Structural Basis and Designing of Peptide Vaccine using PE-PGRS Family Protein of Mycobacterium ulcerans – An Integrated Vaccinomics Approach

Abstract

Buruli ulcer is an emerging-necrotizing skin infection, responsible for permanent deformity if untreated, caused by the pathogen Mycobacterium ulcerans ( M. ulcerans). Despite this debilitating condition, no specific disease-modifying therapeutics or vaccination is available. Therefore, we aimed to design an effective multi-epitope vaccine against M. ulcerans through an integrated vaccinomics approach. Briefly, the highest antigenic PE-PGRS protein was selected from which the promiscuous T- and B-cell epitopes were predicted. After rigorous assessment, 15 promising CTL, HTL and LBL epitopes were selected. The identified T-cell epitopes showed marked interactions towards the HLA binding alleles and provided 99.8% world population coverage. Consequently, a vaccine chimera was designed by connecting these epitopes with suitable linkers and adjuvant (LprG). The vaccine construct was antigenic and immunogenic as well as non-allergenic; hence, subjected to homology modelling. The molecular docking and dynamic simulation revealed strong and stable binding affinity between the vaccine and TLR2 receptor. The binding energy (ΔG) and dissociation constant (K _d) were −15.3 kcal/mol and 5.9×10 ⁻¹² M, respectively. Further, disulfide engineering was applied to improve vaccine’ stability and higher expression in Escherichia coli K12 system was ensured by codon optimization and cloning in silico. The computer-simulated immune responses were characterized by higher levels of IgM and IgG antibodies, helper T-cells with increased IFN-γ production, and macrophage activity crucial for immunity against M. ulcerans. Therefore, our data suggest that, if the designed vaccine is validated experimentally, it will prevent Buruli ulcer by generating robust immune response against M. ulcerans.