tetano
Editor, Senior Moderator
Proc Natl Acad Sci U S A
. 2021 Feb 16;118(7):e2021946118.
doi: 10.1073/pnas.2021946118.
Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP
Katerina Naydenova[SUP] 1 [/SUP], Kyle W Muir[SUP] 1 [/SUP], Long-Fei Wu[SUP] 1 [/SUP], Ziguo Zhang[SUP] 1 [/SUP], Francesca Coscia[SUP] 1 [/SUP], Mathew J Peet[SUP] 1 [/SUP], Pablo Castro-Hartmann[SUP] 2 [/SUP], Pu Qian[SUP] 2 [/SUP], Kasim Sader[SUP] 2 [/SUP], Kyle Dent[SUP] 1 [/SUP], Dari Kimanius[SUP] 1 [/SUP], John D Sutherland[SUP] 3 [/SUP], Jan L?we[SUP] 3 [/SUP], David Barford[SUP] 3 [/SUP], Christopher J Russo[SUP] 3 [/SUP]
Affiliations
Abstract
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
rimer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 ?. 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.
Keywords: COVID-19; T-705; cryoEM; drug design; structural biology.
. 2021 Feb 16;118(7):e2021946118.
doi: 10.1073/pnas.2021946118.
Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP
Katerina Naydenova[SUP] 1 [/SUP], Kyle W Muir[SUP] 1 [/SUP], Long-Fei Wu[SUP] 1 [/SUP], Ziguo Zhang[SUP] 1 [/SUP], Francesca Coscia[SUP] 1 [/SUP], Mathew J Peet[SUP] 1 [/SUP], Pablo Castro-Hartmann[SUP] 2 [/SUP], Pu Qian[SUP] 2 [/SUP], Kasim Sader[SUP] 2 [/SUP], Kyle Dent[SUP] 1 [/SUP], Dari Kimanius[SUP] 1 [/SUP], John D Sutherland[SUP] 3 [/SUP], Jan L?we[SUP] 3 [/SUP], David Barford[SUP] 3 [/SUP], Christopher J Russo[SUP] 3 [/SUP]
Affiliations
- PMID: 33526596
- DOI: 10.1073/pnas.2021946118
Abstract
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
rimer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 ?. 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.Keywords: COVID-19; T-705; cryoEM; drug design; structural biology.