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Research Article

Design and in silico analysis of mRNA vaccine construct against Salmonella

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Pages 7248-7264 | Received 31 May 2022, Accepted 24 Aug 2022, Published online: 12 Sep 2022

References

  • Alberer, M., Gnad-Vogt, U., Hong, H. S., Mehr, K. T., Backert, L., Finak, G., Gottardo, R., Bica, M. A., Garofano, A., Koch, S. D., Fotin-Mleczek, M., Hoerr, I., Clemens, R., & von Sonnenburg, F. (2017). Safety and immunogenicity of a mRNA rabies vaccine in healthy adults: An open-label, non-randomised, prospective, first-in-human phase 1 clinical trial. Lancet (London, England), 390(10101), 1511–1520. https://doi.org/10.1016/S0140-6736(17)31665-3
  • Andries, O., Mc Cafferty, S., De Smedt, S. C., Weiss, R., Sanders, N. N., & Kitada, T. (2015). N1-methylpseudouridine-incorporated mRNA outperforms pseudouridine-incorporated mRNA by providing enhanced protein expression and reduced immunogenicity in mammalian cell lines and mice. Journal of Controlled Release, 217, 337–344. https://doi.org/10.1016/j.jconrel.2015.08.051
  • Argos, P. (1990). An investigation of oligopeptides linking domains in protein tertiary structures and possible candidates for general gene fusion. Journal of Molecular Biology, 211(4), 943–958. https://doi.org/10.1016/0022-2836(90)90085-Z
  • Arockiasamy, A., & Krishnaswamy, S. (2000). Homology model of surface antigen OmpC from Salmonella typhi and its functional implications. Journal of Biomolecular Structure & Dynamics, 18(2), 261–271. https://doi.org/10.1080/07391102.2000.10506664
  • Baden, L. R., El Sahly, H. M., Essink, B., Kotloff, K., Frey, S., Novak, R., Diemert, D., Spector, S. A., Rouphael, N., & Creech, C. (2020). Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine.
  • Bahl, K., Senn, J. J., Yuzhakov, O., Bulychev, A., Brito, L. A., Hassett, K. J., Laska, M. E., Smith, M., Almarsson, Ö., Thompson, J., Ribeiro, A. M., Watson, M., Zaks, T., & Ciaramella, G. (2017). Preclinical and clinical demonstration of immunogenicity by mRNA vaccines against H10N8 and H7N9 influenza viruses. Molecular Therapy, 25(6), 1316–1327. https://doi.org/10.1016/j.ymthe.2017.03.035
  • Bauer, J. A., & Bauerová-Hlinková, V. (2020). Normal mode analysis: A tool for better understanding protein flexibility and dynamics with application to homology models. In. Homology molecular modeling-perspectives and applications. IntechOpen.
  • Benbernou, N., & Nauciel, C. J. I. (1994). Influence of mouse genotype and bacterial virulence in the generation of interferon-gamma-producing cells during the early phase of Salmonella typhimurium infection. Influence of Mouse Genotype and Bacterial Virulence in the Generation of Interferon-Gamma-Producing Cells during the Early Phase of Salmonella typhimurium Infection, 83(2), 245–249.
