In Silico Analysis of Tat Exons to Increase the Efficacy of a Nef-Tat-based HIV-1 Vaccine Candidate

The global human immunodeficiency virus HIV/AIDS pandemic persists without complete eradication. Developing a safe and effective vaccine remains the most promising approach, but ongoing clinical trials have been unsuccessful due to the vaccines' inability to stimulate robust immunity.

The present research endeavor proposes an innovative therapeutic vaccine by employing immunoinformatics strategies. Herein, we aimed to compare the efficiency of the whole sequence of Tat^{(exons 1 + 2)} with its first exon^{(exon 1)} in a fusion vaccine construct harboring the whole sequence of the Nef protein [i.e., Nef-Tat^{(exons 1 + 2)} and Nef-Tat^{(exon 1)} fusion proteins] using in silico studies.

First, the secondary structures of both fusion proteins were predicted. Then, 3D models of the constructs were refined, and their physicochemical properties were determined. After analysis of toxicity, allergenicity, and antigenicity of constructs, the formation of ligand (constructs)-receptor (TLR-2 to TLR-5, and TLR-7 to TLR-9) complexes was examined using the ClusPro and HDOCK servers, and the highest scores of docking analysis were used for molecular dynamics (MDs) simulation. Finally, the JCat server was applied for codon optimization.

Our results indicated that both protein constructs were antigenic, non-allergenic, and capable of eliciting adaptive immune responses. The average values of radius of gyration (Rg) for Nef-Tat^{(exon 1)} and Nef-Tat^{(exons 1+2)} with TLR-4 were 1.74 and 1.90, respectively. Therefore, both constructs were stable. Moreover, the Nef-Tat^{(exon 1)} construct could significantly activate both T- and B-cells as compared to the Nef-Tat^{(exons 1+2)}. Indeed, inclusion of the second exon of Tat^{(exon 2)} did not enhance the immunogenicity of the Nef protein.

Generally, immunoinformatics studies showed the importance of Tat exon 1 in HIV-1 fusion vaccine design.