Iranian
Biomedical Journal
Volume 28, Issue 4 (7-2024)
IBJ 2024, 28(4): 156-167 |
Back to browse issues page
Ethics code: IR.PII.REC.1400.068
Download citation:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:
shahbazi S, Badmasti F, Habibi M, Sabzi S, Noori Goodarzi N, Farokhi M et al . In silico and in vivo Investigations of the Immunoreactivity of Klebsiella pneumoniae OmpA Protein as a Vaccine Candidate. IBJ 2024; 28 (4) :156-167
URL: http://ibj.pasteur.ac.ir/article-1-4023-en.html
URL: http://ibj.pasteur.ac.ir/article-1-4023-en.html
Shahla Shahbazi 
, Farzad Badmasti , Mehri Habibi , Samira Sabzi , Narjes Noori Goodarzi , Mehdi Farokhi * , Mohammad Reza Asadi Karam*
, Farzad Badmasti , Mehri Habibi , Samira Sabzi , Narjes Noori Goodarzi , Mehdi Farokhi * , Mohammad Reza Asadi Karam*
Abstract:
Background: The growing threat of antibiotic resistance and Klebsiella pneumoniae infection in healthcare settings highlights the urgent need for innovative solutions, such as vaccines, to address these challenges. This study sought to assess the potential of using K. pneumoniae outer membrane protein A (OmpA) as a vaccine candidate through both in silico and in vivo analyses.
Methods: The study examined the OmpA protein sequence for subcellular localization, antigenicity, allergenicity, similarity to the human proteome, physicochemical properties, B-cell epitopes, MHC binding sites, tertiary structure predictions, molecular docking, and immune response simulations. The ompA gene was cloned into the pET-28a (+) vector, expressed, purified and confirmed using Western blotting analysis. IgG levels in the serum of the immunized mice were measured using ELISA with dilutions ranging from 1:100 to 1:6400, targeting recombinant outer membrane protein A (rOmpA) and K. pneumoniae ATCC 13883. The sensitivity and specificity of the ELISA method were also assessed.
Results: The bioinformatics analysis identified rOmpA as a promising vaccine candidate. The immunized group demonstrated significant production of specific total IgG antibodies against rOmpA and K. pneumoniae ATCC1 13883, as compared to the control group (p < 0.0001). The titers of antibodies produced in response to bacterial exposure did not show any significant difference when compared to the anti-rOmpA antibodies (p > 0.05). The ELISA test sensitivity was 1:3200, and the antibodies in the serum could accurately recognize K. pneumoniae cells.
Conclusion: This study is a significant advancement in the development of a potential vaccine against K. pneumoniae that relies on OmpA. Nevertheless, additional experimental analyses are required.
Methods: The study examined the OmpA protein sequence for subcellular localization, antigenicity, allergenicity, similarity to the human proteome, physicochemical properties, B-cell epitopes, MHC binding sites, tertiary structure predictions, molecular docking, and immune response simulations. The ompA gene was cloned into the pET-28a (+) vector, expressed, purified and confirmed using Western blotting analysis. IgG levels in the serum of the immunized mice were measured using ELISA with dilutions ranging from 1:100 to 1:6400, targeting recombinant outer membrane protein A (rOmpA) and K. pneumoniae ATCC 13883. The sensitivity and specificity of the ELISA method were also assessed.
Results: The bioinformatics analysis identified rOmpA as a promising vaccine candidate. The immunized group demonstrated significant production of specific total IgG antibodies against rOmpA and K. pneumoniae ATCC1 13883, as compared to the control group (p < 0.0001). The titers of antibodies produced in response to bacterial exposure did not show any significant difference when compared to the anti-rOmpA antibodies (p > 0.05). The ELISA test sensitivity was 1:3200, and the antibodies in the serum could accurately recognize K. pneumoniae cells.
Conclusion: This study is a significant advancement in the development of a potential vaccine against K. pneumoniae that relies on OmpA. Nevertheless, additional experimental analyses are required.
