Mechanism of SARS-CoV-2 polymerase stalling by remdesivir
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Remdesivir is the only FDA-approved drug for the treatment of COVID-19 patients. The active form of remdesivir acts as a nucleoside analog and inhibits the RNA-dependent RNA polymerase (RdRp) of coronaviruses including SARS-CoV-2. Remdesivir is incorporated by the RdRp into the growing RNA product and allows for addition of three more nucleotides before RNA synthesis stalls. Here we use synthetic RNA chemistry, biochemistry and cryo-electron microscopy to establish the molecular mechanism of remdesivir-induced RdRp stalling. We show that addition of the fourth nucleotide following remdesivir incorporation into the RNA product is impaired by a barrier to further RNA translocation. This translocation barrier causes retention of the RNA 3ʹ-nucleotide in the substrate-binding site of the RdRp and interferes with entry of the next nucleoside triphosphate, thereby stalling RdRp. In the structure of the remdesivir-stalled state, the 3ʹ-nucleotide of the RNA product is matched and located with the template base in the active center, and this may impair proofreading by the viral 3ʹ-exonuclease. These mechanistic insights should facilitate the quest for improved antivirals that target coronavirus replication.
Article activity feed
-
-
SciScore for 10.1101/2020.10.28.358481: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization The experiments were not randomized, and the investigators were not blinded to allocation during experiments and outcome assessment. Blinding The experiments were not randomized, and the investigators were not blinded to allocation during experiments and outcome assessment. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources For structure 2, 3.4 million particles were exported from Warp 1.0.9 to cryoSPARC 2.15. Warpsuggested: (Warp, RRID:SCR_018071)For structure 3, 2.2 million particles were exported from Warp 1.0.9 to cryoSPARC 2.15. cryoSPARCsuggested: (cryoSPARC, …SciScore for 10.1101/2020.10.28.358481: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization The experiments were not randomized, and the investigators were not blinded to allocation during experiments and outcome assessment. Blinding The experiments were not randomized, and the investigators were not blinded to allocation during experiments and outcome assessment. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources For structure 2, 3.4 million particles were exported from Warp 1.0.9 to cryoSPARC 2.15. Warpsuggested: (Warp, RRID:SCR_018071)For structure 3, 2.2 million particles were exported from Warp 1.0.9 to cryoSPARC 2.15. cryoSPARCsuggested: (cryoSPARC, RRID:SCR_016501)Model quality was assessed using MolProbity within Phenix38 which revealed excellent stereochemistry for all three structural models (Extended Data Table 1). MolProbitysuggested: (MolProbity, RRID:SCR_014226)Figures were prepared with PyMol and ChimeraX39. Supplementary Information | Synthesis of RMP-containing RNA oligonucleotides. PyMolsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
-
