PT  - JOURNAL ARTICLE
AU  - Katerina Naydenova
AU  - Kyle W. Muir
AU  - Long-Fei Wu
AU  - Ziguo Zhang
AU  - Francesca Coscia
AU  - Mathew J. Peet
AU  - Pablo Castro-Hartmann
AU  - Pu Qian
AU  - Kasim Sader
AU  - Kyle Dent
AU  - Dari Kimanius
AU  - John D. Sutherland
AU  - Jan Löwe
AU  - David Barford
AU  - Christopher J. Russo
TI  - Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP
AID  - 10.1101/2020.10.21.347690
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.10.21.347690
4099  - http://biorxiv.org/content/early/2020/10/21/2020.10.21.347690.short
4100  - http://biorxiv.org/content/early/2020/10/21/2020.10.21.347690.full
AB  - The RNA polymerase inhibitor, favipiravir, is currently in clinical trials as a treatment for infection with 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, non-productive 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.Competing Interest StatementThe authors have declared no competing interest.