A Bioinformatic Approach to Designing a Mosaic Dengue Vaccine with Optimized Immunoreactivity and Safety
DOI:
https://doi.org/10.31674/mjmr.2026.v010i01.012Abstract
Background: Dengue virus infects approximately 390 million people annually and exists as four distinct serotypes. The only licensed dengue vaccine has demonstrated variable efficacy, showing reduced protection in seronegative individuals and against dengue virus serotypes 1 and 2. These limitations highlight the need for improved vaccine strategies that better represent dengue antigenic diversity. Objective: This study aimed to design and evaluate a mosaic vaccine strategy based on the dengue virus envelope (E) protein that could represent conserved antigenic regions across all four serotypes and potentially improve vaccine efficacy. Methods: A novel mosaic E protein composed of nine conserved fragments from dengue virus E proteins was designed using bioinformatics approaches. Sequence similarity analyses were performed to compare the mosaic protein with wild-type E proteins from each serotype and to assess homology with human proteins or other pathogens. Predicted secondary (2D) and tertiary (3D) protein structures were analyzed to determine whether the mosaic protein would mimic the natural E protein structure. Immunoinformatic analyses were conducted to evaluate antigenicity and immunogenicity. Results: The mosaic E protein demonstrated high similarity (>95%) to the wild-type E proteins of all four dengue serotypes. Secondary structure analysis showed a predominance of β-sheet structures, consistent with the flexibility observed in natural E proteins. High-scoring predicted 3D models exhibited acceptable global (>0.4) and local model quality scores, supporting structural reliability. Immunoinformatic analyses indicated that the mosaic proteins had similar or enhanced antigenicity and immunogenicity compared to the native E proteins. Conclusion: The mosaic E protein vaccine strategy effectively represents conserved antigenic diversity across dengue virus serotypes within a single recombinant protein. These findings suggest that this approach holds promise as a next-generation dengue vaccine candidate and warrants further experimental validation in laboratory settings.
Keywords:
Dengue, Vaccine, Mosaic, Envelope, Bioinformatic analysis, ImmunoinformaticDownloads
References
Fitzmaurice, C., Allen, C., Barber, R. M., Barregard, L., Bhutta, Z. A., Brenner, H., ... & Satpathy, M. (2017). Global, regional, and national cancer incidence, mortality, years of life lost, years lived with disability, and disability-adjusted life-years for 32 cancer groups, 1990 to 2015: a systematic analysis for the global burden of disease study. JAMA Oncology, 3(4), 524-548. https://doi.org/10.1001/jamaoncol.2016.5688
World Health Organisation (WHO). (2019a, November 4). Dengue and severe dengue. https://www.who.int/news-room/fact-sheets/detail/dengue-and-severe-dengue
World Health Organisation (WHO). (2019b, November 21). WHO Region of the Americas records highest number of dengue cases in history; cases spike in other regions. https://www.who.int/news-room/detail/21-11-2019-who-region-of-the-americas-records-highest-number-of-dengue-cases-in-history-cases-spike-in-other-regions
Bhatt, S., Gething, P. W., Brady, O. J., Messina, J. P., Farlow, A. W., Moyes, C. L., ... & Hay, S. I. (2013). The global distribution and burden of dengue. Nature, 496(7446), 504-507. https://doi.org/10.1038/nature12060
Ajlan, B. A., Alafif, M. M., Alawi, M. M., Akbar, N. A., Aldigs, E. K., & Madani, T. A. (2019). Assessment of the new World Health Organization's dengue classification for predicting severity of illness and level of healthcare required. PLoS Neglected Tropical Diseases, 13(8), e0007144. https://doi.org/10.1371/journal.pntd.0007144
Whitehorn, J., & Simmons, C. P. (2011). The pathogenesis of dengue. Vaccine, 29(42), 7221-7228. https://doi.org/10.1016/j.vaccine.2011.07.022
Ubol, S., & Halstead, S. B. (2010). How innate immune mechanisms contribute to antibody-enhanced viral infections. Clinical and Vaccine Immunology, 17(12), 1829-1835. https://doi.org/10.1128/CVI.00316-10
