Table 1.
Screening of CTL epitopes.
Table 2.
Screening of HTL epitopes.
Table 3.
Screening of LBL epitopes.
Fig 1.
Full sequence and secondary structure of vaccine construction.
(A) The full-length amino acid sequence of the vaccine; Green represents the β-defensin Ⅱ adjuvant, blue represents the CTL epitope, red represents the HTL epitope, orange represents the linear B cell epitope, purple represents the pan-HTL epitope, and yellow represents the TAT peptide; (B) The secondary structure of the vaccine.
Fig 2.
Refined structure of the vaccine.
(A) Initial structure of the vaccine; (B) Refined structure of the vaccine; (C) Overlayed model of the initial structure and refined structure.
Fig 3.
Construction of multi-epitope vaccine.
(A) Visualization of the vaccine’s refined structure; (B) Ramachandran plot o; (C) Z-score plot; (D) ERRAT score plot.
Table 4.
Screening of conformation B epitopes.
Fig 4.
Conformational epitopes screened from the constructed vaccine.
(A–G) Conformational epitope 1–7 (According to Table 4).
Table 5.
Results of molecular docking.
Fig 5.
(A) Docking model of the vaccine with HLA-A02:01 molecule, blue represents the HLA-A02:01 molecule, and purple represents the vaccine molecule; (B) Docking model of the vaccine with HLA-DRB1*01:01 molecule, blue represents the HLA-DRB1*01:01 molecule, and purple represents the vaccine molecule.
Fig 6.
(A) Docking model of the vaccine with TLR2 molecule, green represents the TLR2 molecule, and purple represents the vaccine molecule; (B) Docking model of the vaccine with TLR4 molecule, red represents the TLR4 molecule, and purple represents the vaccine molecule.
Fig 7.
Molecular dynamic simulation results Blue for vaccine-TLR4 complex, red for vaccine-TLR2 complex, purple for vaccine-HLA-A*02:01 complex, green for vaccine-HLA-DRB1*01:01 complex.
(A) Radius of gyration (Rg) plots of vaccine-receptors complexes, suggesting the compactness of complexes; (B) H-bonds formed in complexes; (C, D) RMSF (root mean square fluctuation) of vaccine-receptors, reflects the flexibility and fluctuation of the amino-acids residues in the side chain of docked complexes, receptors’ RMSF(C) and vaccines’ RMSF(D); (E) Solvent Accessible Surface Area (SASA) of vaccine-receptor complex; (F) RMSD (root mean square deviation) plots of vaccine-receptors, reflects the stability between the vaccine and receptor.
Table 6.
MMPBSA energy analysis.
Fig 8.
MMPBSA residue energy decomposition.
(A) Complex of vaccine-TLR2; (B) Complex of vaccine-TLR4; (C) Complex of vaccine-HLA-A*02:01; (D) Complex of vaccine-HLA-DRB1*01:01. In each figure, B molecular stand for the vaccine and A molecular stand for the receptors.
Fig 9.
Population coverage map (based on pyecharts (https://gitcode.com/gh_mirrors/py/pyecharts/overview?utm_source=highlight_word_gitcode&word=pyecharts)).
Fig 10.
Immunological simulation analysis.
(A) Antibody levels induced by three doses of vaccine injection; (B) Levels of cytokines such as IL2, IFN-γ induced; (C) Levels of B cells induced; (D) Levels of plasma cells; (E) Levels of helper T (TH) cells induced; (F) Levels of cytotoxic T (TC) cells induced; (G) Levels of MA cells induced; (H) Levels of natural killer (NK) cells induced; (I) Levels of dendritic (DC) cells in different states.
Fig 11.
Docking model of the vaccine (mRNA) with TLR3 molecule.