Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance

  1. Ala M. Shaqra
  2. Sarah N. Zvornicanin
  3. Qiu Yu J. Huang
  4. Gordon J. Lockbaum
  5. Mark Knapp
  6. Laura Tandeske
  7. David T. Bakan
  8. Julia Flynn
  9. Daniel N. A. Bolon
  10. Stephanie Moquin
  11. Dustin Dovala
  12. Nese Kurt Yilmaz
  13. Celia A. Schiffer

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Abstract

Coronaviruses can evolve and spread rapidly to cause severe disease morbidity and mortality, as exemplified by SARS-CoV-2 variants of the COVID-19 pandemic. Although currently available vaccines remain mostly effective against SARS-CoV-2 variants, additional treatment strategies are needed. Inhibitors that target essential viral enzymes, such as proteases and polymerases, represent key classes of antivirals. However, clinical use of antiviral therapies inevitably leads to emergence of drug resistance. In this study we implemented a strategy to pre-emptively address drug resistance to protease inhibitors targeting the main protease (M pro ) of SARS-CoV-2, an essential enzyme that promotes viral maturation. We solved nine high-resolution cocrystal structures of SARS-CoV-2 M pro bound to substrate peptides and six structures with cleavage products. These structures enabled us to define the substrate envelope of M pro , map the critical recognition elements, and identify evolutionarily vulnerable sites that may be susceptible to resistance mutations that would compromise binding of the newly developed M pro inhibitors. Our results suggest strategies for developing robust inhibitors against SARS-CoV-2 that will retain longer-lasting efficacy against this evolving viral pathogen.

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  1. Version published to 10.1038/s41467-022-31210-w
  2. ScreenIT

    SciScore for 10.1101/2022.01.25.477757: (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

    Recombinant DNA
    SentencesResources
    Expression and purification of SARS-CoV-2 Mpro: His6-SUMO-SARS-CoV-2 Mpro(C145A) was cloned into a pETite vector.
    pETite
    suggested: None
    Software and Algorithms
    SentencesResources
    Hydrogen bonds were determined using the show_contacts PyMOL Plugin with default parameters where the bond angle is between 63 and 180 degrees and the distance less than 4.0 A for any and 3.6 A for an ideal hydrogen bond between the proton and heavy atom.
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    As a second method to generate the substrate envelope, a custom python script was written to place a 3D grid with a spacing of 0.2 A at the active site and occupancy of each grid cell was counted in the 9 cocrystal structures.
    python
    suggested: (IPython, RRID:SCR_001658)
    The figures were generated using Matplotlib (47), PyMOL and Maestro by Schrödinger LLC.
    Matplotlib
    suggested: (MatPlotLib, RRID:SCR_008624)
    Maestro
    suggested: (Maestro, RRID:SCR_016748)

    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 page 22. 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.

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

    About SciScore

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  3. Version published to 10.1101/2022.01.25.477757v1 on bioRxiv