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Nucleoside analogs targeting viral polymerases are often considered in this context. Here, we employ ensemble biochemical assays and single-molecule magnetic tweezers to characterize the detailed mechanism of action of the adenosine analog CMX521 (developed through Phase 1 clinical studies), a broad-spectrum antiviral against caliciviruses and coronaviruses, against SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). The triphosphate form of CMX521 is efficiently incorporated by RdRp, even against saturating ATP concentrations. Analog incorporation induces only a brief pause in nascent RNA synthesis. When embedded in the template strand, CMX521 causes the polymerase to stall \u223c9 s on average due to impaired uridine opposite incorporation. Multiple CMX521 residues in the template strand completely inhibit polymerase elongation. When the coronavirus polymerase is associated with the viral helicase, CMX521 strongly promotes copy-back RNA synthesis suggesting a second inhibitory mechanism for CMX521. Collectively, our findings establish a two-pronged mode of coronavirus polymerase inhibition by CMX521.<\/jats:p>","DOI":"10.64898\/2026.07.07.737000","type":"posted-content","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T05:25:19Z","timestamp":1783661119000},"source":"Crossref","is-referenced-by-count":0,"title":["The nucleoside analog CMX521 inhibits coronavirus RNA-dependent RNA polymerase via a two-pronged mechanism"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-3405-4136","authenticated-orcid":false,"given":"Asif","family":"Rakib","sequence":"first","affiliation":[{"name":"Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1100, 1081 HZ, Amsterdam, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8259-6201","authenticated-orcid":false,"given":"Calvin","family":"Gordon","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G2E1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas K.","family":"Anderson","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1991-8949","authenticated-orcid":false,"given":"John C.","family":"Marecki","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quinte","family":"Smitskamp","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1100, 1081 HZ, Amsterdam, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathaniel J.","family":"Moorman","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark T.","family":"Heise","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA"},{"name":"Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heidi M.","family":"Colton","sequence":"additional","affiliation":[{"name":"Chimerix, 2505 Meridian Parkway, Suite 100, Durham, NC 27713"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dean","family":"Selleseth","sequence":"additional","affiliation":[{"name":"Chimerix, 2505 Meridian Parkway, Suite 100, Durham, NC 27713"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E. 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