Conference 2021 Live Talk
In-Silico Prediction of T- cell epitopes in VacA: First Step towards the Design of a Helicobacter Pylori Vaccine
Authors and Affiliations
Elijah Kolawole Oladipo1, 2*, Aina Abisola1*, Eko Oluwaseyi1, Olubukola Monisola Oyawoye1
1. Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
2. Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
Helicobacter pylori is indicated in gastritis, gastric cancer, Peptic ulcer, B cell mucosa lymphoid tissue lymphoma. The bacteria has 50% pandemic, a higher prevalence of 75% in developing countries and in 40% prevalence in developed countries. A combination of antibiotics is used to treat Helicobacter pylori infections some of which are Amoxicillin, tetracycline and fluoroquinolones but are ineffective to eliminate the infections and are also compromised by antibiotic resistant strains hence a vaccine to help prevent, control and eliminate Helicobacter pylori infections is needed.
We proposed to predict T-cell epitopes of VacA. Seven VacA protein sequences were retrieved from the NCBI protein database and subjected to antigenicity test using ANTIGENpro database. All the seven (7) sequences with antigenicity score ≥0.8 were submitted to NetCTL server and IEDB (Immune Epitope Database) MHC-II server to predict the cytotoxic T-lymphocyte (CTL) and to predict the Helper T-lymphocyte (HTL) epitopes respectively. The cytotoxic T-lymphocyte epitopes were predicted at the default threshold score of 0.75 while H2-IAb, H2-IAd and H2-IEd mouse alleles were selected for predicting Helper T-lymphocyte epitopes.
The seven amino acid sequences obtained from NCBI subjected to antigenicity test passed by having a score of ≥0.8. Ninety-eight (98) CTL (9-mer) ligands in total were predicted for the seven selected proteins submitted to NetCTL sever. Fifty-six (56) epitopes were selected according to their high scores. Ninety-nine (99) (15-mer) total HTL epitopes were predicted. Their IC50 value not greater than 500nm with percentile rank ranging from 0.030-4.00 while ninety-four (94) epitopes were selected. A total of fifty-six (56) CTL and Ninety-four (94) HTL epitopes were merged together using AAY , EAAY and GPGPG linkers while TLR-4 agonist with sequence APPHALS as an adjuvant to construct the multi epitope vaccine.
The predicted peptides are presumed to be valuable in the multi epitope vaccines without compromising the population coverage. VacA has potential B-cell and T-cell epitopes distributed throughout the sequence. Thus several fragments were identified as valuable candidates for subunit vaccines against Helicobacter pylori.