Author(s): Achmad Makin Amin, Arif Nur Muhammad Ansori, Viol Dhea Kharisma, Days Chelsealani Kaaro, Muhammad Hermawan Widyananda, Arli Aditya Parikesit, Joko Pebrianto Trinugroho, Dora Dayu Rahma Turista, Imam Rosadi, Sergazy Duyssembaev, Maksim Rebezov, Pavel Burkov, Pavel Scherbakov, Vikash Jakhmola, Rahadian Zainul

Email(s): rahadianzmsiphd@fmipa.unp.ac.id

DOI: 10.52711/0974-360X.2024.00317   

Address: Achmad Makin Amin1, Arif Nur Muhammad Ansori2, Viol Dhea Kharisma3, Days Chelsealani Kaaro4, Muhammad Hermawan Widyananda3,5, Arli Aditya Parikesit6, Joko Pebrianto Trinugroho7, Dora Dayu Rahma Turista8, Imam Rosadi9, Sergazy Duyssembaev10, Maksim Rebezov11,12, Pavel Burkov13, Pavel Scherbakov14, Vikash Jakhmola15, Rahadian Zainul16*
1Master Program of Biotechnology, Graduate School, Universitas Gadjah Mada, Yogyakarta, Indonesia.
2Postgraduate School, Universitas Airlangga, Surabaya, Indonesia.
3Division of Molecular Biology and Genetics, Generasi Biologi Indonesia Foundation, Gresik, Indonesia.
4Bachelor Program of Biotechnology, Technical University of Berlin, Berlin, Germany.
5Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Malang, Indonesia
6Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia.
7Bioinformatics and Data Science Research Center, Bina Nusa

Published In:   Volume - 17,      Issue - 5,     Year - 2024


ABSTRACT:
T cell immunity, like responses of CD4+and CD8+ T-cell, plays an important role to fight against viral infections and pathological harm. Several previous studies have shown the results that rabies virus (RABV) protein can act as an ideal receptor for rabies neuroseptic vaccine by inducing a response of T-cell. In this research, we evaluated possible vaccine epitopes based on the Rabies virus sequence and human lymphocyte antigen (HLA) distribution. First, this study used the rabies virus protein P sequence obtained from the NCBI database. Next, we predicted rabies CTL protein epitopes based on the frequency of HLA-I distribution allele locus A, B, and C in Southeast Asia region (> 1%) using Immune Epitope Database and Analysis Resource (iedb.org). Our results predict the presence of 12 epitopes of the protein P RABV. A cluster analysis of epitopes shows that seven P-protein clusters cover 97.47% of the Southeast Asian population. After a conservative epitope analysis, 8 epitopes of protein P showed protection in 11 different types of isolated Rabies virus. Finally, 4 epitopes (SQTVEEIISY119-128; RSSGIFLYNF218-227, ASGPPALEW178-186, IISYVTVNF125-133) were used to vaccinate 97.47% of people in Southeast Asia. Our results suggest that both single and combined CTL epitopes which were predicted in this study can be used as a more effective alternative vaccine against rabies virus’ infections and development


Cite this article:
Achmad Makin Amin, Arif Nur Muhammad Ansori, Viol Dhea Kharisma, Days Chelsealani Kaaro, Muhammad Hermawan Widyananda, Arli Aditya Parikesit, Joko Pebrianto Trinugroho, Dora Dayu Rahma Turista, Imam Rosadi, Sergazy Duyssembaev, Maksim Rebezov, Pavel Burkov, Pavel Scherbakov, Vikash Jakhmola, Rahadian Zainul. T-Cell Epitope Vaccine Prediction Analysis Targeting Phosphoprotein (P) Rabies Virus Based on the Presence of HLA-I Alleles A, B, and C Loci Throughout Southeast Asia: An Immunoinformatics Study. Research Journal of Pharmacy and Technology. 2024; 17(5):2001-2008 doi: 10.52711/0974-360X.2024.00317

