{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T12:21:39Z","timestamp":1766578899156,"version":"build-2065373602"},"reference-count":37,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T00:00:00Z","timestamp":1761004800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T00:00:00Z","timestamp":1761004800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100002383","name":"King Saud University","doi-asserted-by":"publisher","award":["COVID-19 Virus Research Chair.","COVID-19 Virus Research Chair."],"award-info":[{"award-number":["COVID-19 Virus Research Chair.","COVID-19 Virus Research Chair."]}],"id":[{"id":"10.13039\/501100002383","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"DOI":"10.1038\/s41598-025-19353-4","type":"journal-article","created":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T08:44:49Z","timestamp":1761036289000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["An exploratory binding study of molnupiravir efficacy against emerging Omicron SARS-CoV-2 variants"],"prefix":"10.1038","volume":"15","author":[{"given":"Faisal","family":"Ahmad","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zarrin","family":"Basharat","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ayesha","family":"Janjua","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Muzammil Hasan","family":"Najmi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fahad Nasser","family":"Almajhdi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tajamul","family":"Hussain","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dilber Uzun","family":"Ozsahin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yasir","family":"Waheed","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,10,21]]},"reference":[{"key":"19353_CR1","doi-asserted-by":"crossref","unstructured":"Li, H., Liu, S. M., Yu, X. H., Tang, S. L. & Tang, C. K. Coronavirus disease 2019 (COVID-19): current status and future perspective. Int. J. Antimicrob. Agents. 55, 105951 (2020).","DOI":"10.1016\/j.ijantimicag.2020.105951"},{"key":"19353_CR2","doi-asserted-by":"publisher","first-page":"e0000954","DOI":"10.1371\/journal.pgph.0000954","volume":"2","author":"A Aravindakshan","year":"2022","unstructured":"Aravindakshan, A., Boehnke, J., Gholami, E. & Nayak, A. The impact of mask-wearing in mitigating the spread of COVID-19 during the early phases of the pandemic. PLOS Glob Public. Health. 2, e0000954 (2022).","journal-title":"PLOS Glob Public. Health"},{"key":"19353_CR3","doi-asserted-by":"publisher","first-page":"e884","DOI":"10.1002\/hsr2.884","volume":"5","author":"MR Islam","year":"2022","unstructured":"Islam, M. R., Shahriar, M. & Bhuiyan, M. A. The latest Omicron BA.4 and BA.5 lineages are frowning toward COVID-19 preventive measures: A threat to global public health. Health Sci. Rep. 5, e884 (2022).","journal-title":"Health Sci. Rep."},{"key":"19353_CR4","doi-asserted-by":"publisher","first-page":"977","DOI":"10.3349\/ymj.2022.0383","volume":"63","author":"DH Shin","year":"2022","unstructured":"Shin, D. H., Smith, D. M. & Choi, J. Y. SARS-CoV-2 Omicron variant of concern: everything you wanted to know about Omicron but were afraid to ask. Yonsei Med. J. 63, 977\u2013983 (2022).","journal-title":"Yonsei Med. J."},{"key":"19353_CR5","doi-asserted-by":"publisher","first-page":"1308","DOI":"10.3390\/ijms22031308","volume":"22","author":"NA Wong","year":"2021","unstructured":"Wong, N. A. & Saier, M. H. The SARS-Coronavirus infection cycle: A survey of viral membrane proteins, their functional interactions and pathogenesis. Int. J. Mol. Sci. 22, 1308 (2021).","journal-title":"Int. J. Mol. Sci."