Wan, S. W., Wu-Hsieh, B. A., Lin, Y. S., Chen, W. Y., Huang, Y., & Anderson, R. (2018). The monocyte-macrophage-mast cell axis in dengue pathogenesis. Journal of Biomedical Science, 25(1), 77. https://doi.org/10.1186/s12929-018-0482-9
Halstead, S. B. (2018). Safety issues from a Phase 3 clinical trial of a live-attenuated chimeric yellow fever tetravalent dengue vaccine. Human Vaccines & Immunotherapeutics, 14(9), 2158-2162. https://doi.org/10.1080/21645515.2018.1445448
World Health Organisation (WHO). (2017, December 5). Dengue vaccine research. https://www.who.int/immunization/research/development/dengue_vaccines/en/
Biswal, S., Reynales, H., Saez-Llorens, X., Lopez, P., Borja-Tabora, C., Kosalaraksa, P., ... & Wallace, D. (2019). Efficacy of a tetravalent dengue vaccine in healthy children and adolescents. New England Journal of Medicine, 381(21), 2009-2019. https://doi.org/10.1056/NEJMoa1903869
Virus Pathogen Database and Analysis Resource. (2020, July 31). Flaviviridae. https://www.viprbrc.org/brc/vipr_protein_search.spg
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389-3402. https://doi.org/10.1093/nar/25.17.3389
Papadopoulos, J. S., & Agarwala, R. (2007). COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics, 23(9), 1073-1079. https://doi.org/10.1093/bioinformatics/btm076
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673-4680. https://doi.org/10.1093/nar/22.22.4673
Zimmermann, L., Stephens, A., Nam, S. Z., Rau, D., Kübler, J., Lozajic, M., ... & Alva, V. (2018). A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. Journal of Molecular Biology, 430(15), 2237-2243. https://doi.org/10.1016/j.jmb.2017.12.007
McGuffin, L. J. (2008). Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. Bioinformatics, 24(16), 1798-1804. https://doi.org/10.1093/bioinformatics/btn326
Ambuel, Y., Young, G., Brewoo, J. N., Paykel, J., Weisgrau, K. L., Rakasz, E. G., ... & Osorio, J. E. (2014). A rapid immunization strategy with a live-attenuated tetravalent dengue vaccine elicits protective neutralizing antibody responses in non-human primates. Frontiers in Immunology, 5, 263. https://doi.org/10.3389/fimmu.2014.00263
Aziz, S., Almajhdi, F. N., Waqas, M., Ullah, I., Salim, M. A., Khan, N. A., & Ali, A. (2022). Contriving multi-epitope vaccine ensemble for monkeypox disease using an immunoinformatics approach. Frontiers in Immunology, 13, 1004804. https://doi.org/10.3389/fimmu.2022.1004804
Biner, D. W., Grosch, J. S., & Ortoleva, P. J. (2023). B-cell epitope discovery: The first protein flexibility-based algorithm–Zika virus conserved epitope demonstration. Plos One, 18(3), e0262321. https://doi.org/10.26434/chemrxiv.12834977.v1
Chan, Y., Jazayeri, S. D., Ramanathan, B., & Poh, C. L. (2020). Enhancement of tetravalent immune responses to highly conserved epitopes of a dengue peptide vaccine conjugated to polystyrene nanoparticles. Vaccines, 8(3), 417. https://doi.org/10.3390/vaccines8030417
Chen, Q., Li, R., Wu, B., Zhang, X., Zhang, H., & Chen, R. (2023). A tetravalent nanoparticle vaccine elicits a balanced and potent immune response against dengue viruses without inducing antibody-dependent enhancement. Frontiers in Immunology, 14, 1193175. https://doi.org/10.3389/fimmu.2023.1193175
Dixit, N. K. (2021). Design of monovalent and chimeric tetravalent dengue vaccine using an immunoinformatics approach. International Journal of Peptide Research and Therapeutics, 27(4), 2607-2624. https://doi.org/10.1007/s10989-021-10277-x
Fadaka, A. O., Sibuyi, N. R. S., Martin, D. R., Goboza, M., Klein, A., Madiehe, A. M., & Meyer, M. (2021). Immunoinformatics design of a novel epitope-based vaccine candidate against dengue virus. Scientific Reports, 11(1), 19707. https://doi.org/10.1038/s41598-021-99227-7
Ghafoor, D., Kousar, A., Ahmed, W., Khan, S., Ullah, Z., Ullah, N., ... & Riaz, R. (2021). Computational vaccinology guided design of multi-epitopes subunit vaccine designing against Hantaan virus and its validation through immune simulations. Infection, Genetics and Evolution, 93, 104950. https://doi.org/10.1016/j.meegid.2021.104950
