Fig 1.
An overview of the study.
Table 1.
The predicted CTL epitope with their immunogenicity, toxicity, and antigenicity.
Table 2.
The predicted HTL epitopes of the selected proteins with their IFN-γ, IL-4, and IL-10 production capability, toxicity, antigenicity, and allergenicity.
Table 3.
The predicted B-cell (linear) epitopes.
Fig 2.
The vaccine construct contains CTL (green color), HTL (orange color), and B-cell epitopes (blue color) with the linkers (adjacent line) and an adjuvant (olive color).
Table 4.
Physicochemical properties, solubility, allergenicity, and antigenicity of the vaccine construct.
Fig 3.
The secondary structure of the vaccine was predicted by the PSIPRED server.
Table 5.
The vaccine’s secondary structure properties are predicted using GOR4 and SOPMA servers.
Fig 4.
The predicted tertiary structure of the vaccine construct by I-TASSER.
The ribbon (A) and surface (B) model view of the vaccine’s tertiary structure was visualized by PyMol software.
Fig 5.
The Ramachandran plot and the Z-score of the predicted tertiary structure before (A and C) and after structural refinement (B and D).
Table 6.
The quality assessment and structural validation of predicted tertiary structure.
Fig 6.
The docked complex of “Vaccine—TLR-2” and their interacting amino acid residues predicted by the Cluspro 2.0 server.
Fig 7.
The docked complex of “Vaccine—TLR-4” and their interacting amino acid residues predicted by the Cluspro 2.0 server.
Fig 8.
The predicted discontinuous B-cell epitopes of the vaccine (A–I).
Yellow surfaces indicate the predicted discontinuous B-cell epitopes, while cyan sticks reveal the vaccine.
Fig 9.
In silico cloning of the vaccine’s optimized codon sequences into pET28a (+) vector.
Restriction sites indicated in yellow boxes show the two restriction sites (Acc65I and PshAI).
Fig 10.
Exploring the vaccine’s immune simulation using the C-ImmSim server.
The evolution of entire (A) and per state (B) B-cell populations, NK (C) and DC (D) cell populations, the population of Mφ per state (E), and the cytokines and the IL-2 level are illustrated by the primary plot and the sub-plot, respectively (D) (Here, D refers to Simson’s index, which measures the degree of variety. Since an increase in D suggests an increase in the number of epitope-specific T-cells, a lower D value indicates a lower level of diversity).
Fig 11.
T-cells mediated immune responses predicted by the C-ImmSim server.
The evolution of Th with their memory cell life span (A), Th cell population per state cell (B), the development of entire Tc populations (C) and Tc population per state cell (D), the Treg populations per state (E), and the antigen and antibody titers after post vaccination state (F).
Fig 12.
Predicted mRNA structure of the vaccine by RNAfold web server.
The base pair probabilities of the mRNA vaccine with the minimum free energy (A) and centroid (B) structure and the positional entropy of the mRNA vaccine with the minimum free energy (C) and centroid (D) structure.