},{"key":"19353_CR6","doi-asserted-by":"publisher","first-page":"109","DOI":"10.3390\/v13010109","volume":"13","author":"X Xia","year":"2021","unstructured":"Xia, X. Domains and functions of Spike protein in Sars-Cov-2 in the context of vaccine design. Viruses 13, 109 (2021).","journal-title":"Viruses"},{"key":"19353_CR7","doi-asserted-by":"crossref","unstructured":"Kaushal, A. Omicron Variant Could Be an Antigenic Shift of SARS-CoV-2. COVID 5, 73 (2025).","DOI":"10.3390\/covid5050073"},{"key":"19353_CR8","doi-asserted-by":"publisher","first-page":"586","DOI":"10.1007\/s00134-020-05985-9","volume":"46","author":"H Zhang","year":"2020","unstructured":"Zhang, H., Penninger, J. M., Li, Y., Zhong, N. & Slutsky, A. S. Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target. Intensive Care Med. 46, 586\u2013590 (2020).","journal-title":"Intensive Care Med."},{"key":"19353_CR9","doi-asserted-by":"publisher","first-page":"1041","DOI":"10.1097\/JS9.0000000000000246","volume":"109","author":"C Chakraborty","year":"2023","unstructured":"Chakraborty, C. et al. The SARS-CoV-2 Omicron Recombinant subvariants XBB, XBB.1, and XBB.1.5 are expanding rapidly with unique mutations, antibody evasion, and immune escape properties \u2013 an alarming global threat of a surge in COVID-19 cases again? Int. J. Surg. 109, 1041\u20131043 (2023).","journal-title":"Int. J. Surg."},{"key":"19353_CR10","unstructured":"Spread of the SARS-CoV-2 Omicron variant sub lineage BQ.1 in the EU\/EEA. (2022)."},{"key":"19353_CR11","doi-asserted-by":"publisher","first-page":"1329","DOI":"10.1097\/MS9.0000000000000469","volume":"85","author":"S Akash","year":"2023","unstructured":"Akash, S., Islam, M. R., Dhama, K. & Emergence BQ.1 and BQ.1.1 as newly identified Omicron subvariants: current scenario and future outlook \u2013 an update. Ann. Med. Surg. (Lond). 85, 1329\u20131330 (2023).","journal-title":"Ann. Med. Surg. (Lond)"},{"key":"19353_CR12","doi-asserted-by":"publisher","first-page":"e2381","DOI":"10.1002\/rmv.2381","volume":"32","author":"LB Shrestha","year":"2022","unstructured":"Shrestha, L. B., Foster, C., Rawlinson, W., Tedla, N. & Bull, R. A. Evolution of the SARS-CoV-2 Omicron variants BA.1 to BA.5: implications for immune escape and transmission. Rev. Med. Virol. 32, e2381 (2022).","journal-title":"Rev. Med. Virol."},{"key":"19353_CR13","doi-asserted-by":"publisher","first-page":"3284","DOI":"10.1038\/s41467-024-47393-3","volume":"15","author":"C Liu","year":"2024","unstructured":"Liu, C. et al. Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4\/5 infection. Nat. Commun. 15, 3284 (2024).","journal-title":"Nat. Commun."},{"key":"19353_CR14","doi-asserted-by":"publisher","unstructured":"Bekliz, M. et al. Immune escape of Omicron lineages BA.1, BA.2, BA.5.1, BQ.1, XBB.1.5, EG.5.1 and JN.1.1 after vaccination, infection and hybrid immunity. 02.14.579654 Preprint at (2024). https:\/\/doi.org\/10.1101\/2024.02.14.579654 (2024).","DOI":"10.1101\/2024.02.14.579654"},{"key":"19353_CR15","doi-asserted-by":"publisher","first-page":"854","DOI":"10.1056\/NEJMc2214916","volume":"388","author":"J Zou","year":"2023","unstructured":"Zou, J. et al. Neutralization of BA.4-BA.5, BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1 with bivalent vaccine. N. Engl. J. Med. 388, 854\u2013857 (2023).","journal-title":"N. Engl. J. Med."},{"key":"19353_CR16","doi-asserted-by":"publisher","first-page":"146","DOI":"10.2174\/157340911795677602","volume":"7","author":"XY Meng","year":"2011","unstructured":"Meng, X. Y., Zhang, H. X., Mezei, M. & Cui, M. Molecular docking: a powerful approach for structure-based drug discovery. Curr. Comput. Aided Drug Des. 7, 146\u2013157 (2011).","journal-title":"Curr. Comput. Aided Drug Des."},{"key":"19353_CR17","doi-asserted-by":"publisher","first-page":"13398","DOI":"10.1038\/s41598-023-40160-2","volume":"13","author":"PC Agu","year":"2023","unstructured":"Agu, P. C. et al. Molecular Docking as a tool for the discovery of molecular targets of nutraceuticals in diseases management. Sci. Rep. 13, 13398 (2023).","journal-title":"Sci. Rep."