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Computational design of a multi-epitope vaccine against Helicobacter pylori targeting CagA, FliD, urease, and OipA with cholera toxin B subunit (CTB) adjuvant.

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος: Computational design of a multi-epitope vaccine against Helicobacter pylori targeting CagA, FliD, urease, and OipA with cholera toxin B subunit (CTB) adjuvant.
Συγγραφείς: Baniasadi Nejad N; Student Research Committee, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran., Shahbazi B; School of Pharmacy, Semnan University of Medical Sciences, Semnan, Iran.; Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran., Sarkoohi P; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran., Ahmadi N; School of Pharmacy, Semnan University of Medical Sciences, Semnan, Iran., Ahmadi K; The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran. khadijeh_6482@yahoo.com.; Department of Medical Biotechnology, School of Paramedicine, Bushehr University of Medical Sciences, Bushehr, Iran. khadijeh_6482@yahoo.com.
Πηγή: BMC microbiology [BMC Microbiol] 2026 Apr 25; Vol. 26 (1). Date of Electronic Publication: 2026 Apr 25.
Τύπος έκδοσης: Journal Article
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: BioMed Central Country of Publication: England NLM ID: 100966981 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2180 (Electronic) Linking ISSN: 14712180 NLM ISO Abbreviation: BMC Microbiol Subsets: MEDLINE
Imprint Name(s): Original Publication: London : BioMed Central, [2001-
Ιατρικοί όροι (MeSH): Helicobacter pylori*/immunology , Helicobacter pylori*/genetics , Bacterial Proteins*/immunology , Bacterial Proteins*/genetics , Cholera Toxin*/immunology , Bacterial Vaccines*/immunology , Bacterial Vaccines*/genetics , Bacterial Vaccines*/chemistry , Helicobacter Infections*/prevention & control , Helicobacter Infections*/immunology , Helicobacter Infections*/microbiology, Antigens, Bacterial/immunology ; Antigens, Bacterial/genetics ; Urease/immunology ; Urease/genetics ; Epitopes, T-Lymphocyte/immunology ; Epitopes, B-Lymphocyte/immunology ; Toll-Like Receptor 2/immunology ; Toll-Like Receptor 4/immunology ; Virulence Factors/immunology ; Immunodominant Epitopes/immunology ; Molecular Dynamics Simulation ; Molecular Docking Simulation ; Immunoinformatics ; Protein Subunit Vaccines ; Humans ; Adjuvants, Immunologic ; Antibodies, Bacterial ; Computational Biology
Περίληψη: BACKGROUND: Helicobacter pylori, a Gram-negative, microaerophilic bacterium with a characteristic spiral morphology, inhabits the stomachs of approximately half of the world’s population. This study aimed to design a multi-epitope vaccine against H. pylori using immunoinformatics approaches, targeting key virulence factors including FliD, CagA, OipA, and urease. METHODS: A multi-epitope vaccine was constructed by linking nine immunodominant epitopes from FliD, urease, CagA, and OipA and the cholera toxin B subunit (CTB) adjuvant. The resulting construct was rigorously evaluated through computational analyses to assess its physicochemical properties, structural stability, molecular docking with TLR2/TLR4, molecular dynamics (MD) simulations, and immune response profiling. RESULTS: Nine immunodominant epitopes from FliD, urease, CagA, and OipA, selected based on overlapping predictions of B and T cell epitopes, were linked with CTB. Structural modeling and validation predicted a stable tertiary structure, while molecular docking revealed strong interactions with TLR2 and TLR4, key receptors of innate immunity. Molecular dynamics simulations over 100 nanoseconds (ns) demonstrated structural stability for both complexes, with the vaccine-TLR4 complex showing higher stability than TLR2. Immune simulations predicted robust humoral and cellular responses, indicating sustained immunity. CONCLUSION: This study successfully designed a novel multi-epitope vaccine candidate against Helicobacter pylori using a comprehensive immunoinformatics approach. These comprehensive in silico analyses suggest that the proposed vaccine is a highly promising candidate for combating Helicobacter pylori infections; however, further in vitro and in vivo studies are essential to validate its efficacy and safety.
Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.
References: Malfertheiner P, et al. Helicobacter pylori infection. Nat Reviews Disease Primers. 2023;9(1):19. (PMID: 10.1038/s41572-023-00431-8)
Dos Santos Viana I, et al. Vaccine development against Helicobacter pylori: from ideal antigens to the current landscape. Expert Rev Vaccines. 2021;20(8):989–99. (PMID: 10.1080/14760584.2021.1945450)
Martínez LE, et al. Helicobacter pylori strains vary cell shape and flagellum number to maintain robust motility in viscous environments. Mol Microbiol. 2016;99(1):88–110. (PMID: 10.1111/mmi.13218)
Mobley HLT, Mendz GL, Hazell SL, editors. Helicobacter pylori: Physiology and Genetics. Washington (DC): ASM Press; 2001. PMID: 21290711.
Ansari S, Yamaoka Y. Helicobacter pylori Virulence Factors Exploiting Gastric Colonization and its Pathogenicity. Toxins. 2019;11(11):677. (PMID: 10.3390/toxins11110677)
Backert S, Tegtmeyer N, Fischer W. Composition, structure and function of the Helicobacter pylori cag pathogenicity island encoded type IV secretion system. Future Microbiol. 2015;10(6):955–65. (PMID: 10.2217/fmb.15.32)
Gorrell RJ, et al. A novel NOD1- and CagA-independent pathway of interleukin-8 induction mediated by the Helicobacter pylori type IV secretion system. Cell Microbiol. 2013;15(4):554–70. (PMID: 10.1111/cmi.12055)
Backert S, Blaser MJ. The Role of CagA in the Gastric Biology of Helicobacter pylori. Cancer Res. 2016;76(14):4028–31. (PMID: 10.1158/0008-5472.CAN-16-1680)
Yamaoka Y, et al. Importance of Helicobacter pylori oipA in clinical presentation, gastric inflammation, and mucosal interleukin 8 production. Gastroenterology. 2002;123(2):414–24. (PMID: 10.1053/gast.2002.34781)
Horridge DN, Begley AA, Kim J, Aravindan N, Fan K, Forsyth MH. Outer inflammatory protein a (OipA) of Helicobacter pylori is regulated by host cell contact and mediates CagA translocation and interleukin-8 response only in the presence of a functional cag pathogenicity island type IV secretion system. Pathog Dis. 2017;75(8):ftx113. PMID: 29040466; PMCID: PMC6433299. https://doi.org/10.1093/femspd/ftx113 .
Kusters JG, Van Vliet AH, Kuipers EJ. Pathogenesis of Helicobacter pylori infection. Clin Microbiol Rev. 2006;19(3):449–90. (PMID: 10.1128/CMR.00054-05)
Bäckström A, et al. Metastability of Helicobacter pylori bab adhesin genes and dynamics in Lewis b antigen binding. Proc Natl Acad Sci. 2004;101(48):16923–8. (PMID: 10.1073/pnas.0404817101)
Malfertheiner P, et al. Management of Helicobacter pylori infection-the Maastricht V/Florence Consensus Report. Gut. 2017;66(1):6–30. (PMID: 10.1136/gutjnl-2016-312288)
Lee YC, et al. Association Between Helicobacter pylori Eradication and Gastric Cancer Incidence: A Systematic Review and Meta-analysis. Gastroenterology. 2016;150(5):1113–e11245. (PMID: 10.1053/j.gastro.2016.01.028)
Fallone CA, Moss SF, Malfertheiner P. Reconciliation of Recent Helicobacter pylori Treatment Guidelines in a Time of Increasing Resistance to Antibiotics. Gastroenterology. 2019;157(1):44–53. (PMID: 10.1053/j.gastro.2019.04.011)
El-Serag HB, et al. Houston Consensus Conference on Testing for Helicobacter pylori Infection in the United States. Clin Gastroenterol Hepatol. 2018;16(7):992–e10026. (PMID: 10.1016/j.cgh.2018.03.013)
