{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T20:02:53Z","timestamp":1772827373871,"version":"3.50.1"},"reference-count":54,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2021,12,30]],"date-time":"2021-12-30T00:00:00Z","timestamp":1640822400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>The COVID-19 pandemic has caused millions of fatalities since 2019. Despite the availability of vaccines for this disease, new strains are causing rapid ailment and are a continuous threat to vaccine efficacy. Here, molecular docking and simulations identify strong inhibitors of the allosteric site of the SARS-CoV-2 virus RNA dependent RNA polymerase (RdRp). More than one hundred different flavonoids were docked with the SARS-CoV-2 RdRp allosteric site through computational screening. The three top hits were Naringoside, Myricetin and Aureusidin 4,6-diglucoside. Simulation analyses confirmed that they are in constant contact during the simulation time course and have strong association with the enzyme\u2019s allosteric site. Absorption, distribution, metabolism, excretion and toxicity (ADMET) data provided medicinal information of these top three hits. They had good human intestinal absorption (HIA) concentrations and were non-toxic. Due to high mutation rates in the active sites of the viral enzyme, these new allosteric site inhibitors offer opportunities to drug SARS-CoV-2 RdRp. These results provide new information for the design of novel allosteric inhibitors against SARS-CoV-2 RdRp.<\/jats:p>","DOI":"10.3390\/molecules27010223","type":"journal-article","created":{"date-parts":[[2021,12,30]],"date-time":"2021-12-30T23:29:07Z","timestamp":1640906947000},"page":"223","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Computational Study of SARS-CoV-2 RNA Dependent RNA Polymerase Allosteric Site Inhibition"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5105-6982","authenticated-orcid":false,"given":"Shah","family":"Faisal","sequence":"first","affiliation":[{"name":"Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Syed Lal","family":"Badshah","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bibi","family":"Kubra","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5891-7378","authenticated-orcid":false,"given":"Mohamed","family":"Sharaf","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China"},{"name":"Department of Biochemistry, Faculty of Agriculture, AL-Azhar University, Nasr City, Cairo 11751, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9231-3850","authenticated-orcid":false,"given":"Abdul-Hamid","family":"Emwas","sequence":"additional","affiliation":[{"name":"Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mariusz","family":"Jaremko","sequence":"additional","affiliation":[{"name":"Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1682-5547","authenticated-orcid":false,"given":"Mohnad","family":"Abdalla","sequence":"additional","affiliation":[{"name":"Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Jinan 250012, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,12,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1016\/S0140-6736(20)30211-7","article-title":"Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study","volume":"395","author":"Chen","year":"2020","journal-title":"Lancet"},{"key":"ref_2","first-page":"133","article-title":"Deaths from COVID-19","volume":"325","author":"Koh","year":"2021","journal-title":"JAMA J. 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