{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T18:35:43Z","timestamp":1792521343592,"version":"4.5.0"},"reference-count":91,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T00:00:00Z","timestamp":1771027200000},"content-version":"vor","delay-in-days":44,"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\/501100002383","name":"King Saud University","doi-asserted-by":"publisher","award":["ORF-2026-1438"],"award-info":[{"award-number":["ORF-2026-1438"]}],"id":[{"id":"10.13039\/501100002383","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Tropical Medicine"],"published-print":{"date-parts":[[2026,1]]},"abstract":"<jats:p>\n                    As the second most deadly infectious disease worldwide after COVID\u201019, tuberculosis (TB) remains a pressing global health issue, further aggravated by multidrug\u2010resistant TB (MDR\u2010TB) and extensively drug\u2010resistant TB (XDR\u2010TB) strains. There is an urgent need to identify new anti\u2010TB treatments and novel therapeutics to confront drug resistance. The decaprenylphosphoryl\u2010D\u2010ribose oxidase (DprE1) is an essential protein for the biosynthesis of the mycobacterial cell wall, and its inhibition features a promising antitubercular strategy. NPAtlas was utilized as a reference database, comprising natural products with confirmed biological effects. The aim of the current study is to identify and prioritize promising nitro\u2010containing natural products from the NPAtlas as potential covalent DprE1 inhibitors using advanced in silico approaches. Herein, the docking scores of 133 nitro\u2010containing NPAtlas compounds were assessed using a covalent docking technique. Thereafter, NPAtlas compounds with docking scores lower than PBTZ169 (calc. \u22127.8\u2009kcal\u00b7mol\n                    <jats:sup>\u22121<\/jats:sup>\n                    ) were subjected to molecular dynamics simulation (MDS), accompanied by binding energy estimations utilizing the MM\u2010GBSA approach. Based on MM\u2010GBSA\/\/250\u2009ns MDS, NPA011203, NPA013234, NPA016048, NPA012944, NPA001712, and NPA002823 demonstrated higher binding affinities against DprE1 with \u0394\n                    <jats:italic>G<\/jats:italic>\n                    <jats:sub>binding<\/jats:sub>\n                    values of \u221275.6, \u221262.7, \u221261.6, \u221257.6, \u221254.8, and \u221250.7\u2009kcal\u00b7mol\n                    <jats:sup>\u22121<\/jats:sup>\n                    , respectively, than PBTZ169 (calc. \u221249.4\u2009kcal\u00b7mol\n                    <jats:sup>\u22121<\/jats:sup>\n                    ). The identified NPAtlas compounds also demonstrated structural and energetic stability within the DprE1 active site throughout 250\u2009ns MDS. Physicochemical and ADMET predictions of the identified NPAtlas compounds indicated a suitable molecular size, favorable absorption, and negligible toxicity, suggesting their potential oral bioavailability. These in silico outcomes provide preliminary insights into the identified NPAtlas compounds as potential DprE1 inhibitors and can guide subsequent in vitro\/in vivo experiments.\n                  <\/jats:p>","DOI":"10.1155\/jotm\/8879019","type":"journal-article","created":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T15:00:46Z","timestamp":1771081246000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Exploring the Natural Products Atlas (NPAtlas) Database for Hunting Prospective Irreversible Covalent DprE1 Inhibitors With Antitubercular Activity: An Integrated\n                    <i>In-Silico<\/i>\n                    Approach"],"prefix":"10.1155","volume":"2026","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4819-2040","authenticated-orcid":false,"given":"Mahmoud A. A.","family":"Ibrahim","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-3141-9458","authenticated-orcid":false,"given":"Doaa G. M.","family":"Mahmoud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2753-0031","authenticated-orcid":false,"given":"Sherif S.","family":"Ebada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2579-6351","authenticated-orcid":false,"given":"Peter A.","family":"Sidhom","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2474-076X","authenticated-orcid":false,"given":"Gamal A. H.","family":"Mekhemer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0343-4969","authenticated-orcid":false,"given":"Mohamed-Elamir