Fallone CA, et al. The Toronto Consensus for the Treatment of Helicobacter pylori Infection in Adults. Gastroenterology. 2016;151(1):51–e6914. (PMID: 10.1053/j.gastro.2016.04.006)
Graham DY, Fischbach L. Helicobacter pylori treatment in the era of increasing antibiotic resistance. Gut. 2010;59(8):1143–53. (PMID: 10.1136/gut.2009.192757)
Megraud F, et al. Helicobacter pylori resistance to antibiotics in Europe in 2018 and its relationship to antibiotic consumption in the community. Gut. 2021;70(10):1815–22. (PMID: 10.1136/gutjnl-2021-324032)
Savoldi A, et al. Prevalence of Antibiotic Resistance in Helicobacter pylori: A Systematic Review and Meta-analysis in World Health Organization Regions. Gastroenterology. 2018;155(5):1372–e138217. (PMID: 10.1053/j.gastro.2018.07.007)
Bujanda L, Nyssen OP, Vaira D, Saracino IM, Fiorini G, Lerang F, Georgopoulos S, Tepes B, Heluwaert F, Gasbarrini A, Rokkas T, Bordin D, Smith S, Lamy V, Caldas M, Resina E, Muñoz R, Cosme Á, Puig I, Megraud F, O'Morain C, Gisbert JP; The Hp-EuReg Investigators. Antibiotic resistance prevalence and trends in patients infected with helicobacter pylori in the period 2013-2020: results of the European registry on H. pylori Management (Hp-EuReg). Antibiotics (Basel). 2021;10(9):1058. PMID: 34572640; PMCID: PMC8471667. https://doi.org/10.3390/antibiotics10091058 .
Tshibangu-Kabamba E, Yamaoka Y. Helicobacter pylori infection and antibiotic resistance — from biology to clinical implications. Nat Reviews Gastroenterol Hepatol. 2021;18(9):613–29. (PMID: 10.1038/s41575-021-00449-x)
Sutton P, Boag JM. Status of vaccine research and development for Helicobacter pylori. Vaccine. 2019;37(50):7295–9. (PMID: 10.1016/j.vaccine.2018.01.001)
Sánchez J, Holmgren J. Cholera toxin structure, gene regulation and pathophysiological and immunological aspects. Cell Mol Life Sci. 2008;65(9):1347–60. (PMID: 10.1007/s00018-008-7496-5)
Consortium TU. UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Res. 2024;53(D1):D609–17. (PMID: 10.1093/nar/gkae1010)
Jespersen MC, et al. BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res. 2017;45(W1):W24–9. (PMID: 10.1093/nar/gkx346)
Kolaskar AS, Tongaonkar PC. A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett. 1990;276(1–2):172–4. (PMID: 10.1016/0014-5793(90)80535-Q)
El-Manzalawy Y, Dobbs D, Honavar V. Predicting linear B-cell epitopes using string kernels. J Mol Recognit. 2008;21(4):243–55. (PMID: 10.1002/jmr.893)
Kim Y, et al. Immune epitope database analysis resource. Nucleic Acids Res. 2012;40(Web Server issue):W525–30. (PMID: 10.1093/nar/gks438)
Reynisson B, et al. NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res. 2020;48(W1):W449–54. (PMID: 10.1093/nar/gkaa379)
Kaabinejadian S, et al. Accurate MHC Motif Deconvolution of Immunopeptidomics Data Reveals a Significant Contribution of DRB3, 4 and 5 to the Total DR Immunopeptidome. Front Immunol. 2022;13:835454. (PMID: 10.3389/fimmu.2022.835454)
Reche PA, Reinherz EL. Prediction of peptide-MHC binding using profiles. Methods Mol Biol. 2007;409:185–200. (PMID: 10.1007/978-1-60327-118-9_13)
Chen X, Zaro JL, Shen W-C. Fusion protein linkers: property, design and functionality. Adv Drug Deliv Rev. 2013;65(10):1357–69. (PMID: 10.1016/j.addr.2012.09.039)
Wilkins MR, et al. Protein identification and analysis tools in the ExPASy server. Methods Mol Biol. 1999;112:531–52.
