Immunoinformatics-Based Design of Multi-epitope DNA and mRNA Vaccines Against Zika Virus

Abstract

In this study, we used an immunoinformatics approach to predict antigenic epitopes of Zika virus (ZIKV) proteins to assist in designing a vaccine antigen against ZIKV. We performed the prediction of CD8+ T-lymphocyte and antigenic B-cell epitopes of ZIKV proteins. The binding interactions of T-cell epitopes with major histocompatibility complex class I (MHC-I) proteins were assessed. We selected the antigenic, conserved, nontoxic, and immunogenic epitopes, which indicated significant interactions with the human leucocyte antigen (HLA-A and HLA-B) alleles and worldwide population coverage of 76.35%. The predicted epitopes were joined with the help of linkers and an adjuvant. The vaccine antigen was then analyzed through molecular docking with TLR3 and TLR8, and it was in silico cloned in the pVAX1 vector to be used as a DNA vaccine and designed as a mRNA vaccine.

Keywords: Zika virus; immunoinformatics; peptide vaccine.

Figure 1.

Result of molecular analysis of epitopes coupled to HLA-A*02:03 (A), HLA-B*150 (B, C, and D), HLA-A*02:01 (E), HLA-B*57:01 (F), HLA-A*03:01 (G), HLA-A*68:01 (H), and HLA-A*68:02 (I). The molecular surface that forms the groove between the α1 and α2 domains (in gray) is shown. The epitope is represented by lines (magenta), and the red dashed line represents the hydrogen bonds.

Figure 2.

Schematic drawing of vaccine construction after addition of linkers and adjuvant.

Figure 3.

Tertiary structure of the vaccine antigen. Alpha helices are shown in red, β-sheets in light blue, and loops in gray and green.

Figure 4.

Construction of vaccine antigen with TLR3 and TLR8. (A and C) Molecular docking of vaccine antigen with TLR3 and TLR8 in 2 cartoon representations. The TLR3 is displayed in magenta, and the vaccine antigen construct is displayed in green; TLR8 is displayed in gray, and the vaccine antigen construct is displayed in green. (B and D) Enhanced image of the interactions of the vaccine antigen complex and the TLR3 and TLR8. The yellow hatched area represents the interactions of the vaccine antigen complex and the TLR3 and TLR8.

Figure 5.

Molecular dynamics simulation analysis of the vaccine-TLR3 docked complex: (A) the main-chain deformability graph; (B) eigenvalue plot; (C) normal mode variance plot; (D) the covariance matrix; and (E) the elastic network model.

Figure 6.

Molecular dynamics simulation analysis of the vaccine-TLR8 docked complex: (A) the main-chain deformability graph; (B) eigenvalue plot; (C) normal mode variance plot; (D) the covariance matrix; and (E) the elastic network model.

Figure 7.

In silico cloning of the vaccine antigen into the pVAX1 vector. The light pink area represents the vaccine antigen, and the other colored areas represent the ligands and adjuvant.

Figure 8.

Secondary structure prediction and stability analysis of the mRNA vaccine construct: (A) minimum free energy (MFE) structure of the mRNA vaccine construct; (B) centroid free energy (CFE) of the mRNA vaccine construct. The color scale is based on positional entropy; and (C) a mountain plot representation of the secondary structure of the mRNA vaccine constructs and the positional entropy. Red, green, and blue line graphs represent the MFE structure, the thermodynamic ensemble of RNA structures, and the centroid structure, respectively. The height represents the number of base pairs enclosing the base at 1 position. Peaks correspond to hairpin loops, plateaus correspond to loops, and slops correspond to helices.