In Silico Design and Structural Validation of a Multi-Epitope Cytotoxic T Lymphocyte Vaccine Candidate Targeting Membrane-Associated Proteins in Gastric Cancer

Mohammadi, Kianoush; Bakhti, Seyedeh-Zahra

doi:10.61882/gebsj.14.2.3

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Volume 14, Issue 2 (1-2026)

gebsj 2026, 14(2): 180-191

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In Silico Design and Structural Validation of a Multi-Epitope Cytotoxic T Lymphocyte Vaccine Candidate Targeting Membrane-Associated Proteins in Gastric Cancer

Kianoush Mohammadi

, Seyedeh-Zahra Bakhti ^*

Department of Plant, Cell and Molecular Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran. , sz.bakhti@tabrizu.ac.ir

Abstract: (994 Views)

Gastric cancer (GC) is still among the top causes of death from cancer globally. Immunotherapy, in the form of cytotoxic T lymphocyte (CTL) vaccines against tumor-specific antigens, is a promising therapeutic approach. The effective design of multi-epitope vaccines with high immunogenicity, tumor specificity, and structural stability, however, is not straightforward. The study aimed to develop and structurally validate a multi-epitope CTL vaccine targeting membrane-associated proteins overexpressed in GC, utilizing integrated immunoinformatics and structural vaccinology approaches. Experimentally verified 9-mer CTL epitopes were selected from five GC membrane proteins. Immunogenicity was enhanced and antigen processing facilitated by the addition of β-defensin 3 adjuvant and suitable linkers. Vaccine construct physicochemical property analysis, prediction of allergenicity and toxicity, three-dimensional structure modeling, Ramachandran plot validation, and molecular docking into HLA-A*0201 molecules were done. The vaccine developed possessed the desirable physicochemical characteristics of high stability, non-allergenicity, and non-toxicity. Confirmation of structure revealed 87.8% residues in favorable spaces, ascertaining correct folding and structural integrity. Molecular docking analysis revealed strong binding affinity (−874.2 kcal/mol) with HLA-A*0201, indicating efficient MHC-I presentation and the capacity to generate a good CTL response. The in silico rationalized multi-epitope CTL vaccine possesses promising immunogenic and structural characteristics as a personalized GC immunotherapeutic lead. Further studies, including molecular dynamics simulations, broader HLA allele coverage, and experimental validation, are warranted to confirm efficacy and safety and facilitate clinical translation.

Keywords: Gastric cancer, CTL vaccine, Epitope, Immunoinformatics, Docking

Full-Text [PDF 1064 kb] (360 Downloads)

Type of Study: Research | Subject: Animal
Received: 2025/11/18 | Accepted: 2026/01/11 | Published: 2026/01/12

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Mohammadi K, Bakhti S. In Silico Design and Structural Validation of a Multi-Epitope Cytotoxic T Lymphocyte Vaccine Candidate Targeting Membrane-Associated Proteins in Gastric Cancer. gebsj 2026; 14 (2) :180-191
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