Multi-epitope vaccine against nucleoprotein and envelopment polyprotein of Batai orthobunyavirus using molecular docking and molecular dynamics studies

1. Toure, C. T. et al. Genomic characterization of a Bataï Orthobunyavirus, previously classified as ilesha virus, from field-caught mosquitoes in Senegal, Bandia 1969. Viruses 16, 261 (2024).

   Google Scholar 

2. Liu, H., Gao, X. & Liang, G. Newly recognized mosquito-associated viruses in mainland China, in the last two decades. Virol. J. 8, 68 (2011).

   Google Scholar 

3. Mansfield, K. L., Folly, A. J., Hernández-Triana, L. M., Sewgobind, S. & Johnson, N. Batai Orthobunyavirus: An emerging mosquito-borne virus in Europe. Viruses 14, 1868 (2022).

   Google Scholar 

4. Liu, H. et al. Isolation and complete nucleotide sequence of a Batai virus strain in Inner Mongolia. China. Virol. J. 11, 1–8 (2014).

   Google Scholar 

5. Dutuze, M. F., Nzayirambaho, M., Mores, C. N. & Christofferson, R. C. A review of Bunyamwera, Batai, and Ngari viruses: Understudied Orthobunyaviruses with potential one health implications. Front. Veterinary Sci. 5, 69 (2018).

   Google Scholar 

6. Nyaruaba, R., Mwaliko, C., Mwau, M., Mousa, S. & Wei, H. Arboviruses in the East African community partner states: A review of medically important mosquito-borne Arboviruses. Pathogens Glob. Health 113, 209–228 (2019).

   Google Scholar 

7. Mansfield, K. L., Folly, A. J., Hernández-Triana, L. M., Sewgobind, S. & Johnson, N. Batai orthobunyavirus: an emerging mosquito-borne virus in Europe. Viruses 14, 1868 (2022).

8. Koka, H. et al. Evidence of circulation of Orthobunyaviruses in diverse mosquito species in Kwale County Kenya. Virol. J. 18, 1–11 (2021).

   Google Scholar 

9. Ziegler, U. et al. Seroprevalance of Batai virus in ruminants from East Germany. Vet. Microbiol. 227, 97–102 (2018).

   Google Scholar 

10. Lundström, J. O. Mosquito-borne viruses in western Europe: A review. J. Vector Ecol. J. Soc. Vector Ecol. 24, 1–39 (1999).

    Google Scholar 

11. Medlock, J. M., Snow, K. R. & Leach, S. Possible ecology and epidemiology of medically important mosquito-borne arboviruses in Great Britain. Epidemiol. Infect. 135, 466–482 (2007).

    Google Scholar 

12. Huhtamo, E. et al. Isolation and full genomic characterization of Batai virus from mosquitoes, Italy 2009. J. Gen. Virol. 94, 1242–1248 (2013).

    Google Scholar 

13. Nanfack Minkeu, F. & Vernick, K. D. A systematic review of the natural virome of anopheles mosquitoes. Viruses 10, 222 (2018).

    Google Scholar 

14. Nashed, N. W., Olson, J. G. & El-Tigani, A. Isolation of Batai virus (Bunyaviridae: Bunyavirus) from the blood of suspected malaria patients in Sudan. Am. J. Trop. Med. Hyg. 48, 676–681 (1993).

15. Cichon, N. et al. Serological and molecular investigation of Batai virus infections in ruminants from the state of Saxony-Anhalt, Germany, 2018. Viruses 13, 370 (2021).

    Google Scholar 

16. Wilkman, L., Ahlm, C., Evander, M. & Lwande, O. W. Mosquito-borne viruses causing human disease in Fennoscandia—Past, current, and future perspectives. Front. Med. 10, 1152070 (2023).

    Google Scholar 

17. Ahmad, S. et al. The UniProt website API: facilitating programmatic access to protein knowledge. Nucleic Acids Res. 53, W547–W553 (2025).

18. Larsen, J. E., Lund, O. & Nielsen, M. Improved method for predicting linear B-cell epitopes. Immunome Res. 2, 2 (2006).