F.","family":"Hegazy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4897-2998","authenticated-orcid":false,"given":"Yanshuo","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-7732-9933","authenticated-orcid":false,"given":"Tarad","family":"Abalkhail","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,2,14]]},"reference":[{"key":"e_1_2_12_1_2","doi-asserted-by":"publisher","DOI":"10.1038\/31159"},{"key":"e_1_2_12_2_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0000744"},{"key":"e_1_2_12_3_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.0010005"},{"key":"e_1_2_12_4_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.052548299"},{"key":"e_1_2_12_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.01783-05"},{"key":"e_1_2_12_6_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1804.110888"},{"key":"e_1_2_12_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.drup.2020.100695"},{"key":"e_1_2_12_8_2","doi-asserted-by":"publisher","DOI":"10.1111\/jam.14478"},{"key":"e_1_2_12_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2022.03.011"},{"key":"e_1_2_12_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tips.2008.08.001"},{"key":"e_1_2_12_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/s0140-6736(13)62675-6"},{"key":"e_1_2_12_12_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40001-021-00502-0"},{"key":"e_1_2_12_13_2","doi-asserted-by":"publisher","DOI":"10.1596\/978-1-4648-0524-0_ch11"},{"key":"e_1_2_12_14_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21217974"},{"key":"e_1_2_12_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2021.05.003"},{"key":"e_1_2_12_16_2","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms13020396"},{"key":"e_1_2_12_17_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.8b00281"},{"key":"e_1_2_12_18_2","doi-asserted-by":"publisher","DOI":"10.1021\/acschembio.5b00237"},{"key":"e_1_2_12_19_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1171583"},{"key":"e_1_2_12_20_2","doi-asserted-by":"publisher","DOI":"10.1021\/acsinfecdis.5b00065"},{"key":"e_1_2_12_21_2","doi-asserted-by":"publisher","DOI":"10.1021\/cb5007163"},{"key":"e_1_2_12_22_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.8b01356"},{"key":"e_1_2_12_23_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm5002937"},{"key":"e_1_2_12_24_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm500571f"},{"key":"e_1_2_12_25_2","doi-asserted-by":"publisher","DOI":"10.1128\/aac.02020-19"},{"key":"e_1_2_12_26_2","doi-asserted-by":"publisher","DOI":"10.1021\/acschembio.8b00790"},{"key":"e_1_2_12_27_2","doi-asserted-by":"publisher","DOI":"10.1021\/acsmedchemlett.8b00634"},{"key":"e_1_2_12_28_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3004395"},{"key":"e_1_2_12_29_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja106357w"},{"key":"e_1_2_12_30_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja211042r"},{"key":"e_1_2_12_31_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja311058q"},{"key":"e_1_2_12_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jiph.2022.08.016"},{"key":"e_1_2_12_33_2","doi-asserted-by":"publisher","DOI":"10.1002\/emmm.201303575"},{"key":"e_1_2_12_34_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.crphar.2021.100037"},{"key":"e_1_2_12_35_2","doi-asserted-by":"publisher","DOI":"10.1039\/d0ra00750a"},{"key":"e_1_2_12_36_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms24065202"},{"key":"e_1_2_12_37_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00253-013-5218-x"},{"key":"e_1_2_12_38_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bcp.2021.114906"},{"key":"e_1_2_12_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bioorg.2018.12.018"},{"key":"e_1_2_12_40_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1168243"},{"key":"e_1_2_12_41_2","doi-asserted-by":"publisher","DOI":"10.1021\/np9604893"},{"key":"e_1_2_12_42_2","doi-asserted-by":"publisher","DOI":"10.1039\/c9np00068b"},{"key":"e_1_2_12_43_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae1093"},{"key":"e_1_2_12_44_2","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.3"},{"key":"e_1_2_12_45_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki464"},{"key":"e_1_2_12_46_2","doi-asserted-by":"publisher","DOI":"10.1021\/acscentsci.9b00806"},{"key":"e_1_2_12_47_2","volume-title":"OMEGA 4.1.1.0","author":"OpenEye Scientific Software","year":"2021"},{"key":"e_1_2_12_48_2","doi-asserted-by":"publisher","DOI":"10.1021\/ci100031x"},{"key":"e_1_2_12_49_2","doi-asserted-by":"publisher","DOI":"10.1002\/(sici)1096-987x(199905)20:7<720::aid-jcc7>3.0.co;2-x"},{"key":"e_1_2_12_50_2","volume-title":"SZYBKI 2.4.0.0","author":"OpenEye Scientific Software","year":"2021"},{"key":"e_1_2_12_51_2","doi-asserted-by":"publisher","DOI":"10.1107\/s2052520616003954"},{"key":"e_1_2_12_52_2","doi-asserted-by":"publisher","DOI":"10.1016\/0040-4020(80)80168-2"},{"key":"e_1_2_12_53_2","volume-title":"QUACPAC 