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

Wu, Jiqin; Wang, Haofeng; Liu, Qiaojie; Li, Rui; Gao, Yan; Fang, Xiang; Zhong, Yao; Wang, Meihua; Wang, Quan; Rao, Zihe; Gong, Peng

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-angström structure of SARS-CoV-2 RdRP elongation complex (EC) and assess RDV intervention in polymerase elongation phase. While 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 confirm similar delayed intervention and demonstrate that steric hindrance of the RDV-characteristic 1′-cyano at the -4 position is responsible for the “i+3” intervention, while 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.