N-Terminal Finger Stabilizes the S1 Pocket for the Reversible Feline Drug GC376 in the SARS-CoV-2 Mpro Dimer

  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

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Abstract

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  1. Version published to 10.1016/j.jmb.2021.167003
  2. 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.

  3. Version published to 10.1101/2021.02.16.431021v1 on bioRxiv