Type of Study: Full Length/Original Article |
Subject:
Molecular Microbiology
References
1. Shahkolahi S, Shakibnia P, Shahbazi S, Sabzi S, Badmasti F, Asadi Karam MR, et al. Detection of ESBL and AmpC producing Klebsiella pneumoniae ST11 and ST147 from urinary tract infections in Iran. Acta Microbiol Immunol Hung. 2022; 69(4):303-13. [DOI:10.1556/030.2022.01808]
2. Lucena ACR, Ferrarini MG, de Oliveira WK, Marcon BH, Morello LG, Alves LR, et al. Modulation of Klebsiella pneumoniae outer membrane vesicle protein cargo under antibiotic treatment. Biomedicines. 2023; 11(6):1515. [DOI:10.3390/biomedicines11061515]
3. Shivaee A, Shahbazi S, Soltani A, Ahadi E. Evaluation of the prevalence of broad-spectrum beta-lactamases (ESBLs) and carbapenemase genes in Klebsiella pneumoniae strains isolated from burn wounds in patients referred to shahid motahari hospital in Tehran. Med Sci J Islamic Azad Univ. 2019; 29(3): Autumn 2019. [DOI:10.29252/iau.29.3.232]
4. Shahbazi S, Sabzi S, Goodarzi NN, Fereshteh S, Bolourchi N, Mirzaie B, et al. Identification of novel putative immunogenic targets and construction of a multi-epitope vaccine against multidrug-resistant Corynebacterium jeikeium using reverse vaccinology approach. Microb Pathog. 2022; 164:105425. [DOI:10.1016/j.micpath.2022.105425]
5. Choi M, Tennant SM, Simon R, Cross AS. Progress towards the development of Klebsiella vaccines. Expert Rev Vaccines. 2019; 18(7):681-91. [DOI:10.1080/14760584.2019.1635460]
6. Dar HA, Zaheer T, Shehroz M, Ullah N, Naz K, Muhammad SA, et al. Immunoinformatics-aided design and evaluation of a potential multi-epitope vaccine against Klebsiella pneumoniae. Vaccines (Basel). 2019; 7(3):88. [DOI:10.3390/vaccines7030088]
7. Jeannin P, Bottazzi B, Sironi M, Doni A, Rusnati M, Presta M, et al. Complexity and complementarity of outer membrane protein A recognition by cellular and humoral innate immunity receptors. Immunity. 2005; 22(5):551-60. [DOI:10.1016/j.immuni.2005.03.008]
8. Shahbazi S, Habibi M, Badmasti F, Sabzi S, Farokhi M, Karam MRA. Design and fabrication of a vaccine candidate based on rOmpA from Klebsiella pneumoniae encapsulated in silk fibroin-sodium alginate nanoparticles against pneumonia infection. Int Immunopharmacol. 2023; 125(Pt B):111171. [DOI:10.1016/j.intimp.2023.111171]
9. Assoni L, Girardello R, Converso TR, Darrieux M. Current stage in the development of Klebsiella pneumoniae vaccines. Infect Dis Ther. 2021; 10(4):2157-75. [DOI:10.1007/s40121-021-00533-4]
10. Kurupati P, Ramachandran N, Poh CL. Protective efficacy of DNA vaccines encoding outer membrane protein A and OmpK36 of Klebsiella pneumoniae in mice. Clin Vaccine Immunol. 2011; 18(1):82-8. [DOI:10.1128/CVI.00275-10]
11. Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics. 2010; 26(13):1608-15. [DOI:10.1093/bioinformatics/btq249]
12. Emanuelsson O, Brunak S, Von Heijne G, Nielsen H. Locating proteins in the cell using targetp, signalp and related tools. Nat Protoc. 2007;2(4):953-71. [DOI:10.1038/nprot.2007.131]
13. Doytchinova IA, Flower DR. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC bioinform. 2007; 8(1):1-7. [DOI:10.1186/1471-2105-8-4]
14. Sharma N, Patiyal S, Dhall A, Pande A, Arora C, Raghava GP. AlgPred 2.0: an improved method for predicting allergenic proteins and mapping of IgE epitopes. Brief Bioinform. 2021; 22(4):bbaa294. [DOI:10.1093/bib/bbaa294]
15. Bhagwat M, Aravind L. PSI-BLAST tutorial. Methods Mol Biol. 2008; 395:177-86. [DOI:10.1007/978-1-59745-514-5_10]
16. Duvaud S, Gabella C, Lisacek F, Stockinger H, Ioannidis V, Durinx C. Expasy, the swiss bioinformatics resource portal, as designed by its users. Nucleic Acids Res. 2021; 49(W1):W216-W27. [DOI:10.1093/nar/gkab225]
17. He Y, Xiang Z, Mobley HL. Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development. J biotechnol biomed. 2010; 2010:297505. [DOI:10.1155/2010/297505]
18. Sachdeva G, Kumar K, Jain P, Ramachandran S, Ramachandran S. SPAAN: A software for prediction of adhesins and adhesin-like proteins using neural networks. Bioinformatics. 2005; 21(4):483-91. [DOI:10.1093/bioinformatics/bti028]
