Comparative analysis of non structural protein 1 of SARS-CoV2 with SARS-CoV1 and MERS-CoV: An i n silico study

  1. Ankur Chaudhuri

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Abstract

The recently emerged SARS-CoV2 caused a major pandemic of coronavirus disease (COVID-19). Non structural protein 1 (nsp1) is found in all beta coronavirus that causes several severe respiratory diseases. This protein is considered as a virulence factor and has an important role in pathogenesis. This study aims to elucidate the structural conformations of non structural protein 1 (nsp1), prediction of epitope sites and identification of important residues for targeted therapy against COVID-19. In this study, molecular modelling coupled with molecular dynamics simulations were performed to analyse the conformational change of nsp1 of SARS-CoV1, SARS-CoV2 and MERS-CoV at molecular level. Principal component analysis escorted by free energy landscape revealed that SARS-CoV2 nsp1 protein shows greater flexibility, compared to SARS-CoV1 and MERS-CoV nsp1. From the sequence alignment, it was observed that 28 mutations are present in SERS-CoV2 nsp1 protein compared to SERS-CoV1 nsp1. Several B-cell and T-cell epitopes were identified by immunoinformatics approach. SARS-CoV2 nsp1 protein binds with the interface region of the palm and finger domain of POLA1 by using hydrogen bond and salt bridge interactions. These findings can be used to develop therapeutics specific against COVID-19.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.09.142570: (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
    The pairwise sequence identity between COVID-19 nsp1 protein and each of the other HCoV nsp1 proteins (SERS-COV1 and MERS-COV) was calculated using the BLASTp (basic local alignment tool) [17].
    BLASTp
    suggested: (BLASTP, RRID:SCR_001010)
    To check the conservation pattern, multiple sequence alignment (MSA) of all of the nsp1 sequences was performed using the Clustal Omega programme of the European Bioinformatics Institute (EMBL-EBI) [18].
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    So, in silico modelling study was employed to predict the three dimensional structure of nsp1 of SARS-COV2 and MERS-COV by using the I-TASSER web server [20]
    I-TASSER
    suggested: (I-TASSER, RRID:SCR_014627)
    These two methods recognize ligand-binding templates from the BioLiP database [28] by sequence profile comparisons and binding-specific substructure.
    BioLiP
    suggested: None
    , Pymol [42], and also the plots were created using xmgrace [43].
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)

    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 24 and 22. 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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

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  2. Version published to 10.1101/2020.06.09.142570 on bioRxiv