He, L., Sun, W., Yang, L., Liu, W., & Li, J. (2022). A multiple-target mRNA-LNP vaccine induces protective immunity against experimental multi-serotype DENV in mice. Virologica Sinica, 37(5), 746-757. https://doi.org/10.1016/j.virs.2022.07.003
Hou, J., Shrivastava, S., Fraser, C. C., Loo, H. L., Wong, L. H., Ho, V., ... & Chen, J. (2019). Dengue mosaic vaccines enhance cellular immunity and expand the breadth of neutralizing antibody against all four serotypes of dengue viruses in mice. Frontiers in Immunology, 10, 1429. https://doi.org/10.3389/fimmu.2019.01429
Invenção, M. D. C. V., Macêdo, L. S. D., Moura, I. A. D., Santos, L. A. B. D. O., Espinoza, B. C. F., Pinho, S. S. D., ... & Freitas, A. C. D. (2025). Design and immune profile of multi-epitope synthetic antigen vaccine against SARS-coV-2: An in silico and in vivo approach. Vaccines, 13(2), 149. https://doi.org/10.3390/vaccines13020149
Izmirly, A. M., Alturki, S. O., Alturki, S. O., Connors, J., & Haddad, E. K. (2020). Challenges in dengue vaccines development: pre-existing infections and cross-reactivity. Frontiers in immunology, 11, 1055. https://doi.org/10.3389/fimmu.2020.01055
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
Khalid, K., Saeed, U., Aljuaid, M., Ali, M. I., Anjum, A., & Waheed, Y. (2022). Immunoinformatic approach to contrive a next generation multi-epitope vaccine against Achromobacter xylosoxidans infections. Frontiers in Medicine, 9, 902611. https://doi.org/10.3389/fmed.2022.902611
Liu, X. (2025). Opportunities and challenges of mRNA technologies in development of Dengue Virus Vaccine. Frontiers in Immunology, 16, 1520968. https://doi.org/10.3389/fimmu.2025.1520968
Mahata, D., Mukherjee, D., Malviya, V., & Mukherjee, G. (2021). Targeting “Immunogenic Hotspots” in Dengue and Zika Virus: A Novel Approach to a Common Vaccine. bioRxiv, 2021-07. https://doi.org/10.1101/2021.07.23.453561
Medits, I., Heinz, F. X., & Stiasny, K. (2021). An absolutely conserved tryptophan in the stem of the envelope protein E of flaviviruses is essential for the formation of stable particles. Viruses, 13(9), 1727. https://doi.org/10.3390/v13091727
Norshidah, H., Vignesh, R., & Lai, N. S. (2021). Updates on dengue vaccine and antiviral: where are we heading?. Molecules, 26(22), 6768. https://doi.org/10.3390/molecules26226768
Pérez, M., Álvarez, M., Perez, L., Benitez, A. J., Serrano, S., Adelino, T. E. R., ... & Guzman, M. G. (2025). Establishing a Dengue Genomic Monitoring in Cuba: Uncovering Virus Dynamics to Enhance Local Response. IJID Regions, 100683. https://doi.org/10.1016/j.ijregi.2025.100683
Rasheed, M. A., Raza, S., Alonazi, W. B., Ashraf, M. A., Navid, M. T., Aslam, I., ... & Riaz, M. I. (2023). Design and Assessment of a Novel in Silico Approach for Developing a Next-Generation Multi-Epitope Universal Vaccine Targeting Coronaviruses. Microorganisms, 11(9), 2282. https://doi.org/10.3390/microorganisms11092282
Roy, U. (2020). Structural and molecular analyses of functional epitopes and escape mutants in Japanese encephalitis virus envelope protein domain III. Immunologic Research, 68(2), 81-89. https://doi.org/10.1007/s12026-020-09130-y
See, K. C. (2025). Dengue vaccination: A practical guide for clinicians. Vaccines, 13(2), 145. https://doi.org/10.3390/vaccines13020145
Shanshin, D. V., Borisevich, S. S., Bondar, A. A., Porozov, Y. B., Rukhlova, E. A., Protopopova, E. V., ... & Shcherbakov, D. N. (2022). Can modern molecular modeling methods help find the area of potential vulnerability of flaviviruses?. International Journal of Molecular Sciences, 23(14), 7721. https://doi.org/10.3390/ijms23147721
Torres-Flores, J. M., Reyes-Sandoval, A., & Salazar, M. I. (2022). Dengue vaccines: an update. BioDrugs, 36(3), 325-336. https://doi.org/10.1007/s40259-022-00531-z
Yong, Y. K., Wong, W. F., Vignesh, R., Chattopadhyay, I., Velu, V., Tan, H. Y., ... & Shankar, E. M. (2022). Dengue infection-recent advances in disease pathogenesis in the era of COVID-19. Frontiers in Immunology, 13, 889196. https://doi.org/10.3389/fimmu.2022.889196
Published
How to Cite
Issue
Section
License
Copyright (c) 2026 Malaysian Journal of Medical Research (MJMR)
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
