{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,11]],"date-time":"2026-05-11T09:11:42Z","timestamp":1778490702920,"version":"3.51.4"},"reference-count":15,"publisher":"Walter de Gruyter GmbH","issue":"3","license":[{"start":{"date-parts":[[2020,12,31]],"date-time":"2020-12-31T00:00:00Z","timestamp":1609372800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    COVID-19 was declared a pandemic by the World Health Organization (WHO) in March 2020. The disease is caused by severe acute respiratory syndrome coronavirus 2 (SARSCoV-2). The aim of this study is to target the SARS-CoV-2 virus main protease (M\n                    <jats:sup>pro<\/jats:sup>\n                    )\n                    <jats:italic>via<\/jats:italic>\n                    structure-based virtual screening. Consequently, &gt; 580,000 ligands were processed\n                    <jats:italic>via<\/jats:italic>\n                    several filtration and docking steps, then the top 21 compounds were analysed extensively\n                    <jats:italic>via<\/jats:italic>\n                    MM-GBSA scoring and molecular dynamic simulations. Interestingly, the top compounds showed favorable binding energies and binding patterns to the protease enzyme, forming interactions with several key residues. Trihydroxychroman and pyrazolone derivatives, SN02 and SN18 ligands, exhibited very promising binding modes along with the best MM-GBSA scoring of \u201340.9 and \u201341.2 kcal mol\n                    <jats:sup>\u22121<\/jats:sup>\n                    , resp. MD simulations of 300 ns for the ligand-protein complexes of SN02 and SN18 affirmed the previously attained results of the potential inhibition activity of these two ligands. These potential inhibitors can be the starting point for further studies to pave way for the discovery of new antiviral drugs for SARS-CoV-2.\n                  <\/jats:p>","DOI":"10.2478\/acph-2021-0040","type":"journal-article","created":{"date-parts":[[2021,1,22]],"date-time":"2021-01-22T21:07:52Z","timestamp":1611349672000},"page":"325-333","source":"Crossref","is-referenced-by-count":4,"title":["Computer-aided approaches reveal trihydroxychroman and pyrazolone derivatives as potential inhibitors of SARS-CoV-2 virus main protease"],"prefix":"10.2478","volume":"71","author":[{"given":"Noor","family":"Atatreh","sequence":"first","affiliation":[{"name":"College of Pharmacy , Al Ain University Abu Dhabi , UAE, P.O. Box 112612"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shaima","family":"Hasan","sequence":"additional","affiliation":[{"name":"College of Pharmacy , Al Ain University Abu Dhabi , UAE, P.O. Box 112612"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bassam R.","family":"Ali","sequence":"additional","affiliation":[{"name":"Department of Pathology , College of Medicine and Health Sciences , United Arab Emirates University Al Ain , UAE"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammad A.","family":"Ghattas","sequence":"additional","affiliation":[{"name":"College of Pharmacy , Al Ain University Abu Dhabi , UAE, P.O. Box 112612"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"374","published-online":{"date-parts":[[2020,12,31]]},"reference":[{"key":"2026051108212946459_j_acph-2021-0040_ref_001_w2aab3b7c23b1b6b1ab1ab1Aa","doi-asserted-by":"crossref","unstructured":"1. R. Lu, X. Zhao, J. Li, P. Niu, B. Yang, H. Wu, W. Wang, H. Song, B. Huang, N. Zhu, Y. Bi, X. Ma, F. Zhan, L Wang, T. Hu, H. Zhou, Z Hu, W. Zhou, L. Zhao, J. Chen, Y. Meng, J.Wang, Y. Lin, J. Yuan, Z. Xie, J. Ma, W. J. Liu, D. Wang, W. Xu, E. C. Holmes, G. F. Gao, G. Wu, W. Chen, W. Shi and