SARS-cov-2 Polymerase Selectively incorporates Remdesivir, But resistance can Develop Thru Single Mutation
Structural analyses reveal how the antiviral drug remdesivir is incorporated into the SARS-CoV-2 genome by the virus’s RNA-dependent RNA polymerase (RdRp), and pinpoint the mechanism behind resistance conferred by a specific mutation.
Researchers have determined, through a combination of enzymatic assays, mass spectrometry, and cryo-electron microscopy (cryo-EM), that the SARS-CoV-2 RdRp readily incorporates remdesivir triphosphate (RTP) – the active form of the antiviral drug – even when adenosine triphosphate (ATP) is present in 10-fold excess. However, subsequent incorporation of RTP is considerably hindered by the presence of ATP.
Structural studies show the remdesivir:UMP base pair formed during incorporation is unusually stable and resists the translocation necessary for continued RNA synthesis, limiting remdesivir’s overall occupancy to less than 16% of positions within a copied RNA strand. This suggests remdesivir acts as a “non-obligate” chain terminator, meaning it doesn’t always halt replication instantly.
Importantly, the study identified the S759A mutation in RdRp as conferring resistance to remdesivir. Cryo-EM structures of the S759A RdRp reveal this resistance stems from alterations in the positioning of the primer’s 3′-end nucleotide and a change in the ribose ring’s conformation,effectively preventing efficient RTP incorporation.
These findings provide critical insights into the mechanism of remdesivir action and resistance, offering a foundation for the design of novel nucleoside analogs with possibly improved antiviral efficacy and resistance profiles.