  • Bhati, M., Lee, M., Nancarrow, A. L., Bach, I., Guss, J. M., Matthews, J., & Communications, C. (2008). Crystallization of an Lhx3–Isl1 complex. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications, 64(Pt 4), 297–299. https://doi.org/10.1107/S174430910800691X
  • Briard, B., Place, D. E., & Kanneganti, T.-D. (2020). DNA sensing in the innate immune response. Physiology (Bethesda, Md.), 35(2), 112–124. https://doi.org/10.1152/physiol.00022.2019
  • Cervantes-Barragán, L., Cruz, G. C., Pastelin‐Palacios, R., Lang, K. S., Isibasi, A., Ludewig, B., & López‐Macías, C. (2009). TLR2 and TLR4 signaling shapes specific antibody responses to Salmonella typhi antigens. European Journal of Immunology, 39(1), 126–135. https://doi.org/10.1002/eji.200838185
  • Das, S., Chowdhury, R., Pal, A., Okamoto, K., & Das, S. J. I. (2019). Salmonella Typhi outer membrane protein STIV is a potential candidate for vaccine development against typhoid and paratyphoid fever. Immunobiology, 224(3), 371–382. https://doi.org/10.1016/j.imbio.2019.02.011
  • Deane, J. E., Maher, M. J., Langley, D. B., Graham, S. C., Visvader, J. E., Guss, J. M., & Matthews, J. (2003). Crystallization of FLINC4, an intramolecular LMO4–ldb1 complex. Acta Crystallographica. Section D, Biological Crystallography, 59(Pt 8), 1484–1486. https://doi.org/10.1107/s0907444903011843
  • Deane, J. E., Ryan, D. P., Sunde, M., Maher, M. J., Guss, J. M., Visvader, J. E., & Matthews, J. (2004). Tandem LIM domains provide synergistic binding in the LMO4: Ldb1 complex. The EMBO Journal, 23(18), 3589–3598. https://doi.org/10.1038/sj.emboj.7600376
  • Delcour, A. H. (2009). Outer membrane permeability and antibiotic resistance. Biochimica et Biophysica Acta, 1794(5), 808–816. https://doi.org/10.1016/j.bbapap.2008.11.005
  • Dey, J., Mahapatra, S. R., Lata, S., Patro, S., Misra, N., & Suar, M. (2022a). Exploring Klebsiella pneumoniae capsule polysaccharide proteins to design multiepitope subunit vaccine to fight against pneumonia. Expert Review of Vaccines, 21(4), 569–587. https://doi.org/10.1080/14760584.2022.2021882
  • Dey, J., Mahapatra, S. R., Patnaik, S., Lata, S., Kushwaha, G. S., Panda, R. K., Misra, N., & Suar, M. (2022b). Molecular characterization and designing of a novel multiepitope vaccine construct against Pseudomonas aeruginosa. International Journal of Peptide Research and Therapeutics, 28, 1–19.
  • Feasey, N. A., Dougan, G., Kingsley, R. A., Heyderman, R. S., & Gordon, M. (2012). Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa. Lancet (London, England), 379(9835), 2489–2499. https://doi.org/10.1016/S0140-6736(11)61752-2
  • Galdiero, M., Galdiero, M., Finamore, E., Rossano, F., Gambuzza, M., Catania, M. R., Teti, G., Midiri, A., & Mancuso, G. (2004). Haemophilus influenzae porin induces Toll-like receptor 2-mediated cytokine production in human monocytes and mouse macrophages. Infection and Immunity, 72(2), 1204–1209. https://doi.org/10.1128/IAI.72.2.1204-1209.2004
  • Galdiero, F., Tufano, M. A., Sommese, L., Folgore, A., & Tedesco, F. (1984). Activation of complement system by porins extracted from Salmonella typhimurium. Infection and Immunity, 46(2), 559–563. https://doi.org/10.1128/iai.46.2.559-563.1984
  • González, C. R., Isibasi, A., Ortiz-Navarrete, V., Paniagua, J., García, J. A., Blanco, F., & Kumate, J. J. M. (1993). Lymphocytic proliferative response to outer-membrane proteins isolated from Salmonella. Microbiology and Immunology, 37(10), 793–799. immunology https://doi.org/10.1111/j.1348-0421.1993.tb01707.x
  • Honda, S., & Selker, E. U. J. G. (2009). Tools for fungal proteomics: multifunctional neurospora vectors for gene replacement, protein expression and protein purification. Genetics, 182(1), 11–23. https://doi.org/10.1534/genetics.108.098707
  • Hou, X., Zaks, T., Langer, R., & Dong, Y. (2021). Lipid nanoparticles for mRNA delivery. Nature Reviews. Materials, 6(12), 1078–1094. https://doi.org/10.1038/s41578-021-00358-0
  • Howlader, D. R., Koley, H., Maiti, S., Bhaumik, U., Mukherjee, P., & Dutta, S. J. V. (2017). A brief review on the immunological scenario and recent developmental status of vaccines against enteric fever. Vaccine, 35(47), 6359–6366. https://doi.org/10.1016/j.vaccine.2017.09.066
  • Hussain, M., Amanullah, A., Aslam, A., Raza, F., Arzoo, S., Qureshi, I. W., Waheed, H., Jabeen, N., Shabbir, S., Sayeed, M. A., & Quraishy, S. (2022). Design and immunoinformatic assessment of candidate multivariant mRNA vaccine construct against immune escape variants of SARS-CoV-2. Polymers, 14(16), 3263. https://doi.org/10.3390/polym14163263
  • Hynes, T. R., Kautz, R. A., Goodman, M. A., Gill, J. F., & Fox, R. O. J. N. (1989). Transfer of a β-turn structure to a new protein context. Nature, 339(6219), 73–76. https://doi.org/10.1038/339073a0
  • Isibasi, A., Ortiz, V., Vargas, M., Paniagua, J., Gonzalez, C., Moreno, J., & Kumate, J. J. I. (1988). Protection against Salmonella typhi infection in mice after immunization with outer membrane proteins isolated from Salmonella typhi 9,12,d, Vi. Infection and Immunity, 56(11), 2953–2959.
