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Advances in Bioinformatics
Volume 2019, Article ID 1270485, 23 pages
https://doi.org/10.1155/2019/1270485
Research Article

Immunoinformatics Approach for Multiepitopes Vaccine Prediction against Glycoprotein B of Avian Infectious Laryngotracheitis Virus

1Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan
2Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, Sudan University of Science and Technology, Sudan
3Department of Pharmaceutical Technology, College of Pharmacy, University of Medical Science and Technology (MUST), Khartoum, Sudan

Correspondence should be addressed to Sumaia A. Ali; moc.oohay@looldahaimos

Received 7 November 2018; Accepted 17 February 2019; Published 18 March 2019

Academic Editor: Nurit Haspel

Copyright © 2019 Sumaia A. Ali et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. K. R. Menendez, M. García, S. Spatz, and N. L. Tablante, “Molecular epidemiology of infectious laryngotracheitis: a review,” Avian Pathology, vol. 43, no. 2, pp. 108–117, 2014. View at Publisher · View at Google Scholar · View at Scopus
  2. H. Hidalgo, “Infectious laryngotracheitis: a review,” Revista Brasileira de Ciência Avícola, vol. 5, no. 3, pp. 157–168, 2003. View at Publisher · View at Google Scholar
  3. T. J. Bagust, R. C. Jones, and J. S. Guy, “Avian infectious laryngotracheitis,” Revue Scientifique et Technique de l'OIE, vol. 19, no. 2, pp. 483–492, 2000. View at Publisher · View at Google Scholar · View at Scopus
  4. I. Oldoni, A. Rodríguez-Avila, S. Riblet, and M. García, “Characterization of infectious laryngotracheitis virus (ILTV) isolates from commercial poultry by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP),” Avian Diseases, vol. 52, no. 1, pp. 59–63, 2008. View at Publisher · View at Google Scholar · View at Scopus
  5. S. Parra, L. Nuñez, and A. Ferreira, “Epidemiology of avian infectious laryngotracheitis with special focus to south america: an update,” Revista Brasileira de Ciência Avícola, vol. 18, no. 4, pp. 551–562, 2016. View at Publisher · View at Google Scholar
  6. A. Moreno, A. Piccirillo, A. Mondin, E. Morandini, L. Gavazzi, and P. Cordioli, “Epidemic of infectious laryngotracheitis in Italy: Characterization of virus isolates by PCR-restriction fragment length polymorphism and sequence analysis,” Avian Diseases, vol. 54, no. 4, pp. 1172–1177, 2010. View at Publisher · View at Google Scholar · View at Scopus
  7. M. G. Han and S. J. Kim, “Analysis of Korean strains of infectious laryngotracheitis virus by nucleotide sequences and restriction fragment length polymorphism,” Veterinary Microbiology, vol. 83, no. 4, pp. 321–331, 2001. View at Publisher · View at Google Scholar · View at Scopus
  8. L. H. Keller, C. E. Benson, S. Davison, and R. J. Eckroade, “Differences among restriction endonuclease DNA fingerprints of Pennsylvania field isolates, vaccine strains, and challenge strains of infectious laryngotracheitis virus,” Avian Diseases, vol. 36, no. 3, pp. 575–581, 1992. View at Publisher · View at Google Scholar · View at Scopus
  9. F. T. Jordan, “A review of the literature on infectious laryngotracheitis (ILT),” Avian Diseases, vol. 10, no. 1, pp. 1–26, 1966. View at Publisher · View at Google Scholar
  10. L. Dufour-Zavala, “Epizootiology of infectious laryngotracheitis and presentation of an industry control program,” Avian Diseases, vol. 52, no. 1, pp. 1–7, 2008. View at Publisher · View at Google Scholar · View at Scopus
  11. A. H. Abu haraz, K. A. Abd elrahman, M. S. Ibrahim et al., “Multi epitope peptide vaccine prediction against sudan ebola virus using immuno-informatics approaches,” Advanced Techniques in Biology & Medicine, vol. 5, no. 203, Article ID 1000203, pp. 2379–1764, 2017. View at Publisher · View at Google Scholar
  12. S. O. Abd Albagi, O. Hashim Ahmed, M. A. Gumaa, K. A. Abd elrahman, A. H. Abu Haraz, and M. A. Hassan, “Immunoinformatics-peptide driven vaccine and in silico modeling for duvenhage rabies virus glycoprotein G,” Journal of Clinical & Cellular Immunology, vol. 8, no. 517, p. 2, 2017. View at Publisher · View at Google Scholar
