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Research Article

A novel immunoinformatics approach for developing a poly-epitope vaccine targeting foot and mouth disease virus, exploiting structural VP proteins

ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon
Received 20 Oct 2023, Accepted 05 Mar 2024, Published online: 15 Mar 2024

References

  • Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
  • Alizadeh, M., Amini-Khoei, H., Tahmasebian, S., Ghatrehsamani, M., Ghatreh Samani, K., Edalatpanah, Y., Rostampur, S., Salehi, M., Ghasemi-Dehnoo, M., Azadegan-Dehkordi, F., Sanami, S., & Bagheri, N. (2022). Designing a novel multi‑epitope vaccine against Ebola virus using reverse vaccinology approach. Scientific Reports, 12(1), 7757. https://doi.org/10.1038/s41598-022-11851-z
  • Bachanek-Bankowska, K., Di Nardo, A., Wadsworth, J., King, D., & Knowles, N. (2019). A47 reconstructing the evolutionary history of pandemic foot-and-mouth disease viruses: The impact of recombination within the emerging O/ME-SA/Ind-2001 lineage. Virus Evolution, 5(Supplement_1), vez002.046. https://doi.org/10.1093/ve/vez002.046
  • Bayry, J., & Tough, D. F. (2005). Is RNA interference feasible for the control of foot-and-mouth disease outbreaks? Trends in Immunology, 26(5), 238–239. https://doi.org/10.1016/j.it.2005.03.003
  • Cao, Y., Lu, Z., Li, Y., Sun, P., Li, D., Li, P., Bai, X., Fu, Y., Bao, H., Zhou, C., Xie, B., Chen, Y., & Liu, Z. (2013). Poly (I: C) combined with multi-epitope protein vaccine completely protects against virulent foot-and-mouth disease virus challenge in pigs. Antiviral Research, 97(2), 145–153. https://doi.org/10.1016/j.antiviral.2012.11.009
  • Chang, K. Y., & Yang, J. R. (2013). Analysis and prediction of highly effective antiviral peptides based on random forests. PLoS One, 8(8), e70166. https://doi.org/10.1371/journal.pone.0070166
  • Chang, Y., Dou, Y., Bao, H., Luo, X., Liu, X., Mu, K., Liu, Z., Liu, X., & Cai, X. (2014). Multiple microRNAs targeted to internal ribosome entry site against foot-and-mouth disease virus infection in vitro and in vivo. Virology Journal, 11(1), 1–12. https://doi.org/10.1186/1743-422X-11-1
  • Christoffer, C., Chen, S., Bharadwaj, V., Aderinwale, T., Kumar, V., Hormati, M., & Kihara, D. (2021). LZerD webserver for pairwise and multiple protein–protein docking. Nucleic Acids Research, 49(W1), W359–W365. https://doi.org/10.1093/nar/gkab336
  • Cianci, R., & Franza, L. (2022). Recent advances in vaccine technology and design. Vaccines, 10(4), 624. https://doi.org/10.3390/vaccines10040624
  • Cox, S. J., Aggarwal, N., Statham, R. J., & Barnett, P. V. (2003). Longevity of antibody and cytokine responses following vaccination with high potency emergency FMD vaccines. Vaccine, 21(13-14), 1336–1347. https://doi.org/10.1016/s0264-410x(02)00691-6
  • Dar, H. A., Zaheer, T., Shehroz, M., Ullah, N., Naz, K., Muhammad, S. A., Zhang, T., & Ali, A. (2019). Immunoinformatics-aided design and evaluation of a potential multi-epitope vaccine against Klebsiella pneumoniae. Vaccines, 7(3), 88. https://doi.org/10.3390/vaccines7030088
  • Denny, J. C. (2012). Chapter 13: Mining electronic health records in the genomics era. PLoS Computational Biology, 8(12), e1002823. https://doi.org/10.1371/journal.pcbi.1002823
  • Dimitrov, I., Bangov, I., Flower, D. R., & Doytchinova, I. (2014). AllerTOP v. 2—A server for in silico prediction of allergens. Journal of Molecular Modeling, 20(6), 2278. https://doi.org/10.1007/s00894-014-2278-5
