Fig 1.
(a) Schematic representation of the in-silico workflow for the prediction of potential B- and T-cell epitopes of structural proteins (spike [S], envelope [E], membrane [M], and nucleocapsid [N] of SARS-CoV-2 and SARS-CoV. Summary of SARS-CoV-2-derived B-cell epitopes. Heat map showing the distribution of (b) linear (continuous) and (c) conformational (discontinuous) B-cell epitopes across the protein sequences of spike (1273 aa), nucleocapsid (419 aa), membrane (222 aa), and envelope (75 aa) proteins of SARS-CoV-2. Red represents the antigenic epitopes predicted using the methods described in Fig 1a.
Table 1.
A summary of literature review showing the bioinformatically predicted B- and T-cell epitopes identified in the structural proteins of SARS-CoV-2.
Table 2.
Linear B-cell epitopes of structural proteins of SARS-CoV-2.
Fig 2.
Mapping of linear B-cell epitopes on the three-dimensional structure of SARS-CoV-2 structural proteins.
Localization of top predicted monomeric B-cell epitopes (inset table) on the (a) modeled structure and (b) crystal structure (PDB: 6VSB) of the spike protein, (c) nucleocapsid, (d) membrane, and (e) envelope proteins, as observed using BIOVIA Discovery Studio 2017 R2.
Table 3.
Linear B-cell epitopes common to SARS-CoV-2 and SARS-CoV.
Fig 3.
Mapping of conformational B-cell epitopes on the three-dimensional structure of SARS-CoV-2 structural proteins.
The selected B-cell epitopes are listed in the inset table, and the corresponding color shows the localization of predicted epitopes on the (a) modeled structure and (b) crystal structure (PDB: 6VSB) of the spike, (c) nucleocapsid, (d) membrane, and (e) envelope proteins, as observed using BIOVIA Discovery Studio 2017 R2.
Table 4.
Conformational B-cell epitopes of structural proteins of SARS-CoV-2.
Table 5.
Conformational B-cell epitopes common to SARS-CoV-2 and SARS-CoV.
Fig 4.
Sequence alignment of receptor-binding domains (RBDs) of SARS-CoV-2 and SARS-CoV spike (S) proteins.
GenBank accession numbers of the S protein of SARS-CoV-2 and SARS-CoV are QHR63250.2 (SARS-CoV-2) and AAP30030.1 (SARS-CoV BJ01), respectively. ACE2-binding residues are colored magenta, and CR3022 epitope residues are colored bright green. The alignment was performed using Clustal Omega. The inset table shows the antigenic linear and conformational B-cell epitopes predicted in the RBD of the S protein of SARS-CoV-2.
Table 6.
List of predicted SARS-CoV-2-derived T-cell epitopes with high-affinity binding to MHC I molecules.
Table 7.
List of predicted T-cell epitopes with high-affinity binding to MHC I molecules common to SARS-CoV-2 and SARS-CoV.
Fig 5.
Summary of SARS-CoV-2-derived T-cell epitopes.
Heat map showing the distribution of (a) HLA class I and (b) HLA class II epitopes across the protein sequences of spike (1273 aa), nucleocapsid (419 aa), membrane (222 aa), and envelope (75 aa) proteins of SARS-CoV-2. Red color represents antigenic epitopes predicted using the methods described in Fig 1.
Table 8.
List of predicted SARS-CoV-2-derived T-cell epitopes with high affinity binding to MHC II molecules.
Table 9.
T-cell epitopes predicted with high affinity to MHC II molecules common to SARS-CoV-2 and SARS-CoV.
Table 10.
List of SARS-CoV-2 proteins that were predicted as common and overlapping B- and T- cell epitopes.
Table 11.
Design of multi-epitope vaccine constructs of SARS-CoV-2.
Fig 6.
Schematic diagram of multi-epitope vaccine constructs of SARS-CoV-2.
The multi-epitope vaccine constructs consisted of top-ranked predicted and experimentally validated B- and T-cell epitopes. Cytotoxic T lymphocytes (CTL) epitopes were joined by the AAY linker, whereas helper T lymphocytes (HTL) and B-cell epitopes were joined by KK and GGGGS linkers, respectively. (a) The receptor-binding domain (RBD) of the spike (S) protein (B- and T-cell epitopes); (b) The S protein (B- and T-cell epitopes), (c) The structural protein construct (B- and T-cell epitopes of S, N, M, and E proteins); (d) The chimeric construct of S and N proteins (B- and T-cell epitopes of S and N proteins).
Fig 7.
In silico immune simulation of multi-epitope vaccine constructs of SARS-CoV-2.
C-ImmSim simulation of the cytokine levels induced by three injections administered four weeks apart. The main plot shows cytokine levels after the injections. The inset plot shows IL-2 levels with the Simpson index (D), which is indicated by the dotted line, is a measure of diversity. Increase in D over time indicates the emergence of different epitope-specific dominant clones of T cells. The smaller the D value, the lower the diversity. (a) The receptor-binding domain (RBD) of the spike (S) protein (B- and T-cell epitopes); (b) The S protein (B- and T-cell epitopes); (c) The structural protein construct (B- and T-cell epitopes of S, N, M, and E proteins); (d) The chimeric construct of S and N proteins (B- and T-cell epitopes of S and N proteins).