Tehran University of Medical Sciences

Science Communicator Platform

Stay connected! Follow us on X network (Twitter):
Share this content! On (X network) By
In Silico Design and Immunoinformatics Analysis of a Chimeric Vaccine Construct Based on Salmonella Pathogenesis Factors Publisher Pubmed



Jafari Najaf Abadi MH1 ; Abdi Abyaneh F2 ; Zare N3 ; Zamani J4 ; Abdoli A2, 5 ; Aslanbeigi F2, 5 ; Hamblin MR6 ; Tarrahimofrad H4 ; Rahimi M7, 8 ; Hashemian SM9 ; Mirzaei H10
Authors
Show Affiliations
Authors Affiliations
  1. 1. Research Center for Health Technology Assessment and Medical Informatics, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
  2. 2. School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
  3. 3. Faculty of Pharmacy, International Campus, Tehran University of Medical Science, Tehran, Iran
  4. 4. Department of Animal Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
  5. 5. Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
  6. 6. Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028, South Africa
  7. 7. Infectious Diseases Research Center, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
  8. 8. Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
  9. 9. Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, 1983535511, Iran
  10. 10. Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran

Source: Microbial Pathogenesis Published:2023


Abstract

Currently, there are two vaccines based on killed and/or weakened Salmonella bacteria, but no recombinant vaccine is available for preventing or treating the disease. We used an in silico approach to design a multi-epitope vaccine against Salmonella using OmpA, OmpS, SopB, SseB, SthA and FilC antigens. We predicted helper T lymphocyte, cytotoxic T lymphocyte, and IFN-γ epitopes. The FilC sequence was used as a bovine TLR5 agonist, and the linkers KK, AAY, GPGPG and EAAAK were used to connect epitopes. The final sequence consisted of 747 amino acid residues, and the expressed soluble protein (∼79.6 kDa) was predicted to be both non-allergenic and antigenic. The tertiary structure of modeled protein was refined and validated, and the interactions of vaccine 3D structure were evaluated using molecular docking, and molecular dynamics simulation (RMSD, RMSF and Gyration). This structurally stable protein could interact with human TLR5. The C-ImmSim server predicted that this proposed vaccine likely induces an immune response by stimulating T and B cells, making it a potential candidate for further evaluation for the prevention and treatment of Salmonella infection. © 2023 Elsevier Ltd
Related Docs
View other Related Docs
1. Rational Design of B-Cell and T-Cell Multi Epitope-Based Vaccine Against Zika Virus, an in Silico Study, Journal of Biomolecular Structure and Dynamics (2024)
2. Immunoinformatics Approach: Developing a Multi-Epitope Vaccine With Novel Carriers Targeting Monkeypox Virus, FASEB Journal (2024)
3. In Silico Studying of the Whole Protein Structure and Dynamics of Dickkopf Family Members Showed That N-Terminal Domain of Dickkopf 2 in Contrary to Other Dickkopfs Facilitates Its Interaction With Low Density Lipoprotein Receptor Related Protein 5/6, Journal of Biomolecular Structure and Dynamics (2019)
4. Impacts of the G145r Mutation on the Structure and Immunogenic Activity of the Hepatitis B Surface Antigen: A Computational Analysis, Hepatitis Monthly (2016)
5. Immunoinformatics: In Silico Approaches and Computational Design of a Multi-Epitope, Immunogenic Protein, International Reviews of Immunology (2019)
6. Rational Design of Anti-Angiogenic Peptides to Inhibit Vegf/Vegfr2 Interactions for Cancer Therapeutics, Anti-Cancer Agents in Medicinal Chemistry (2022)
7. Immunoinformatics Design of Multivalent Chimeric Vaccine for Modulation of the Immune System in Pseudomonas Aeruginosa Infection, Infection# Genetics and Evolution (2020)
8. Structure-Based Study of Immune Receptors As Eligible Binding Targets of Coronavirus Sars-Cov-2 Spike Protein, Journal of Molecular Graphics and Modelling (2021)
Experts (# of related papers)
View all Related Experts
Massoud Amanlou (4)
Seyed Mohammad Jazayeri (2)
Other Related Docs
9. Computational Design of a Novel Vlp-Based Vaccine for Hepatitis B Virus, Frontiers in Immunology (2020)
10. Investigation of Biological Activities of Two Cultivars of Cicer Arietinum Proteins Mass Associated With Alzheimer's Disease, Proteins: Structure# Function and Bioinformatics (2023)
11. In Silico Approach for Designing a Novel Recombinant Fusion Protein As a Candidate Vaccine Against Hpv, Current Proteomics (2021)
12. Functional Variation (Q63r) in the Cannabinoid Cb2 Receptor May Affect the Severity of Covid-19: A Human Study and Molecular Docking, Archives of Virology (2021)
13. Cd171 Multi-Epitope Peptide Design Based on Immuno-Informatics Approach As a Cancer Vaccine Candidate for Glioblastoma, Journal of Biomolecular Structure and Dynamics (2023)
14. Hpv16-E7 Protein T Cell Epitope Prediction and Global Therapeutic Peptide Vaccine Design Based on Human Leukocyte Antigen Frequency: An In-Silico Study, International Journal of Peptide Research and Therapeutics (2021)
15. Conformational Analysis of Hepatitis B Virus Surface Antigen Mutations Among Hiv-Positive Patients Diagnosed With Occult Hepatitis B Virus, Future Virology (2020)
