Design of a Recombinant Multi-Epitope Subunit Vaccine Targeting Glycoproteins of Herpes Simplex Virus Type 2 Using an Immunoinformatics Approach
DOI:
https://doi.org/10.47352/bioactivities.2963-654X.280Keywords:
HSV-2, glycoprotein, multi-epitope vaccine, immunoinformaticsAbstract
Herpes simplex virus type 2 (HSV-2) is a major global cause of genital herpes, characterized by its lifelong latency and high transmission rate, yet no licensed vaccine currently exists. This study aimed to design a recombinant multi-epitope subunit vaccine targeting HSV-2 envelope glycoproteins (gB, gC, gD, gH, and gL) using an immunoinformatics-guided approach. A total of 37 epitopes comprising cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B cell targets were selected based on high antigenicity and confirmed to be non-allergenic and non-toxic. The final construct included adjuvants and immunostimulatory elements to enhance immune recognition. Structural analysis showed a favorable molecular weight of 92.7 kDa, high stability (instability index 39.16), and strong hydrophilicity (GRAVY score -0.367). Validation of the 3D model yielded an ERRAT score of 74.77 and 82.60% of residues within the most favored regions in the Ramachandran plot, indicating a high-quality and reliable conformation. Molecular docking simulations demonstrated strong binding affinities of the vaccine construct with MHC class I, MHC class II, TLR2, and TLR4. Highest binding affinity value of -335.03 kcal/mol for TLR4, supported by the formation of optimal hydrogen bonds and salt bridges indicating potential to elicit robust adaptive and innate immune responses. These findings indicate that the designed vaccine is structurally robust, immunologically promising, and suitable for further in vitro and in vivo evaluation against HSV-2 infection.
References
[1] R. Krishnan and P. M. Stuart. (2021). "Developments in Vaccination for Herpes Simplex Virus". Frontiers in Microbiology. 12 : 798927. 10.3389/fmicb.2021.798927.
[2] L. Khadr, M. Harfouche, R. Omori, G. Schwarzer, H. Chemaitelly, and L. J. Abu-Raddad. (2019). "The Epidemiology of Herpes Simplex Virus Type 1 in Asia: Systematic Review, Meta-analyses, and Meta-regressions". Clinical Infectious Diseases. 68 (5): 757-772. 10.1093/cid/ciy562.
[3] D. Sharma, S. Sharma, N. Akojwar, A. Dondulkar, N. Yenorkar, D. Pandita, S. K. Prasad, and M. Dhobi. (2023). "An Insight into Current Treatment Strategies, Their Limitations, and Ongoing Developments in Vaccine Technologies against Herpes Simplex Infections". Vaccines (Basel). 11 (2). 10.3390/vaccines11020206.
[4] J. B. Suzich and A. R. Cliffe. (2018). "Strength in diversity: Understanding the pathways to herpes simplex virus reactivation". Virology. 522 : 81-91. 10.1016/j.virol.2018.07.011.
[5] S. Awasthi, J. J. Knox, A. Desmond, M. G. Alameh, B. T. Gaudette, J. M. Lubinski, A. Naughton, L. M. Hook, K. P. Egan, Y. K. Tam, N. Pardi, D. Allman, E. T. Luning Prak, M. P. Cancro, D. Weissman, G. H. Cohen, and H. M. Friedman. (2021). "Trivalent nucleoside-modified mRNA vaccine yields durable memory B cell protection against genital herpes in preclinical models". Journal of Clinical Investigation. 131 (23). 10.1172/JCI152310.
[6] N. Jambunathan, C. M. Clark, F. Musarrat, V. N. Chouljenko, J. Rudd, and K. G. Kousoulas. (2021). "Two Sides to Every Story: Herpes Simplex Type-1 Viral Glycoproteins gB, gD, gH/gL, gK, and Cellular Receptors Function as Key Players in Membrane Fusion". Viruses. 13 (9). 10.3390/v13091849.
[7] S. Zhu and A. Viejo-Borbolla. (2021). "Pathogenesis and virulence of herpes simplex virus". Virulence. 12 (1): 2670-2702. 10.1080/21505594.2021.1982373.
[8] S. S. Rawat, A. K. Keshri, R. Kaur, and A. Prasad. (2023). "Immunoinformatics Approaches for Vaccine Design: A Fast and Secure Strategy for Successful Vaccine Development". Vaccines (Basel). 11 (2). 10.3390/vaccines11020221.
[9] T. Kar, U. Narsaria, S. Basak, D. Deb, F. Castiglione, D. M. Mueller, and A. P. Srivastava. (2020). "A candidate multi-epitope vaccine against SARS-CoV-2". Scientific Reports. 10 (1): 10895. 10.1038/s41598-020-67749-1.