Dimitrov I, et al. AllerTOP v.2–a server for in silico prediction of allergens. J Mol Model. 2014;20(6):2278. (PMID: 10.1007/s00894-014-2278-5)
Diaz AA, et al. Prediction of protein solubility in Escherichia coli using logistic regression. Biotechnol Bioeng. 2010;105(2):374–83. (PMID: 10.1002/bit.22537)
Doytchinova IA, Flower DR. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics. 2007;8(1):4. (PMID: 10.1186/1471-2105-8-4)
Gupta S, et al. Peptide toxicity prediction. Methods Mol Biol. 2015;1268:143–57. (PMID: 10.1007/978-1-4939-2285-7_7)
Kouza M, et al. The GOR Method of Protein Secondary Structure Prediction and Its Application as a Protein Aggregation Prediction Tool. Methods Mol Biol. 2017;1484:7–24. (PMID: 10.1007/978-1-4939-6406-2_2)
Ko J, et al. GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Res. 2012;40(Web Server issue):W294–7. (PMID: 10.1093/nar/gks493)
Williams CJ, et al. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 2018;27(1):293–315. (PMID: 10.1002/pro.3330)
Laskowski RA, et al. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR. 1996;8(4):477–86. (PMID: 10.1007/BF00228148)
Colovos C, Yeates TO. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci. 1993;2(9):1511–9. (PMID: 10.1002/pro.5560020916)
Wiederstein M, Sippl MJ. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007;35(suppl2):W407–10. (PMID: 10.1093/nar/gkm290)
Ponomarenko J, et al. ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics. 2008;9:514. (PMID: 10.1186/1471-2105-9-514)
Kozakov D, et al. The ClusPro web server for protein-protein docking. Nat Protoc. 2017;12(2):255–78. (PMID: 10.1038/nprot.2016.169)
Pettersen EF, et al. UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–12. (PMID: 10.1002/jcc.20084)
Xue LC, et al. PRODIGY: a web server for predicting the binding affinity of protein–protein complexes. Bioinformatics. 2016;32(23):3676–8. (PMID: 10.1093/bioinformatics/btw514)
Laskowski RA, et al. PDBsum: Structural summaries of PDB entries. Protein Sci. 2018;27(1):129–34. (PMID: 10.1002/pro.3289)
Grote A, et al. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 2005;33(Web Server issue):W526–31. (PMID: 10.1093/nar/gki376)
Kudla G, et al. High guanine and cytosine content increases mRNA levels in mammalian cells. PLoS Biol. 2006;4(6):e180. (PMID: 10.1371/journal.pbio.0040180)
Puigbò P, Bravo IG, Garcia-Vallve S. CAIcal: a combined set of tools to assess codon usage adaptation. Biol Direct. 2008;3:38. (PMID: 10.1186/1745-6150-3-38)
Pronk S, et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics. 2013;29(7):845–54. (PMID: 10.1093/bioinformatics/btt055)
Weng G, et al. HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA. Nucleic Acids Res. 2019;47(W1):W322–30. (PMID: 10.1093/nar/gkz397)
Rapin N, et al. Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system. PLoS ONE. 2010;5(4):e9862. (PMID: 10.1371/journal.pone.0009862)
Cyster JG, Allen CDC. B Cell Responses: Cell Interact Dynamics Decisions Cell. 2019;177(3):524–40.
Pan X, et al. Protection Against Helicobacter pylori Infection in BALB/c Mouse Model by Oral Administration of Multivalent Epitope-Based Vaccine of Cholera Toxin B Subunit-HUUC. Front Immunol. 2018;9:1003. (PMID: 10.3389/fimmu.2018.01003)
Xie W, et al. Oral multivalent epitope vaccine, based on UreB, HpaA, CAT, and LTB, for prevention and treatment of Helicobacter pylori infection in C57BL / 6 mice. Helicobacter. 2021;26(3):e12807. (PMID: 10.1111/hel.12807)
Guo L, et al. Oral Immunization with a Multivalent Epitope-Based Vaccine, Based on NAP, Urease, HSP60, and HpaA, Provides Therapeutic Effect on H. pylori Infection in Mongolian gerbils. Front Cell Infect Microbiol. 2017;7:349. (PMID: 10.3389/fcimb.2017.00349)
Larussa T, et al. Helicobacter pylori and T Helper Cells: Mechanisms of Immune Escape and Tolerance. J Immunol Res. 2015;2015(1):981328.