  • Domingo, E., Pariente, N., Airaksinen, A., Gonzaĺez-Lopez, C., Sierra, S., Herrera, M., Grande-Pérez, A., Lowenstein, P. R., Manrubia, S. C., Lázaro, E., & Escarmís, C. (2005). Foot-and-mouth disease virus evolution: Exploring pathways towards virus extinction. Current Topics in Microbiology and Immunology, 288, 149–173. https://doi.org/10.1007/3-540-27109-0_7
  • Domingo, E., Ruiz-Jarabo, C. M., Sierra, S., Arias, A., Pariente, N., Baranowski, E., & Escarmis, C. (2001). Emergence and selection of RNA virus variants: Memory and extinction. Virus Research, 82(1-2), 39–44. https://doi.org/10.1016/s0168-1702(01)00385-9
  • Forouharmehr, A. (2021). Engineering an efficient poly-epitope vaccine against Toxoplasma gondii infection: A computational vaccinology study. Microbial Pathogenesis, 152, 104646. https://doi.org/10.1016/j.micpath.2020.104646
  • Forouharmehr, A., Nassiri, M., Ghovvati, S., & Javadmanesh, A. (2018). Evaluation of different signal peptides for secretory production of recombinant bovine pancreatic ribonuclease A in gram negative bacterial system: An in silico study. Current Proteomics, 15(1), 24–33. https://doi.org/10.2174/1570164614666170725144424
  • Forouharmehr, A., Nazifi, N., Mousavi, S. M., & Jaydari, A. (2022). Designing an efficient epitope-based vaccine conjugated with a molecular adjuvant against Bovine Babesiosis: A computational study. Process Biochemistry, 121, 170–177. https://doi.org/10.1016/j.procbio.2022.06.016
  • Foroutan, M., Ghaffarifar, F., Sharifi, Z., & Dalimi, A. (2020). Vaccination with a novel multi-epitope ROP8 DNA vaccine against acute Toxoplasma gondii infection induces strong B and T cell responses in mice. Comparative Immunology, Microbiology and Infectious Diseases, 69, 101413. https://doi.org/10.1016/j.cimid.2020.101413
  • Grubman, M. (1980). The 5′ end of foot-and-mouth disease virion RNA contains a protein covalently linked to the nucleotide pUp. Archives of Virology, 63(3-4), 311–315. https://doi.org/10.1007/BF01315038
  • Grubman, M. J., & De Los Santos, T. (2005). Rapid control of foot-and-mouth disease outbreaks: Is RNAi a possible solution? Trends in Immunology, 26(2), 65–68. https://doi.org/10.1016/j.it.2004.12.002
  • Guo, H.-C., Sun, S.-Q., Jin, Y., Yang, S.-L., Wei, Y.-Q., Sun, D.-H., Yin, S.-H., Ma, J.-W., Liu, Z.-X., Guo, J.-H., Luo, J.-X., Yin, H., Liu, X.-T., & Liu, D. X. (2013). Foot-and-mouth disease virus-like particles produced by a SUMO fusion protein system in Escherichia coli induce potent protective immune responses in guinea pigs, swine and cattle. Veterinary Research, 44(1), 48. https://doi.org/10.1186/1297-9716-44-48
  • Haydon, D., Samuel, A., & Knowles, N. (2001). The generation and persistence of genetic variation in foot-and-mouth disease virus. Preventive Veterinary Medicine, 51(1-2), 111–124. https://doi.org/10.1016/s0167-5877(01)00210-0
  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
  • Kalita, P., Padhi, A. K., Zhang, K. Y. J., & Tripathi, T. (2020). Design of a peptide-based subunit vaccine against novel coronavirus SARS-CoV-2. Microbial Pathogenesis, 145, 104236. https://doi.org/10.1016/j.micpath.2020.104236
  • Kaushik, V., G, S. K., Gupta, L. R., Kalra, U., Shaikh, A. R., Cavallo, L., & Chawla, M. (2022). Immunoinformatics aided design and in-vivo validation of a cross-reactive peptide based multi-epitope vaccine targeting multiple serotypes of dengue virus. Frontiers in Immunology, 13, 865180. https://doi.org/10.3389/fimmu.2022.865180
  • Khan, M. T., Islam, R., Jerin, T. J., Mahmud, A., Khatun, S., Kobir, A., Islam, M. N., Akter, A., & Mondal, S. I. (2021). Immunoinformatics and molecular dynamics approaches: Next generation vaccine design against West Nile virus. PLoS One, 16(6), e0253393. https://doi.org/10.1371/journal.pone.0253393