Cite(Electronic):
Achmad Makin Amin, Arif Nur Muhammad Ansori, Viol Dhea Kharisma, Days Chelsealani Kaaro, Muhammad Hermawan Widyananda, Arli Aditya Parikesit, Joko Pebrianto Trinugroho, Dora Dayu Rahma Turista, Imam Rosadi, Sergazy Duyssembaev, Maksim Rebezov, Pavel Burkov, Pavel Scherbakov, Vikash Jakhmola, Rahadian Zainul. T-Cell Epitope Vaccine Prediction Analysis Targeting Phosphoprotein (P) Rabies Virus Based on the Presence of HLA-I Alleles A, B, and C Loci Throughout Southeast Asia: An Immunoinformatics Study. Research Journal of Pharmacy and Technology. 2024; 17(5):2001-2008 doi: 10.52711/0974-360X.2024.00317   Available on: https://rjptonline.org/AbstractView.aspx?PID=2024-17-5-13


REFERENCES:
1.    CDC. https://www.cdc.gov/rabies/about.html. 2020; U.S. Department of Health & Human Services.
2.    WHO. https://www.who.int/health-topics/rabies#tab=tab_1. 2022; World Health Organization.
3.    WHO. https://www.who.int/news-room/fact-sheets/detail/rabies. 2021; World Health Organization.
4.    Zhang Y, Chen C, Deng C, Zhang C, Li N, Wang Z, Zhao L, & Zhang B. A Novel Rabies Vaccine Based on Infectious Propagating Particles dericed from Hybrid VEEV-Rabies Replicon. EBioMedicine. 2020; 56-102819. DOI: 10.1016/j.ebiom.2020.102819
5.    Horwitz JA, Jenni S, Harrison SC, Whelan SPJ. Structure of a rabies virus polymerase complex from electron cryo-microscopy. Proc Natl Acad Sci U S A. 2020; 117(4): 2099-2107. DOI: 10.1073/pnas.1918809117.
6.    Fouquet B, Nikolic J, Larrous F, Bourhy H, Wirblich C, Lagaudrière-Gesbert C, Blondel D. Focal adhesion kinase is involved in rabies virus infection through its interaction with viral phosphoprotein P. J Virol. 2015; 89(3): 1640-51. DOI: 10.1128/JVI.02602-14.
7.    Okada K, Ito N, Yamaoka S, Masatani T, Ebihara H, Goto H, Nakagawa K, Mitake H, Okadera K, Sugiyama M. Roles of the Rabies Virus Phosphoprotein Isoforms in Pathogenesis. J Virol. 2016; 90(18): 8226-37. DOI: 10.1128/JVI.00809-16.
8.    Lu Y, Cheng L, Liu J. Optimization of Inhibitory Peptides Targeting Phosphoprotein of Rabies Virus. Int J Pept Res Ther. 2020; 26(2): 1043-1049. DOI: 10.1007/s10989-019-09906-3.
9.    Kammouni W, Wood H, Saleh A, Appolinario CM, Fernyhough P, Jackson AC. Rabies virus phosphoprotein interacts with mitochondrial Complex I and induces mitochondrial dysfunction and oxidative stress. J Neurovirol. 2015; 21(4): 370-82. DOI: 10.1007/s13365-015-0320-8.
10.    Kammouni W, Wood H, Jackson AC. Serine residues at positions 162 and 166 of the rabies virus phosphoprotein are critical for the induction of oxidative stress in rabies virus infection. J Neurovirol. 2017; 23(3): 358-368. DOI: 10.1007/s13365-016-0506-8.
11.    Albertini AA, Ruigrok RW, Blondel D. Rabies virus transcription and replication. Adv Virus Res. 2011; 79:1-22. DOI: 10.1016/B978-0-12-387040-7.00001-9.
12.    Zumla A. Mandell, Douglas, and Bennett's principles and practice of infectious diseases. Lancet Infect Dis. 2010;10(5): 303–4. DOI: 10.1016/S1473-3099(10)70089-X.
13.    De Groot AS, Moise L, Terry F, Gutierrez AH, Hindocha P, Richard G, Hoft DF, Ross TM, Noe AR, Takahashi Y, Kotraiah V, Silk SE, Nielsen CM, Minassian AM, Ashfield R, Ardito M, Draper SJ, Martin WD. Better Epitope Discovery, Precision Immune Engineering, and Accelerated Vaccine Design Using Immunoinformatics Tools. Front Immunol. 2020; 11: 442. DOI: 10.3389/fimmu.2020.00442.