  13. M. A. Awad Elkareem, S. Ahmed Osman, H. A. Mohamed et al., “Prediction and conservancy analysis of multiepitope based peptide vaccine against merkel cell polyomavirus: an immunoinformatics approach,” Immunome Research, vol. 13, no. 134, p. 2, 2017. View at Publisher · View at Google Scholar
  14. M. M. Shawan, H. A. Mahmud, M. M. Hasan, A. Parvin, M. N. Rahman, and S. M. Rahman, “In silico modeling and immunoinformatics probing disclose the epitope based peptidevaccine against zika virus envelope glycoprotein,” Indian Journal of Pharmaceutical and Biological Research, vol. 2, no. 4, 2014. View at Publisher · View at Google Scholar
  15. P. A. Reche, E. Fernandez-Caldas, D. R. Flower, M. Fridkis-Hareli, and Y. Hoshino, “Peptide-based immunotherapeutics and vaccines,” Journal of Immunology Research, vol. 2014, Article ID 256784, 2 pages, 2014. View at Publisher · View at Google Scholar
  16. D. R. Flower, “Designing immunogenic peptides,” Nature Chemical Biology, vol. 9, no. 12, pp. 749–753, 2013. View at Publisher · View at Google Scholar · View at Scopus
  17. F. Bande, S. S. Arshad, M. Hair Bejo, S. Kadkhodaei, and A. R. Omar, “Prediction and in silico identification of novel B-cells and T-cells epitopes in the S1-spike glycoprotein of M41 and CR88 (793/B) infectious bronchitis virus serotypes for application in peptide vaccines,” Advances in Bioinformatics, vol. 2016, 2016. View at Google Scholar · View at Scopus
  18. J. Zheng, X. Lin, X. Wang et al., “In silico analysis of epitope-based vaccine candidates against hepatitis B virus polymerase protein,” Viruses, vol. 9, no. 5, p. 112, 2017. View at Publisher · View at Google Scholar
  19. A. Dereeper, V. Guignon, G. Blanc et al., “Phylogeny. fr: robust phylogenetic analysis for the non-specialist,” Nucleic Acids Research, vol. 36, supplement 2, pp. W465–W469, 2008. View at Publisher · View at Google Scholar · View at Scopus
  20. T. Hall, “BioEdit: an important software for molecular biology,” Gerf Bulletin of Bioscience, vol. 2, no. 1, pp. 60-61, 2011. View at Google Scholar
  21. R. Vita, J. A. Overton, J. A. Greenbaum et al., “The immune epitope database (IEDB) 3.0,” Nucleic Acids Research, vol. 43, pp. D405–D412, 2015. View at Publisher · View at Google Scholar
  22. J. E. Larsen, O. Lund, and M. Nielsen, “Improved method for predicting linear B-cell epitopes,” Immunome Research, vol. 2, no. 1, p. 2, 2006. View at Publisher · View at Google Scholar
  23. E. A. Emini, J. V. Hughes, D. S. Perlow, and J. Boger, “Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide,” Journal of Virology, vol. 55, no. 3, pp. 836–839, 1985. View at Google Scholar · View at Scopus
  24. A. S. Kolaskar and P. C. Tongaonkar, “A semi-empirical method for prediction of antigenic determinants on protein antigens,” FEBS Letters, vol. 276, no. 1-2, pp. 172–174, 1990. View at Publisher · View at Google Scholar · View at Scopus
  25. C. Lundegaard, O. Lund, and M. Nielsen, “Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers,” Bioinformatics, vol. 24, no. 11, pp. 1397-1398, 2008. View at Publisher · View at Google Scholar · View at Scopus
  26. M. Abdelbagi, T. Hassan, M. Shihabeldin et al., “Immunoinformatics prediction of peptide-based vaccine against african horse sickness virus,” Immunome Research, vol. 13, no. 135, p. 2, 2017. View at Publisher · View at Google Scholar
  27. A. Patronov and I. Doytchinova, “T-cell epitope vaccine design by immunoinformatics,” Open Biology, vol. 3, Article ID 120139, p. 1, 2013. View at Google Scholar · View at Scopus
  28. M. Nielsen and O. Lund, “NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction,” BMC Bioinformatics, vol. 10, article 296, 2009. View at Publisher · View at Google Scholar · View at Scopus
  29. W. M. Chan, “User’s manual for Chimera grid tools, version 1.8,” NASA Ames Research Center, 2003, http://people.nas.nasa.gov/~rogers/cgt/doc/man.html.
  30. M. Källberg, H. P. Wang, and S. Wang, “Template-based protein structure modeling using the RaptorX web server,” Nature Protocols, vol. 7, no. 8, pp. 1511–1522, 2012. View at Publisher · View at Google Scholar · View at Scopus
