Subtractive proteomics-based vaccine targets annotation and reverse vaccinology approaches to identify multiepitope vaccine against Plesiomonas shigelloides

Abstract

Plesiomonas shigelloides, an aquatic bacterium belonging to the Enterobacteriaceae family, is a frequent cause of gastroenteritis with diarrhea and gastrointestinal severe disease. Despite decades of research, discovering a licensed and globally accessible vaccine is still years away. Developing a putative vaccine that can combat the Plesiomonas shigelloides infection by boosting population immunity against P. shigelloides is direly needed. In the framework of the current study, the entire proteome of P. shigelloides was explored using subtractive genomics integrated with the immunoinformatics approach for designing an effective vaccine construct against P. shigelloides. The overall stability of the vaccine construct was evaluated using molecular docking, which demonstrated that MEV showed higher binding affinities with toll-like receptors (TLR4: 51.5 ± 10.3, TLR2: 60.5 ± 9.2) and MHC receptors(MHCI: 79.7 ± 11.2 kcal/mol, MHCII: 70.4 ± 23.7). Further, the therapeutic efficacy of the vaccine construct for generating an efficient immune response was evaluated by computational immunological simulation. Finally, computer-based cloning and improvement in codon composition without altering amino acid sequence led to the development of a proposed vaccine. In a nutshell, the findings of this study add to the existing knowledge about the pathogenesis of this infection. The schemed MEV can be a possible prophylactic agent for individuals infected with P. shigelloides. Nevertheless, further authentication is required to guarantee its safeness and immunogenic potential.

Keywords: Codon optimization; Immunoinformatics; Molecular docking; Molecular docking simulation; Plesiomonas shigelloides.

Fig. 1

Graphical synopsis representing the complete methodology used for prediction of multiepitope based vaccine against Plesiomonas shigelloides.

Fig. 2

Details of vaccine construct (A) Sequence of multi-epitope subunit vaccine construct (B) graphical representation of vaccine construction. AAY Linker represented Grey, CPGPG linker represented Yellow, and KK linker represented Brown in construction of vaccine. (C) Secondary structure of vaccine construct; (D) PROCHECK results for Ramachandran plot to validate the integrity of constructed vaccine (E) Tertiary structure of vaccine construct. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3

Docked complexes of MESV with (A) MHCI, (B) MHCII and with human receptor TLR4.

Fig. 4

Molecular dynamic simulation of the vaccine–TLR4 complex, showing: (A) eigenvalue; (B) deformability; (c) B-factor; (d) Residue index.

Fig. 5

Response of the immune system to vaccine: (A) Post antigen exposure production of immunoglobulin and B-cell isotypes in various states with the Simpson index (B) development of cytokine interleukins.

Fig. 6

Codon-optimized vaccine computationally cloned using the expression system of E. coli K12’. Black and red colors represent the plasmid backbone and inserted DNA, respectively. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 7

MHC-I Vaccine A (RMSD), B(RMSF), C(SSE), D(SSE) TLR4-Vaccine E(RMSD), F(RMSF), G(SSE), H(SSE) and MHC-II Vaccine I(RMSD),J(RMSF),K(SSE), L(SSE) are all vaccine showing their stability and fluctuation at different stages with protein-protein interactions.