  • Jackson, N. A., Kester, K. E., Casimiro, D., Gurunathan, S., & DeRosa, F. (2020). The promise of mRNA vaccines: A biotech and industrial perspective. npj Vaccines, 5, 1–6.
  • Jin, C., Gibani, M. M., Moore, M., Juel, H. B., Jones, E., Meiring, J., Harris, V., Gardner, J., Nebykova, A., Kerridge, S. A., Hill, J., Thomaides-Brears, H., Blohmke, C. J., Yu, L.-M., Angus, B., & Pollard, A. J. (2017). Efficacy and immunogenicity of a Vi-tetanus toxoid conjugate vaccine in the prevention of typhoid fever using a controlled human infection model of Salmonella Typhi: A randomised controlled, phase 2b trial. Lancet (London, England), 390(10111), 2472–2480. https://doi.org/10.1016/S0140-6736(17)32149-9
  • Karikó, K., Muramatsu, H., Ludwig, J., & Weissman, D. (2011). Generating the optimal mRNA for therapy: HPLC purification eliminates immune activation and improves translation of nucleoside-modified, protein-encoding mRNA. Nucleic Acids Research, 39(21), e142. https://doi.org/10.1093/nar/gkr695
  • Kringelum, J. V., Lundegaard, C., Lund, O., & Nielsen, M. (2012). Reliable B cell epitope predictions: impacts of method development and improved benchmarking. PLoS Computational Biology, 8(12), e1002829. https://doi.org/10.1371/journal.pcbi.1002829
  • Levine, M. M., Ferreccio, C., Black, R. E., Lagos, R., Martin, O. S., & Blackwelder, W. (2007). Ty21a live oral typhoid vaccine and prevention of paratyphoid fever caused by Salmonella enterica Serovar Paratyphi B. Clinical Infectious Diseases, 45(Supplement_1), S24–S28. https://doi.org/10.1086/518141
  • Li, S., Liu, L., Zhuang, X., Yu, Y., Liu, X., Cui, X., Ji, L., Pan, Z., Cao, X., Mo, B., Zhang, F., Raikhel, N., Jiang, L., & Chen, X. (2013). MicroRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis. Cell, 153(3), 562–574. https://doi.org/10.1016/j.cell.2013.04.005
  • Lopéz-Blanco, J. R., Garzón, J. I., & Chacón, P. J. B. (2011). iMod: multipurpose normal mode analysis in internal coordinates. Bioinformatics (Oxford, England), 27(20), 2843–2850. https://doi.org/10.1093/bioinformatics/btr497
  • Mahapatra, S. R., Dey, J., Kushwaha, G. S., Puhan, P., Mohakud, N. K., Panda, S. K., Lata, S., Misra, N., & Suar, M. (2021). Immunoinformatic approach employing modeling and simulation to design a novel vaccine construct targeting MDR efflux pumps to confer wide protection against typhoidal Salmonella serovars. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2021.1964600
  • Malone, R. W., Felgner, P. L., & Verma, I. (1989). Cationic liposome-mediated RNA transfection. Proceedings of the National Academy of Sciences of the United States of America, 86(16), 6077–6081. https://doi.org/10.1073/pnas.86.16.6077
