{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T14:52:33Z","timestamp":1784559153882,"version":"3.55.0"},"reference-count":83,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T00:00:00Z","timestamp":1769817600000},"content-version":"vor","delay-in-days":30,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100006662","name":"Ardabil University of Medical Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006662","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["BioMed Research International"],"published-print":{"date-parts":[[2026,1]]},"abstract":"<jats:p>\n                    This study presents an integrated computational framework that combines three\u2010dimensional quantitative structure\u2013activity relationship (3D\u2010QSAR) modeling with molecular dynamics (MD) simulations to advance the rational design of triazole\u2010based urease inhibitors. Given the role of urease as a central virulence factor in\n                    <jats:italic>Helicobacter pylori<\/jats:italic>\n                    and its increasing relevance in antibiotic\u2010resistant infections, effective predictive methodologies are essential for early\u2010stage inhibitor development. A dataset of 54 triazole derivatives was examined using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA), generating statistically robust and predictive models that elucidate the steric, hydrophobic, and hydrogen\u2010bonding features underlying inhibitory potency. These insights, supported by molecular docking and structure\u2013activity relationship analyses, informed the construction of a pharmacophore model used to screen the ZINC database. Several candidate molecules, including ZINC84668437, ZINC84669798, and ZINC244633273, emerged as computationally promising and demonstrated favorable predicted druglikeness and ADMET characteristics. MD simulations were subsequently employed to evaluate the dynamic stability and conformational behavior of the ligand\u2013urease complexes, reinforcing the coherence of the integrated computational workflow. The primary contribution of this work resides in its methodological integration of complementary in silico approaches rather than in experimental validation. Although the findings offer mechanistic insights and prioritize potential lead compounds, they remain predictive and necessitate future empirical confirmation. Overall, the study establishes a rigorous and academically grounded computational strategy that can guide subsequent efforts in the design of selective urease inhibitors for\n                    <jats:italic>H. pylori<\/jats:italic>\n                    \u2013associated diseases.\n                  <\/jats:p>","DOI":"10.1155\/bmri\/4138899","type":"journal-article","created":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T13:57:30Z","timestamp":1769867850000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Rational Design of Novel Inhibitors: Integrating 3D\u2010QSAR and Molecular Dynamics"],"prefix":"10.1155","volume":"2026","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9874-1397","authenticated-orcid":false,"given":"Neda","family":"Shakour","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8436-9336","authenticated-orcid":false,"given":"Aida","family":"Fayyaz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7680-8191","authenticated-orcid":false,"given":"Farzin","family":"Hadizadeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7340-0468","authenticated-orcid":false,"given":"Saghi","family":"Sepehri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,1,31]]},"reference":[{"key":"e_1_2_10_1_2","doi-asserted-by":"publisher","DOI":"10.1002\/ardp.202000023"},{"key":"e_1_2_10_2_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.9b00355"},{"key":"e_1_2_10_3_2","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2015-309252"},{"key":"e_1_2_10_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.catcom.2015.09.006"},{"key":"e_1_2_10_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molstruc.2020.128740"},{"key":"e_1_2_10_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bioorg.2019.01.061"},{"key":"e_1_2_10_7_2","doi-asserted-by":"publisher","DOI":"10.1002\/jms.443"},{"key":"e_1_2_10_8_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13065-019-0556-0"},{"key":"e_1_2_10_9_2","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2012-302254"},{"key":"e_1_2_10_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bmc.2020.115759"},{"key":"e_1_2_10_11_2","doi-asserted-by":"publisher","DOI":"10.3390\/molecules26071952"},{"key":"e_1_2_10_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bmcl.2019.126846"},{"key":"e_1_2_10_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molstruc.2020.128234"},{"key":"e_1_2_10_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejmech.2010.08.034"},{"key":"e_1_2_10_15_2","doi-asserted-by":"publisher","DOI":"10.1002\/ardp.201800005"},{"key":"e_1_2_10_16_2","doi-asserted-by":"publisher","DOI":"10.1590\/S0103-50532012000500010"},{"key":"e_1_2_10_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ica.2014.09.012"},{"key":"e_1_2_10_18_2","doi-asserted-by":"publisher","DOI":"10.1002\/slct.202502280"},{"key":"e_1_2_10_19_2","doi-asserted-by":"publisher","DOI":"10.1007\/s42250-025-01244-w"},{"key":"e_1_2_10_20_2","doi-asserted-by":"publisher","DOI":"10.1002\/slct.202404972"},{"key":"e_1_2_10_21_2","doi-asserted-by":"publisher","DOI":"10.22036\/pcr.2023.394159.2326"},{"key":"e_1_2_10_22_2","doi-asserted-by":"publisher","DOI":"10.1186\/1752-153X-7-88"},{"key":"e_1_2_10_23_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11696-021-01653-4"},{"key":"e_1_2_10_24_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00894-010-0684-x"},{"key":"e_1_2_10_25_2","doi-asserted-by":"publisher","DOI":"10.2174\/156802610790232260"},{"key":"e_1_2_10_26_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms17050657"},{"key":"e_1_2_10_27_2","doi-asserted-by":"publisher","DOI":"10.1080\/14756360802166665"},{"key":"e_1_2_10_28_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bmcl.2018.08.025"},{"key":"e_1_2_10_29_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00044-012-9999-8"},{"key":"e_1_2_10_30_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejmech.2009.12.065"},{"key":"e_1_2_10_31_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiolchem.2016.12.008"},{"key":"e_1_2_10_32_2","doi-asserted-by":"publisher","DOI":"10.3390\/molecules23051191"},{"key":"e_1_2_10_33_2","doi-asserted-by":"publisher","DOI":"10.1155\/2021\/6380336"},{"key":"e_1_2_10_34_2","doi-asserted-by":"publisher","DOI":"10.3389\/fphar.2023.1177282"},{"key":"e_1_2_10_35_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejmech.2022.114273"},{"key":"e_1_2_10_36_2","doi-asserted-by":"publisher","DOI":"10.1002\/ardp.202300252"},{"key":"e_1_2_10_37_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bmcl.2015.05.069"},{"key":"e_1_2_10_38_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bioorg.2019.103024"},{"key":"e_1_2_10_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bioorg.2015.06.004"},{"key":"e_1_2_10_40_2","doi-asserted-by":"publisher","DOI":"10.1002\/ardp.202200158"},{"key":"e_1_2_10_41_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejmech.2013.07.047"},{"key":"e_1_2_10_42_2","doi-asserted-by":"publisher","DOI":"10.1002\/cbdv.202300054"},{"key":"e_1_2_10_43_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-005-4788-9"},{"key":"e_1_2_10_44_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm800562d"},{"key":"e_1_2_10_45_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms17020144"},{"key":"e_1_2_10_46_2","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbx030"},{"key":"e_1_2_10_47_2","doi-asserted-by":"publisher","DOI":"10.2174\/1381612033454595"},{"key":"e_1_2_10_48_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1359-0278(98)00019-4"},{"key":"e_1_2_10_49_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2003.10.027"},{"key":"e_1_2_10_50_2","doi-asserted-by":"publisher","DOI":"10.1002\/minf.201600060"},{"key":"e_1_2_10_51_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejmech.2023.115211"},{"key":"e_1_2_10_52_2","doi-asserted-by":"publisher","DOI":"10.1080\/07391102.2023.2279281"},{"key":"e_1_2_10_53_2","doi-asserted-by":"publisher","DOI":"10.1080\/07391102.2022.2087103"},{"key":"e_1_