[10] A. Ullah, S. Ahmad, S. Ismail, Z. Afsheen, M. Khurram, M. Tahir Ul Qamar, N. AlSuhaymi, M. H. Alsugoor, and K. S. Allemailem. (2021). "Towards A Novel Multi-Epitopes Chimeric Vaccine for Simulating Strong Immune Responses and Protection against Morganella morganii". International Journal of Environmental Research and Public Health. 18 (20). 10.3390/ijerph182010961.
[11] A. Albutti. (2021). "An integrated computational framework to design a multi-epitopes vaccine against Mycobacterium tuberculosis". Scientific Reports. 11 (1): 21929. 10.1038/s41598-021-01283-6.
[12] M. Alharbi, A. Alshammari, A. F. Alasmari, S. M. Alharbi, M. Tahir Ul Qamar, A. Ullah, S. Ahmad, M. Irfan, and A. A. K. Khalil. (2022). "Designing of a Recombinant Multi-Epitopes Based Vaccine against Enterococcus mundtii Using Bioinformatics and Immunoinformatics Approaches". International Journal of Environmental Research and Public Health. 19 (6). 10.3390/ijerph19063729.
[13] S. Zaib, N. Rana, Areeba, N. Hussain, H. Alrbyawi, A. A. Dera, I. Khan, M. Khalid, A. Khan, and A. Al-Harrasi. (2023). "Designing multi-epitope monkeypox virus-specific vaccine using immunoinformatics approach". Journal of Infection and Public Health. 16 (1): 107-116. 10.1016/j.jiph.2022.11.033.
[14] M. Andreatta and M. Nielsen. (2016). "Gapped sequence alignment using artificial neural networks: application to the MHC class I system". Bioinformatics. 32 (4): 511-7. 10.1093/bioinformatics/btv639.
[15] J. Guo, Z. Jia, Y. Yang, N. Wang, Y. Xue, L. Xiao, F. Wang, L. Wang, X. Wang, Y. Liu, J. Wang, W. Gong, H. Zhao, Y. Liang, and X. Wu. (2025). "Bioinformatics analysis, immunogenicity, and therapeutic efficacy evaluation of a novel multi-stage, multi-epitope DNA vaccine for tuberculosis". International Immunopharmacology. 152 : 114415. 10.1016/j.intimp.2025.114415.
[16] K. A. Galanis, K. C. Nastou, N. C. Papandreou, G. N. Petichakis, D. G. Pigis, and V. A. Iconomidou. (2021). "Linear B-Cell Epitope Prediction for In Silico Vaccine Design: A Performance Review of Methods Available via Command-Line Interface". International Journal of Molecular Sciences. 22 (6). 10.3390/ijms22063210.
[17] I. Dimitrov, D. R. Flower, and I. Doytchinova. (2013). "AllerTOP--a server for in silico prediction of allergens". BMC Bioinformatics. 14 Suppl 6 (Suppl 6): S4. 10.1186/1471-2105-14-S6-S4.
[18] S. Gupta, P. Kapoor, K. Chaudhary, A. Gautam, R. Kumar, and G. P. S. Raghava.(2015)." Computational Peptidology. 10.1007/978-1-4939-2285-7.
[19] J. Hou, Y. Liu, J. Hsi, H. Wang, R. Tao, and Y. Shao. (2014). "Cholera toxin B subunit acts as a potent systemic adjuvant for HIV-1 DNA vaccination intramuscularly in mice". Human Vaccines & Immunotherapeutics. 10 (5): 1274-83. 10.4161/hv.28371.
[20] B. Denes, R. N. Fuller, W. Kelin, T. R. Levin, J. Gil, A. Harewood, M. Lorincz, N. R. Wall, A. F. Firek, and W. H. R. Langridge. (2023). "A CTB-SARS-CoV-2-ACE-2 RBD Mucosal Vaccine Protects Against Coronavirus Infection". Vaccines (Basel). 11 (12). 10.3390/vaccines11121865.
[21] P. Sadana, M. Monnich, C. Unverzagt, and A. Scrima. (2017). "Structure of the Y. pseudotuberculosis adhesin InvasinE". Protein Science. 26 (6): 1182-1195. 10.1002/pro.3171.
[22] J. Yang and Y. Zhang. (2015). "I-TASSER server: new development for protein structure and function predictions". Nucleic Acids Research. 43 (W1): W174-81. 10.1093/nar/gkv342.
[23] G. R. Lee, J. Won, L. Heo, and C. Seok. (2019). "GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure". Nucleic Acids Research. 47 (W1): W451-W455. 10.1093/nar/gkz288.
[24] N. Lawko, C. Plaskasovitis, C. Stokes, L. Abelseth, I. Fraser, R. Sharma, R. Kirsch, M. Hasan, E. Abelseth, and S. M. Willerth. (2021). "3D Tissue Models as an Effective Tool for Studying Viruses and Vaccine Development". Frontiers in Materials. 8. 10.3389/fmats.2021.631373.
