Design of a multi-epitope-based vaccine targeting M-protein of SARS-CoV2: an immunoinformatics approach

Abstract

In the present study, one of the targets present on the envelopes of coronaviruses, membrane glycoprotein (M) was chosen for the design of a multi-epitope vaccine by Immunoinformatics approach. The B-cell and T-cell epitopes used for the construction of vaccine were antigenic, nonallergic and nontoxic. An adjuvant, β-defensin and PADRE sequence were included at the N-terminal end of the vaccine. All the epitopes were joined by linkers for decreasing the junctional immunogenicity. Various physicochemical parameters of the vaccine were evaluated. Secondary and tertiary structures were predicted for the vaccine construct. The tertiary structure was further refined, and various parameters related to the refinement of the protein structure were validated by using different tools. Humoral immunity induced by B-cells relies upon the identification of antigenic determinants on the surface of the vaccine construct. In this regard, the vaccine construct was found to consist of several B-cell epitopes in its three-dimensional conformation. Molecular docking of the vaccine was carried out with TLR-3 receptor to study their binding and its strength. Further, protein-protein interactions in the docked complex were visualized using LigPlot+. Population coverage analysis had shown that the multi-epitope vaccine covers 94.06% of the global population. The vaccine construct was successfully cloned in silico into pET-28a (+). Immune simulation studies showed the induction of primary, secondary and tertiary immune responses marked by the increased levels of antibodies, INF-γ, IL-2, TGF-β, B- cells, CD4+ and CD8+ cells. Finally, the vaccine construct was able to elicit immune response as desired.Communicated by Ramaswamy H. Sarma.

Keywords: COVID-19; SARS-CoV2; immunoinformatics; membrane glycoprotein; multi-epitope vaccine.

Figure 1.

Flowchart summarizing the steps involved in the rational design of vaccine.

Figure 2.

Tertiary structure of the vaccine with discontinuous B-cell epitopes. The side chain of each predicted B-cell epitopes by DiscoTope is highlighted in yellow.

Figure 3.

Production of various cytokines in response to the administration of vaccine obtained from c-ImmSim (Inset figure: Simpson Index, D).

Figure 4.

Prediction of secondary structure of the vaccine by PSIPRED.

Figure 5.

3D structure of the vaccine refined by GalaxyRefine2.

Figure 6.

z-score of the vaccine determined using ProSA-web.

Figure 7.

Ramachandran plot analysis of the vaccine.

Figure 8.

Docked complex of TLR-3 and the vaccine construct. In the complex, vaccine is depicted in ‘Magenta’ color, whereas TLR-3 is depicted in ‘Cyan’ color.

Figure 9.

Representation of the molecular interactions between Chain A (TLR-3) and Chain B (vaccine) in the docked complex obtained using DIMPLOT module in LigPlot+. Dashed lines in Pink color indicate salt bridge interactions and dashed lines in blue indicate Hydrogen bonds.

Figure 10.

In silico restriction cloning of the vaccine into pET-28a (+) vector in between Pae71-PspXI-XhoI and MluI restriction sites. Vaccine constrict is depicted in ‘Red’ color.

Figure 11.

In silico immune simulation results obtained using c-ImmSim server after administration of three injections of the vaccine. (a) Production of various types of immunoglobulins, (b) B-cell population, (c) T_H cell population per state, (d) T-helper cell population, (e) T_C lymphocytes count per entity-state.