An integrative reverse vaccinology, immunoinformatic, docking and simulation approaches towards designing of multi-epitopes based vaccine against monkeypox virus

Abstract

Monkeypox is a viral zoonotic disease that is caused by the monkeypox virus (MPXV) and is mainly transmitted to human through close contact with an infected person, animal, or fomites which is contaminated by the virus. In the present research work, reverse vaccinology and several other bioinformatics and immunoinformatics tools were utilized to design multi-epitopes-based vaccine against MPXV by exploring three probable antigenic extracellular proteins: cupin domain-containing protein, ABC transporter ATP-binding protein and DUF192 domain-containing protein. Both cellular and humoral immunity induction were the main concerning qualities of the vaccine construct, hence from selected proteins both B and T-cells epitopes were predicted. Antigenicity, allergenicity, toxicity, and water solubility of the predicted epitopes were assessed and only probable antigenic, non-allergic, non-toxic and good water-soluble epitopes were used in the multi-epitopes vaccine construct. The developed vaccine was found to be potentially effective against MPXV and to be highly immunogenic, cytokine-producing, antigenic, non-toxic, non-allergenic, and stable. Additionally, to increase stability and expression efficiency in the host E. coli, disulfide engineering, codon adaptation, and in silico cloning were employed. Molecular docking and other biophysical approaches were utilized to evaluate the binding mode and dynamic behavior of the vaccine construct with TLR-2, TLR-4, and TLR-8. The outcomes of the immune simulation demonstrated that both B and T cells responded more strongly to the vaccination component. The detailed in silico analysis concludes that the proposed vaccine will induce a strong immune response against MPXV infection, making it a promising target for additional experimental trials.Communicated by Ramaswamy H. Sarma.

Keywords: Monkeypox; binding free energies calculation; molecular docking; molecular dynamic simulation.

Figure 1.

Schematic representation of research methodology used herein.

Figure 2.

The number of proteins obtained at each step of subtractive proteomics.

Figure 3.

Schematic view of MPXV vaccine construct that shows 180 amino acids long and containing selected epitopes and adjuvant linked in the construct via EAAAK linker at N- terminal.

Figure 4.

3D structure of MPXV vaccine construct. Black color represents selected epitopes, red color represents EAAAK linker, yellow color represents GPGPG linkers and blue color represents adjuvant.

Figure 5.

Population coverage map of MPXV vaccine covering 99.78% of the world population.

Figure 6.

Docked confirmation of immune cells receptors with vaccine. (A) Docked structure of TLR-2 with MPXV, (B) Docked structure of TLR-4 with MPXV, (C) Docked structure of TLR-8 with MPXV. Purple color represent MPXV vaccine, while brown, pink, and red color represents TLR-2, TLR-4, and TLR-8, respectively.

Figure 7.

Simulation graphs of vaccine with immune cells receptors. (A) RMSD (B) RMSF.

Figure 8.

Number of hydrogen bonds formed in each frame of the MD simulation.

Figure 9.

In silico restriction cloning of the final multi-epitope vaccine using the pET28a (+) expression vector. The black circle represents the vector, and the blue portion is where the vaccine is inserted.

Figure 10.

(A)Wild and (B) mutated structure of designed vaccine. Yellow color represents the mutated residues.

Figure 11.

Immune simulation of the vaccine Construct. A. Immunoglobulin concentrations in relation to antigen concentration. B. Simpson index for cytokine and interleukin production.