Modeling SARS-CoV-2 spike/ACE2 protein–protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context

  1. Vincenzo Tragni
  2. Francesca Preziusi
  3. Luna Laera
  4. Angelo Onofrio
  5. Ivan Mercurio
  6. Simona Todisco
  7. Mariateresa Volpicella
  8. Anna De Grassi
  9. Ciro Leonardo Pierri

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Abstract

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  1. Version published to 10.1007/s13167-021-00267-w
  2. ScreenIT

    SciScore for 10.1101/2021.05.26.445422: (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
    Furthermore, the FoldX AnalyseComplex assay was used for determining the binding affinity between SARS-CoV-2 spike RBD and the ACE2 structurally related receptors ACE, THOP1, and NLN, identified through pGenTHREADER and/or ITASSER analyses.
    pGenTHREADER
    suggested: None
    Software and Algorithms
    SentencesResources
    With this aim, the amino acid sequence of ACE2 (NP_001358344.1) was used as query sequence for running pGenThreader (http://bioinf.cs.ucl.ac.uk/psipred/) and I-Tasser (https://zhanglab.ccmb.med.umich.edu/I-TASSER/) to screen the Protein Data Bank (PDB), searching for ACE2 structurally related crystallized proteins [1, 29–35].
    http://bioinf.cs.ucl.ac.uk/psipred/
    suggested: (PSIPRED, RRID:SCR_010246)
    https://zhanglab.ccmb.med.umich.edu/I-TASSER/
    suggested: (I-TASSER, RRID:SCR_014627)
    The variation in the number of interactions (H-bonds, ionic and aromatic interactions) at the SARS-CoV-2 spike RBD/ACE2 interface in presence of the investigated amino acid replacements have been calculated by using the PIC webserver [37] and verified by manual inspection by using PyMOL.
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    Furthermore, the FoldX AnalyseComplex assay was used for determining the binding affinity between SARS-CoV-2 spike RBD and the ACE2 structurally related receptors ACE, THOP1, and NLN, identified through pGenTHREADER and/or ITASSER analyses.
    FoldX
    suggested: (FoldX, RRID:SCR_008522)

    Results from OddPub: Thank you for sharing your data.

    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 pages 8, 16, 19 and 21. 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 10.1101/2021.05.26.445422v1 on bioRxiv