In Silico design of a multi-epitope mRNA vaccine targeting BabA, SabA, HopQ and UreB proteins of helicobacter pylori using immuno informatics.

Abstract

Helicobacter pylori infects nearly half of the global population, with higher prevalence in developing countries. This gram-negative, microaerophilic bacterium causes gastric ulcers and is a major risk factor for gastric cancer, the third deadliest and fifth most common malignancy globally earning it WHO’s group 1 carcinogen status. Rising antibiotic resistance, frequent reinfections, and the lack of a licensed vaccine underscore the need for alternative therapies. This study employed immunoinformatics to design a novel multi-epitope mRNA vaccine using CTL, HTL, and B-cell epitopes derived from key virulence proteins: BabA, SabA, HopQ, and UreB. CTL and HTL epitopes were predicted using NetMHCpan-4.1 and NetMHCIIpan-4.0, respectively, while B cell candidate motifs were identified via MEME Suite. T cell epitopes were screened for antigenicity (VaxiJen), toxicity (ToxinPred), allergenicity (AllerTOP), and conservancy (IEDB). B cell epitopes underwent evaluation for linearity, beta turns, surface accessibility, flexibility, antigenicity, and hydrophilicity using IEDB tools. A total of 11 epitopes (6 T cell and 5 B cell) were selected based on the criteria, combined with a tissue plasminogen activator (tPA) signal sequence, the adjuvant hBD-3, and the immune co-stimulatory molecule CD40L using appropriate linkers. The final vaccine construct as predicted by the ProtParam sever was 560 amino acids long, with a predicted molecular weight of 61641.58 Da, pI of 9.43, hydrophilic (GRAVY: −0.390), soluble, and thermostable (aliphatic index: 76.12). The vaccine was non-allergenic, a probable non-toxin and had a VaxiJen antigenicity score of 0.93, confirming it as highly antigenic. GOR4-predicted secondary structure showed 34.11% alpha helices, 20% beta strands, and 45.89% coils. The 3D structure from I-TASSER (model 2) was selected based on a C-score of -0.91. Codon optimization in R yielded a CAI of 1.0 and GC content of 64.42%, suggesting efficient expression in humans. RNAfold analysis revealed an MFE of -1463.40 kcal/mol, ensemble free energy of -1505.17 kcal/mol, and a diversity of 1001.24, indicating thermodynamic stability. Collectively, these parameters support the vaccine's potential as an effective intervention against Helicobacter pylori.