W. Tan, Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding, Lancet395 (2020) 565\u2013574; https:\/\/doi.org\/10.1016\/S0140-6736(20)30251-810.1016\/S0140-6736(20)30251-8","DOI":"10.1016\/S0140-6736(20)30251-8"},{"key":"2026051108212946459_j_acph-2021-0040_ref_002_w2aab3b7c23b1b6b1ab1ab2Aa","doi-asserted-by":"crossref","unstructured":"2. M. Yuan, N. C. Wu, X. Zhu, C. D. Lee, R. T. Y. So, H. Lv, C. K. P. Mok and I. A. Wilson, A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV, Science368 (2020) 630\u2013633; https:\/\/doi.org\/10.1126%2Fscience.abb726910.1126\/science.abb7269716439132245784","DOI":"10.1126\/science.abb7269"},{"key":"2026051108212946459_j_acph-2021-0040_ref_003_w2aab3b7c23b1b6b1ab1ab3Aa","doi-asserted-by":"crossref","unstructured":"3. A. Wu, Y. Peng, B. Huang, X. Ding, X. Wang, P. Niu, J. Meng, Z. Zhu, Z. Zhang, J. Wang, J. Sheng, L. Quan, Z. Xia, W. Tan, G. Cheng and T. Jiang, Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China, Cell Host Microbe27 (2020) 325\u2013328; https:\/\/doi.org\/10.1016\/j.chom.2020.02.00110.1016\/j.chom.2020.02.001715451432035028","DOI":"10.1016\/j.chom.2020.02.001"},{"key":"2026051108212946459_j_acph-2021-0040_ref_004_w2aab3b7c23b1b6b1ab1ab4Aa","doi-asserted-by":"crossref","unstructured":"4. Z. Jin, X. Du, Y. Xu, Y. Deng, M. Liu, Y. Zhao, B. Zhang, X. Li, L. Zhang, C. Peng, Y. Duan, J. Yu, L. Wang, K. Yang, F. Liu, R. Jiang, X. Yang, T. You, X. Liu, X. Yang, F. Bai, H. Liu, X. Liu, L. W. Guddat, W. Xu, G. Xiao, C. Qin, Z. Shi, H. Jiang, Z. Rao and H. Yang, Structure of M(pro) from SARS-CoV-2 and discovery of its inhibitors, Nature582 (2020) 289\u2013293; https:\/\/doi.org\/10.1038\/s41586-020-2223-y10.1038\/s41586-020-2223-y32272481","DOI":"10.1038\/s41586-020-2223-y"},{"key":"2026051108212946459_j_acph-2021-0040_ref_005_w2aab3b7c23b1b6b1ab1ab5Aa","doi-asserted-by":"crossref","unstructured":"5. A. Shulla, T. Heald-Sargent, G. Subramanya, J. Zhao, S. Perlman and T. Gallagher, A transmembrane serine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry, J. Virol. 85 (2011) 873\u2013882; https:\/\/doi.org\/10.1128\/JVI.02062-1010.1128\/JVI.02062-10302002321068237","DOI":"10.1128\/JVI.02062-10"},{"key":"2026051108212946459_j_acph-2021-0040_ref_006_w2aab3b7c23b1b6b1ab1ab6Aa","doi-asserted-by":"crossref","unstructured":"6. S. Lam, A. Lombardi and A. Ouanounou, COVID-19: A review of the proposed pharmacological treatments, Eur. J. Pharmacol.886 (2020) Article ID 173451 (11 pages); https:\/\/doi.org\/10.1016\/j.ejphar.2020.17345110.1016\/j.ejphar.2020.173451740647732768505","DOI":"10.1016\/j.ejphar.2020.173451"},{"key":"2026051108212946459_j_acph-2021-0040_ref_007_w2aab3b7c23b1b6b1ab1ab7Aa","unstructured":"7. Chemical Computing Group, Manual Version 2018.09, Molecular Operating Environment (MOE), Montreal 2018; http:\/\/www.chemcomp.com"},{"key":"2026051108212946459_j_acph-2021-0040_ref_008_w2aab3b7c23b1b6b1ab1ab8Aa","doi-asserted-by":"crossref","unstructured":"8. G. M. Sastry, M. Adzhigirey, T. Day, R. Annabhimoju and W. Sherman, Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments, J. Comp. Aided Mol. Des. 27 (2013) 221\u2013234; https:\/\/doi.org\/10.1007\/s10822-013-9644-810.1007\/s10822-013-9644-823579614","DOI":"10.1007\/s10822-013-9644-8"},{"key":"2026051108212946459_j_acph-2021-0040_ref_009_w2aab3b7c23b1b6b1ab1ab9Aa","doi-asserted-by":"crossref","unstructured":"9. R. A. Friesner, J. L. Banks, R. B. Murphy, T. A. Halgren, J. J. Klicic, D. T. Mainz, M. P. Repasky, E. H. Knoll, M. Shelley, J. K. Perry, D. E. Shaw, P. Francis, P. S. Shenkin, Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy, J. Med. Chem. 47 (2004) 