  • Klein, J. (2009). Understanding the molecular epidemiology of foot-and-mouth-disease virus. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 9(2), 153–161. https://doi.org/10.1016/j.meegid.2008.11.005
  • Knowles, N., & Samuel, A. (2003). Molecular epidemiology of foot-and-mouth disease virus. Virus Research, 91(1), 65–80. https://doi.org/10.1016/s0168-1702(02)00260-5
  • Kony, D., Damm, W., Stoll, S., & Van Gunsteren, W. F. (1997). OPLS all‐atom force field for carbohydrates. Journal of Computational Chemistry, 23(15), 1416–1429. https://doi.org/10.1002/jcc.10139
  • Kotecha, A., Seago, J., Scott, K., Burman, A., Loureiro, S., Ren, J., Porta, C., Ginn, H. M., Jackson, T., Perez-Martin, E., Siebert, C. A., Paul, G., Huiskonen, J. T., Jones, I. M., Esnouf, R. M., Fry, E. E., Maree, F. F., Charleston, B., & Stuart, D. I. (2015). Structure-based energetics of protein interfaces guides foot-and-mouth disease virus vaccine design. Nature Structural & Molecular Biology, 22(10), 788–794. https://doi.org/10.1038/nsmb.3096
  • Kotecha, A., Wang, Q., Dong, X., Ilca, S. L., Ondiviela, M., Zihe, R., Seago, J., Charleston, B., Fry, E. E., Abrescia, N. G. A., Springer, T. A., Huiskonen, J. T., & Stuart, D. I. (2017). Rules of engagement between αvβ6 integrin and foot-and-mouth disease virus. Nature Communications, 8(1), 15408. https://doi.org/10.1038/ncomms15408
  • Li, Q., Wubshet, A. K., Wang, Y., Heath, L., & Zhang, J. (2023). B and T cell epitopes of the incursionary foot-and-mouth disease virus serotype SAT2 for vaccine development. Viruses, 15(3), 797. https://doi.org/10.3390/v15030797
  • Li, S.-F., Gong, M.-J., Sun, Y.-F., Shao, J.-J., Zhang, Y.-G., & Chang, H.-Y. (2019). In vitro and in vivo antiviral activity of mizoribine against foot-and-mouth disease virus. Molecules, 24(9), 1723. https://doi.org/10.3390/molecules24091723
  • Mahapatra, M., & Parida, S. (2018). Foot and mouth disease vaccine strain selection: Current approaches and future perspectives. Expert Review of Vaccines, 17(7), 577–591. https://doi.org/10.1080/14760584.2018.1492378
  • Mathew, S., Fakhroo, A. D., Smatti, M., Al Thani, A. A., & Yassine, H. M. (2022). sImmunoinformatics prediction of potential immunodominant epitopes from human coronaviruses and association with autoimmunity. Immunogenetics, 74(2), 213–229. https://doi.org/10.1007/s00251-021-01250-5
  • Nielsen, M., Andreatta, M., Peters, B., & Buus, S. (2020). Immunoinformatics: Predicting peptide–MHC binding. Annual Review of Biomedical Data Science, 3(1), 191–215. https://doi.org/10.1146/annurev-biodatasci-021920-100259
  • Nishiya, T., Kajita, E., Miwa, S., & Defranco, A. L. (2005). TLR3 and TLR7 are targeted to the same intracellular compartments by distinct regulatory elements. The Journal of Biological Chemistry, 280(44), 37107–37117. https://doi.org/10.1074/jbc.M504951200
  • Nosrati, M., Hajizade, A., Nazarian, S., Amani, J., Namvar Vansofla, A., & Tarverdizadeh, Y. (2019). Designing a multi-epitope vaccine for cross-protection against Shigella spp: An immunoinformatics and structural vaccinology study. Molecular Immunology, 116, 106–116. https://doi.org/10.1016/j.molimm.2019.09.018
  • Omoniyi, A. A., Adebisi, S. S., Musa, S. A., Nzalak, J. O., Bauchi, Z. M., Bako, K. W., Olatomide, O. D., Zachariah, R., & Nyengaard, J. R. (2022). In silico design and analyses of a multi-epitope vaccine against Crimean-Congo hemorrhagic fever virus through reverse vaccinology and immunoinformatics approaches. Scientific Reports, 12(1), 8736. https://doi.org/10.1038/s41598-022-12651-1