2_10_54_2","doi-asserted-by":"publisher","DOI":"10.34172\/PS.2021.4"},{"key":"e_1_2_10_55_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molstruc.2024.140228"},{"key":"e_1_2_10_56_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiolchem.2022.107642"},{"key":"e_1_2_10_57_2","doi-asserted-by":"publisher","DOI":"10.1021\/ci100427j"},{"key":"e_1_2_10_58_2","doi-asserted-by":"publisher","DOI":"10.1007\/s0089400060438"},{"key":"e_1_2_10_59_2","doi-asserted-by":"publisher","DOI":"10.2174\/1381612828666220926095922"},{"key":"e_1_2_10_60_2","doi-asserted-by":"publisher","DOI":"10.1021\/ci0342526"},{"key":"e_1_2_10_61_2","doi-asserted-by":"publisher","DOI":"10.4155\/fmc-2017-0049"},{"key":"e_1_2_10_62_2","doi-asserted-by":"publisher","DOI":"10.1002\/qsar.19880070105"},{"key":"e_1_2_10_63_2","doi-asserted-by":"publisher","DOI":"10.1002\/cem.1180010306"},{"key":"e_1_2_10_64_2","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1145\/267460.267491","volume-title":"roceedings of the Tenth Annual Conference on Computational Learning Theory","author":"Kearns M.","year":"1997"},{"key":"e_1_2_10_65_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molstruc.2019.126961"},{"key":"e_1_2_10_66_2","doi-asserted-by":"publisher","DOI":"10.1039\/C9FO03018B"},{"key":"e_1_2_10_67_2","doi-asserted-by":"publisher","DOI":"10.1021\/ci200579f"},{"key":"e_1_2_10_68_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11030-012-9395-9"},{"key":"e_1_2_10_69_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jics.2022.100582"},{"key":"e_1_2_10_70_2","doi-asserted-by":"publisher","DOI":"10.17179\/excli2020-2932"},{"key":"e_1_2_10_71_2","doi-asserted-by":"publisher","DOI":"10.2174\/0118715206296355240325113920"},{"key":"e_1_2_10_72_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-025-10545-6"},{"key":"e_1_2_10_73_2","doi-asserted-by":"publisher","DOI":"10.1089\/mdr.2022.0134"},{"key":"e_1_2_10_74_2","doi-asserted-by":"publisher","DOI":"10.1142\/S2737599424500038"},{"key":"e_1_2_10_75_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jocs.2024.102497"},{"key":"e_1_2_10_76_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-030-64872-5_7"},{"key":"e_1_2_10_77_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1056-8719(00)00107-6"},{"key":"e_1_2_10_78_2","doi-asserted-by":"publisher","DOI":"10.1021\/ci300367a"},{"key":"e_1_2_10_79_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep42717"},{"key":"e_1_2_10_80_2","doi-asserted-by":"publisher","DOI":"10.1080\/07391102.2023.2298734"},{"key":"e_1_2_10_81_2","doi-asserted-by":"crossref","DOI":"10.1007\/s40203-025-00407-4","article-title":"In-Silico Identification of COX-2 Inhibitory Phytochemicals From Traditional Medicinal Plants: Molecular Docking, Dynamics, and Safety Predictions","volume":"13","author":"Abdollahi F.","year":"2025","journal-title":"Silico Pharmacology"},{"key":"e_1_2_10_82_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0191838"},{"key":"e_1_2_10_83_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bioorg.2021.105162"}],"container-title":["BioMed Research International"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1155\/bmri\/4138899","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1155\/bmri\/4138899","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1155\/bmri\/4138899","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T13:57:32Z","timestamp":1769867852000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1155\/bmri\/4138899"}},"subtitle":[],"editor":[{"given":"Baisakhi","family":"Banerjee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":83,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1]]}},"alternative-id":["10.1155\/bmri\/4138899"],"URL":"https:\/\/doi.org\/10.1155\/bmri\/4138899","archive":["Portico"],"relation":{},"ISSN":["2314-6133","2314-6141"],"issn-type":[{"value":"2314-6133","type":"print"},{"value":"2314-6141","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1]]},"assertion":[{"value":"2025-06-11","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-12-17","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-01-31","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"4138899"}}