19. Jespersen MC, Peters B, Nielsen M, Marcatili P. BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res. 2017; 45(W1):W24-9. [DOI:10.1093/nar/gkx346]
20. Astle WJ, Elding H, Jiang T, Allen D, Ruklisa D, Mann AL, et al. The allelic landscape of human blood cell trait variation and links to common complex disease. Cell. 2016; 167(5):1415-29. [DOI:10.1016/j.cell.2016.10.042]
21. Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 2010; 5(4):725-38. [DOI:10.1038/nprot.2010.5]
22. Badmasti F, Siadat S, Bouzari S, Nasiri O, Nemati H, Shahcheraghi F. Molecular analysis of AbOmpA type-1 as immunogenic target for therapeutic interventions against MDR Acinetobacter baumannii infection. Vac Res. 2015; 2(1):9-18. [DOI:10.18869/acadpub.vacres.2.3.9]
23. Ponomarenko J, Bui H-H, Li W, Fusseder N, Bourne PE, Sette A, et al. ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinform. 2008; 9:1-8. [DOI:10.1186/1471-2105-9-514]
24. Bui H-H, Sidney J, Li W, Fusseder N, Sette A. Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC bioinform. 2007; 8:1-6. [DOI:10.1186/1471-2105-8-361]
25. De Vries SJ, Van Dijk M, Bonvin AM. The HADDOCK web server for data-driven biomolecular docking. Nat Protoc. 2010; 5(5):883-97. [DOI:10.1038/nprot.2010.32]
26. Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng Des Sel. 1995; 8(2):127-34. [DOI:10.1093/protein/8.2.127]
27. Rapin N, Lund O, Bernaschi M, Castiglione F. 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. [DOI:10.1371/journal.pone.0009862]
28. He Y, Xiang Z. Databases and in silico tools for vaccine design. Methods Mol Biol. 2013; 993:115-27. [DOI:10.1007/978-1-62703-342-8_8]
29. Sabzi S, Badmasti F, Noori Goodarzi N, Habibi M, Shahbazi S, Asadi Karam MR, et al. In silico evaluation, cloning, and expression of omp22 as a promising vaccine candidate against Acinetobacter baumannii. Vac Res. 2023; 10(1):11-7. [DOI:10.61186/vacres.10.1.11]
30. Sabzi S, Shahbazi S, Noori Goodarzi N, Haririzadeh Jouriani F, Habibi M, Bolourchi N, et al. genome-wide subtraction analysis and reverse vaccinology to detect novel drug targets and potential vaccine candidates against Ehrlichia chaffeensis. Appl Biochem Biotechnol. 2023; 195(1):107-24. [DOI:10.1007/s12010-022-04116-y]
31. Kar T, Narsaria U, Basak S, Deb D, Castiglione F, Mueller DM, et al. A candidate multi-epitope vaccine against SARS-CoV-2. Sci Rep. 2020; 10(1):1-24. [DOI:10.1038/s41598-020-67749-1]
32. Casadevall A, Pirofski La. Host‐pathogen interactions: the attributes of virulence. J Infect Dis. 2001; 184(3):337-44. [DOI:10.1086/322044]
33. Mehdinejadiani K, Bandehpour M, Hashemi A, Ranjbar MM, Taheri S, Jalali SA, et al. In silico design and evaluation of Acinetobacter baumannii outer membrane protein A (OmpA) antigenic peptides as vaccine candidate in immunized mice. Iran J Allergy Asthma Immunol. 2019; 18(6):655-63. [DOI:10.18502/ijaai.v18i6.2178]
34. Smith SG, Mahon V, Lambert MA, Fagan RP. A molecular Swiss army knife: OmpA structure, function and expression. FEMS Microbiol Lett. 2007; 273(1):1-11. [DOI:10.1111/j.1574-6968.2007.00778.x]
35. Farhadi T, Nezafat N, Ghasemi Y, Karimi Z, Hemmati S, Erfani N. Designing of complex multi-epitope peptide vaccine based on omps of Klebsiella pneumoniae: an in silico approach. Int J Pept Res Ther. 2015; 21:325-41. [DOI:10.1007/s10989-015-9461-0]
36. Goodarzi NN, Fereshteh S, Sabzi S, Shahbazi S, Badmasti F. Construction of a chimeric FliC including epitopes of OmpA and OmpK36 as a multi-epitope vaccine against Klebsiella pneumonia. Health Biotechnol Biopharma. 2021; 5:44-60.
37. Hu G, Chen X, Chu W, Ma Z, Miao Y, Luo X, et al. Immunogenic characteristics of the outer membrane phosphoporin as a vaccine candidate against Klebsiella pneumoniae. Vet Res. 2022; 53(1):1-13. [DOI:10.1186/s13567-022-01023-2]
| Rights and permissions | |
 |
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
IBJ is a member of Committee on Publication Ethics (COPE)
and follows its guidelines |
The articles of this journal are licensed under
a Creative Commons Attribution-NonDerivatives 4.0 International License. .png) |
 IBJ is owned and published by Pasteur Institute of Iran |