  • Pan, Q., Wang, H., Ouyang, W., Wang, X., Bi, Z., Xia, X., Wang, Y., & He, K. (2016). Immunogenicity of adenovirus-derived porcine parvovirus-like particles displaying B and T cell epitopes of foot-and-mouth disease. Vaccine, 34(4), 578–585. https://doi.org/10.1016/j.vaccine.2015.11.003
  • Parida, S. (2009). Vaccination against foot-and-mouth disease virus: Strategies and effectiveness. Expert Review of Vaccines, 8(3), 347–365. https://doi.org/10.1586/14760584.8.3.347
  • Parvizpour, S., Pourseif, M. M., Razmara, J., Rafi, M. A., & Omidi, Y. (2020). Epitope-based vaccine design: A comprehensive overview of bioinformatics approaches. Drug Discovery Today, 25(6), 1034–1042. https://doi.org/10.1016/j.drudis.2020.03.006
  • Peng, J., Yi, J., Yang, W., Ren, J., Wen, Y., Zheng, H., & Li, D. (2020). Advances in foot-and-mouth disease virus proteins regulating host innate immunity. Frontiers in Microbiology, 11, 2046. https://doi.org/10.3389/fmicb.2020.02046
  • Ponomarenko, J., Bui, H.-H., Li, W., Fusseder, N., Bourne, P. E., Sette, A., & Peters, B. (2008). ElliPro: A new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics, 9(1), 514. (https://doi.org/10.1186/1471-2105-9-514
  • Porta, C., Kotecha, A., Burman, A., Jackson, T., Ren, J., Loureiro, S., Jones, I. M., Fry, E. E., Stuart, D. I., & Charleston, B. (2013). Rational engineering of recombinant picornavirus capsids to produce safe, protective vaccine antigen. PLoS Pathogens, 9(3), e1003255. https://doi.org/10.1371/journal.ppat.1003255
  • Rana, A., & Akhter, Y. (2016). A multi-subunit based, thermodynamically stable model vaccine using combined immunoinformatics and protein structure based approach. Immunobiology, 221(4), 544–557. https://doi.org/10.1016/j.imbio.2015.12.004
  • Rodriguez, L. L., & Gay, C. G. (2011). Development of vaccines toward the global control and eradication of foot-and-mouth disease. Expert Review of Vaccines, 10(3), 377–387. https://doi.org/10.1586/erv.11.4
  • Rodriguez, L. L., & Grubman, M. J. (2009). Foot and mouth disease virus vaccines. Vaccine, 27 (Suppl 4), D90–D94. https://doi.org/10.1016/j.vaccine.2009.08.039
  • Ruiz, V., Mozgovoj, M. V., Dus Santos, M. J., & Wigdorovitz, A. (2015). Plant‐produced viral bovine vaccines: What happened during the last 10 years? Plant Biotechnology Journal, 13(8), 1071–1077. https://doi.org/10.1111/pbi.12440
  • Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
  • Sahu, T. K., Meher, P. K., Choudhury, N. K., & Rao, A. R. (2022). A comparative analysis of amino acid encoding schemes for the prediction of flexible length linear B-cell epitopes. Briefings in Bioinformatics, 23(5), 1–14. https://doi.org/10.1093/bib/bbac356
  • Samad, A., Meghla, N. S., Nain, Z., Karpiński, T. M., & Rahman, M. S. (2022). Immune epitopes identification and designing of a multi-epitope vaccine against bovine leukemia virus: A molecular dynamics and immune simulation approaches. Cancer Immunology, Immunotherapy, 71(10), 2535–2548. https://doi.org/10.1007/s00262-022-03181-w
  • Sanches, R. C. O., Tiwari, S., Ferreira, L. C. G., Oliveira, F. M., Lopes, M. D., Passos, M. J. F., Maia, E. H. B., Taranto, A. G., Kato, R., Azevedo, V. A. C., & Lopes, D. O. (2021). Immunoinformatics design of multi-epitope peptide-based vaccine against Schistosoma mansoni using transmembrane proteins as a target. Frontiers in Immunology, 12, 621706. https://doi.org/10.3389/fimmu.2021.621706
  • Shao, J.-J., Wong, C. K., Lin, T., Lee, S. K., Cong, G.-Z., Sin, F. W. Y., Du, J.-Z., Gao, S.-D., Liu, X.-T., Cai, X.-P., Xie, Y., Chang, H.-Y., & Liu, J.-X. (2011). Promising multiple-epitope recombinant vaccine against foot-and-mouth disease virus type O in swine. Clinical and Vaccine Immunology: CVI, 18(1), 143–149. https://doi.org/10.1128/CVI.00236-10