14.    Oli AN, Obialor WO, Ifeanyichukwu MO, Odimegwu DC, Okoyeh JN, Emechebe GO, Adejumo SA, Ibeanu GC. Immunoinformatics and Vaccine Development: An Overview. Immunotargets Ther. 2020; 9: 13-30. DOI: 10.2147/ITT.S241064.
15.    Patronov A, Doytchinova I. T-cell epitope vaccine design by immunoinformatics. Open Biol. 2013; 3(1): 120139. DOI: 10.1098/rsob.120139.
16.    Bui HH, Sidney J, Dinh K, Southwood S, Newman MJ, Sette A. Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics. 2006; 7: 153. DOI: 10.1186/1471-2105-7-153.
17.    Calis JJ, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, Keşmir C, Peters B. Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol. 2013; 9(10): e1003266. DOI: 10.1371/journal.pcbi.1003266.
18.    Hoa BK, Hang NT, Kashiwase K, Ohashi J, Lien LT, Horie T, Shojima J, Hijikata M, Sakurada S, Satake M, Tokunaga K, Sasazuki T, Keicho N. HLA-A, -B, -C, -DRB1 and -DQB1 alleles and haplotypes in the Kinh population in Vietnam. Tissue Antigens. 2008; 71(2): 127-34. DOI: 10.1111/j.1399-0039.2007.00982.x.
19.    Jinam TA, Saitou N, Edo J, Mahmood A, Phipps ME. Molecular analysis of HLA Class I and Class II genes in four indigenous Malaysian populations. Tissue Antigens. 2010; 75(2): 151-8. DOI: 10.1111/j.1399-0039.2009.01417.x.
20.    Pillai NE, Okada Y, Saw WY, Ong RT, Wang X, Tantoso E, Xu W, Peterson TA, Bielawny T, Ali M, Tay KY, Poh WT, Tan LW, Koo SH, Lim WY, Soong R, Wenk M, Raychaudhuri S, Little P, Plummer FA, Lee EJ, Chia KS, Luo M, De Bakker PI, Teo YY. Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations. Hum Mol Genet. 2014; 23(16): 4443-51. DOI: 10.1093/hmg/ddu149.
21.    Kongmaroeng C, Romphruk A, Puapairoj C, Leelayuwat C, Kulski JK, Inoko H, Dunn DS, Romphruk AV. HLA alleles and haplotypes in Burmese (Myanmarese) and Karen in Thailand. Tissue Antigens. 2015; 86(3): 199-204. DOI: 10.1111/tan.12637.
22.    Pradana KA, Widjaya MA, Wahjudi M. Indonesians Human Leukocyte Antigen (HLA) Distributions and Correlations with Global Diseases. Immunol Invest. 2020; 49(3): 333-363. DOI: 10.1080/08820139.2019.1673771.
23.    Satapornpong P, Jinda P, Jantararoungtong T, Koomdee N, Chaichan C, Pratoomwun J, Na Nakorn C, Aekplakorn W, Wilantho A, Ngamphiw C, Tongsima S, Sukasem C. Genetic Diversity of HLA Class I and Class II Alleles in Thai Populations: Contribution to Genotype-Guided Therapeutics. Front Pharmacol. 2020; 11: 78. DOI: 10.3389/fphar.2020.00078.
24.    Do MD, Le LGH, Nguyen VT, Dang TN, Nguyen, NH, Vu HA, Mai TP. High-Resolution HLA Typing of HLA-A, -B, -C -DRB1, and -DQB1 Kinh Vietnamese by Using Next-Generation Sequencing. Front in Genetics. 2020; 11(383): 1-10. DOI: 10.3389/fgene.2020.00383
25.    Long T, Zhang B, Fan R, Wu Y, Mo M, Luo J, Chang Y, Tian Q, Mei M, Jiang H, Luo Y, Guo X. Phosphoprotein Gene of Wild-Type Rabies Virus Plays a Role in Limiting Viral Pathogenicity and Lowering the Enhancement of BBB Permeability. Front Microbiol. 2020; 11: 109. DOI: 10.3389/fmicb.2020.00109.
26.    Husen SA, Setyawan MF, Syadzha MF, Susilo RJK, Hayaza S, Ansori ANM, Alamsjah MA, Ilmi ZN, Wulandari PAC, Pudjiastuti P, Awang P, Winarni D. A Novel Therapeutic effects of Sargassum ilicifolium Alginate and Okra (Abelmoschus esculentus) Pods extracts on Open wound healing process in Diabetic Mice. Research J. Pharm. and Tech 2020; 13(6): 2764-2770. DOI: 10.5958/0974-360X.2020.00491.6