16. Decoding the Structure–Function Relationship of the Muramidase Domain in E. Coli O157.H7 Bacteriophage Endolysin: A Potential Building Block for Chimeric Enzybiotics, Protein Journal (2024)
17. Immunopotentiation of the Engineered Low-Molecular-Weight Pilin Targeting Pseudomonas Aeruginosa: A Combination of Immunoinformatics Investigation and Active Immunization, Molecular Immunology (2020)
18. Design of a Multi-Epitope Vaccine Against Sars-Cov-2 Using Immunoinformatics Approach, International Journal of Biological Macromolecules (2020)
19. Construction of a Chimeric Flic Including Epitopes of Ompa and Ompk36 As a Multi-Epitope Vaccine Against Klebsiella Pneumonia, Health Biotechnology and Biopharma (2021)
20. Discovery of Potential Fgfr3 Inhibitors Via Qsar, Pharmacophore Modeling, Virtual Screening and Molecular Docking Studies Against Bladder Cancer, Journal of Translational Medicine (2023)
21. In Silico Development of a Multi-Epitope-Based Vaccine Against Burkholderia Cepacia Complex Using Reverse Vaccinology, Frontiers in Virology (2025)
22. In Silico Analysis for Determination and Validation of Human Cd20 Antigen 3D Structure, International Journal of Peptide Research and Therapeutics (2019)
23. The Effect of in Silico Targeting Pseudomonas Aeruginosa Patatin-Like Protein D, for Immunogenic Administration, Computational Biology and Chemistry (2018)
24. Rational Design of Dkk3 Structure-Based Small Peptides As Antagonists of Wnt Signaling Pathway and in Silico Evaluation of Their Efficiency, PLoS ONE (2017)
25. In Silico Characterization of Epitopes for Vaccine Design Against Escherichia Coli Based on Heme-Utilization Protein, Journal of Applied Biotechnology Reports (2024)
26. A Bioinformatics Approach to Introduce Novel Multi-Epitope Vaccines Against Acinetobacter Baumannii Retrieved From Immunogenic Extracellular Loops of Outer Membrane Proteins, Informatics in Medicine Unlocked (2022)
27. Computational Design and Analysis of a Poly-Epitope Fusion Protein: A New Vaccine Candidate for Hepatitis and Poliovirus, International Journal of Peptide Research and Therapeutics (2020)
28. Investigation of Specific Binding of Designed Oligodeoxynucleotide Decoys to Transcription Factors in Ht29 Cell Line Undergoing Epithelial–Mesenchymal Transition (Emt), Journal of Cellular Physiology (2019)
29. Computational Structure-Based Design of Antiviral Peptides As Potential Protein–Protein Interaction Inhibitors of Rabies Virus Phosphoprotein and Human Lc8, Heliyon (2025)
30. Immunomodulatory Effects of a Rationally Designed Peptide Mimetic of Human Ifnβ in Eae Model of Multiple Sclerosis, Progress in Neuro-Psychopharmacology and Biological Psychiatry (2018)
31. In Silico Analysis for Determination and Validation of Iron-Regulated Protein From Escherichia Coli, International Journal of Peptide Research and Therapeutics (2019)
32. Covid-19: A Systematic Review and Update on Prevention, Diagnosis, and Treatment, MedComm (2022)
33. Deletion of Loop Fragment Adjacent to Active Site Diminishes the Stability and Activity of Exo-Inulinase, International Journal of Biological Macromolecules (2016)
34. Characterization of the Dna Mismatch Repair Proteins Muts and Mutl in a Hypermutator Acinetobacter Baumannii, Microbial Pathogenesis (2017)
35. In Silico Homology Modeling and Epitope Prediction of Nada As a Potential Vaccine Candidate in Neisseria Meningitidis, International Journal of Molecular and Cellular Medicine (2018)
36. Reverse Vaccinology Approaches to Introduce Promising Immunogenic and Drug Targets Against Antibiotic-Resistant Neisseria Gonorrhoeae: Thinking Outside the Box in Current Prevention and Treatment, Infection# Genetics and Evolution (2023)
37. Identification of Novel Putative Immunogenic Targets and Construction of a Multi-Epitope Vaccine Against Multidrug-Resistant Corynebacterium Jeikeium Using Reverse Vaccinology Approach, Microbial Pathogenesis (2022)
38. A Knowledge-Based Protein-Protein Interaction Inhibition (Kpi) Pipeline: An Insight From Drug Repositioning for Covid-19 Inhibition, Journal of Biomolecular Structure and Dynamics (2023)
39. High-Throughput Analysis of the Interactions Between Viral Proteins and Host Cell Rnas, Computers in Biology and Medicine (2021)
40. In Silico Mutagenesis in Recombinant Human Keratinocyte Growth Factor: Improvement of Stability and Activity in Addition to Decrement Immunogenicity, Journal of Molecular Graphics and Modelling (2020)
41. Hbsag Mutations Related to Occult Hepatitis B Virus Infection in Hiv-Positive Patients Result in a Reduced Secretion and Conformational Changes of Hbsag, Journal of Medical Virology (2017)
42. Subtractive Genomic Approach Toward Introduction of Novel Immunogenic Targets Against Clostridioides Difficile: Thinking Out of the Box, Microbial Pathogenesis (2022)
43. Computational Designing of the Ligands of Protein L Affinity Chromatography Based on Molecular Docking and Molecular Dynamics Simulations, Journal of Biomolecular Structure and Dynamics (2023)
44. Computer-Assisted Multi-Epitopes T-Cell Subunit Covid-19 Vaccine Design, Biomedical and Biotechnology Research Journal (2021)
45. Identification of New Dna Gyrase Inhibitors Based on Bioactive Compounds From Streptomyces: Structure-Based Virtual Screening and Molecular Dynamics Simulations Approaches, Journal of Biomolecular Structure and Dynamics (2020)
46. Computational Design of a Potential Therapeutic Peptide Against Spike Protein of Sars-Cov-2, Journal of Computational Biophysics and Chemistry (2021)