    Google Scholar 

19. Andreatta, M. & Nielsen, M. Gapped sequence alignment using artificial neural networks: Application to the MHC class I system. Bioinformatics 32, 511–517 (2016).

    Google Scholar 

20. Nilsson, J. B. et al. Accurate prediction of HLA class II antigen presentation across all loci using tailored data acquisition and refined machine learning. Sci. Adv. 9, eadj6367 (2023).

    Google Scholar 

21. Doytchinova, I. A. & Flower, D. R. VaxiJen: A server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics 8, 4 (2007).

    Google Scholar 

22. Dimitrov, I., Bangov, I., Flower, D. R. & Doytchinova, I. AllerTOP v. 2—a server for in silico prediction of allergens. J. Mol. Model. 20, 2278 (2014).

    Google Scholar 

23. Naveed, M. et al. Rational computational design and development of an immunogenic multiepitope vaccine incorporating transmembrane proteins of Fusobacterium necrophorum. Sci. Rep. 15, 15587 (2025).

    Google Scholar 

24. Kuri, P. R. & Goswami, P. Reverse vaccinology-based multi-epitope vaccine design against Indian group A rotavirus targeting VP7, VP4, and VP6 proteins. Microb. Pathog. 193, 106775 (2024).

    Google Scholar 

25. Wang, J. et al. Multi-epitope-based peptide vaccine against bovine parainfluenza virus type 3: Design and immunoinformatics approach. Veterinary sciences 12, 1074 (2025).

    Google Scholar 

26. Sahoo, S., Lee, H.-K. & Shin, D. An integrated structural and immunoinformatic approach to design a multi-epitope based vaccine against the foot-and-mouth disease virus. Sci. Rep. 15, 35911 (2025).

    Google Scholar 

27. Naveed, M. et al. Development of a broad-spectrum multiepitope vaccine against dabie bandavirus through immunoinformatic approaches. Int. Immunopharmacol. 166, 115492 (2025).

    Google Scholar 

28. Bui, H. H. et al. Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics 7, 153 (2006).

    Google Scholar 

29. Wilkins, M. R. et al. Protein identification and analysis tools in the ExPASy server. Methods Mol. Biol. 112, 531–552 (1999).

    Google Scholar 

30. Hanif, N. et al. Computational drug design targeting MYH7 for hypertrophic cardiomyopathy integrating molecular docking, Density Functional Theory, and Molecular Dynamics Simulations. J. Appl. Biol. Sci. 19, 179–192 (2025).

    Google Scholar 

31. Hon, J. et al. SoluProt: Prediction of soluble protein expression in Escherichia coli. Bioinformatics 37, 23–28 (2021).

    Google Scholar 

32. Buchan, D. W. A., Moffat, L., Lau, A., Kandathil, S. M. & Jones, D. T. Deep learning for the PSIPRED protein analysis workbench. Nucleic Acids Res. 52, W287-w293 (2024).

    Google Scholar 

33. Hanif, N. et al. In silico characterization of hypothetical protein AZJ53_10480 in streptococcus pneumoniae. BioSci. Rev. 6, 1–12 (2024).

    Google Scholar 

34. Bryant, P., Pozzati, G. & Elofsson, A. Improved prediction of protein-protein interactions using AlphaFold2. Nat. Commun. 13, 1265 (2022).

    Google Scholar 

35. Ko, J., Park, H., Heo, L. & Seok, C. GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Res. 40, W294–W297 (2012).

36. Colovos, C. & Yeates, T. O. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci. 2, 1511–1519 (1993).

37. Naveed, M. et al. Molecular identification of the blaOXA gene in Bacillus cereus and AI-driven optimization of natural phytochemicals for foodborne illness treatment. Antonie Van Leeuwenhoek 119, 29 (2026).

    Google Scholar 

38. Naveed, M. et al. Nanoinformatics-guided inhibition of blaOXA in staphylococcus nepalensis using cysteine-conjugated silver nanoparticles. ChemistrySelect 11, e04545 (2026).

