Remdesivir overcomes the S861 roadblock in SARS-CoV-2 polymerase elongation complex

Highlights

• SARS-CoV-2 RdRP elongation complex assembled via multiple nucleotide addition cycles

• Remdesivir overcomes the S861 roadblock in the SARS-CoV-2 RdRP elongation complex

• Remdesivir induces delayed intervention at the equivalent site in EV71 RdRP

• Delayed intervention of RdRP by 1′-modified nucleotide analogs may generally occur

Summary

Remdesivir (RDV), a nucleotide analog with broad-spectrum features, has exhibited effectiveness in COVID-19 treatment. However, the precise working mechanism of RDV when targeting the viral RNA-dependent RNA polymerase (RdRP) has not been fully elucidated. Here, we solve a 3.0-Å structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRP elongation complex (EC) and assess RDV intervention in polymerase elongation phase. Although RDV could induce an “i+3” delayed termination in meta-stable complexes, only pausing and subsequent elongation are observed in the EC. A comparative investigation using an enterovirus RdRP further confirms similar delayed intervention and demonstrates that steric hindrance of the RDV-characteristic 1′-cyano at the −4 position is responsible for the “i+3” intervention, although two representative Flaviviridae RdRPs do not exhibit similar behavior. A comparison of representative viral RdRP catalytic complex structures indicates that the product RNA backbone encounters highly conserved structural elements, highlighting the broad-spectrum intervention potential of 1′-modified nucleotide analogs in anti-RNA virus drug development.