},{"key":"19353_CR18","doi-asserted-by":"publisher","unstructured":"Lokhande, K. B., Doiphode, S., Vyas, R. & Swamy, K. V. Molecular Docking and simulation studies on SARS-CoV-2 Mpro reveals mitoxantrone, leucovorin, birinapant, and dynasore as potent drugs against COVID-19. J Biomol. Struct. Dyn 1\u201312 https:\/\/doi.org\/10.1080\/07391102.2020.1805019","DOI":"10.1080\/07391102.2020.1805019"},{"key":"19353_CR19","doi-asserted-by":"publisher","first-page":"5795","DOI":"10.3390\/molecules26195795","volume":"26","author":"M Imran","year":"2021","unstructured":"Imran, M. et al. Discovery, development, and patent trends on molnupiravir: A prospective oral treatment for COVID-19. Molecules 26, 5795 (2021).","journal-title":"Molecules"},{"key":"19353_CR20","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1002\/em.22471","volume":"63","author":"MD Waters","year":"2022","unstructured":"Waters, M. D., Warren, S., Hughes, C., Lewis, P. & Zhang, F. Human genetic risk of treatment with antiviral nucleoside analog drugs that induce lethal mutagenesis: the special case of molnupiravir. Environ. Mol. Mutagen. 63, 37\u201363 (2022).","journal-title":"Environ. Mol. Mutagen."},{"key":"19353_CR21","doi-asserted-by":"publisher","first-page":"107322","DOI":"10.1016\/j.compbiolchem.2020.107322","volume":"87","author":"LP Kagami","year":"2020","unstructured":"Kagami, L. P., das Neves, G. M., Timmers, L. F. S. M., Caceres, R. A. & Eifler-Lima, V. L. Geo-Measures: A PyMOL plugin for protein structure ensembles analysis. Comput. Biol. Chem. 87, 107322 (2020).","journal-title":"Comput. Biol. Chem."},{"key":"19353_CR22","unstructured":"Desmond | Schr\u00f6dinger. https:\/\/www.schrodinger.com\/products\/desmond"},{"key":"19353_CR23","unstructured":"ProtParam, E. ExPASy-ProtParam Tool. (2017)."},{"key":"19353_CR24","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen, E. F. et al. UCSF Chimera?A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605\u20131612 (2004).","journal-title":"J. Comput. Chem."},{"key":"19353_CR25","doi-asserted-by":"crossref","unstructured":"Baroroh, S., Muscifa, U., Destiarani, Z. S., Rohmatullah, W. & Yusuf, M. F. G. Molecular interaction analysis and visualization of protein-ligand docking using Biovia Discovery Studio Visualizer. IJCB 2, 22 (2023).","DOI":"10.24198\/ijcb.v2i1.46322"},{"key":"19353_CR26","doi-asserted-by":"publisher","first-page":"6474","DOI":"10.1021\/jp003919d","volume":"105","author":"GA Kaminski","year":"2001","unstructured":"Kaminski, G. A., Friesner, R. A., Tirado-Rives, J. & Jorgensen, W. L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B. 105, 6474\u20136487 (2001).","journal-title":"J. Phys. Chem. B"},{"key":"19353_CR27","doi-asserted-by":"crossref","unstructured":"Halder, S. K. et al. In Silico Identification and Analysis of Potentially Bioactive Antiviral Phytochemicals against SARS-CoV-2: A Molecular Docking and Dynamics Simulation Approach. BioMed Research International 5469258 (2023). (2023).","DOI":"10.1155\/2023\/5469258"},{"key":"19353_CR28","doi-asserted-by":"publisher","first-page":"749","DOI":"10.3390\/bioengineering9120749","volume":"9","author":"Y Ali","year":"2022","unstructured":"Ali, Y. et al. Structural evaluation and conformational dynamics of ZNF141T474I mutation provoking postaxial polydactyly type A. Bioengineering 9, 749 (2022).","journal-title":"Bioengineering"},{"key":"19353_CR29","doi-asserted-by":"publisher","first-page":"803","DOI":"10.3390\/ph16060803","volume":"16","author":"HA Khan","year":"2023","unstructured":"Khan, H. A. et al. In Silico characterization and analysis of clinically significant variants of Lipase-H (LIPH Gene) protein associated with hypotrichosis. Pharmaceuticals 16, 803 (2023).","journal-title":"Pharmaceuticals"},{"key":"19353_CR30","doi-asserted-by":"publisher","first-page":"918101","DOI":"10.3389\/fmolb.2022.918101","volume":"9","author":"A Chandra Manivannan","year":"2022","unstructured":"Chandra Manivannan, A. et al. Evaluation of clove phytochemicals as potential antiviral drug candidates targeting SARS-CoV-2 main protease: computational docking, molecular dynamics simulation, and Pharmacokinetic profiling. Front. Mol. Biosci. 