Towards the design of multiepitope-based peptide vaccine candidate against SARS-CoV-2

  1. Hasanain Abdulhameed Odhar
  2. Salam Waheed Ahjel
  3. Suhad Sami Humadi

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Abstract

Coronavirus disease 2019 is a current pandemic health threat especially for elderly patients with comorbidities. This respiratory disease is caused by a beta coronavirus known as severe acute respiratory syndrome coronavirus 2. The disease can progress into acute respiratory distress syndrome that can be fatal. Currently, no specific drug or vaccine are available to combat this pandemic outbreak. Social distancing and lockdown have been enforced in many places worldwide. The spike protein of coronavirus 2 is essential for viral entry into host target cells via interaction with angiotensin converting enzyme 2. This viral protein is considered a potential target for design and development of a drug or vaccine. Previously, we have reported several potential epitopes on coronavirus 2 spike protein with high antigenicity, low allergenicity and good stability against specified proteases. In the current study, we have constructed and evaluated a peptide vaccine from these potential epitopes by using in silico approach. This construct is predicted to have a protective immunogenicity, low allergenicity and good stability with minor structural flaws in model build. The population coverage of the used T-cells epitopes is believed to be high according to the employed restricted alleles. The vaccine construct can elicit efficient and long-lasting immune response as appeared through simulation analysis. This multiepitope-based peptide vaccine may represent a potential candidate against coronavirus 2. However, further in vitro and in vivo verification are required.

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    SciScore for 10.1101/2020.07.07.186122: (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
    Prediction of physicochemical properties, immunogenicity and allergenicity of vaccine design: We have used ProtParam web-based tool to predict different physical and chemical characteristics of vaccine construct [26].
    ProtParam
    suggested: (ProtParam Tool, RRID:SCR_018087)
    VaxiJen v2.0 tool can predict protective antigens with no need for sequence alignment, it depends mainly on physicochemical properties of the submitted peptide [27].
    VaxiJen
    suggested: (VaxiJen, RRID:SCR_018514)
    Secondary and tertiary structures prediction of vaccine design: The secondary structure of vaccine construct was predicted by using PSIPRED 4.0 tool [29].
    PSIPRED
    suggested: (PSIPRED, RRID:SCR_010246)
    To further improve vaccine tertiary structure, the generated PDB file was then submitted to Galaxy refine server.
    Galaxy
    suggested: (Galaxy, RRID:SCR_006281)
    Molecular docking and dynamics simulation study: The vaccine PDB was then docked into Toll-like receptor 8 (TLR8) crystal by using PatchDock web server.
    PatchDock
    suggested: (PatchDock, RRID:SCR_017589)
    The generated docking complex with the highest geometric shape complementarity score was then downloaded as PDB file and visualized by using PyMOL version 2.3 and DIMPLOT [40,41].
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    Later, this docking complex was subject to molecular dynamics (MD) analysis by using YASARA Dynamics version 19.12.14 [42].
    YASARA
    suggested: (YASARA, RRID:SCR_017591)

    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.

    About SciScore

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  2. Version published to 10.1101/2020.07.07.186122v1 on bioRxiv