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To this end, we describe structural binding-site insights for facilitating COVID-19 drug design when targeting RNA-dependent RNA polymerase (RDRP), a common conserved component of RNA viruses. We combined an RDRP structure data set, including 384 RDRP PDB structures and all corresponding RDRP\u2013ligand interaction fingerprints, thereby revealing the structural characteristics of the active sites for application to RDRP-targeted drug discovery. Specifically, we revealed the intrinsic ligand-binding modes and associated RDRP structural characteristics. Four types of binding modes with corresponding binding pockets were determined, suggesting two major subpockets available for drug discovery. We screened a drug data set of 7894 compounds against these binding pockets and presented the top-10 small molecules as a starting point in further exploring the prevention of virus replication. In summary, the binding characteristics determined here help rationalize RDRP-targeted drug discovery and provide insights into the specific binding mechanisms important for containing the SARS-CoV-2 virus.<\/jats:p>","DOI":"10.1021\/acs.jproteome.0c00623","type":"journal-article","created":{"date-parts":[[2020,9,18]],"date-time":"2020-09-18T19:48:04Z","timestamp":1600458484000},"page":"4698-4705","source":"Crossref","is-referenced-by-count":20,"title":["Structural Insights\ninto the Binding Modes of Viral\nRNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint\nMethod for RNA Virus Drug Discovery"],"prefix":"10.1021","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1453-3230","authenticated-orcid":true,"given":"Zheng","family":"Zhao","sequence":"first","affiliation":[{"name":"University of Virginia , , , ,","place":["Charlottesville, Virginia, United States of America, 22904"]},{"name":"University of Virginia , , , ,","place":["Charlottesville, Virginia, United States of America, 22904"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip E.","family":"Bourne","sequence":"additional","affiliation":[{"name":"University of Virginia , , , ,","place":["Charlottesville, Virginia, United States of America, 22904"]},{"name":"University of Virginia , , , ,","place":["Charlottesville, Virginia, United States of America, 22904"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2020,9,18]]},"reference":[{"key":"2026081714252184000_cit1","unstructured":"The WHO situation report. https:\/\/www.who.int\/emergencies\/diseases\/novel-coronavirus-2019\/situation-reports (accessed June 30, 2020)."},{"issue":"7798","key":"2026081714252184000_cit2","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak\nassociated with a new coronavirus of probable bat origin","volume":"579","author":"Zhou","year":"2020","journal-title":"Nature"},{"issue":"3","key":"2026081714252184000_cit3","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1021\/acscentsci.0c00272","article-title":"Research and\nDevelopment on Therapeutic\nAgents and Vaccines for COVID-19 and Related Human Coronavirus Diseases","volume":"6","author":"Liu","year":"2020","journal-title":"ACS Cent. 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