Multiepitope Subunit Vaccine Design against COVID-19 Based on the Spike Protein of SARS-CoV-2: An In Silico Analysis

Abstract

The global health crisis caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19, has resulted in a negative impact on human health and on social and economic activities worldwide. Researchers around the globe need to design and develop successful therapeutics as well as vaccines against the novel COVID-19 disease. In the present study, we conducted comprehensive computer-assisted analysis on the spike glycoprotein of SARS-CoV-2 in order to design a safe and potent multiepitope vaccine. In silico epitope prioritization shortlisted six HLA I epitopes and six B-cell-derived HLA II epitopes. These high-ranked epitopes were all connected to each other via flexible GPGPG linkers, and at the N-terminus side, the sequence of Cholera Toxin β subunit was attached via an EAAAK linker. Structural modeling of the vaccine was performed, and molecular docking analysis strongly suggested a positive association of a multiepitope vaccine with Toll-like Receptor 3. The structural investigations of the vaccine-TLR3 complex revealed the formation of fifteen interchain hydrogen bonds, thus validating its integrity and stability. Moreover, it was found that this interaction was thermodynamically feasible. In conclusion, our data supports the proposition that a multiepitope vaccine will provide protective immunity against COVID-19. However, further in vivo and in vitro experiments are needed to validate the immunogenicity and safety of the candidate vaccine.

Figure 1

Here, the overall design of our study is shown. The sequence of SARS-CoV-2 spike protein was subjected to in silico epitope prediction and prioritization steps to select promiscuous T-cell epitopes. These epitopes were linked together to construct a multiepitope vaccine which was subjected to molecular docking analysis with TLR3. Based on these results, a multiepitope vaccine was proposed against COVID-19.

Figure 2

Structure-based assessments of the vaccine construct obtained after molecular modelling and refinements. (a) The three-dimensional refined model of the vaccine is visualized. (b) Ramachandran plot analysis of the structural model suggests high quality. (c) The ProSA Z-score of the best model is found to be good, i.e., -4.48, thus indicating near-native configuration.

Figure 3

(a) Here, we show the interaction pose of a representative complex of the vaccine-TLR3 refined cluster. The designed vaccine is colored red while the TLR3 structure is colored dark green. The interacting residues are focused, and some interchain hydrogen bonds are highlighted. Residues Tyr198, Lys200, and Asn210 of the vaccine construct participated in hydrogen bond formation with some residues in the TLR3 structure. (b) Interacting residues as well as bonding interactions between the vaccine and TLR3 protein chains.

Figure 4

Normal mode analysis of the vaccine-TLR3 complex. The structural strength of refined protein-protein complex was analyzed as per generated graphs: mobility (a), eigenvalue vis-à-vis modes (b), B-factor vis-à-vis atoms (c), deformability vis-à-vis atoms (d), covariance vis-à-vis residue (e), and elastic network vis-à-vis atoms (f).