[25] M. A. Asad, S. A. Shorna, M. Mizan, R. D. Nath, A. S. M. Saikat, and M. E. Uddin. (2024). "Bioinformatics Approaches for the Molecular Characterization and Structural Elucidation of a Hypothetical Protein of Aedes albopictus". The 3rd International Electronic Conference on Processes. 10.3390/engproc2024067014.
[26] A. Hashempour, N. Khodadad, S. Akbarinia, F. Ghasabi, Y. Ghasemi, M. Matin Karbalaei Ali Nazar, and S. Falahi. (2024). "Correction: Reverse vaccinology approaches to design a potent multiepitope vaccine against the HIV whole genome: immunoinformatic, bioinformatics, and molecular dynamics approaches". BMC Infectious Diseases. 24 (1): 1023. 10.1186/s12879-024-09951-4.
[27] Y. Yan, H. Tao, J. He, and S. Y. Huang. (2020). "The HDOCK server for integrated protein-protein docking". Nature Protocols. 15 (5): 1829-1852. 10.1038/s41596-020-0312-x.
[28] Y. Wang, M. Liu, and J. Gao. (2020). "Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions". Proceedings of the National Academy of Sciences. 117 (25): 13967-13974. 10.1073/pnas.2008209117.
[29] Z. Nain, F. Abdulla, M. M. Rahman, M. M. Karim, M. S. A. Khan, S. B. Sayed, S. Mahmud, S. M. R. Rahman, M. M. Sheam, Z. Haque, and U. K. Adhikari. (2020). "Proteome-wide screening for designing a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches". Journal of Biomolecular Structure and Dynamics. 38 (16): 4850-4867. 10.1080/07391102.2019.1692072.
[30] V. T. Adeleke, A. A. Adeniyi, M. A. Adeleke, M. Okpeku, and D. Lokhat. (2021). "The design of multiepitope vaccines from plasmids of diarrheagenic Escherichia coli against diarrhoea infection: Immunoinformatics approach". Infection, Genetics and Evolution. 91 : 104803. 10.1016/j.meegid.2021.104803.
[31] F. Khan and A. Kumar. (2021). "An integrative docking and simulation-based approach towards the development of epitope-based vaccine against enterotoxigenic Escherichia coli". Network Modeling Analysis in Health Informatics and Bioinformatics. 10 (1): 11. 10.1007/s13721-021-00287-6.
[32] K. K. Jensen, M. Andreatta, P. Marcatili, S. Buus, J. A. Greenbaum, Z. Yan, A. Sette, B. Peters, and M. Nielsen. (2018). "Improved methods for predicting peptide binding affinity to MHC class II molecules". Immunology. 154 (3): 394-406. 10.1111/imm.12889.
[33] S. Paul, J. Sidney, B. Peters, and A. Sette. (2014). "Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes". Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. 10.1145/2649387.2660842.
[34] M. Tahir Ul Qamar, A. Rehman, K. Tusleem, U. A. Ashfaq, M. Qasim, X. Zhu, I. Fatima, F. Shahid, and L. L. Chen. (2020). "Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics and in silico approaches". PLoS One. 15 (12): e0244176. 10.1371/journal.pone.0244176.
[35] S. F. Ahmed, A. A. Quadeer, J. P. Barton, and M. R. McKay. (2020). "Cross-serotypically conserved epitope recommendations for a universal T cell-based dengue vaccine". PLOS Neglected Tropical Diseases. 14 (9): e0008676. 10.1371/journal.pntd.0008676.
[36] M. C. Jespersen, B. Peters, M. Nielsen, and P. Marcatili. (2017). "BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes". Nucleic Acids Research. 45 (W1): W24-W29. 10.1093/nar/gkx346.
[37] R. Umitaibatin, A. H. Harisna, M. M. Jauhar, P. H. Syaifie, A. G. Arda, D. W. Nugroho, D. Ramadhan, E. Mardliyati, W. Shalannanda, and I. Anshori. (2023). "Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein". Vaccines (Basel). 11 (2). 10.3390/vaccines11020399.
[38] D. D. Martinelli. (2022). "In silico vaccine design: A tutorial in immunoinformatics". Healthcare Analytics. 2. 10.1016/j.health.2022.100044.
[39] M. Yu, Y. Zhu, Y. Li, Z. Chen, Z. Li, J. Wang, Z. Li, F. Zhang, and J. Ding. (2022). "Design of a Recombinant Multivalent Epitope Vaccine Based on SARS-CoV-2 and Its Variants in Immunoinformatics Approaches". Frontiers in Immunology. 13 : 884433. 10.3389/fimmu.2022.884433.
