Multi-epitope chimeric vaccine design against emerging Monkeypox virus via reverse vaccinology techniques- a bioinformatics and immunoinformatics approach

Abstract

The emerging monkeypox virus (MPXV) is a zoonotic orthopoxvirus that causes infections in humans similar to smallpox. Since May 2022, cases of monkeypox (MPX) have been increasingly reported by the World Health Organization (WHO) worldwide. Currently, there are no clinically validated treatments for MPX infections. In this study, an immunoinformatics approach was used to identify potential vaccine targets against MPXV. A total of 190 MPXV-2022 proteins were retrieved from the ViPR database and subjected to various analyses including antigenicity, allergenicity, toxicity, solubility, IFN-γ, and virulence. Three outer membrane and extracellular proteins were selected based on their respective parameters to predict B-cell and T-cell epitopes. The epitopes are conserved among different strains of MPXV and the population coverage is 100% worldwide, which will provide broader protection against various strains of the virus globally. Nine overlapping MHC-I, MHC-II, and B-cell epitopes were selected to design multi-epitope vaccine constructs linked with suitable linkers in combination with different adjuvants to enhance the immune responses of the vaccine constructs. Molecular modeling and structural validation ensured high-quality 3D structures of vaccine constructs. Based on various immunological and physiochemical properties and docking scores, MPXV-V2 was selected for further investigation. In silico cloning revealed a high level of gene expression for the MPXV-V2 vaccine within the bacterial expression system. Immune and MD simulations confirmed the molecular stability of the MPXV-V2 construct, with high immune responses within the host cell. These results may aid in the development of experimental vaccines against MPXV with increased potency and improved safety.

Keywords: immune simulation; molecular dynamic simulation; monkeypox virus; multi-epitope vaccine construct; reverse vaccinology; vaccine candidates.

Figure 1

Global surveillance of MPX confirmed cases from January 2022 to 15 June 2022, data as of 15 June 2022. (A) CDC report; 2022 MPXV and Orthopoxvirus Outbreak Global Map - https://www.cdc.gov/. (B) Confirmed cases of MPXV by WHO report.

Figure 2

Systematic workflow of the designed study.

Figure 3

Subcellular localization results predicted by CELLO2GO.

Figure 4

Population coverage of MHC epitopes in highly infected regions of the world calculated by IEDB.

Figure 5

Three-dimensional structure analysis, structure refinement, and structure validation of MPXV-V2. (A) The 3D model of the multi-epitope vaccine was built by the Swiss Model using a homology modeling approach. (B) Refine 3D structure of MPXV-V2 obtained from DeepRefiner web-server. (C) Ramachandran plot analysis shows 84.5% residues in the favored region, 13.4% residues in the allowed region, and 2.1% residues in the disallowed region of the plot. (D) ProSA-web results with a Z-score of -1.66.

Figure 6

MPXV-V2 docked complex with TLR4 receptor. Blue indicates TLR4 and Green indicates the vaccine construct.

Figure 7

In silico restricted cloning of MPXV-V2 vaccine into E.coli expression vector pET28a (+).

Figure 8

In silico immune simulation to predict the immunological potential of designed vaccine MPXV-V2 chimeric peptide predicted by C-ImmSim Server. (A) Increased level of immunoglobin antibodies with a decrease in antigen levels upon vaccine injections. (B) Increased levels of B-cell populations with a decrease in antigen levels upon vaccine injections. (C) Rising B-cell populations after repeated exposure to antigen. (D, E) The increase in the population of T-cytotoxic and T-helper cells upon repeated antigen exposure. (F–H) The population increase of dendritic cells, macrophages, and natural killer cells during the immunization period. (I) Increased concentrations of cytokine and interleukin levels after the repeated antigen exposure. The inset plot shows the danger signal together with leukocyte growth factor IL-2.

Figure 9

The results of molecular dynamics simulation of vaccine MPXV-V2 and TLR4 complex achieved by iMODS server. (A) NMA mobility, (B) deformability, (C) B-factor which indicates an averaged RMS, (D) eigenvalues (E) colored bars show the individual (purple) and cumulative (green) variances (F) Covariance matrix indicates correlated (red), uncorrelated (white), and anti-correlated (blue) motions of paired residues and (G) The elastic network model (grey regions indicates stiffer regions).