Immunoinformatics and Structural Analysis for Identification of Immunodominant Epitopes in SARS-CoV-2 as Potential Vaccine Targets

Abstract

A new coronavirus infection, COVID-19, has recently emerged, and has caused a global pandemic along with an international public health emergency. Currently, no licensed vaccines are available for COVID-19. The identification of immunodominant epitopes for both B- and T-cells that induce protective responses in the host is crucial for effective vaccine design. Computational prediction of potential epitopes might significantly reduce the time required to screen peptide libraries as part of emergent vaccine design. In our present study, we used an extensive immunoinformatics-based approach to predict conserved immunodominant epitopes from the proteome of SARS-CoV-2. Regions from SARS-CoV-2 protein sequences were defined as immunodominant, based on the following three criteria regarding B- and T-cell epitopes: (i) they were both mapped, (ii) they predicted protective antigens, and (iii) they were completely identical to experimentally validated epitopes of SARS-CoV. Further, structural and molecular docking analyses were performed in order to understand the binding interactions of the identified immunodominant epitopes with human major histocompatibility complexes (MHC). Our study provides a set of potential immunodominant epitopes that could enable the generation of both antibody- and cell-mediated immunity. This could contribute to developing peptide vaccine-based adaptive immunotherapy against SARS-CoV-2 infections and prevent future pandemic outbreaks.

Designing of Nucleocapsid Protein Based Novel Multi-epitope Vaccine Against SARS-COV-2 Using Immunoinformatics Approach

“…On the basis of several parameters including antigenic, immunogenic, non-allergenic, non-toxic and number of MHC-I & II binding allele properties, five CTL and one HTL epitopes were selected from SARS-CoV-2 N protein. Importantly, selected HTL epitope was found to be immunogenic during in vitro T cell assays (Lee and Koohy 2020 ) and also one of the CTL epitopes (KTFPPTEPK) has been utilized in other recent reports to construct vaccine candidate for SARS-CoV-2 (Kalita et al 2020 ; Mukherjee et al 2020 ). Simultaneously, one linear B-cell epitope was selected on the basis of various criteria like antigenicity, allergenicity, surface accessibility and flexibility etc.…”

Computational Immune Proteomics Approach to Target COVID-19

“… 75 By following another immunoinformatics approach, Mukherjee and colleagues predicted both B and T epitopes of SARS-CoV-2 with the potential for development of a vaccinal formulation. 76 The study provides a list of candidate immunodominant epitopes capable of eliciting both humoral and cell-mediated immunity in a rapid and cost-effective manner, whose efficiency is to be tested experimentally. Another study specifically targeting the surface glycoprotein provides a list of five cytotoxic T-cell epitopes, three linear, and five more structural B-cell epitopes.…”

Immunoinformatic Analysis of SARS-CoV-2 Nucleocapsid Protein and Identification of COVID-19 Vaccine Targets

“…Approaches which use overlapping peptides, spaced other than single amino acid displacement, may exclude the key peptides. There have been several reports of bioinformatics analyses of SARS-CoV-2 using a variety of platforms (25)(26)(27)(28)(29). Herein, we applied bioinformatics analysis to determine the antigenic potential of the SARS-CoV-2 N protein.…”