9, 918101 (2022).","journal-title":"Front. Mol. Biosci."},{"key":"19353_CR31","doi-asserted-by":"publisher","DOI":"10.1002\/9780470015902.a0003011.pub2","volume-title":"Encyclopedia of Life Sciences","author":"RE Hubbard","year":"2010","unstructured":"Hubbard, R. E. & Kamran Haider, M. Hydrogen bonds in proteins: role and strength. In Encyclopedia of Life Sciences (John Wiley & Sons, Ltd, 2010). https:\/\/doi.org\/10.1002\/9780470015902.a0003011.pub2."},{"key":"19353_CR32","doi-asserted-by":"crossref","unstructured":"Biswas, P. et al. Evaluation of Melongosides as Potential Inhibitors of NS2B-NS3 Activator-Protease of Dengue Virus (Serotype 2) by Using Molecular Docking and Dynamics Simulation Approach. Journal of Tropical Medicine (2022). (2022).","DOI":"10.1155\/2022\/7111786"},{"key":"19353_CR33","doi-asserted-by":"publisher","first-page":"2794","DOI":"10.1002\/prot.23106","volume":"79","author":"J Li","year":"2011","unstructured":"Li, J. et al. The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling. Proteins 79, 2794\u20132812 (2011).","journal-title":"Proteins"},{"key":"19353_CR34","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1016\/j.jpha.2020.03.009","volume":"10","author":"M Tahir Ul Qamar","year":"2020","unstructured":"Tahir Ul Qamar, M., Alqahtani, S. M., Alamri, M. A. & Chen, L. L. Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. J. Pharm. Anal. 10, 313\u2013319 (2020).","journal-title":"J. Pharm. Anal."},{"key":"19353_CR35","doi-asserted-by":"publisher","first-page":"1763","DOI":"10.1126\/science.1085658","volume":"300","author":"K Anand","year":"2003","unstructured":"Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J. R. & Hilgenfeld, R. Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science 300, 1763\u20131767 (2003).","journal-title":"Science"},{"key":"19353_CR36","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1099\/0022-1317-81-4-853","volume":"81","author":"J Ziebuhr","year":"2000","unstructured":"Ziebuhr, J., Snijder, E. J. & Gorbalenya, A. E. Virus-encoded proteinases and proteolytic processing in the nidovirales. J. Gen. Virol. 81, 853\u2013879 (2000).","journal-title":"J. Gen. Virol."},{"key":"19353_CR37","doi-asserted-by":"publisher","first-page":"100719","DOI":"10.1016\/j.drup.2020.100719","volume":"53","author":"S Dro\u017cd\u017cal","year":"2020","unstructured":"Dro\u017cd\u017cal, S. et al. FDA approved drugs with pharmacotherapeutic potential for SARS-CoV-2 (COVID-19) therapy. Drug Resist. Updat. 53, 100719 (2020).","journal-title":"Drug Resist. Updat"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-19353-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-19353-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-19353-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T08:44:54Z","timestamp":1761036294000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-19353-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,21]]},"references-count":37,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["19353"],"URL":"https:\/\/doi.org\/10.1038\/s41598-025-19353-4","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,21]]},"assertion":[{"value":"22 April 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 September 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 October 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no conflicts of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"36549"}}