27.    Husen SA, Wahyuningsih SPA, Ansori ANM, Hayaza S, Susilo RJK, Winarni D, Punnapayak H, Darmanto W. Antioxidant Potency of Okra (Abelmoschus esculentus Moench) Pods Extract on SOD Level and Tissue Glucose Tolerance in Diabetic Mice. Res J Pharm Technol. 2019; 12(12): 5683. DOI: 10.5958/0974-360X.2019.00983.1
28.    Fadholly A, Ansori ANM, Utomo B. Anticancer Effect of Naringin on Human Colon Cancer (WiDr Cells): In Vitro Study. Research Journal of Pharmacy and Technology. 2022; 15(2): 885-888. DOI: 10.52711/0974-360X.2022.00148
29.    Fadholly A, Ansori ANM, Sucipto TH. An overview of naringin: Potential anticancer compound of citrus fruits. Res J Pharm Technol. 2020; 13(11): 5613-5619. DOI: 10.5958/0974-360X.2020.00979.8
30.    Ansori ANM, Kharisma VD, Solikhah TI. Medicinal properties of Muntingia calabura L.: A Review. Res J Pharm Technol. 2021; 14(8): 4509-2. DOI: 10.52711/0974-360X.2021.00784
31.    Fadholly A, Ansori ANM, Kharisma VD, Rahmahani J, Tacharina MR. Immunobioinformatics of Rabies Virus in Various Countries of Asia: Glycoprotein Gene. Res J Pharm Technol. 2021; 14(2): 883-886. DOI: 10.5958/0974-360X.2021.00157.8
32.    Kharisma VD, Ansori ANM, Jakhmola V, Rizky WC, Widyananda MH, Probojati RT, Murtadlo AAA, Rebezov M, Scherbakov P, Burkov P, Matrosova Y, Romanov A, Sihombing MAEM, Antonius Y, Zainul R. Multi-strain human papillomavirus (HPV) vaccine innovation via computational study: A mini review. Res J Pharm Technol. 2022; 15(8): 3802-7. DOI: 10.52711/0974-360X.2022.00638
33.    Galvez-Romero G, Salas-Roja M, Pompa-Mera EN, Chavez-Rueda K, Aguilar-Setien A. Addition of C3d-P28 Adjuvant to a Rabies DNA Vaccine Encoding the G5 Linear Epiotpr Enhances the Humoral Immune System Response and Confers Protein. Vaccine. 2018; 36(2018): 292-298. DOI: 10.1016/j.vaccine.2017.11.047
34.    Proboningrat A, Kharisma VD, Ansori ANM, Rahmawati R, Fadholly A, Posa GAV, Sudjarwo SA, Rantam FA, Achmad AB. In silico Study of Natural inhibitors for Human papillomavirus-18 E6 protein. Res J Pharm Technol. 2022; 15(3):1251-6. DOI: 10.52711/0974-360X.2022.00209
35.    Husen SA, Ansori ANM, Hayaza S, Susilo RJK, Zuraidah AA, Winarni D, Punnapayak H, Darmanto W. Therapeutic Effect of Okra (Abelmoschus esculentus Moench) Pods Extract on Streptozotocin-Induced Type-2 Diabetic Mice. Res J Pharm Technol. 2019; 12(8): 3703-3708. DOI: 10.5958/0974-360X.2019.00633.4
36.    Kharisma VD, Kharisma SD, Ansori ANM, Kurniawan HP, Witaningrum AM, Fadholly A, Tacharina MR. Antiretroviral Effect Simulation from Black Tea (Camellia sinensis) via Dual Inhibitors Mechanism in HIV-1 and its Social Perspective in Indonesia. Res J Pharm Technol. 2021; 14(1): 455-460. DOI: 10.5958/0974-360X.2021.00083.4
37.    Panagioti E, Klenerman P, Lee LN, van der Burg SH, & Arens R. Features of Effective T Cell-Inducing Vaccine Against Chronic Viral Infections. Front Immunol. 2018; 9(276): 1-11. DOI: 10.3389/fimmu.2018.002

Recomonded Articles:

Research Journal of Pharmacy and Technology (RJPT) is an international, peer-reviewed, multidisciplinary journal.... Read more >>>

RNI: CHHENG00387/33/1/2008-TC                     
DOI: 10.5958/0974-360X 

1.3
2021CiteScore
 
56th percentile
Powered by  Scopus


SCImago Journal & Country Rank


Recent Articles




Tags


Not Available