[40] N. Khatoon, R. K. Pandey, and V. K. Prajapati. (2017). "Exploring Leishmania secretory proteins to design B and T cell multi-epitope subunit vaccine using immunoinformatics approach". Scientific Reports. 7 (1): 8285. 10.1038/s41598-017-08842-w.
[41] S. Kanse, M. Khandelwal, R. K. Pandey, M. Khokhar, N. Desai, and B. V. Kumbhar. (2023). "Designing a Multi-Epitope Subunit Vaccine against VP1 Major Coat Protein of JC Polyomavirus". Vaccines (Basel). 11 (7). 10.3390/vaccines11071182.
[42] E. Behmard, B. Soleymani, A. Najafi, and E. Barzegari. (2020). "Immunoinformatic design of a COVID-19 subunit vaccine using entire structural immunogenic epitopes of SARS-CoV-2". Scientific Reports. 10 (1): 20864. 10.1038/s41598-020-77547-4.
[43] O. O. Oluwagbemi, E. K. Oladipo, E. O. Dairo, A. E. Ayeni, B. A. Irewolede, E. M. Jimah, M. P. Oyewole, B. M. Olawale, H. M. Adegoke, and A. J. Ogunleye. (2022). "Computational construction of a glycoprotein multi-epitope subunit vaccine candidate for old and new South-African SARS-CoV-2 virus strains". Informatics in Medicine Unlocked. 28 : 100845. 10.1016/j.imu.2022.100845.
[44] R. Uddin and K. Khan. (2022). "A Comparative Computational Analysis Approach to Predict Significant Protein-Protein Interactions of Human and Vancomycin Resistant Enterococcus faecalis (VRE) to Prioritize Potential Drug Targets". Letters in Drug Design & Discovery. 19 (2): 123-143. 10.2174/1570180818666211006125332.
[45] N. Chinthakunta, S. Cheemanapalli, S. Chinthakunta, C. M. Anuradha, and S. K. Chitta. (2018). "A new insight into identification of in silico analysis of natural compounds targeting GPR120". Network Modeling Analysis in Health Informatics and Bioinformatics. 7 (1): 8. 10.1007/s13721-018-0166-0.
[46] A. Singh, R. Kaushik, A. Mishra, A. Shanker, and B. Jayaram. (2016). "ProTSAV: A protein tertiary structure analysis and validation server". Biochimica et Biophysica Acta. 1864 (1): 11-9. 10.1016/j.bbapap.2015.10.004.
[47] R. A. Laskowski, N. Furnham, and J. M. Thornton. (2013). "The Ramachandran Plot And Protein Structure Validation". Biomolecular Forms and Functions. 62-75. 10.1142/9789814449144_0005.
[48] N. Alam, I. M. Budiarsa, and D. Tureni. (2020). "Prediksi Struktur Tiga Dimensi Protein β-NGF (Nerve Growth Factor) Burung Merpati (Columba livia)". Jurnal Ilmiah Sains. 20 (2). 10.35799/jis.20.2.2020.28857.
[49] G. A. Jeffrey.(1997)." An Introduction to Hydrogen Bonding". Oxford University Press, New York.
[50] Z. Mao, H. Xiao, P. Shen, Y. Yang, J. Xue, Y. Yang, Y. Shang, L. Zhang, X. Li, Y. Zhang, Y. Du, C. C. Chen, R. T. Guo, and Y. Zhang. (2022). "KRAS(G12D) can be targeted by potent inhibitors via formation of salt bridge". Cell Discovery. 8 (1): 5. 10.1038/s41421-021-00368-w.
[51] F. Naufa, R. Mutiah, and Y. Y. A. Indrawijaya. (2022). "In Silico Studies on The Potential of Green Tea Catechin Compounds (Camellia sinensis) as Antiviral of SARS CoV-2 Againts Spike Glycoprotein (6LZG) and Main Protease (5R7Y)". Journal of Food and Pharmaceutical Sciences. 584-596. 10.22146/jfps.3580.
[52] K. P. Tan, K. Singh, A. Hazra, and M. S. Madhusudhan. (2021). "Peptide bond planarity constrains hydrogen bond geometry and influences secondary structure conformations". Current Research in Structural Biology. 3 : 1-8. 10.1016/j.crstbi.2020.11.002.
[53] H. Li, H. Liu, K. Chen, W. Feng, and J. Guo. (2014). "HSV-2 increases TLR4-dependent phosphorylated IRFs and IFN-beta induction in cervical epithelial cells (INM9P.460)". The Journal of Immunology. 192 (Supplement_1): 189.13-189.13. 10.4049/jimmunol.192.Supp.189.13.
[54] J. A. West, S. M. Gregory, and B. Damania. (2012). "Toll-like receptor sensing of human herpesvirus infection". Front Cell Infect Microbiol. 2 : 122. 10.3389/fcimb.2012.00122.
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