N-Terminal finger stabilizes the reversible feline drug GC376 in SARS-CoV-2 M pro

  1. Elena Arutyunova
  2. Muhammad Bashir Khan
  3. Conrad Fischer
  4. Jimmy Lu
  5. Tess Lamer
  6. Wayne Vuong
  7. Marco J. van Belkum
  8. Ryan T. McKay
  9. D. Lorne Tyrrell
  10. John C. Vederas
  11. Howard S. Young
  12. M. Joanne Lemieux

Reviewed by

Read the full article See related articles

Discuss this preprint

Start a discussion What are Sciety discussions?

Listed in

Log in to save this article

Abstract

The main protease (M pro , also known as 3CL protease) of SARS-CoV-2 is a high priority drug target in the development of antivirals to combat COVID-19 infections. A feline coronavirus antiviral drug, GC376, has been shown to be effective in inhibiting the SARS-CoV-2 main protease and live virus growth. As this drug moves into clinical trials, further characterization of GC376 with the main protease of coronaviruses is required to gain insight into the drug’s properties, such as reversibility and broad specificity. Reversibility is an important factor for therapeutic proteolytic inhibitors to prevent toxicity due to off-target effects. Here we demonstrate that GC376 has nanomolar K i values with the M pro from both SARS-CoV-2 and SARS-CoV strains. Restoring enzymatic activity after inhibition by GC376 demonstrates reversible binding with both proteases. In addition, the stability and thermodynamic parameters of both proteases were studied to shed light on physical chemical properties of these viral enzymes, revealing higher stability for SARS-CoV-2 M pro . The comparison of a new X-ray crystal structure of M pro from SARS-CoV complexed with GC376 reveals similar molecular mechanism of inhibition compared to SARS-CoV-2 M pro , and gives insight into the broad specificity properties of this drug. In both structures, we observe domain swapping of the N-termini in the dimer of the M pro , which facilitates coordination of the drug’s P1 position. These results validate that GC376 is a drug with an off-rate suitable for clinical trials.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2021.02.16.431021: (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
    Kinetic data corresponding the interaction of SARS-CoV Mpro and SARS CoV-2 Mpro with GC376 compound were analyzed using computer-fit calculation (Prism 4.0, GraphPad Software).
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    All three structures were determined by molecular replacement with the crystal structure of the free enzyme of the SARS-CoV-2 Mpro (PDB entry 6Y7M as search model, using the Phaser program from Phenix[49], version v1.18.1-3855).
    Phaser
    suggested: (Phaser, RRID:SCR_014219)
    Refinement of all the structures was performed with phenix.refine in Phenix software.
    Phenix
    suggested: (Phenix, RRID:SCR_014224)
    Final models displayed using PyMOL molecular graphics software (Version 2.0 Schrödinger, LLC).
    PyMOL
    suggested: (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.

    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.

  2. Version published to 10.1101/2021.02.16.431021 on bioRxiv