Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

  1. Anna Pavlova
  2. Diane L. Lynch
  3. Isabella Daidone
  4. Laura Zanetti-Polzi
  5. Micholas Dean Smith
  6. Chris Chipot
  7. Daniel W. Kneller
  8. Andrey Kovalevsky
  9. Leighton Coates
  10. Andrei A. Golosov
  11. Callum J. Dickson
  12. Camilo Velez-Vega
  13. José S. Duca
  14. Josh V. Vermaas
  15. Yui Tik Pang
  16. Atanu Acharya
  17. Jerry M. Parks
  18. Jeremy C. Smith
  19. James C. Gumbart

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Abstract

The main protease (M pro ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics.

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  1. Version published to 10.1039/d0sc04942e
  2. ScreenIT

    SciScore for 10.1101/2020.09.07.286344: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    NAMD 2.13 was used for a set of 20-ns simulations of each potential protonation-state combination.
    NAMD
    suggested: (NAMD, RRID:SCR_014894)
    All distribution plots were generated by applying Gaussian kernel density estimation on normalized histograms using the seaborn python package.
    python
    suggested: (IPython, RRID:SCR_001658)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 24 and 26. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

    About SciScore

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  3. Version published to 10.1101/2020.09.07.286344v1 on bioRxiv