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

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) <i>Onchocerca volvulus</i> 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.

Novel “GaEl Antigenic Patches” Identified by a “Reverse Epitomics” Approach to Design Multipatch Vaccines against NIPAH Infection, a Silent Threat to Global Human Health

“…A total of 30 GaEl Ag-Patches from 362 CTL and 27 GaEl Ag-Patches from 414 HTL overlapping epitopes were identified. To identify the GaEl Ag-Patches, a novel “reverse epitomics” approach involving the “overlapping-epitope-clusters-to-patches” method was utilized − (Tables and ). The herewith suggested GaEl Ag-Patches are expected to result in up to 776 overlapping epitopes upon intercellular proteolytic chop down by antigen presenting cells (APCs).…”

“…The constructs include hBD-2 with sequence: GIGDPVTCLKSGAICHPVFCPRRYKQIGTCGLPGTKCCKKP and 3D structure deposited in the Protein Data Bank (PDB code 1FD3) and hBD-3 with sequence: GIINTLQKYYCRVRGGRCAVLSCLPKEEQIGKCSTRGRKCCRRKK and 3D structure (PDB code 1KJ6). hBD 2 and 3 are utilized here as adjuvants to enhance the immunogenic response. − ,,− The multipatch vaccine design and the method thereof are included in the field patents 202011037939, 202011037939, PCT/IN2021/050841, and previous publications. − …”

“…These vaccines are composed of “GaEL antigenic patches” (GaEl Ag-Patches) identified from the proteome of NiV. The “GaEl Ag-Patches” were identified by the reverse epitomics approach as introduced in our earlier studies. − All nine proteins of the NiV proteome () were used in this study, viz., C protein (gi-1859635642), glycoprotein (gi-253559848), fusion protein (gi-13559813), nucleoprotein (gi-1679387250), matrix protein (gi-13559811), phosphoprotein (gi-1802790259), W protein (gi-374256971), V protein (gi-1802790260), and RNA polymerase (gi-15487370). The full-length amino acid sequences of NiV proteins were retrieved from the National Center for Biotechnology Information (NCBI).…”

“…The consensus amino acid sequence of overlapping epitopes was identified as “GaEl Ag-Patches”. This novel approach of search and identification of “GaEl antigenic patches” from a source protein is named as “reverse epitomics” as introduced and explained in our earlier studies. − This approach is applicable to proteins/antigens of any pathogen and not only to SARS-CoV-2 or NiV.…”

“…This is to acknowledge the inventors of “reverse epitomics”, and the prefix GaEl is derived from river Ganga and Elna of the inventors’ home countries. The novel “reverse epitomics” approach to identify “GaEl Ag-Patch” has been introduced in our earlier study on SARS-CoV-2. − In the present study, we have utilized the “reverse epitomics” approach to identify “GaEl Ag-Patch” from NiV proteins. The reverse epitomics approach applies the novel “overlapping-epitope-clusters-to-patches” method to identify the “GaEl Ag-Patches”.…”