In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins

  1. Gunderao H Kathwate

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Abstract

COVID 19 is disease caused by novel corona virus, SARS-CoV2 originated in China most probably of Bat origin. Till date, no specific vaccine or drug has been discovered to tackle the infections caused by SARS-CoV2. In response to this pandemic, we utilized bioinformatics knowledge to develop efficient vaccine candidate against SARS-CoV2. Designed vaccine was rich in effective BCR and TCR epitopes screened from the sequence of S-protein of SARS-CoV2. Predicted BCR and TCR epitopes were antigenic in nature non-toxic and probably non-allergen. Modelled and refined tertiary structure was predicted as valid for further use. Protein-Protein interaction prediction of TLR2/4 and designed vaccine indicates promising binding. Designed multiepitope vaccine has induced cell mediated and humoral immunity along with increased interferon gamma response. Macrophages and dendritic cells were also found increased over the vaccine exposure. In silico codon optimization and cloning in expression vector indicates that vaccine can be efficiently expressed in E. coli . In conclusion, predicted vaccine is a good antigen, probable no allergen and has potential to induce cellular and humoral immunity.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.03.131755: (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
    Selection of protein for epitope prediction: Complete Spike protein sequence (P0DTC2) of SARS-CoV2 was downloaded in fasta format from UniProt protein database.
    UniProt
    suggested: (UniProtKB, RRID:SCR_004426)
    Antigenicity of epitopes was analyzed by online server VaxiJen v2.0 (http://www.ddg-harmfac.net/vaxijen/VaxiJen/VaxiJen.html).
    VaxiJen
    suggested: (VaxiJen, RRID:SCR_018514)
    AllerTop v2.0 and AllergenFP were two online tools utilized for the prediction of allergenicity of chimeric protein.
    AllerTop
    suggested: (AllerTop, RRID:SCR_018496)
    PROSO II server works on an approach of classifier which utilizes difference between TargetDB and PDB and insoluble proteins of TargetDB.
    TargetDB
    suggested: None
    PSIPRED 3.2 attains average Q3 score of 81.6% obtained using very stringent cross approval strategies to assess its performance.
    PSIPRED
    suggested: (PSIPRED, RRID:SCR_010246)
    Tertiary structure of multi-epitopes chimeric vaccine candidate was built using I TASSER online server (https://zhanglab.ccmb.med.umich.edu/I-TASSER/).
    https://zhanglab.ccmb.med.umich.edu/I-TASSER/
    suggested: (I-TASSER, RRID:SCR_014627)
    Structure refined by Galaxy server of best quality in accordance with community-wide CASP10 experiments(58).
    Galaxy
    suggested: (Galaxy, RRID:SCR_006281)
    ProSA-web (https://prosa.services.came.sbg.ac.at/prosa.php), The ERRAT server (http://services.mbi.ucla.edu/ERRAT/) and RAMPAGE (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php) web servers were utilized for 3D structure validation obtained after galaxy server refinement(59)
    RAMPAGE
    suggested: (RAMPAGE, RRID:SCR_017590)

    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: 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.

    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.

  2. Version published to 10.1101/2020.06.03.131755 on bioRxiv