Identification of low micromolar SARS-CoV-2 M pro inhibitors from hits identified by in silico screens

  1. Giacomo G. Rossetti
  2. Marianna Ossorio
  3. Samia Barriot
  4. Laurence Tropia
  5. Vasilis S. Dionellis
  6. Christoph Gorgulla
  7. Haribabu Arthanari
  8. Peter Mohr
  9. Remo Gamboni
  10. Thanos D. Halazonetis

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Abstract

M pro , also known as 3CL pro , is the main protease of the SARS-CoV-2 coronavirus and, as such, is essential for the viral life cycle. Two studies have each screened and ranked in silico more than one billion chemical compounds in an effort to identify putative inhibitors of M pro . More than five hundred of the seven thousand top-ranking hits were synthesized by an external supplier and examined with respect to their activity in two biochemical assays: a protease activity assay and a thermal shift assay. Two clusters of chemical compounds with M pro inhibitory activity were identified. An additional five hundred molecules, analogues of the compounds in the two clusters described above, were also synthesized and characterized in vitro . The study of the analogues revealed that the compounds of the first cluster acted by denaturing M pro and might denature other proteins as well. In contrast, the compounds of the second cluster targeted M pro with much greater specificity and enhanced its melting temperature, consistent with the formation of stable M pro -inhibitor complexes. The most active compounds of the second cluster exhibited IC 50 values between 4 and 7 μM and their chemical structure suggests that they could serve as leads for the development of potent M pro inhibitors.

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    SciScore for 10.1101/2020.12.03.409441: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    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.

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  2. Version published to 10.1101/2020.12.03.409441v1 on bioRxiv