Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP

Abstract

Significance While the current COVID-19 pandemic continues, the US Food and Drug Administration (FDA) has approved only one drug against the virus—remdesivir. It is a nucleotide analogue inhibitor of the SARS-CoV-2 RNA-dependent RNA polymerase; favipiravir is another member of the same class. These nucleoside analogs were originally developed against other viral polymerases, and can be quickly repurposed against SARS-CoV-2 should they prove efficacious. We used cryoEM to visualize how favipiravir-RTP binds to the replicating SARS-CoV-2 polymerase and determine how it slows RNA replication. This structure explains the mechanism of action, and will help guide the design of more potent drugs targeting SARS-CoV-2. The RNA polymerase inhibitor favipiravir is currently in clinical trials as a treatment for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, nonproductive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp, which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.