An Immunoinformatics Approach for SARS-CoV-2 in Latam Populations and Multi-Epitope Vaccine Candidate Directed towards the World's Population

Abstract

The coronavirus pandemic is a major public health crisis affecting global health systems with dire socioeconomic consequences, especially in vulnerable regions such as Latin America (LATAM). There is an urgent need for a vaccine to help control contagion, reduce mortality and alleviate social costs. In this study, we propose a rational multi-epitope candidate vaccine against SARS-CoV-2. Using bioinformatics, we constructed a library of potential vaccine peptides, based on the affinity of the most common major human histocompatibility complex (HLA) I and II molecules in the LATAM population to predict immunological complexes among antigenic, non-toxic and non-allergenic peptides extracted from the conserved regions of 92 proteomes. Although HLA-C, had the greatest antigenic peptide capacity from SARS-CoV-2, HLA-B and HLA-A, could be more relevant based on COVID-19 risk of infection in LATAM countries. We also used three-dimensional structures of SARS-CoV-2 proteins to identify potential regions for antibody production. The best HLA-I and II predictions (with increased coverage in common alleles and regions evoking B lymphocyte responses) were grouped into an optimized final multi-epitope construct containing the adjuvants Beta defensin-3, TpD, and PADRE, which are recognized for invoking a safe and specific immune response. Finally, we used Molecular Dynamics to identify the multi-epitope construct which may be a stable target for TLR-4/MD-2. This would prove to be safe and provide the physicochemical requirements for conducting experimental tests around the world.

Keywords: LATAM; SARS-CoV-2; in silico; vaccine.

Figure 1

Vaccine development pipeline: the design stages of the multi-epitope vaccine proposal are shown. Each stage is important for meeting the objective of identifying peptides capable of generating an immune response, taking into account the most frequent alleles in Latin America. The important servers and cutoff values used in the process are specified.

Figure 2

Antigenic presentation from the proposed vaccine: The assembly of peptides with vaccine potential are recognised by cell membrane receptors capable of recognising patterns associated with pathogens, such as TLR2 and 4 from dendritic cells. After recognition, the construct is phagocytized by the cell together with TLR, allowing its interaction with MyD88 and the maturation of the phagosome. From the phagosome, the peptide can take two routes: the first route is towards the proteasome, where the peptide is degraded, internalised in the ER and assembled with HLA-I molecules; the second route involves the internalization of the peptide in the late endosome, where it is assembled with HLA-II molecules and subsequently presented on the cell membrane of the LT [103,104,105].

Figure 3

Estimation of flexible molecular protein-peptide coupling: In the complexes (upper panels) are two non-redundant HLA-I molecules most frequently found in the Latin American population coupled with a peptide with vaccine potential from SP, namely FAMQMAYRF. (a), Cluster 1, density of 239, $\Delta$G of −5.2. (b), Cluster 1, density of 355, $\Delta$G of −4.9. In the complexes (lower panels) are two non-redundant HLA-II molecules most frequently found in the Latin American population coupled with a peptide with vaccine potential from MG, namely SFRLFARTRSMWSFN. (c), Cluster 1, density of 138, $\Delta$G of −4.6. (d), Cluster 2, density of 168, $\Delta$G of −4.4.

Figure 4

Construction of the Proposed Multi-Epitope Vaccine. Structure of the multi-epitope construct: three-dimensional diagrammatic structure of the multi-epitope construct showing (a), the separators, origin of the peptides and adjuvants used; (b), the location of the adjuvants PADRE, TpD and M cell ligand; and (c), the location of the epitope’s cytotoxic T lymphocytes (CTLs), T helper lymphocytes (HTLs) and B lymphocytes (BLs). (d), Ribbon diagram of the multiepitope construct.

Figure 5

Analysis of trajectory. (a), Root mean square deviation (RMSD) C$\alpha$ atoms. (b), Root mean square fluctuation for C$\alpha$ atoms (RMSF), TLR-4 receptor initialize at amino acid 1 and goes to amino acid number 1482, and the vaccine from amino acid number 1483 to 1992. (c), Rg plot; vaccine construct is stable in its compact form during the simulation time. (d), Changes in the number of hydrogen bonds between the TLR-4 receptor and multi-epitope vaccine molecule during MD simulation.

Figure 6

Immune simulation using the multi-epitope construct. (a), BLs, (b), CD4+ TLs and (d), CD8+ TLs were simulated, presenting a cumulative effect towards the third injection on the 56th day of simulation. This suggests the early presence of TLs memory and a change towards the immunoglobulin isotype, immunoglobulin G (IgG), being more predominant. While the antigenic stimulus lasts, there is a polarization towards a certain type of response (c), HTL-1, which is consistent with (e), the active antigenic presentation of professional antigen-presenting cells. This could be partly stimulated by other non-presenters, as well as the production of interleukins, such as (f), IFN $\gamma$, TGF-$\beta$ and IL-2. An infection challenge, composed of a virus responding to the sequence of SARS-CoV-2 proteins covered by the multi-epitope construct, was simulated on day 366. (g), An indifference in immunoglobulin M (IgM) production and increased IgG response suggests favourable conditions for viral antibody clearance in the BLs. (h), The duplication and antigenic presentation of BLs correspond to the stimulated response by the simulated virus, which lasts beyond the viral challenge. (i), An IgG isotype shows a substantial response to the viral challenge, with subtype IgG1 most notably responding. (j), The CD4+ TLs population is globally stimulated; the memory response results in consolidation, which increases cell numbers and is still available over 100 days after the viral challenge. (k), The population of memory CD8+ cells is stimulated by the viral challenge, acting directly on viral clearance.