Immunoinformatic approach to design a multiepitope vaccine targeting non-mutational hotspot regions of structural and non-structural proteins of the SARS CoV2

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Biochemistry, Biophysics and Molecular Biology

Main article text

 

Introduction

Materials and Methods

Protein sequence collection

Analysis of protein antigenicity and trans-membrane helicity

Cytotoxic T cell epitopes prediction with potential antigenicity, allergenicity and Toxicity

Immunogenicity prediction

Helper T cell epitope prediction

B cell epitope prediction

Comparative cross-reactivity, IFN gamma induction analysis of MHC I, II and B cell epitopes

Multi-epitope vaccine designing

Evaluation of potential vaccine candidate or construct

Molecular docking

Molecular dynamics simulation

Binding affinity and dissociation constant calculation

Validation of potential vaccine candidate or construct with the human microbiome

Mutational sensitivity profiling of VTC3 and experimental mutation database analysis

Immune simulations

Codon adaptation for vaccine construct and in-silico cloning

Result

Analysis of protein antigenicity and trans-membrane helicity

Cytotoxic T cell epitopes prediction with potential antigenicity, no allergenicity and toxicity

Immunogenicity prediction

Helper T cell epitopes prediction with antigenicity, no allergenicity and toxicity

B cell epitope prediction with antigenicity, no allergenicity and no toxicity

Cross-reactivity, IFN gamma induction analysis of MHC I, II and B cell epitopes

Analysis of physicochemical properties of selected vaccine construct VTC3

Molecular docking analysis confirms the interaction of VTC3 with TLR and HLA

MDS analysis confirms the strong interaction of VTC3 with TLR1/2 heterodimer and HLA

Strong binding affinity and favorable dissociation constant between VTC3 with HLA and TLRs during MDS analysis

Multiepitope vaccine VTC3 does not have significant similarity with the human gut microbiome

Mutational profiling of multiepitope vaccine VTC3 showed less mutation sensitivity

Immune simulation confirms the strong immune response against the VTC3, as well as virus protection

Codon adaptation and in silico cloning

Discussion

Conclusion

Supplemental Information

Supplemental Figures 1–2 and Tables 1–5.

DOI: 10.7717/peerj.11126/supp-1

Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Vandana Solanki performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Monalisa Tiwari performed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Vishvanath Tiwari conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

Raw data are available as a Supplemental File.

Funding

The authors received no funding for this work.

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