Peptide-based epitope design on non-structural proteins of SARS-CoV-2

  1. R S Swathika
  2. S Vimal
  3. E Bhagyashree
  4. Elakkiya Elumalai
  5. Krishna Kant Gupta

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Abstract

The SARS-CoV-2 virus has caused the severe pandemic, COVID19 and since then its been critical to produce a potent vaccine to prevent the quick transmission and also to avoid alarming deaths. Among all type of vaccines peptide based epitope design tend to outshine with respect to low cost production and more efficacy. Therefore, we started with obtaining the necessary protein sequences from NCBI database of SARS-CoV-2 virus and filtered with respect to antigenicity, virulency, pathogenicity and non-homologous nature with human proteome using different available online tools and servers. The promising proteins was checked for containing common B and T-cell epitopes. The structure for these proteins were modeled from I-TASSER server followed by its refinement and validation. The predicted common epitopes were mapped on modeled structures of proteins by using Pepitope server. The surface exposed epitopes were docked with the most common allele DRB1*0101 using the GalaxyPepDock server. The epitopes, ELEGIQYGRS from Leader protein (NSP1), YGPFVDRQTA from 3c-like proteinase (nsp5), DLKWARFPKS from NSP9 and YQDVNCTEVP from Surface glycoprotein (spike protein) are the epitopes which has more hydrogen bonds. Hence these four epitopes could be considered as a more promising epitopes and these epitopes can be used for future studies.

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    SciScore for 10.1101/2021.12.27.474315: (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
    BLASTp with default parameters were used to find essential proteins.
    BLASTp
    suggested: (BLASTP, RRID:SCR_001010)
    Prediction and analysis of 3D structure: The 3D structure of the target proteins was predicted using online software I-TASSER [20]
    I-TASSER
    suggested: (I-TASSER, RRID:SCR_014627)
    The obtained structures were refined using GALAXYWEB server [21] and the appropriate models were made choice by considering highest C-score value.
    GALAXYWEB
    suggested: (GalaxyWEB, RRID:SCR_018558)
    To perform docking GALAXY Pepdock server [22] was used.
    GALAXY
    suggested: (Galaxy, RRID:SCR_006281)

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  2. Version published to 10.1101/2021.12.27.474315v1 on bioRxiv