Application of reverse vaccinology to design a multi-epitope subunit vaccine against a new strain of Aeromonas veronii

Abstract

Background: Aeromonas veronii is one of the most common pathogens of freshwater fishes that cause sepsis and ulcers. There are increasing numbers of cases showing that it is a significant zoonotic and aquatic agent. Epidemiological studies have shown that A. veronii virulence and drug tolerance have both increased over the last few years as a result of epidemiological investigations. Cadaverine reverse transporter (CadB) and maltoporin (LamB protein) contribute to the virulence of A. veronii TH0426. TH0426 strain is currently showing severe cases on fish species, and its resistance against therapeutic has been increasing. Despite these devastating complications, there is still no effective cure or vaccine for this strain of A.veronii.

Results: In this regard, an immunoinformatic method was used to generate an epitope-based vaccine against this pathogen. The immunodominant epitopes were identified using the CadB and LamB protein of A. veronii. The final constructed vaccine sequence was developed to be immunogenic, non-allergenic as well as have better solubility. Molecular dynamic simulation revealed significant binding stability and structural compactness. Finally, using Escherichia coli K12 as a model, codon optimization yielded ideal GC content and a higher CAI value, which was then included in the cloning vector pET2+ (a).

Conclusion: Altogether, our outcomes imply that the proposed peptide vaccine might be a good option for A. veronii TH0426 prophylaxis.

Keywords: A. Veronii TH0426; E. coli K12; Epitopes; MD simulation; Vaccine.

Fig. 1

Constructed vaccine sequence

Fig. 2

Prediction of the secondary structure of designed multi-epitope vaccines using PSI-PRED

Fig. 3

3D structure of the designed vaccine construct

Fig. 4

A, B Analysis of Ramachandran plot by PROCHECK server. A Ramachandran plot of the crude model of the vaccine and B Ramachandran plot of the refine model of the vaccine. The MFR, AAR, GAR, and DR have represented the most favored, additional allowed, generously allowed, and disallowed regions of the vaccine. C A 3D structure validation with a Z-score by Pro-SA server of the vaccine crude model. D A 3D structure validation with a Z-score by Pro-SA server of the vaccine refine model

Fig. 5

A three-dimensional representation of the developed epitope-based vaccine’s conformational or discontinuous B cell epitopes. A–F The conformational or discontinuous B cell epitopes are depicted by yellow surfaces, while the majority of the polyprotein is represented by grey sticks

Fig. 6

Discontinuous B cell epitopes and the ligand-protein (multi-epitope subunit vaccine)-receptor protein interaction (TLR-5). A Inside this epitope-based subunit vaccine, the specific value of discontinuous B cell epitopes was anticipated. B, C The ligand-protein is shown in yellow, whereas the receptor protein is highlighted in red

Fig. 7

Analysis of EBV–immune receptor binding conformation and interaction. Intermolecular binding mode and residue-level chemical interactions of MEBV-TLR5

Fig. 8

Simulation of the multi-epitope vaccine complex at the molecular level. The backbone atoms of the complexes were plotted using the RMSD method

Fig. 9

Simulation of the multi-epitope vaccine complex at the molecular level. The multi-epitope docked vaccine candidate RMSF plot. Red and blue backgrounds emphasize the alpha-helical and beta-strand sections, respectively. These areas are defined by helices or strands that last for 70% of the simulation time

Fig. 10

The vaccine has elicited an immune response. The graph shows A primary, secondary, and tertiary immune responses, B B cell population, C cytotoxic T cell population, D helper T cell population, E induction of cytokines and interleukins, and F dendritic cell population per state

Fig. 11

Codon adaptation of EBV to E. coli K12 strain

Fig. 12

The proposed vaccine was cloned into the pET-28a (+) vector in silico

Fig. 13

Predicted secondary structure of mRNA for the vaccine. The 5′ end of the predicted mRNA structure does not contain any pseudoknot or hairpin