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Structural basis to design multi-epitope vaccines against Novel Coronavirus 19 (COVID19) infection, the ongoing pandemic emergency: an in silico approach

View ORCID ProfileSukrit Srivastava, Sonia Verma, Mohit Kamthania, Rupinder Kaur, Ruchi Kiran Badyal, Ajay Kumar Saxena, Ho-Joon Shin, Michael Kolbe, Kailash C Pandey
doi: https://doi.org/10.1101/2020.04.01.019299
Sukrit Srivastava
aDepartment of Biotechnology, Institute of Bio-Medical Education and Research, Mangalayatan University, 202146 Aligarh, India
bMolecular Medicine Lab., School of Life Science, Jawaharlal Nehru University, 110067 New Delhi, India
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  • ORCID record for Sukrit Srivastava
  • For correspondence: sukrit.srivastav@mangalayatan.edu.in srivastav.sukrit@gmail.com
Sonia Verma
cParasite-Host Biology Group, Protein Biochemistry & Engineering Lab, ICMR-National Institute of Malaria Research, New Delhi, India
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Mohit Kamthania
dDepartment of Biotechnology, Institute of Applied Medicines and Research, 201206 Ghaziabad, India
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Rupinder Kaur
eDepartment of Chemistry, Guru Nanak Dev University, Amritsar, India
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Ruchi Kiran Badyal
fDepartment of economics, Mangalayata University, India
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Ajay Kumar Saxena
bMolecular Medicine Lab., School of Life Science, Jawaharlal Nehru University, 110067 New Delhi, India
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Ho-Joon Shin
gDepartment of Microbiology,School of Medicine, Ajou University, South Korea
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Michael Kolbe
hDepartment for Structural Infection Biology, Centre for Structural Systems Biology (CSSB) & Helmholtz-Centre for Infection Research, Notkestraße 85, 22607 Hamburg, Germany
iFaculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Rothenbaumchaussee 19, 20148 Hamburg, Germany
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Kailash C Pandey
cParasite-Host Biology Group, Protein Biochemistry & Engineering Lab, ICMR-National Institute of Malaria Research, New Delhi, India
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  • Abstract
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Abstract

The 2019 novel coronavirus (COVID19 / Wuhan coronavirus), officially named as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is a positive-sense single-stranded RNA coronavirus. SARS-CoV-2 causes the contagious COVID19 disease also known as 2019-nCoV acute respiratory disease and has led to the ongoing 2019–20 pandemic COVID19 outbreak. The effective counter measures against SARS-CoV-2 infection require the design and development of specific and effective vaccine candidate. In the present study, we have screened and shortlisted 38 CTL, 33 HTL and 12 B cell epitopes from the eleven Protein sequences of SARS-CoV-2 by utilizing different in silico tools. The screened epitopes were further validated for their binding with their respective HLA allele binders and TAP (Transporter associated with antigen processing) molecule by molecular docking. The shortlisted screened epitopes were further utilized to design novel two multi-epitope vaccines (MEVs) composed of CTL, HTL and B cell epitopes overlaps with potential to elicit humoral as well as cellular immune response against SARS-CoV-2. To enhance the immune response for our vaccine design, truncated (residues 10-153) Onchocerca volvulus activation-associated secreted protein-1 (Ov-ASP-1) has been utilized as an adjuvant at N terminal of both the MEVs. Further molecular models for both the MEVs were prepared and validated for their stable molecular interactions with Toll-Like Receptor 3 (TLR 3). The codon-optimized cDNA of both the MEVs were further analyzed for their potential of high level of expression in a human cell line. The present study is very significant in terms of molecular designing of prospective CTL and HTL vaccine against SARS-CoV-2 infection with the potential to elicit cellular as well as humoral immune response. (SARS-CoV-2), Coronavirus, Human Transporter associated with antigen processing (TAP), Toll-Like Receptor (TLR), Epitope, Immunoinformatics, Molecular Docking, Molecular dynamics simulation, Multi-epitope Vaccine

Graphical abstract The designed CTL (Cytotoxic T lymphocyte) and HTL (Helper T lymphocyte) multi-epitope vaccines (MEV) against COVID19 infection. Both the CTL and HTL MEV models show a very stable and well fit conformational complex formation tendency with the Toll like receptor 3. CTL and HTL MEVs: ribbon; Toll like receptor 3: gray cartoon; Adjuvant [truncated (residues 10-153) Onchocerca volvulus activation-associated secreted protein-1]: orange ribbon regions; Epitopes: cyan ribbons regions; 6xHis Tag: magenta ribbon regions.

