Introduction
Helicobacter pylori (H. pylori) is responsible for various chronic or acute diseases, such as stomach ulcers, peptic ulcers, gastroesophageal reflux, gastritis, lymphoma, and stomach cancers, yet its management is increasingly compromised by the rapid emergence of multidrug-resistant strains. Globally, the efficacy of standard eradication therapies has plummeted due to alarming resistance rates to first-line antibiotics such as metronidazole, which often exceeds 80% in specific clinical settings. This crisis, coupled with the high genetic plasticity of the bacterium, creates an urgent need for innovative, non-antibiotic-based preventive strategies that reduce pharmacological dependency. In Colombia, this challenge is particularly acute in the Southwestern Andean region, specifically in Nariño, where gastric cancer incidence and mortality rates are among the highest in the world, necessitating a precision medicine approach tailored to the local immunogenetic landscape.
Aims & Methods
The objective was to design and in silico evaluate a multi-epitope vaccine against H. pylori using local consensus sequences from Andean Nariño isolates. Virulence-associated proteins CagA, UreB, and VacA from H.pylori were selected based on their pathogenic relevance. Consensus sequences from Andean Nariño isolates were generated and screened for antigenicity using VaxiJen, and non-homology with human proteins was confirmed via BLASTp. Linear B-cell (LBL) epitopes were predicted using ABCpred and IEDB B-cell, while HTL and CTL epitopes were identified using IEDB T-cell tools (Table 1). Selected epitopes were assembled into a multi-epitope construct using GPGPG (HTL), AAY (CTL), and KK (LBL) linkers, with cholera toxin B subunit (CTB) as an N-terminal adjuvant linked via EAAAK. Allergenicity (AllerTOP), physicochemical properties (ProtParam), secondary structure (SOPMA/Prabi), and solubility (Protein-Sol) were evaluated. The 3D structure was modeled using SWISS-MODEL and molecular docking with human TLR4 was performed using PatchDock.
Results
The designed multi-epitope vaccine was predicted to be antigenic and non-allergenic, with 276 amino acids, a theoretical pI of 9.67, and a molecular weight of 29,918.79 Da. Physicochemical analysis indicated a stable and mildly hydrophilic protein, with an instability index of 30.92, an aliphatic index of 83.55, and a GRAVY value of -0.174. Structural evaluation supported the model quality, showing 39.86% alpha helix, 19.20% extended strand, 40.94% random coil, 96.72% residues in favored Ramachandran regions, and a MolProbity score of 0.88.
Table 1. Antigens and predicted epitopes of B lymphocytes (LBL), helper T lymphocytes (HTL), and cytotoxic T lymphocytes (CTL).
| Protein | Subcellular Localization | Human Homology | Epitope | Location | Sequence | Allele | Length (aa) | Score | Antigenicity |
| CagA | Cytoplasmic / Secreted | Non-homologous | LBL | 237-252 | QPDIATTTTDIQGLPP |
| 16 | 0.92 | 1.0744 (Probable ANTIGEN) |
|
|
| HTL | 666-680 | DARAIAYAQNLKGIK | HLA-DRB1*04:07 | 15 | 0.9192 | 0.4829 (Probable ANTIGEN) |
|
|
| CTL | 527-535 | HLDAGFSKV | HLA-A*02:01 | 9 | 0.833525 | 0.5460 (Probable ANTIGEN) |
| UreB | Outer Membrane / Cytoplasmic | Non-homologous | LBL | 213 -228 | AGAIGFKIHEDWGTTP |
| 16 | 0.98 | 1.0385 (Probable ANTIGEN) |
|
|
| HTL | 438-452 | SPAFFGVKPNMIIKG | HLA-DRB1*07:01 | 15 | 0.9385 | 0.8775 (Probable ANTIGEN) |
|
|
| CTL | 467-475 | IPTPQPVYY | HLA-B*35:01 | 9 | 0.995265 | 0.7004 (Probable ANTIGEN) |
| VacA | Extracellular/ Outer Membrane | Non-homologous | LBL | 81-96 | VWRIQAGKGFNEFPNK |
| 16 | 0.96 | 0.4941 (Probable ANTIGEN) |
|
|
| HTL | 545-589 | GQSFLGVLNLKAAKN | HLA-DRB1*04:07 | 15 | 0.9191 | 0.7954 (Probable ANTIGEN) |
|
|
| CTL | 492-502 | MLIQLILKV | HLA-A*02:01 | 9 | 0.875382 | 0.8003 (Probable ANTIGEN) |
Conclusion
This immunoinformatics approach yielded a promising chimeric multi-epitope vaccine candidate against Helicobacter pylori with favorable antigenic, non-allergenic, physicochemical, and structural properties. These findings support its potential as a non-antibiotic preventive strategy for high-risk gastric cancer populations in Colombia and justify further in vitro and in vivo validation.
References
Cui M, Ji X, Guan F, Su G, Du L. Design of a Helicobacter pylori multi-epitope vaccine based on immunoinformatics. Front Immunol. 2024;15:1432968.
Guzman K, Igua D, Casas Cruz HM, Pazos A, Hidalgo A. Genomic epidemiology of Helicobacter pylori in regions with high and low risk of gastric cancer, Colombia. Front Microbiol. 2026;16:1742406.
Guzman KA, Hidalgo A, Pazos AJ. Point mutations in furazolidone and rifampicin resistance genes in Helicobacter pylori strains from Colombia. Antibiotics. 2024;13:643.