    Google Scholar 

39. Kozakov, D. et al. The ClusPro web server for protein-protein docking. Nat Protoc. 12, 255–278 (2017).

    Google Scholar 

40. Laskowski, R. A. & Swindells, M. B. LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J. Chem. Inf. Model. 51, 2778–2786 (2011).

41. Laubenbacher, R. et al. Toward mechanistic medical digital twins: Some use cases in immunology. Front Digit Health 6, 1349595 (2024).

    Google Scholar 

42. Madeira, F. et al. The EMBL-EBI job dispatcher sequence analysis tools framework in 2024. Nucleic Acids Res. 52, W521–W525 (2024).

    Google Scholar 

43. Naveed, M. et al. Designing IL-24–P18 fusion protein through computational engineering for targeted breast cancer therapy. J. Comput. Biophys. Chem. 25, 109–123 (2026).

    Google Scholar 

44. Tian, C. Improving the accuracy of Amber force field for biomolecular simulation. PhD thesis, State University of New York at Stony Brook (2019).

45. Naveed, M. et al. Immunoinformatics-based design and evaluation of a multi-epitope vaccine against Vibrio fluvialis. Sci. Rep. 16, 4100 (2026).

46. Naveed, M. et al. Computational drug design for neurosyphilis disease by targeting Phosphoglycerate Kinase in Treponema pallidum with enhanced binding affinity and reduced toxicity. Sci. Rep. 15, 1–22 (2025).

    Google Scholar 

47. Naveed, M. et al. Combining network pharmacology and computational approaches for screening of Apiaceae-derived phytochemicals as inhibitors of DNA polymerase III in Streptococcus pyogenes causing streptococcal toxic shock syndrome. Chin. J. Anal. Chem. 100632 (2025).

48. Naveed, M. et al. Identification of phytochemical inhibitors targeting the hylEfm gene in multidrug-resistant enterococcus faecium using different approaches. ChemistrySelect 11, e04341 (2026).

    Google Scholar 

49. Naveed, M. et al. In silico design and immunoinformatics assessment of a multiepitope vaccine targeting borealpox virus. Sci. Rep. 16, 3885 (2026).

50. Hernández-Triana, L. M. et al. Oral susceptibility of aedine and culicine mosquitoes (Diptera: Culicidae) to Batai Orthobunyavirus. Parasit. Vectors 14, 566 (2021).

    Google Scholar 

51. Mansfield, K. L., Folly, A. J., Hernández-Triana, L. M., Sewgobind, S. & Johnson, N. Batai orthobunyavirus: an emerging mosquito-borne virus in Europe. Viruses 14, 1868 (2022).

52. Dutuze, M. F., Nzayirambaho, M., Mores, C. N. & Christofferson, R. C. A review of bunyamwera, Batai, and Ngari Viruses: Understudied orthobunyaviruses with potential one health implications. Front. Vet. Sci. 5, 69 (2018).

    Google Scholar 

53. Liu, H. et al. Isolation and complete nucleotide sequence of a Batai virus strain in Inner Mongolia. China. Virol. J. 11, 138 (2014).

    Google Scholar 

54. O’Connor, T. W., Hick, P. M., Finlaison, D. S., Kirkland, P. D. & Toribio, J.-A.L.M.L. Revisiting the importance of Orthobunyaviruses for animal health: A scoping review of livestock disease, diagnostic tests, and surveillance strategies for the simbu serogroup. Viruses 16, 294 (2024).

    Google Scholar 

55. Dutuze, M. F. et al. Identification of Bunyamwera and possible other Orthobunyavirus infections and disease in cattle during a Rift Valley fever outbreak in Rwanda in 2018. Am. J. Trop. Med. Hyg. 103, 183 (2020).

    Google Scholar 

56. Basmenj, E. R. et al. Computational epitope-based vaccine design with bioinformatics approach; a review. Heliyon 11, e41714 (2025).

57. Bravi, B. Development and use of machine learning algorithms in vaccine target selection. NPJ. Vaccines 9, 15 (2024).

    Google Scholar 

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