Design of multivalent-epitope vaccine models directed toward the world's population against HIV-Gag polyprotein: Reverse vaccinology and immunoinformatics

Abstract

Significant progress has been made in HIV-1 research; however, researchers have not yet achieved the objective of eradicating HIV-1 infection. Accordingly, in this study, eucaryotic and procaryotic in silico vaccines were developed for HIV-Gag polyproteins from 100 major HIV subtypes and CRFs using immunoinformatic techniques to simulate immune responses in mice and humans. The epitopes located in the conserved domains of the Gag polyprotein were evaluated for allergenicity, antigenicity, immunogenicity, toxicity, homology, topology, and IFN-γ induction. Adjuvants, linkers, CTLs, HTLs, and BCL epitopes were incorporated into the vaccine models. Strong binding affinities were detected between HLA/MHC alleles, TLR-2, TLR-3, TLR-4, TLR-7, and TLR-9, and vaccine models. Immunological simulation showed that innate and adaptive immune cells elicited active and consistent responses. The human vaccine model was matched with approximately 93.91% of the human population. The strong binding of the vaccine to MHC/HLA and TLR molecules was confirmed through molecular dynamic stimulation. Codon optimization ensured the successful translation of the designed constructs into human cells and E. coli hosts. We believe that the HIV-1 Gag vaccine formulated in our research can reduce the challenges faced in developing an HIV-1 vaccine. Nevertheless, experimental verification is necessary to confirm the effectiveness of these vaccines in these models.

Fig 1. Flowchart of Gag vaccine design in this research.

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.

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.

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.