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Structure paper

TitleStructure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 118, Issue 7, Year 2021
Publish dateFeb 16, 2021
AuthorsKaterina Naydenova / Kyle W Muir / Long-Fei Wu / Ziguo Zhang / Francesca Coscia / Mathew J Peet / Pablo Castro-Hartmann / Pu Qian / Kasim Sader / Kyle Dent / Dari Kimanius / John D Sutherland / Jan Löwe / David Barford / Christopher J Russo /
PubMed AbstractThe 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 ...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.
External linksProc Natl Acad Sci U S A / PubMed:33526596 / PubMed Central
MethodsEM (single particle)
Resolution2.5 Å
Structure data

11692

7aap

EMDB-11692, PDB-7aap:
Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex with template:primer dsRNA and favipiravir-RTP
Method: EM (single particle) / Resolution: 2.5 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-POP:
PYROPHOSPHATE 2- / Pyrophosphate

ChemComp-GE6:
[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-5-fluoranyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / RNA-dependent RNA polymerase / Favipiravir / SARS-CoV2 / nCovid19

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