2.1.3.0","author":"OpenEye Scientific Software","year":"2021"},{"key":"e_1_2_12_54_2","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.1666"},{"key":"e_1_2_12_55_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21256"},{"key":"e_1_2_12_56_2","doi-asserted-by":"publisher","DOI":"10.1002\/pro.2733"},{"key":"e_1_2_12_57_2","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2016.051"},{"key":"e_1_2_12_58_2","volume-title":"AMBER 2020","author":"University of California","year":"2020"},{"key":"e_1_2_12_59_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0314422"},{"key":"e_1_2_12_60_2","doi-asserted-by":"publisher","DOI":"10.1002\/open.202500237"},{"key":"e_1_2_12_61_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-025-24162-w"},{"key":"e_1_2_12_62_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20035"},{"key":"e_1_2_12_63_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b00255"},{"key":"e_1_2_12_64_2","volume-title":"Gaussian 09, Revision E.01","author":"Frisch Gwt J.","year":"2009"},{"key":"e_1_2_12_65_2","doi-asserted-by":"publisher","DOI":"10.1021\/j100142a004"},{"key":"e_1_2_12_66_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.445869"},{"key":"e_1_2_12_67_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540130805"},{"key":"e_1_2_12_68_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.464397"},{"key":"e_1_2_12_69_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.448118"},{"key":"e_1_2_12_70_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.1332996"},{"key":"e_1_2_12_71_2","volume-title":"BIOVIA DSV, Version 2019","author":"Dassault Syst\u00e8mes","year":"2019"},{"key":"e_1_2_12_72_2","doi-asserted-by":"publisher","DOI":"10.1023\/a:1008763014207"},{"key":"e_1_2_12_73_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20033"},{"key":"e_1_2_12_74_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21666"},{"key":"e_1_2_12_75_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.chemrev.9b00055"},{"key":"e_1_2_12_76_2","doi-asserted-by":"publisher","DOI":"10.1039\/c7cp07623a"},{"key":"e_1_2_12_77_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm011027b"},{"key":"e_1_2_12_78_2","doi-asserted-by":"publisher","DOI":"10.1016\/s1359-6446(99)01451-8"},{"key":"e_1_2_12_79_2","first-page":"540","article-title":"Guiding Molecules Towards Drug-Likeness","volume":"5","author":"Egan W. J.","year":"2002","journal-title":"Current Opinion in Drug Discovery & Development"},{"key":"e_1_2_12_80_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.addr.2016.05.007"},{"key":"e_1_2_12_81_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.drudis.2021.11.005"},{"key":"e_1_2_12_82_2","doi-asserted-by":"publisher","DOI":"10.1016\/s0040-4020(97)10396-9"},{"key":"e_1_2_12_83_2","doi-asserted-by":"publisher","DOI":"10.1002\/anie.201409964"},{"key":"e_1_2_12_84_2","doi-asserted-by":"publisher","DOI":"10.1002\/chem.202000117"},{"key":"e_1_2_12_85_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.phytochem.2008.02.002"},{"key":"e_1_2_12_86_2","doi-asserted-by":"publisher","DOI":"10.7164\/antibiotics.47.1219"},{"key":"e_1_2_12_87_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.5b01684"},{"key":"e_1_2_12_88_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-62703-342-8_7"},{"key":"e_1_2_12_89_2","doi-asserted-by":"publisher","DOI":"10.1186\/1758-2946-4-31"},{"key":"e_1_2_12_90_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrd.2018.197"},{"key":"e_1_2_12_91_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.5b00104"}],"container-title":["Journal of Tropical Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1155\/jotm\/8879019","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1155\/jotm\/8879019","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1155\/jotm\/8879019","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T10:06:34Z","timestamp":1773914794000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1155\/jotm\/8879019"}},"subtitle":[],"editor":[{"given":"Rajib","family":"Chowdhury","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":91,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1]]}},"alternative-id":["10.1155\/jotm\/8879019"],"URL":"https:\/\/doi.org\/10.1155\/jotm\/8879019","archive":["Portico"],"relation":{},"ISSN":["1687-9686","1687-9694"],"issn-type":[{"value":"1687-9686","type":"print"},{"value":"1687-9694","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1]]},"assertion":[{"value":"2025-07-23","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-01-09","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-02-14","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"8879019"}}