  31. J. Peng and J. Xu, “Raptorx: Exploiting structure information for protein alignment by statistical inference,” Proteins: Structure, Function, and Bioinformatics, vol. 79, no. S10, pp. 161–171, 2011. View at Publisher · View at Google Scholar
  32. J. Peng and J. Xu, “A multiple-template approach to protein threading,” Proteins: Structure, Function, and Bioinformatics, vol. 79, no. 6, pp. 1930–1939, 2011. View at Publisher · View at Google Scholar · View at Scopus
  33. J. Maupetit, P. Derreumaux, and P. Tufféry, “A fast method for large-scale de novo peptide and miniprotein structure prediction,” Journal of Computational Chemistry, vol. 31, no. 4, pp. 726–738, 2010. View at Publisher · View at Google Scholar · View at Scopus
  34. J. Beaufays, L. Lins, A. Thomas, and R. Brasseur, “In silico predictions of 3D structures of linear and cyclic peptides with natural and non-proteinogenic residues,” Journal of Peptide Science, vol. 18, no. 1, pp. 17–24, 2012. View at Publisher · View at Google Scholar · View at Scopus
  35. Y. Shen, J. Maupetit, P. Derreumaux, and P. Tufféry, “Improved PEP-FOLD approach for peptide and miniprotein structure prediction,” Journal of Chemical Theory and Computation, vol. 10, no. 10, pp. 4745–4758, 2014. View at Publisher · View at Google Scholar · View at Scopus
  36. D. Duhovny, R. Nussinov, and H. J. Wolfson, “Efficient unbound docking of rigid molecules,” in Proceedings of the International Workshop on Algorithms in Bioinformatics, Springer, 2002.
  37. D. Schneidman-Duhovny, Y. Inbar, R. Nussinov, and H. J. Wolfson, “PatchDock and SymmDock: servers for rigid and symmetric docking,” Nucleic Acids Research, vol. 33, supplement 2, pp. W363–W367, 2005. View at Publisher · View at Google Scholar · View at Scopus
  38. N. Andrusier, R. Nussinov, and H. J. Wolfson, “FireDock: Fast interaction refinement in molecular docking,” Proteins: Structure, Function, and Genetics, vol. 69, no. 1, pp. 139–159, 2007. View at Publisher · View at Google Scholar · View at Scopus
  39. M. M. Osman, E. E. Elamin, M. Al-Nour et al., “In silico design of epitope based peptide vaccine against virulent strains of hn-newcastle disease virus (NDV) in poultry species,” IJMCR: International Journal of Multidisciplinary and Current Research, vol. 4, 2016. View at Google Scholar
  40. A. Ingale, “In silico homology modeling and epitope prediction of nucleocapsid protein region from japanese encephalitis virus,” Journal of Computer Science & Systems Biology, vol. 3, no. 2, pp. 53–58, 2010. View at Publisher · View at Google Scholar
  41. A. G. Ingale and S. Goto, “Prediction of CTL epitope, in silico modeling and functional analysis of cytolethal distending toxin (CDT) protein of Campylobacter jejuni,” BMC Research Notes, vol. 7, no. 1, article 92, 2014. View at Publisher · View at Google Scholar · View at Scopus
  42. S. H. Abro, K. Ullman, S. Belák, and C. Baule, “Bioinformatics and evolutionary insight on the spike glycoprotein gene of QX-like and Massachusetts strains of infectious bronchitis virus,” Virology Journal, vol. 9, article 211, 2012. View at Publisher · View at Google Scholar · View at Scopus
  43. M. Koch, S. Camp, T. Collen et al., “Structures of an MHC class I molecule from B21 chickens illustrate promiscuous peptide binding,” Immunity, vol. 27, no. 6, pp. 885–899, 2007. View at Publisher · View at Google Scholar · View at Scopus
  44. M. M. Pourseif, G. Moghaddam, B. Naghili et al., “A novel in silico minigene vaccine based on CD4 + T-helper and B-cell epitopes of EG95 isolates for vaccination against cystic echinococcosis,” Computational Biology and Chemistry, vol. 72, pp. 150–163, 2018. View at Publisher · View at Google Scholar
  45. O. Vainio, C. Koch, and A. Toivanen, “B-L antigens (class II) of the chicken major histocompatibility complex control T-B cell interaction,” Immunogenetics, vol. 19, no. 2, pp. 131–140, 1984. View at Google Scholar
  46. K. Hála, R. Boyd, and G. Wick, “Chicken major histocompatibility complex and disease,” Scandinavian Journal of Immunology, vol. 14, no. 6, pp. 607–616, 1981. View at Publisher · View at Google Scholar · View at Scopus