Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design

  1. Dénes Berta
  2. Magd Badaoui
  3. Sam Alexander Martino
  4. Pedro J. Buigues
  5. Andrei V. Pisliakov
  6. Nadia Elghobashi-Meinhardt
  7. Geoff Wells
  8. Sarah A. Harris
  9. Elisa Frezza
  10. Edina Rosta

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Abstract

The RNA helicase (non-structural protein 13, NSP13) of SARS-CoV-2 is essential for viral replication, and it is highly conserved among the coronaviridae family, thus a prominent drug target to treat COVID-19.

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  1. Version published to 10.1039/d1sc02775a
  2. ScreenIT

    SciScore for 10.1101/2020.11.03.366609: (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
    Homologous Sequence Analysis: Sequence alignments were done using BLAST with default settings and BLOSUM62 distance matrix, requesting the most similar 1000 hits from UniProtKB.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    UniProtKB
    suggested: (UniProtKB, RRID:SCR_004426)
    9 Missing residues and the I570V mutagenesis were constructed in pymol.
    pymol
    suggested: (PyMOL, RRID:SCR_000305)
    These constraints were subsequently progressively reduced and removed during the next 20 ns, using the colvar function implemented in NAMD.
    NAMD
    suggested: (NAMD, RRID:SCR_014894)
    To compare simulation results obtained with MD, we also carried out MD simulations using GROMACS 201818–21 with the Amber ff99+ parmbsc0+chioL3 force field22,23 for ssRNA and Amber14SB24 for the helicase.
    GROMACS
    suggested: (GROMACS, RRID:SCR_014565)
    Amber
    suggested: (AMBER, RRID:SCR_016151)

    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

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  3. Version published to 10.1101/2020.11.03.366609v1 on bioRxiv