Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP
Top Cited Papers
Open Access
- 16 February 2021
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 118 (7)
- https://doi.org/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: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.Keywords
Funding Information
- RCUK | Medical Research Council (MC UP 120117)
- RCUK | Medical Research Council (MC UP 1201/6)
- RCUK | Medical Research Council (U105184326)
- RCUK | Medical Research Council (MC UP A024 1009)
- Wellcome (202754/Z/16/Z)
- Cancer Research UK (C576/A14109)
This publication has 36 references indexed in Scilit:
- A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysisIUCrJ, 2019
- Measuring the effects of particle orientation to improve the efficiency of electron cryomicroscopyNature Communications, 2017
- Understanding the Mechanism of the Broad-Spectrum Antiviral Activity of Favipiravir (T-705): Key Role of the F1 Motif of the Viral PolymeraseJournal of Virology, 2017
- A precision cryostat design for manual and semi-automated cryo-plunge instrumentsReview of Scientific Instruments, 2016
- Recombinant expression and reconstitution of multiprotein complexes by the USER cloning method in the insect cell-baculovirus expression systemMethods, 2016
- Favipiravir elicits antiviral mutagenesis during virus replication in vivoeLife, 2014
- Mechanism of Action of T-705 Ribosyl Triphosphate against Influenza Virus RNA PolymeraseAntimicrobial Agents and Chemotherapy, 2013
- Features and development of CootActa crystallographica. Section D, Structural biology, 2010
- Protein production by auto-induction in high-density shaking culturesProtein Expression and Purification, 2005
- Controlled environment vitrification system: An improved sample preparation techniqueJournal of Electron Microscopy Technique, 1988