Table 1.
List of links used in this study.
Fig 1.
Flowchart of Gag vaccine design in this research.
Table 2.
A list of conserved domains of the Gag gene sequence of HIV-1.
Fig 2.
Linear B-cell epitopes predicted on the Gag vaccine construct (1–9).
The purple color displays each linear B-cell epitope, such as amino acids 8–116, with a score ranging from 0.50–0.78.
Table 3.
A list of BCL-selected epitopes of the Gag vaccine.
Table 4.
Potential antigenic and immunogenic HTL epitopes of the Gag vaccine.
Table 5.
Potential antigenic and immunogenic CTL epitopes.
Fig 3.
Percentage of combined (MHC I and MHC II) coverage of the selected epitopes (CTL and HTL) of the Gag vaccine in the global population (Generated by https://certmapper.cr.usgs.gov/data/apps/world-energy/?resource=continuous).
Fig 4.
Gag vaccine designed: a) Proposed Gag-HIV vaccine construct; b) Best 3D model of designed Gag vaccine; c) Confirmation of vaccine structure defined by crystallography using the ERRAT tool; d) Ramachandran plot of the refined Gag vaccine was created with the PDBsum software; e) Protein structure analysis of vaccine designed by Prosa-web tool.
Fig 5.
Discontinuous B-cell epitopes on the vaccine construct (1–6) are indicated by the orange region of the Gag vaccine, which depicts each discontinuous B-cell epitope comprising residues 4 to 63 with score values ranging from 0.532 to 0.841.
Table 6.
Discontinuous epitopes found in the Gag vaccine construct overlap with linear epitopes.
Table 7.
AutoDock VINA results between the CTL and HTL epitopes of Gag and related alleles.
Fig 6.
Docked complex of the Gag vaccine construct with a) TLR-2, b) TLR-3, c) TLR-4, d) TLR-7, and e) TLR-9. The 3D molecule of the vaccine is shown in green and red according to the ClusPro server.
Fig 7.
Molecular dynamics simulation analysis of A) TLR-2, B) TLR-3, C) TLR-4, D) TLR-7, and E) TLR-9 with Gag vaccine constructs. RMSD results (A1-E1); RMSF results (A2-E2); Rg results (A3-E3).
Fig 8.
Immune simulation outcomes obtained from C-IMMSIM after administration of the Gag vaccine are shown in plots a-j.
Fig 9.
In silico cloning of the Gag vaccine construct A1) pET-30a(+) plasmid and A2) pcDNA3.1(+) vector.