Efficient incorporation and template-dependent polymerase inhibition are major determinants for the broad-spectrum antiviral activity of remdesivir

  1. Calvin J. Gordon
  2. Hery W. Lee
  3. Egor P. Tchesnokov
  4. Jason K. Perry
  5. Joy Y. Feng
  6. John P. Bilello
  7. Danielle P. Porter
  8. Matthias Götte

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

No abstract available

Article activity feed

  1. Version published to 10.1016/j.jbc.2021.101529
  2. ScreenIT

    SciScore for 10.1101/2021.10.14.464416: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Experimental Models: Organisms/Strains
    SentencesResources
    The protein identities of the purified HCV nsp5b RdRp and NiV RdRp P/L complex were confirmed by mass spectrometry (MS) analysis (Alberta Proteomics and Mass Spectrometry, Edmonton, AB, Canada).
    AB
    suggested: RRID:BDSC_203)
    Recombinant DNA
    SentencesResources
    The pFastBac-1 (Invitrogen, Burlington, ON, Canada) plasmid with the codon-optimized synthetic DNA sequences (GenScript, Piscataway, NJ, USA) coding for HCV nsp5b RdRp (CAB46677.1 polyprotein, residues 2420 to 3010) minus the 21 C-terminus residues was used as a starting material for protein expression in insect cells (Sf9, Invitrogen, Burlington, ON, Canada).
    pFastBac-1
    suggested: None
    Software and Algorithms
    SentencesResources
    Data were analyzed using GraphPad Prism 7.0 (GraphPad Software, Inc
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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: We detected the following sentences addressing limitations in the study:
    Structures of EBOV, NiV, CCHFV RdRp enzymes are not available, and structure of RSV and LASV RdRp lack the RNA substrate, which is a limitation of our modeling approach. Clear evidence for delayed chain-termination following a single incorporation of RDV-TP has so far only been demonstrated for SARS-CoV, MERS-CoV, and SARS-CoV-2 RdRp complexes. In these cases, a conserved serine clashes with the 1’-cyano group of the incorporated RDV-MP at position “i+3”(26,27,29,31,32). However, NTP concentrations > 10 μM are often sufficient to overcome the inhibition(26,27,29,31). The clash between the 1’-cyano group of RDV-MP and S861 in SARS-CoV-2 occurs in a region of the RdRp away from the active site. Indeed, tested polymerases of other viruses did not show any significant inhibition in primer extension reactions, although previous studies have shown that multiple consecutive incorporations of the inhibitor can also lead to delayed chain-termination at positions “i+3” and “i+5” with EBOV, RSV, and NiV RdRp complexes(11,16). In this work, we have also shown a subtle inhibitory effect at position “i” with HCV RdRp. Overall, this analysis suggests that the inhibitory effect in primer extension reactions is heterogeneous and generally weak. In contrast, the template-dependent inhibition of RNA synthesis seems to provide a unifying mechanism that shows strong inhibition of UTP incorporation opposite RDV-MP. The template nucleotide that base-pairs with the incoming nucleotide substrate is p...

    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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.10.14.464416v1 on bioRxiv