In silicodesign of Multi-epitope-based peptide vaccine against SARS-CoV-2 using its spike protein

Abstract

<jats:title>Abstract</jats:title><jats:p>SARS CoV-2 has particularly been efficient in ensuring that many countries are brought to a standstill. With repercussions ranging from rampant mortality, fear, paranoia and economic recession, the virus has brought together countries in order to look at possible therapeutic countermeasures. With prophylactic interventions possibly months away from being particularly effective, a slew of measures and possibilities concerning the design of vaccines are being worked upon. We attempted a structure-based approach utilizing a combination of epitope prediction servers to develop a multi-epitope-based subunit vaccine that involves the two major domains of the spike glycoprotein of SARS CoV-2 (S1 and S2) coupled with a substantially effective chimeric adjuvant to create stable vaccine constructs through MD simulations. The designed constructs were evaluated based on their docking with Toll Like Receptor (TLR) 4. Our findings provide an epitope-based peptide fragment; which can be a potential candidate for the development of a vaccine against SARS-CoV-2. Recent experimental studies based on determining immunodominant regions across the spike glycoprotein of SARS-CoV-2 indicate the presence of the predicted epitopes included in this study.</jats:p>

Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma

“…Other antibodies with neutralizing activities have been discovered through different methodologies [20][21][22][23][24][25]. The rapid propagation of SARS-CoV-2 stimulated several studies predicting the antigenic parts of the viral proteins in silico [26][27][28][29][30][31][32], and analyzing SARS-CoV-1 epitopes that were conserved in this new coronavirus [33][34][35][36]. More recently, the first reports of experimental epitope mapping of the SARS-CoV-2 were deposited on repositories [37][38][39][40][41][42].…”

Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions

“…We used EvalVax to evaluate peptide vaccines and megapools proposed by other publications ( Lee and Koohy, 2020 ; Fast et al., 2020 ; Poran et al., 2020 ; Bhattacharya et al., 2020 ; Baruah and Bose, 2020 ; Abdelmageed et al., 2020 ; Ahmed et al., 2020 ; Srivastava et al., 2020 ; Herst et al., 2020 ; Vashi et al., 2020 ; Akhand et al., 2020 ; Mitra et al., 2020 ; Khan et al., 2020 ; Banerjee et al., 2020 ; Ramaiah and Arumugaswami, 2020 ; Gupta et al., 2020 ; Saha and Prasad, 2020 ; Tahir ul Qamar et al, 2020 ; Singh et al., 2020 ; Yarmarkovich et al., 2020 ; Grifoni et al., 2020a ; Nerli and Sgourakis, 2020 ; Yazdani et al., 2020 ; Ismail et al., 2020 ) on metrics including EvalVax-Unlinked and EvalVax-Robust population coverage at different per-individual number of peptide-HLA hits thresholds, expected per-individual number of peptide-HLA hits in White, Black, and Asian populations, percentage of peptides that are predicted to be glycosylated, peptides observed to mutate with a probability greater than 0.001, or peptides that sit on known cleavage sites. We define “normalized coverage” as the mean expected per-individual number of peptide-HLA hits for a vaccine divided by the number of peptides in the vaccine.…”

Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch vaccines, designed by reverse epitomics approach, show potential to cover large ethnically distributed human population worldwide

“…On the other hand, the multi-epitope vaccine involves fusion of multiple epitopes identified from the proteome of the SARS-CoV-2 by short peptide linkers. Several subunit and multi-epitope-based vaccine designs have been published claiming potential to activate CD4 and CD8 T-cell immune response driving long-term robust adaptive immunity in the vast majority of the population (Abdelmageed et al, 2020 ; Ahmed et al, 2020 ; Akhand et al, 2020 ; An et al, 2000 ; Banerjee et al, 2020 ; Baruah & Bose, 2020 ; Bhattacharya et al, 2020 ; Fast & Chen, 2020 ; Gragert et al, 2013 ; Gupta et al, 2020 ; Herst et al, 2020 ; Ismail et al, 2020 ; Khan et al, 2020 ; Lee & Koohy, 2020 ; Liu et al, 2020 ; Lu et al, 2014 ; Mitra et al, 2020 ; Nerli & Sgourakis, 2020 ; Poran et al, 2020 ; Ramaiah & Arumugaswami, 2020 ; Saha & Prasad, 2020 ; Sheikhshahrokh et al, 2020 ; Singh et al, 2020 ; Srivastava et al, 2020a ; 2020b ; Ul Qamar et al, 2020 ; Vashi et al, 2020 ; Yarmarkovich, Farrel et al, 2020; Yazdani et al, 2020 ). Numerous highly antigenic regions have also been reported from SARS-CoV-2 proteins, which have been recognized with a large population coverage by favorable binding with large number of HLA allele distributed among different ethnic human population across the world (Grifoni et al, 2020b ; Yarmarkovich, Warrington, et al, 2020 ).…”