Structural Basis for Designing Multiepitope Vaccines Against COVID-19 Infection: In Silico Vaccine Design and Validation

Abstract

Background The novel coronavirus disease (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to the ongoing 2019-2020 pandemic. SARS-CoV-2 is a positive-sense single-stranded RNA coronavirus. Effective countermeasures against SARS-CoV-2 infection require the design and development of specific and effective vaccine candidates. Objective To address the urgent need for a SARS-CoV-2 vaccine, in the present study, we designed and validated one cytotoxic T lymphocyte (CTL) and one helper T lymphocyte (HTL) multi-epitope vaccine (MEV) against SARS-CoV-2 using various in silico methods. Methods Both designed MEVs are composed of CTL and HTL epitopes screened from 11 structural and nonstructural proteins of the SARS-CoV-2 proteome. Both MEVs also carry potential B-cell linear and discontinuous epitopes as well as interferon gamma–inducing epitopes. To enhance the immune response of our vaccine design, truncated (residues 10-153) Onchocerca volvulus activation-associated secreted protein-1 was used as an adjuvant at the N termini of both MEVs. The tertiary models for both the designed MEVs were generated, refined, and further analyzed for stable molecular interaction with toll-like receptor 3. Codon-biased complementary DNA (cDNA) was generated for both MEVs and analyzed in silico for high level expression in a mammalian (human) host cell line. Results In the present study, we screened and shortlisted 38 CTL, 33 HTL, and 12 B cell epitopes from the 11 protein sequences of the SARS-CoV-2 proteome. Moreover, the molecular interactions of the screened epitopes with their respective human leukocyte antigen allele binders and the transporter associated with antigen processing (TAP) complex were positively validated. The shortlisted screened epitopes were utilized to design two novel MEVs against SARS-CoV-2. Further molecular models of both MEVs were prepared, and their stable molecular interactions with toll-like receptor 3 were positively validated. The codon-optimized cDNAs of both MEVs were also positively analyzed for high levels of overexpression in a human cell line. Conclusions The present study is highly significant in terms of the molecular design of prospective CTL and HTL vaccines against SARS-CoV-2 infection with potential to elicit cellular and humoral immune responses. The epitopes of the designed MEVs are predicted to cover the large human population worldwide (96.10%). Hence, both designed MEVs could be tried in vivo as potential vaccine candidates against SARS-CoV-2.

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

“…The identified Ag-Patches were highly conserved in nature and were identified on the basis of significant number of overlapping epitope forming clusters (Figure 2, 3 & 4). Ag-Patches together, and to facilitate folding of the protein into its tertiary conformation (Hu et al, 2004;Wilson et al, 2013;Duits et al, 2003;Chen et al, 2013;Hajighahramani et al, 2017;Srivastava et al, 2019;Srivastava et al, 2018;Srivastava et al, 2020a;Srivastava et al, 2020b) ( Figure 1A, 1B, 2 (Table 3). from CTL-MPV-3); likewise, a total of IFN-γ inducing epitopes were screened from two HTL MPVs (83 from HTL-MPV-1 and 98 from HTL-MPV-2).…”

“…All the three CTL and two HTL MPVs were fitting into the ectodomain region of TLR3 receptor (Figure 7). 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 et al, 2020;Bhattacharya et al, 2020;Fast et al, 2020;Gragert et al, 2013;Gupta et al, 2020;Herst et al, 2020;Ismail et al, 2020;Khan et al, 2020;Lee et al, 2020;Liu et al, 2020;Lu et al, 2014;Mitra et al, 2020;Nerli et al, 2020;Poran et al, 2020;Ramaiah et al, 2020;Saha et al, 2020;Sheikhshahrokh et al, 2020;Singh et al, 2020;Srivastava et al, 2020a;Srivastava et al, 2020b;ul Qamar et al, 2020;Vashi et al, 2020;Yazdani et al, 2020). Numerous highly antigenic regions have also been reported from SARS-CoV-2 proteins which have been recognized on the basis of large population coverage by favorable binding with large number of HLA allele distributed amongst different ethnic human population worldwide (Grifoni et al, 2020b;Yarmarkovich and Warrington et al, 2020).…”

“…The proteasome and lysosomal chop down processing of MPVs by the Antigen Presenting cells would release larger number of epitopes in their intact form for which the MEVs would have a challenge. Moreover the Ag-Patch based MPVs will cover larger number of overlapping epitopes in comparison to the limited number of epitopes covered by epitope based MEVs (Srivastava et al, 2020a;Srivastava et al, 2020b). The larger the number of epitopes covered larger would be the number of HLA alleles targeted and hence larger human population with ethnic distribution of HLA alleles will be covered.…”

“…The immunogenicity analysis of all the screened CTL epitopes was also performed by the tool "MHC I Immunogenicity" of IEDB. The higher immunogenicity score of all the screened CTL epitopes suggest the high immunogenic potential of the CTL epitopes (Supplementary table S1, S2;Srivastava et al 2020a;Srivastava et al 2020b;and Grifoni et al, 2020a). MHC-II Binding Predictions" tool of IEDB.…”

“…Furthermore, the higher Percentile rank suggests a higher affinity of the peptide to bind its respective HLA allele binders. A total of 314 HTL epitopes-HLA II allele pairs with high percentile rank were screened from the entire proteome of the SARS-CoV-2 virus(Supplementary table S3;Srivastava et al 2020a;Srivastava et al 2020b;and Grifoni et al, 2020a).CTL and HTL epitope Toxicity prediction. Toxicity analysis of all the screened CTL and HTL epitopes was also performed by the tool "ToxinPred".…”