Akhiani AA, et al. Protection against Helicobacter pylori infection following immunization is IL-12-dependent and mediated by Th1 cells. J Immunol. 2002;169(12):6977–84. (PMID: 10.4049/jimmunol.169.12.6977)
Gupte TM, Ritt M, Sivaramakrishnan S. ER/K-link-Leveraging a native protein linker to probe dynamic cellular interactions. Methods Enzymol. 2021;647:173–208. Epub 2020. PMID: 33482988; PMCID: PMC8009693. https://doi.org/10.1016/bs.mie.2020.10.002 .
Chen VB, et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 2010;66(Pt 1):12–21. (PMID: 10.1107/S0907444909042073)
Marshall BJ, Warren JR. Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration. Lancet. 1984;1(8390):1311–5. (PMID: 10.1016/S0140-6736(84)91816-6)
Kuo CH, et al. Helicobacter pylori and Systemic Disease. Gastroenterol Res Pract. 2014;2014:358494. (PMID: 10.1155/2014/358494)
Kim JS, et al. Molecular cloning and characterization of the Helicobacter pylori fliD gene, an essential factor in flagellar structure and motility. J Bacteriol. 1999;181(22):6969–76. (PMID: 10.1128/JB.181.22.6969-6976.1999)
Yong X, et al. Helicobacter pylori virulence factor CagA promotes tumorigenesis of gastric cancer via multiple signaling pathways. Cell Communication Signal. 2015;13(1):30. (PMID: 10.1186/s12964-015-0111-0)
Teymournejad O, et al. Binding of the Helicobacter pylori OipA causes apoptosis of host cells via modulation of Bax/Bcl-2 levels. Sci Rep. 2017;7(1):8036. (PMID: 10.1038/s41598-017-08176-7)
Kawai T, Akira S. Toll-like receptors and their crosstalk with other innate receptors in infection and immunity. Immunity. 2011;34(5):637–50. (PMID: 10.1016/j.immuni.2011.05.006)
Duthie MS, et al. Use of defined TLR ligands as adjuvants within human vaccines. Immunol Rev. 2011;239(1):178–96. (PMID: 10.1111/j.1600-065X.2010.00978.x)
Luchner M, Reinke S, Milicic A. TLR Agonists as Vaccine Adjuvants Targeting Cancer and Infectious Diseases. Pharmaceutics. 2021;13(2):142. (PMID: 10.3390/pharmaceutics13020142)
Reed SG, et al. The science of vaccine adjuvants: advances in TLR4 ligand adjuvants. Curr Opin Immunol. 2016;41:85–90. (PMID: 10.1016/j.coi.2016.06.007)
Contributed Indexing: Keywords: Helicobacter pylori; CTB; Molecular docking; Molecular dynamics simulation; Multi-epitope vaccine
Substance Nomenclature: 0 (Bacterial Proteins)
0 (Antigens, Bacterial)
9012-63-9 (Cholera Toxin)
0 (cagA protein, Helicobacter pylori)
EC 3.5.1.5 (Urease)
0 (Bacterial Vaccines)
0 (Epitopes, T-Lymphocyte)
0 (Epitopes, B-Lymphocyte)
0 (Protein Subunit Vaccines)
0 (Toll-Like Receptor 2)
0 (Adjuvants, Immunologic)
0 (Toll-Like Receptor 4)
0 (Antibodies, Bacterial)
0 (Virulence Factors)
0 (Immunodominant Epitopes)
Entry Date(s): Date Created: 20260426 Date Completed: 20260628 Latest Revision: 20260726
Update Code: 20260726
PubMed Central ID: PMC13251020
DOI: 10.1186/s12866-026-05078-5
PMID: 42035012
Βάση Δεδομένων: MEDLINE
Περιγραφή
ISSN:1471-2180
DOI:10.1186/s12866-026-05078-5