Epitope-Based Vaccine of NiV Targeting Glycoprotein and Fusion Protein: An Integrated Immunoinformatics and Bioinformatics Approach

• Glycoprotein and fusion proteins were systematically analyzed to identify immunogenic epitopes for rational vaccine design. • 3 vaccine constructs were formulated, and VC2 was prioritized based on the variability and incorporation of different adjuvants. • The formulated vaccine constructs exhibited strong immunodominant features. • Docking analysis demonstrated favorable interaction of the vaccine with TLR3 compared to other TLRs, and the complexes were further evaluated for stability using Normal Mode Analysis (NMA) and 100 ns molecular dynamics simulation. • Dose-dependent immune simulation demonstrated robust immune activity, and GC content analysis suggested high expression potential of the construct. NiV is an ongoing infection that causes severe complications, and its frequent outbreaks make its treatment more complicated in terms of the proper therapeutic design. No viable vaccine candidate exists to combat NiV; however, efforts are underway, and some vaccines are in clinical trials. Therefore, an integrated immunoinformatics and bioinformatics approach was employed to design a promising epitope-based vaccine targeting glycoprotein and fusion protein, which are critical for host–pathogen interactions. The two targets, i.e., glycoprotein and fusion protein, were examined to identify B- and T-cell epitopes. A total of 3 B cell, 13 MHC I and 7 MHC II epitopes from both targets were chosen for vaccine formulation. Epitopes were joined using specific linkers and combined with three different adjuvants to generate 3 vaccines, i.e., VC1, VC2, and VC3, enabling selection of the best construct based on antigenicity. PADRE and a 6 × His-tag were also included. Analysis resulted in VC2 as a highly immunodominant profile. The incorporated epitopes resulted in broad global population coverage (e.g., 98.97%) and remarkable stereochemical properties of the modelled vaccine, as assessed via 2D and 3D analyses. Subsequently, the VC2 were docked to the toll-like receptors (TLR2, TLR3, and TLR4) and showed high binding affinities of -14.2 to -23.1kcal/mol, along with H-bonds (9 to 20). Among them, the VC2–TLR3 complex showed the most promising interaction and demonstrated stability based on the NMA analysis (eigenvalue = 1.710065e-06), followed by a 100-ns simulation and RMSD, RMSF, etc. Furthermore, the immune simulation and expression analysis revealed remarkable immune activity in a dose-dependent manner, yielding GC% and CAI values. Based on the integrated framework, the study demonstrated that the designed vaccine, incorporating variations in the adjuvant, may exhibit significant immunodominant activity and could help combat NiV.