1739\u20131749; https:\/\/doi.org\/10.1021\/jm030643010.1021\/jm030643015027865","DOI":"10.1021\/jm0306430"},{"key":"2026051108212946459_j_acph-2021-0040_ref_010_w2aab3b7c23b1b6b1ab1ac10Aa","doi-asserted-by":"crossref","unstructured":"10. J. Wang, W. Wang, P. A. Kollman and D. A. Case, Automatic atom type and bond type perception in molecular mechanical calculations, J. Mol. Graph. Mod. 25 (2006) 247\u2013260; https:\/\/doi.org\/10.1016\/j.jmgm.2005.12.00510.1016\/j.jmgm.2005.12.00516458552","DOI":"10.1016\/j.jmgm.2005.12.005"},{"key":"2026051108212946459_j_acph-2021-0040_ref_011_w2aab3b7c23b1b6b1ab1ac11Aa","doi-asserted-by":"crossref","unstructured":"11. A. Jakalian, D. B. Jack and C. I. Bayly, Fast, efficient generation of high-quality atomic charges, AM1-BCC model: II. Parameterization and validation, J. Comp. Chem. 23 (2002) 1623\u20131641; https:\/\/doi.org\/10.1002\/jcc.1012810.1002\/jcc.1012812395429","DOI":"10.1002\/jcc.10128"},{"key":"2026051108212946459_j_acph-2021-0040_ref_012_w2aab3b7c23b1b6b1ab1ac12Aa","unstructured":"12. T. S. Lee, B. K. Allen, T. J. Giese, Z. Guo, P. Li, C. Lin, T. D. McGee, D. A. Pearlman, B. K. Radak, Y. Tao, H. Tsai, H. Xu, W. Sherman and D. M. York, Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery, J. Chem. Inf. Model. 2020, in press; https:\/\/doi.org\/10.1021\/acs.jcim.0c0061310.1021\/acs.jcim.0c00613768602632936637"},{"key":"2026051108212946459_j_acph-2021-0040_ref_013_w2aab3b7c23b1b6b1ab1ac13Aa","doi-asserted-by":"crossref","unstructured":"13. C. R. Guimar\u00e3es and M. Cardozo, MM-GB\/SA rescoring of docking poses in structure-based lead optimization, J. Chem. Inf. Model.48 (2008) 958\u2013970; https:\/\/doi.org\/10.1021\/ci800004w10.1021\/ci800004w18422307","DOI":"10.1021\/ci800004w"},{"key":"2026051108212946459_j_acph-2021-0040_ref_014_w2aab3b7c23b1b6b1ab1ac14Aa","doi-asserted-by":"crossref","unstructured":"14. J. Shao, S. W. Tanner, N. Thompson and T. E. Cheatham, Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms, J. Chem. Theory Comp. 3 (2007) 2312\u20132334; https:\/\/doi.org\/10.1021\/ct700119m10.1021\/ct700119m26636222","DOI":"10.1021\/ct700119m"},{"key":"2026051108212946459_j_acph-2021-0040_ref_015_w2aab3b7c23b1b6b1ab1ac15Aa","doi-asserted-by":"crossref","unstructured":"15. W. Dai, B. Zhang, X. M. Jiang, H. Su, J. Li, Y. Zhao, X. Xie, Z. Jin, J. Peng, F. Liu, C. Li, Y. Li, F. Bai, H. Wang, X. Cheng, X. Cen, S. Hu, X. Yang, J. Wang, X. Liu, G. Xiao, H. Jiang, Z. Rao, L. K. Zhang, Y. Xu, H. Yang and H. Liu, Structure-based design of antiviral drug candidates targeting the SARSCoV-2 main protease, Science368 (2020) 1331\u20131335; https:\/\/doi.org\/10.1126\/science.abb448910.1126\/science.abb4489717993732321856","DOI":"10.1126\/science.abb4489"}],"container-title":["Acta Pharmaceutica"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/content.sciendo.com\/view\/journals\/acph\/71\/3\/article-p325.xml","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/reference-global.com\/pdf\/10.2478\/acph-2021-0040","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,11]],"date-time":"2026-05-11T08:54:10Z","timestamp":1778489650000},"score":1,"resource":{"primary":{"URL":"https:\/\/reference-global.com\/article\/10.2478\/acph-2021-0040"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,12,31]]},"references-count":15,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2020,12,31]]},"published-print":{"date-parts":[[2021,9,1]]}},"alternative-id":["10.2478\/acph-2021-0040"],"URL":"https:\/\/doi.org\/10.2478\/acph-2021-0040","relation":{},"ISSN":["1846-9558"],"issn-type":[{"value":"1846-9558","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,12,31]]}}}