  • Singh, S., Qureshi, I. A., & Jyotisha, Multi-epitope vaccine against SARS-CoV-2 applying immunoinformatics and molecular dynamics simulation approaches. Journal of Biomolecular Structure & dynamics 2022. 40(7): p. 2917–2933. https://doi.org/10.1080/07391102.2020.1844060
  • Subramaniam, S., Mohapatra, J. K., Das, B., Sanyal, A., & Pattnaik, B. (2015). Genetic and antigenic analysis of foot-and-mouth disease virus serotype O responsible for outbreaks in India during 2013. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 30, 59–64. https://doi.org/10.1016/j.meegid.2014.12.009
  • Tolawak, D., & Pal, M. (2022). A review on the FMD in Ethiopia. Research in Veterinary Science and Medicine, 2, 6. https://doi.org/10.25259/RVSM_4_2022
  • Tomar, S., Mahajan, S., & Kumar, R. (2020). Advances in structure-assisted antiviral discovery for animal viral diseases. In Genomics and biotechnological advances in veterinary, poultry, and fisheries (pp. 435–468). Elsevier.
  • Triwijaya, R., Hasuki, W., Mustika Kresnia, G., Natasya, J., Natalia Satya, P. G. A., & Parikesit, A. A. (2022). In-silico studies reveal potential epitope based vaccine against M. leprae phosphoglycerate mutase protein. Malaysian Journal of Fundamental and Applied Sciences, 18(1), 19–29. https://doi.org/10.11113/mjfas.v18n1.2286
  • Uddowla, S., Hollister, J., Pacheco, J. M., Rodriguez, L. L., & Rieder, E. (2012). A safe foot-and-mouth disease vaccine platform with two negative markers for differentiating infected from vaccinated animals. Journal of Virology, 86(21), 11675–11685. https://doi.org/10.1128/JVI.01254-12
  • Vakili, B., Eslami, M., Hatam, G. R., Zare, B., Erfani, N., Nezafat, N., & Ghasemi, Y. (2018). Immunoinformatics-aided design of a potential multi-epitope peptide vaccine against Leishmania infantum. International Journal of Biological Macromolecules, 120(Pt A), 1127–1139. https://doi.org/10.1016/j.ijbiomac.2018.08.125
  • Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). gmx_MMPBSA: A new tool to perform end-state free energy calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645
  • Validi, M., Karkhah, A., Prajapati, V. K., & Nouri, H. R. (2018). Immuno-informatics based approaches to design a novel multi epitope-based vaccine for immune response reinforcement against Leptospirosis. Molecular Immunology, 104, 128–138. https://doi.org/10.1016/j.molimm.2018.11.005
  • Vieira, I. H. P., Botelho, E. B., de Souza Gomes, T. J., Kist, R., Caceres, R. A., & Zanchi, F. B. (2023). Visual dynamics: A WEB application for molecular dynamics simulation using GROMACS. BMC Bioinformatics, 24(1), 107. https://doi.org/10.1186/s12859-023-05234-y
  • Yao, B., Zhang, L., Liang, S., & Zhang, C. (2012). SVMTriP: A method to predict antigenic epitopes using support vector machine to integrate tri-peptide similarity and propensity. PLoS One, 7(9), e45152. https://doi.org/10.1371/journal.pone.0045152
  • Yılmaz Çolak, Ç. (2021). Computational design of a multi-epitope vaccine against Clostridium chauvoei: An immunoinformatics approach. International Journal of Peptide Research and Therapeutics, 27(4), 2639–2649. https://doi.org/10.1007/s10989-021-10279-9
  • Zhang, J., & Tao, A. (2015). Antigenicity, immunogenicity, allergenicity. In Allergy bioinformatics (pp. 175–186). Springer.
  • Zhong, J., Rist, M., Cooper, L., Smith, C., & Khanna, R. (2008). Induction of pluripotent protective immunity following immunisation with a chimeric vaccine against human cytomegalovirus. PLoS One, 3(9), e3256. https://doi.org/10.1371/journal.pone.0003256

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