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Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Additional result of Molecular dynamics simulation validation to our multi-epitope vaccine has been added (Fig. 10).

  • Abbreviations

    (APCs)
    Antigen-presenting cell
    (CAI)
    Codon Adaptation Index
    (COVID19)
    Coronavirus ID 19
    (CoV)
    Coronavirus
    (CoV)
    Coverage
    (Cryo-EM)
    Cryo-Electron Microscopy
    (CTL)
    Cytotoxic T lymphocyte
    (ECD)
    ectodomain
    (E Protein)
    Envelope Protein
    (ER)
    endoplasmic reticulum
    (EBI)
    European Bioinformatics Institute
    (N Protein)
    Nucleocapsid Protein
    (ORF)
    Ope reading Frame
    (GDT)
    global distance test
    (GRAVY)
    Grand average of hydropathicity
    (RMSD)
    root mean square deviation
    (RMSF)
    root mean square fluctuation
    (S Protein)
    Surface protein
    (IC50)
    half maximal inhibitory concentration
    (HTL)
    Helper T lymphocyte
    (HLA)
    Human Leukocyte Antigen
    (IEDB)
    Immune Epitope Database
    (IPD)
    Immuno Polymorphism Database
    (IFN-γ)
    Interferon Gama
    (IMGT)
    International ImMunoGeneTics project
    (MHC)
    major histocompatibility complex
    (M Protein)
    Membrane Protein
    (MERCI)
    Motif-EmeRging with ClassesIdentification
    (MD simulation)
    Molecular dynamics simulation
    (MEV)
    Multi-epitope Vaccine
    (MSA)
    Multiple Sequence Alignment
    (nsp)
    non-structural protein
    (NCBI)
    National Center for Biotechnology Information
    (pMHC)
    peptide-MHC
    (SARS-CoV-2)
    Severe Acute Respiratory Syndrome Coronavirus 2
    (SMM)
    Stabilization Matrix alignment method
    (TM)
    Transmembrane
    (PDB)
    Protein Data Bank
    (QMEAN)
    Qualitative Model Energy ANalysis
    (RMSD)
    root mean square deviation
    (SVM)
    Support Vector Machine
    (TLR3)
    Toll-Like Receptor 3
    (TAP)
    Transporter associated with antigen processing
    (uGDT)
    un-normalized global distance test
    (YASARA)
    Yet Another Scientifc Artifcial Reality Application
  • Copyright 
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    Structural basis to design multi-epitope vaccines against Novel Coronavirus 19 (COVID19) infection, the ongoing pandemic emergency: an in silico approach
    Sukrit Srivastava, Sonia Verma, Mohit Kamthania, Rupinder Kaur, Ruchi Kiran Badyal, Ajay Kumar Saxena, Ho-Joon Shin, Michael Kolbe, Kailash C Pandey
    bioRxiv 2020.04.01.019299; doi: https://doi.org/10.1101/2020.04.01.019299
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    Structural basis to design multi-epitope vaccines against Novel Coronavirus 19 (COVID19) infection, the ongoing pandemic emergency: an in silico approach
    Sukrit Srivastava, Sonia Verma, Mohit Kamthania, Rupinder Kaur, Ruchi Kiran Badyal, Ajay Kumar Saxena, Ho-Joon Shin, Michael Kolbe, Kailash C Pandey
    bioRxiv 2020.04.01.019299; doi: https://doi.org/10.1101/2020.04.01.019299

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