  • MedNet. WHOJDW. (2020). Messenger RNA encoding the full-length SARS-CoV-2 spike glycoprotein. Retrieved 2021, February 25. Available online: https://web.archive.org/web/20210105162941/https://mednet-communities.net/inn/db/media/docs/11889.doc
  • Meyer, M., Huang, E., Yuzhakov, O., Ramanathan, P., Ciaramella, G., & Bukreyev, A. (2018). Modified mRNA-based vaccines elicit robust immune responses and protect guinea pigs from Ebola virus disease. The Journal of Infectious Diseases, 217(3), 451–455. https://doi.org/10.1093/infdis/jix592
  • Milligan, R., Paul, M., Richardson, M., & Neuberger, A. (2018). Vaccines for preventing typhoid fever. The Cochrane Database of Systematic Reviews, 5, CD001261. https://doi.org/10.1002/14651858.CD001261.pub4
  • Mogasale, V., Maskery, B., Ochiai, R. L., Lee, J. S., Mogasale, V. V., Ramani, E., Kim, Y. E., Park, J. K., & Wierzba, T. (2014). Burden of typhoid fever in low-income and middle-income countries: A systematic, literature-based update with risk-factor adjustment. The Lancet. Global Health, 2(10), e570–e80. https://doi.org/10.1016/S2214-109X(14)70301-8
  • Nagi, A. D., & Regan, L. J. F. (1997). An inverse correlation between loop length and stability in a four-helix-bundle protein. Folding and Design, 2(1), 67–75. https://doi.org/10.1016/S1359-0278(97)00007-2
  • Pakkanen, S. H., Kantele, J. M., Savolainen, L. E., Rombo, L., & Kantele, A. J. V. (2015). Specific and cross-reactive immune response to oral Salmonella Typhi Ty21a and parenteral Vi capsular polysaccharide typhoid vaccines administered concomitantly. Vaccine, 33(3), 451–458. https://doi.org/10.1016/j.vaccine.2014.11.030
  • Pardi, N., Hogan, M. J., Porter, F. W., & Weissman, D. (2018). mRNA vaccines—A new era in vaccinology. Nature Reviews. Drug Discovery, 17(4), 261–279. https://doi.org/10.1038/nrd.2017.243
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Meng, E. C., Couch, G. S., Croll, T. I., Morris, J. H., & Ferrin, T. (2021). UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Science, 30(1), 70–82. https://doi.org/10.1002/pro.3943
  • Polack, F. P., Thomas, S. J., Kitchin, N., Absalon, J., Gurtman, A., Lockhart, S., Perez, J. L., Marc, G. P., Moreira, E. D., & Zerbini, C. (2020). Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine. The New England Journal of Medicine, 383, 2603–2615. https://doi.org/10.1056/NEJMoa2034577
  • Richner, J. M., Himansu, S., Dowd, K. A., Butler, S. L., Salazar, V., Fox, J. M., Julander, J. G., Tang, W. W., Shresta, S., Pierson, T. C., Ciaramella, G., & Diamond, M. S. (2017). Modified mRNA vaccines protect against Zika virus infection. Cell, 168(6), 1114–1125. e10. https://doi.org/10.1016/j.cell.2017.02.017
  • Rollauer, S. E., Sooreshjani, M. A., Noinaj, N., & Buchanan, S. (2015). Outer membrane protein biogenesis in Gram-negative bacteria. Philosophical Transactions of the Royal Society B: Biological Sciences, 370, 20150023.
