synthesis of \u03b1-trifluoromethyl-\u03b1-amino-\u03b2-sulfone hydroxamates: novel nanomolar inhibitors of matrix metalloproteinases","volume":"46","author":"R Sinisi","year":"2005","journal-title":"Tetrahedron Letters"},{"issue":"2","key":"pone.0337544.ref044","doi-asserted-by":"crossref","first-page":"146","DOI":"10.2174\/157340911795677602","article-title":"Molecular docking: a powerful approach for structure-based drug discovery","volume":"7","author":"X-Y Meng","year":"2011","journal-title":"Curr Comput Aided Drug Des"},{"issue":"26","key":"pone.0337544.ref045","doi-asserted-by":"crossref","first-page":"6507","DOI":"10.1021\/jm070593p","article-title":"A flexible approach to induced fit docking","volume":"50","author":"SB Nabuurs","year":"2007","journal-title":"J Med Chem"},{"key":"pone.0337544.ref046","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.ejmech.2015.04.023","article-title":"Synthesis, crystal structure and effect of indeno[1,2-b]indole derivatives on prostate cancer in vitro. Potential effect against MMP-9","volume":"96","author":"G Lobo","year":"2015","journal-title":"Eur J Med Chem"},{"issue":"5","key":"pone.0337544.ref047","doi-asserted-by":"crossref","first-page":"762","DOI":"10.2174\/1871520616666160802115737","article-title":"The effects of 1,3,5-trisubstituted indole derivatives on cell growth, apoptosis and MMP-2\/9 mRNA expression of MCF-7 human breast cancer cells","volume":"17","author":"F Bakar","year":"2017","journal-title":"Anticancer Agents Med Chem"},{"issue":"2","key":"pone.0337544.ref048","doi-asserted-by":"crossref","first-page":"265","DOI":"10.4103\/jcrt.jcrt_1256_21","article-title":"Indole curcumin combats metastatic HBV-positive hepatocellular carcinoma by inhibiting cell proliferation, migration, and matrix metalloproteinase-9 activity","volume":"19","author":"S Subramanian","year":"2023","journal-title":"J Cancer Res Ther"},{"issue":"13","key":"pone.0337544.ref049","doi-asserted-by":"crossref","first-page":"8917","DOI":"10.1021\/acs.jmedchem.3c00511","article-title":"Newly synthesized 3-indolyl furanoid inhibits matrix metalloproteinase-9 activity and prevents nonsteroidal anti-inflammatory drug-induced gastric ulceration","volume":"66","author":"DS Rudra","year":"2023","journal-title":"J Med Chem"},{"issue":"8","key":"pone.0337544.ref050","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1080\/1062936X.2021.1955414","article-title":"Insight into the structural requirement of aryl sulphonamide based gelatinases (MMP-2 and MMP-9) inhibitors - Part I: 2D-QSAR, 3D-QSAR topomer CoMFA and Na\u00efve Bayes studies - First report of 3D-QSAR Topomer CoMFA analysis for MMP-9 inhibitors and jointly inhibitors of gelatinases together","volume":"32","author":"S Das","year":"2021","journal-title":"SAR QSAR Environ Res"},{"key":"pone.0337544.ref051","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/j.ejmech.2017.02.014","article-title":"Arylsulfonamides and selectivity of matrix metalloproteinase-2: An overview","volume":"129","author":"N Adhikari","year":"2017","journal-title":"Eur J Med Chem"},{"issue":"2","key":"pone.0337544.ref052","doi-asserted-by":"crossref","first-page":"216","DOI":"10.23893\/1307-2080.APS.05913","article-title":"Synthesis of New 1,2,4-Triazole Derivatives and Investigation of Their Matrix Metalloproteinase-9 (MMP-9) Inhibition Properties","volume":"59","author":"L Yurtta\u015f","year":"2021","journal-title":"actapharm"},{"issue":"2","key":"pone.0337544.ref053","doi-asserted-by":"crossref","first-page":"415","DOI":"10.3390\/molecules23020415","article-title":"4-Thiazolidinone derivatives as MMP inhibitors in tissue damage: synthesis, biological evaluation and docking studies","volume":"23","author":"M Incerti","year":"2018","journal-title":"Molecules"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0337544","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T18:51:01Z","timestamp":1771354261000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0337544"}},"subtitle":[],"editor":[{"given":"Ahmed","family":"Elkamhawy","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,2,17]]},"references-count":53,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2,17]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0337544","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,17]]}}}