Design of HIV-1 Peptide-Based Vaccine from Matrix Protein p17: Immunoinformatics Approach

Rosario Trijuliamos Manalu; Meilisa Rahmasari; Fathin Hamida

doi:10.55927/ajha.v2i1.4134

Authors

Rosario Trijuliamos Manalu National Institute of Science and Technology
Meilisa Rahmasari National Institute of Science and Technology
Fathin Hamida National Institute of Science and Technology

DOI:

https://doi.org/10.55927/ajha.v2i1.4134

Keywords:

Epitop, HIV, Immunoinformatic, Vaccine Design

Abstract

HIV/AIDS infection is a spectrum of infectious diseases of the immune system. Rapid transmission causes difficulty in overcoming this disease. This studied aims to determine potential peptides as vaccine candidates, and to determine the physicochemical properties and homologous properties of vaccine candidates. This studied used a processing method with an immunoinformatics approached and used samples from the p17 matrix protein sequence with PDB code 2HMX. All stages were carried out used the appropriate web server and application. From sequence analysis, selected T-cell and B-cell epitopes was obtained. After designing the vaccine candidate from T-cell and B-cell epitopes, the final stepped was to perform 2D and 3D visualization of the vaccine candidate. The researched shows that the peptide were as follows, adjuvant-EAAAK-GSEELRSLY-AAY-NNSQVSQNY-GPG PG-TGSEELRSLYNTIAV-KK-QPSLQTGSEELRS -KK-DVKDTKEALDK. The physicochemical properties of the HIV vaccine candidate had a total of 116 amino acids, a molecular weight of 12871.66 g/mol, a theoretical pI of 9.58, a number of negative residues 13, a number of positively charged residues 24, the extinction coefficient was 7825 m²/mol, the stability index was 59, 77, aliphatic index 64.74, average hydrophobicity -0.958. The results of the homologous analysis of the matrix protein p17 vaccine candidate stated that the amino acid residues that made up the peptide were not homologous or did not caused an autoimmune response when used as a vaccine candidate.

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References

Adhiputra, Anak Agung Ngurah. (2018). HIV/AIDS Model Layanan Profesional Konseling Berbasis Front and Analysis. Psikosian : Yogyakarta.

Ahmad, M. M., & Komari, N. (2022). Pemodelan Calponin Ikan Gabus (Channa striata) dengan Phyre2 dan Interaksi dengan Protein Lain. Jurnal Natural Scientiae, 2(1), 19–31. https://doi.org/10.20527/jns.v2i1.4790.

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), 1–15. https://doi.org/10.1038/s41598-022-11851-z.

Alom, M. W., Shehab, M. N., Sujon, K. M., & Akter, F. (2021). Exploring E, NS3, and NS5 proteins to design a novel multi-epitope vaccine candidate against West Nile Virus: An in-silico approach. Informatics in Medicine Unlocked, 25, 100644. https://doi.org/10.1016/j.imu.2021.100644.

Balupuri, A., & Cho, S. J. (2013). Exploration of the Binding Mode of Indole Derivatives as Potent HIV-1 Inhibitors Using Molecular Docking Simulations. Journal of the Chosun Natural Science, 6(3), 138–142. https://doi.org/10.13160/ricns.2013.6.3.138.

Behera, S. K., Sabarinath, T., Mishra, P. K. K., Deneke, Y., Kumar, A., Chandrasekar, S., Senthilkumar, K., Verma, M., Ganesh, B., Gurav, A., & Hota, A. (2021). Immunoinformatic Study of Recombinant LigA/BCon1-5 Antigen and Evaluation of Its Diagnostic Potential in Primary and Secondary Binding Tests for Serodiagnosis of Porcine Leptospirosis. Pathogens, 10(9). https://doi.org/10.3390/PATHOGENS10091082.

Behmard, E., Soleymani, B., Najafi, A., & Barzegari, E. (2020). Immunoinformatic design of a COVID-19 subunit vaccine using entire structural immunogenic epitopes of SARS-CoV-2. Scientific Reports, 10(1), 1–12. https://doi.org/10.1038/s41598-020-77547-4.

Caccuri, F., Neves, V., Gano, L., Correia, J. D. G., Oliveira, M. C., Mazzuca, P., Caruso, A., & Castanho, M. (2022). The HIV-1 Matrix Protein p17 Does Cross the Blood-Brain Barrier. Journal of Virology, 96(1). https://doi.org/10.1128/jvi.01200-21.

Chatanaka, M. K., Ulndreaj, A., Sohaei, D., & Prassas, I. (2022). Immunoinformatics: Pushing the boundaries of immunology research and medicine. ImmunoInformatics, 5(December 2021), 100007. https://doi.org/10.1016/j.immuno.2021.100007.

Chen, J., Li, C., Li, R., Chen, H., Chen, D., & Li, W. (2021). Exosomes in HIV infection. Current Opinion in HIV and AIDS, 16(5), 262–270. https://doi.org/10.1097/COH.0000000000000694.

Emanuele Fanales-Belasio, Mariangela Raimondo, B. S. and S. B. (2011). HIV virology and pathogenetic mechanisms of infection: a brief overview. Ann Ist Super Sanità, 47(4), 363–372. https://doi.org/10.4415/ANN.

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), 1–23. https://doi.org/10.1038/s41598-021-99227-7.

