Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection

Abstract

Dengue is considered as a major health issue which causes a number of deaths worldwide each year; tropical countries are majorly affected by dengue outbreaks. It is considered as life threatening issue because, since many decades not a single effective approach for treatment and prevention of dengue has been developed. Therefore, to find new preventive measure, we used immunoinformatics approaches to develop a multi-epitope based subunit vaccine for dengue which can generate various immune responses inside the host. Different B-cell, T_C cell, and T_H cell binding epitopes were predicted for structural and non-structural proteins of dengue virus. Final vaccine constructs consisting of T_C and T_H cell epitopes and an adjuvant (β-defensin) at N-terminal of the construct. Presence of B-cell and IFN-γ inducing epitopes confirms the humoral and cell mediated immune response developed by designed vaccine. Designed vaccine was not found allergic and was potentially antigenic in nature. Modeling of tertiary structure and the refined model was used for molecular docking with TLR-3 (immune receptor). Molecular docking and dynamics simulation confirms the microscopic interactions between ligand and receptor. In silico cloning approach was used to ensure the expression and translation efficiency of vaccine within an expression vector.

Figure 1

Schematic diagram of multi-epitope vaccine construct: A 457 amino acid long multi-epitope vaccine sequence consisting an adjuvant (green) at N-terminal end linked with a multi-epitope sequence with the help of EAAAK linker (pink). CTL epitopes were linked with the help of AAY linkers (brown) while HTL epitopes were fused with the help of GPGPG linkers (yellow).

Figure 2

IFN-γ inducing and discontinuous B-cell epitopes representation in final vaccine model (A) Red color sequences depict IFN-γ inducing epitopes in the modeled structure. (B) Magenta color spheres show discontinuous B-cell epitopes in the 3D model of multi-epitope vaccine.

Figure 3

Schematic representation of secondary structure prediction of the multi-epitope vaccine, secondary structure prediction result represents the arrangement of α-helix (15.31%), β-strands (8.91%) and coils (75.71%).

Figure 4

Multi-epitope vaccine modeling and validation (A) Represents tertiary structure of multi-epitope vaccine after modeling and refinement. (B) Shows validation of multi-epitope vaccine tertiary structure by ramachandran plot where 93% residues were found in favored region, 5.3% residues were found in allowed region and 1.8% residues were lies in outlier region.

Figure 5

Ligand-receptor docked complex: figure obtained after molecular docking which represents multi-epitope vaccine as a ligand in green color while TLR-3 (PDB ID: 2A0Z) as a receptor in purple color.

Figure 6

Molecular dynamics simulation of the ligand-receptor complex (vaccine & TLR-3) (A) Temperature progression plot of ligand-receptor complex shows that temperature of the system reaches to 300K and remains nearly constant around 300K throughout equilibration phase (100 ps). (B) Ligand-receptor complex pressure progression plot indicates fluctuation of pressure throughout the equilibration phase of 100 ps with an average pressure value 1 bar. (C) RMSD-Root Mean Square Deviation of docked complex shows very minute deviation which reflects the stable microscopic interaction between ligand and receptor molecule. (D) RMSF-Root Mean Square Fluctuation plot of docked protein complex side chain fluctuation in plot generates peak which reflects the flexibility of side chain of docked protein complex.