  • Routy, J.-P., Boulassel, M.-R., Yassine-Diab, B., Nicolette, C., Healey, D., Jain, R., Landry, C., Yegorov, O., Tcherepanova, I., Monesmith, T., Finke, L., & Sékaly, R.-P. (2010). Immunologic activity and safety of autologous HIV RNA-electroporated dendritic cells in HIV-1 infected patients receiving antiretroviral therapy. Clinical Immunology (Orlando, Fla.), 134(2), 140–147. https://doi.org/10.1016/j.clim.2009.09.009
  • Sabourin, M., Tuzon, C. T., Fisher, T. S., & Zakian, V. A. J. Y. (2007). A flexible protein linker improves the function of epitope‐tagged proteins in Saccharomyces cerevisiae. Yeast (Chichester, England), 24(1), 39–45. https://doi.org/10.1002/yea.1431
  • Schlake, T., Thess, A., Fotin-Mleczek, M., & Kallen, K.-J. (2012). Developing mRNA-vaccine technologies. RNA Biology, 9(11), 1319–1330. https://doi.org/10.4161/rna.22269
  • Schoenmaker, L., Witzigmann, D., Kulkarni, J. A., Verbeke, R., Kersten, G., Jiskoot, W., & Crommelin, D. J. A. (2021). mRNA-lipid nanoparticle COVID-19 vaccines: Structure and stability. International Journal of Pharmaceutics, 601, 120586. https://doi.org/10.1016/j.ijpharm.2021.120586
  • Seder, R. A., Darrah, P. A., & Roederer, M. (2008). T-cell quality in memory and protection: Implications for vaccine design. Nature Reviews. Immunology, 8(4), 247–258. https://doi.org/10.1038/nri2274
  • Singh, S. P., Upshaw, Y., Abdullah, T., Singh, S. R., & Klebba, P. E. (1992). Structural relatedness of enteric bacterial porins assessed with monoclonal antibodies to Salmonella typhimurium OmpD and OmpC. Journal of Bacteriology, 174(6), 1965–1973. https://doi.org/10.1128/jb.174.6.1965-1973.1992
  • Tennant, S. M., MacLennan, C. A., Simon, R., Martin, L. B., & Khan, M. I. J. V. (2016). Nontyphoidal salmonella disease: Current status of vaccine research and development. Vaccine, 34(26), 2907–2910. https://doi.org/10.1016/j.vaccine.2016.03.072
  • Tjalsma, H., Bolhuis, A., Jongbloed, J. D., Bron, S., & van Dijl, J. M. (2000). Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome. Microbiology and Molecular Biology Reviews: MMBR, 64(3), 515–547. https://doi.org/10.1128/MMBR.64.3.515-547.2000
  • Trotta, E. (2014). On the normalization of the minimum free energy of RNAs by sequence length. PloS One, 9(11), e113380. https://doi.org/10.1371/journal.pone.0113380
  • Verma, S., Sugadev, R., Kumar, A., Chandna, S., Ganju, L., & Bansal, A. J. V. (2018). Multi-epitope DnaK peptide vaccine against S. Typhi: an in silico approach. Vaccine, 36(28), 4014–4022. https://doi.org/10.1016/j.vaccine.2018.05.106
  • Wadhwa, A., Aljabbari, A., Lokras, A., Foged, C., & Thakur, A. J. P. (2020). Opportunities and challenges in the delivery of mRNA-based vaccines. Pharmaceutics, 12(2), 102. https://doi.org/10.3390/pharmaceutics12020102
  • Wahid, R., Fresnay, S., Levine, M. M., & Sztein, M. (2016). Cross-reactive multifunctional CD4+ T cell responses against Salmonella enterica serovars Typhi, Paratyphi A and Paratyphi B in humans following immunization with live oral typhoid vaccine Ty21a. Clinical Immunology (Orlando, Fla.), 173, 87–95. https://doi.org/10.1016/j.clim.2016.09.006
  • Wootton, J., & Drummond, M. J. P. E. (1989). The Q-linker: a class of interdomain sequences found in bacterial multidomain regulatory proteins. Protein Engineering, 2(7), 535–543. https://doi.org/10.1093/protein/2.7.535
  • Zeng, C., Hou, X., Yan, J., Zhang, C., Li, W., Zhao, W., Du, S., & Dong, Y. J. A. M. (2020). Leveraging mRNA sequences and nanoparticles to deliver SARS‐CoV‐2 antigens in vivo. Advanced Materials, 32(40), 2004452. https://doi.org/10.1002/adma.202004452
  • Zhang, J., Tan, D., DeRose, E. F., Perera, L., Dominski, Z., Marzluff, W. F., Tong, L., & Hall, T. M. T. (2014). Molecular mechanisms for the regulation of histone mRNA stem-loop–binding protein by phosphorylation. Proceedings of the National Academy of Sciences of the United States of America, 111(29), E2937–46E2946. https://doi.org/10.1073/pnas.1406381111

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