Fiorentini, S., Giagulli, C., Caccuri, F., Magiera, A. K., & Caruso, A. (2010). HIV-1 matrix protein p17: A candidate antigen for therapeutic vaccines against AIDS. Pharmacology and Therapeutics, 128(3), 433–444. https://doi.org/10.1016/j.pharmthera.2010.08.005.

Gustiananda, M., Sulistyo, B. P., Agustriawan, D., & Andarini, S. (2021). Immunoinformatics analysis of sars-cov-2 orf1ab polyproteins to identify promiscuous and highly conserved t-cell epitopes to formulate vaccine for indonesia and the world population. Vaccines, 9(12). https://doi.org/10.3390/vaccines9121459.

Khalili, S., Jahangiri, A., Borna, H., Ahmadi Zanoos, K., & Amani, J. (2014). Computational vaccinology and epitope vaccine design by immunoinformatics. Acta Microbiologica et Immunologica Hungarica, 61(3), 285–307. https://doi.org/10.1556/AMicr.61.2014.3.4.

Langton, D. J., Bourke, S. C., Lie, B. A., Reiff, G., Natu, S., Darlay, R., Burn, J., & Echevarria, C. (2021). The influence of HLA genotype on the severity of COVID-19 infection. Hla, 98(1), 14–22. https://doi.org/10.1111/tan.14284.

Li, L., & Petrovsky, N. (2017). Molecular Adjuvants for DNA Vaccines. Current Issues in Molecular Biology, 22, 17–40. https://doi.org/10.21775/CIMB.022.017.

Massiah, M. A., Starich, M. R., Paschall, C., Summers, M. F., Christensen, A. M., & Sundquist, W. I. (1994). Three-dimensional Structure of the Human Immunodeficiency Virus Type 1 Matrix Protein. Journal of Molecular Biology, 244(2), 198–223. https://doi.org/10.1006/JMBI.1994.1719.

Oenarta, D. G. (2019). Hiv Dan Hpv. Widya Medika, 5(2).

Patronov, A., & Doytchinova, I. (2013). T-cell epitope vaccine design by immunoinformatics. Open Biology, 3(JAN). https://doi.org/10.1098/rsob.120139.

Rahadianti, D. (2022). Sistem Imunitas Alamiah dan Sistem Imunitas Adaptif. Natural Immunity System and Adaptive Immunity System. Nusantara Hasana Journal, 2(3).

Rezaldi, F., Taupiqurrohman., Fadillah, M., Rochmat, Agus., Humaedi, Aji., Fadhilah, Fitri. (2021). Identifikasi Kandidat Vaksin COVID-19 Berbasis Peptida dari Glikoprotein Spike SARS CoV-2 untuk Ras Asia secara In Silico. Jurnal Biotek Medisiana Indonesia, 10 (1), 77–85. http://ejournal2.litbang.kemkes.go.id/index.php/jbmi/article/view/5031%0A2299

Sanami, S., Rafieian-Kopaei, M., Dehkordi, K. A., Pazoki-Toroudi, H., Azadegan-Dehkordi, F., Mobini, G. R., Alizadeh, M., Nezhad, M. S., Ghasemi-Dehnoo, M., & Bagheri, N. (2022). In silico design of a multi-epitope vaccine against HPV16/18. BMC Bioinformatics, 23(1), 1–24. https://doi.org/10.1186/s12859-022-04784-x.

Setiarto, Haryo Bimo. (2021). Penanganan Virus HIV/AIDS. Deepublish : Yogyakarta.

Sharma, S., Kumari, V., Kumbhar, B. V., Mukherjee, A., Pandey, R., & Kondabagil, K. (2021). Immunoinformatics approach for a novel multi-epitope subunit vaccine design against various subtypes of Influenza A virus. Immunobiology, 226(2), 152053. https://doi.org/10.1016/j.imbio.2021.152053.

Simarmata, S. N., Toepak, E. P., Rahman, S., & Angga, S. C. (2022). Design of Vaccine Candidate Based on Ebola Virus Epitop With In Silico Approach. Jurnal Sains dan Terapan Kimia, 16(1), 57. https://doi.org/10.20527/jstk.v16i1.12167.

Sinha, S., Grewal, R. K., & Roy, S. (2020). Modeling phage–bacteria dynamics. In Methods in Molecular Biology (Vol. 2131). https://doi.org/10.1007/978-1-0716-0389-5_18.

Subekti, D. T., Artama, W., Poerwanto, S., Sulistyaningsih, E., & Sari, Y. (2012). Analisis Imunogenisitas Protein GRA1 dari Hasil Kloning Gen GRA1 Takizoit Toxoplasma gondii. Berita Biologi, 11(1), 43–52.

Tambunan, U. S. F., & Alamudi, S. (2010). Designing cyclic peptide inhibitor of dengue virus NS3-NS2B protease by using molecular docking approach. Bioinformation, 5(6), 250–254. https://doi.org/10.6026/97320630005250.

Zeinolabediny, Y., Caccuri, F., Colombo, L., Morelli, F., Romeo, M., Rossi, A., Schiarea, S., Ciaramelli, C., Airoldi, C., Weston, R., Donghui, L., Krupinski, J., Corpas, R., García-Lara, E., Sarroca, S., Sanfeliu, C., Slevin, M., Caruso, A., Salmona, M., & Diomede, L. (2017). HIV-1 matrix protein p17 misfolding forms toxic amyloidogenic assemblies that induce neurocognitive disorders. Scientific Reports, 7(1), 1–18. https://doi.org/10.1038/s41598-017-10875-0