Cytotoxic T-lymphocyte elicited vaccine against SARS-CoV-2 employing immunoinformatics framework

Abstract

Development of effective counteragents against the novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains, requires clear insights and information for understanding the immune responses associated with it. This global pandemic has pushed the healthcare system and restricted the movement of people and succumbing of the available therapeutics utterly warrants the development of a potential vaccine to contest the deadly situation. In the present study, highly efficacious, immunodominant cytotoxic T-lymphocyte (CTL) epitopes were predicted by advanced immunoinformatics assays using the spike glycoprotein of SARS-CoV2, generating a robust and specific immune response with convincing immunological parameters (Antigenicity, TAP affinity, MHC binder) engendering an efficient viral vaccine. The molecular docking studies show strong binding of the CTL construct with MHC-1 and host membrane specific TLR2 receptors. The molecular dynamics simulation in an explicit system confirmed the stable and robust binding of CTL epitope with TLR2. Steep magnitude RMSD variation and compelling residual fluctuations existed in terminal residues and various loops of the β linker segments of TLR2-epitope (residues 105-156 and 239-254) to about 0.4 nm. The reduced R_g value (3.3 nm) and stagnant SASA analysis (275 nm/S²/N after 8 ns and 5 ns) for protein surface and its orientation in the exposed and buried regions suggests more compactness due to the strong binding interaction of the epitope. The CTL vaccine candidate establishes a high capability to elicit the critical immune regulators, like T-cells and memory cells as proven by the in silico immunization assays and can be further corroborated through in vitro and in vivo assays.

Figure 1

(A) Three-dimensional structure of HLA-A*0201 receptor. (B) Ramachandran plot analysis of HLA-A*0201 protein receptor, suggesting structure existence in the allowed region. (C) Three-dimensional structure of Toll-like receptor-2 receptor. (D) Ramachandran plot analysis of TLR2 receptor, presence in the permitted area with optimal quality of structures.

Figure 2

Binding analyses of lead CTL epitope with host membrane specific TLR2 receptor (A) Interacting complex of lead CTL epitope with TLR2, mesh network, TLR2 residues shown in sky blue and CTL epitope in orange color. (B) Molecular interactions involved in the strong binding of lead CTL epitope to TLR2 receptor. (C) Surface view of a binding grove of TLR2 during interaction of CTL epitope. (D) CTL epitope binding cavity network responsible strong and stable binding with TLR2.

Figure 3

The stability of the TLR2 and TLR2-CTL epitope complex as predicted by molecular dynamics simulations. (A) RMSD profile of TLR2 (black traces) and TLR2-CTL(red traces) epitope. (B) RMSF profile of TLR2 (black traces) and TLR2-CTL epitope (blue traces). (C) Radius of gyration plots of TLR2 (black traces) and TLR2-CTL epitope (green traces). (D) SASA profile of TLR2 (black traces) and TLR2-CTL epitope (green traces). The comprehensive computational strategy was utilized to attain insights towards the epitope’s antigenicity against TLR2.

Figure 4

(A) The statics of consistent high number of hydrogen bonds involved in strong binding of CTL epitope to TLR2 receptor. (B) Depiction of TLR2 receptor-CTL epitope stabilized hydrogen bond throughout the simulation run. (C) The binding energies calculation of CTL epitope to TLR2 receptor, which showing the stringent interaction in all cluster frames in 20 ns run.

Figure 5

The secondary structure analyses of the stable trajectory for both the simulation systems were performed using DSSP tool of GROMACS (A) TLR2, (B) TLR2-CTL epitope, (C) most dominant cluster of TLR2 (Cyan) and TLR2-CTL epitope (Pink); stable conformation after binding of CTL.

Figure 6

Vaccine constructs in silico immunization analysis. (A) CTL response to elicit the Cytotoxic T-cell population for long span. (B) Elevated level of Cytotoxic T-cell population in resting state for 30 days.

Figure 7

(A) The three-dimensional globular structure of CTL epitope (Vaccine candidate). (B) Local secondary structure analysis of CTL epitope, Structural profile is shown by helicity (red), extended coils (green) and coils (blue). (C) Ramachandran plot analysis of vaccine candidate, depiction residues were lying in a favorable region.