Viroinformatics study: polytope mapping of envelope glycoprotein to tackle HIV-2 infection and develop vaccine candidate

Viol Dhea Kharisma; Muhammad Hermawan Widyananda; Rasyadan Taufiq Probojati; Arif Nur Muhammad Ansori; Ahmad Affan Ali Murtadlo; Muhammad Badrut Tamam; Adhityo Wicaksono; Dora Dayu Rahma Turista

doi:10.55655/genbinesia.v1i1.6

Viol Dhea Kharisma Department of Biology, Faculty of Mathematic and Natural Sciences, Universitas Brawijaya, Malang, Indonesia
Muhammad Hermawan Widyananda Department of Biology, Faculty of Mathematic and Natural Sciences, Universitas Brawijaya, Malang, Indonesia
Rasyadan Taufiq Probojati Department of Agrotechnology, Faculty of Agriculture, Universitas Kadiri, Kediri, Indonesia
Arif Nur Muhammad Ansori Doctoral Program in Veterinary Science, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
Ahmad Affan Ali Murtadlo Computational Virology and Complexity Sciences Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia Foundation, Gresik, Indonesia
Muhammad Badrut Tamam Department of Biology, Faculty of Sciences and Technology, Universitas Muhammadiyah Lamongan, Lamongan, Indonesia
Adhityo Wicaksono Independent Researcher of Biotechnology in Jakarta, Indonesia
Dora Dayu Rahma Turista Biology Education Department, Faculty of Teacher Training and Education, Mulawarman University, Samarinda, Indonesia

DOI: https://doi.org/10.55655/genbinesia.v1i1.6

Keywords: Acquired Immune Deficiency Syndrome, B-cell, Bioinformatics, Human Immunodeficiency Virus, Retrovirus

Abstract

Human Immunodeficiency Virus type 2 (HIV-2) has been identified to exhibit an ability to resist antiretroviral administration and many scientists has predicted increases in the pathogenicity of HIV-2. The development of a vaccine against the type 1 virus (HIV-1) infection has reached the phase 3 clinical trial stage, but currently there is no information on the development of a vaccine against HIV-2. Vaccine development to trigger an increase in the coverage of the expansion of protection can be done through B cell polytope. This study aims to provide an important preliminary for the construction of vaccine candidates by identifying the peptides that make up the B cell polytope in the HIV-2 envelope glycoprotein region. The HIV-2 sequence was obtained from the database. The study followed by 3D modelling, prediction of linear B-cell epitope mapping, antigenicity, allergenicity, peptide properties, and immune simulation was carried out via a webserver. The 3D structure of the peptide was displayed through molecular visualization software. The results showed that the 23-mer peptides E1 'HPRYTGVKNIRDITLTEPGRGSD', F1 'NFIENRKGTQHN' 12-mer, M1 'YLKDQARLNS' 10-mer, N1 'PWVNDSIQPNWNNMTWQQWELQVRD' 25-mer, and O1 'KLQNSWNMGVQTO' can be used as a candidate polytope HIV-2 vaccine because it is recognized by B cells is an antigenic peptide with stable molecule, non-allergenic. The peptides trigger proliferation and activation of B cells to produces a humoral response and work as functionally protective antibody for neutralization of HIV-2.

Key words: Acquired Immune Deficiency Syndrome, B-cell, Bioinformatics, Human Immunodeficiency Virus, Retrovirus

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Author Biography

Arif Nur Muhammad Ansori, Doctoral Program in Veterinary Science, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia

Doctoral Program in Veterinary Science

References

1. Esbjörnsson J, Jansson M, Jespersen S, et al. HIV-2 as a model to identify a functional HIV cure. AIDS research and therapy. 2019; 16(1): 24
2. Campbell-Yesufu OT and Gandhi RT. Update on human immunodeficiency virus (HIV)-2 infection. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America. 2011; 52(6): 780–787
3. Nsagha DS, Njunda AL, Kamga HL, et al. HIV-1/HIV-2 co-infection among voluntary counselling and testing subjects at a regional hospital in Cameroon. African health sciences. 2012; 12(3): 276–281
4. Raugi DN, Nixon RS, Leong S, et al. HIV-2 Drug Resistance Genotyping from Dried Blood Spots. Journal of clinical microbiology. 2020; 59(1): e02303-20
5. Lee JH and Crotty S. HIV vaccinology: 2021 update. Seminars in immunology. 2021; 51: 101470
6. Baden LR, Stieh DJ, Sarnecki M, et al. Safety and immunogenicity of two heterologous HIV vaccine regimens in healthy, HIV-uninfected adults (TRAVERSE): a randomised, parallel-group, placebo-controlled, double-blind, phase 1/2a study. The lancet. HIV. 2020; 7(10): e688–e698
7. Agrawal L, Poullikkas T, Eisenhower S, et al. Viroinformatics-Based Analysis of SARS-CoV-2 Core Proteins for Potential Therapeutic Targets. Antibodies (Basel, Switzerland). 2021; 10(1): 3
8. Pouyanfard S, Spagnoli G, Bulli L, et al. Minor Capsid Protein L2 Polytope Induces Broad Protection against Oncogenic and Mucosal Human Papillomaviruses. Journal of virology. 2018; 92(4): e01930-17
9. Kharisma VD, Ansori ANM, Posa GAV, et al. Conserved B-cell epitope identification of envelope glycoprotein (GP120) HIV-1 to develop multi-strain vaccine candidate through bioinformatics approach. J Tekno Lab. 2021; 10(1): 06-13
10. Hartati FK, Djauhari AB, VD Kharisma (2021) Evaluation of Pharmacokinetic Properties, Toxicity, and Bioactive Cytotoxic Activity of Black Rice (Oryza sativa L.) as Candidates for Diabetes Mellitus Drugs by in silico. Biointerface Research in Applied Chemistry 11 (4), 12301-12311
11. Fahmi M, Kharisma VD, Ansori ANM, et al. Retrieval and Investigation of Data on SARS-CoV-2 and COVID-19 Using Bioinformatics Approach. Advances in Experimental Medicine and Biology. 2021; 1318: 839-857
12. Fadholly A, Ansori ANM, Kharisma VD, et al. Immunobioinformatics of Rabies Virus in Various Countries of Asia: Glycoprotein Gene. Research Journal of Pharmacy and Technology. 2021: 86(85): 85
13. Rantam FA, Kharisma VD, Sumartono C, et al. Molecular docking and dynamic simulation of conserved B cell epitope of SARS-CoV-2 glycoprotein Indonesian isolates: an immunoinformatic approach. F1000Research. 2021; 10(813): 813
14. Banerjee S, Majumder K, Gutierrez GJ, et al. Immuno-informatics approach for multi-epitope vaccine designing against SARS-CoV-2. bioRxiv: the preprint server for biology. 2020; 07(23): 218529
15. Widyananda MH, Pratama SK, Samoedra RS, et al. Molecular docking study of sea urchin (Arbacia lixula) peptides as multi-target inhibitor for non-small cell lung cancer (NSCLC) associated proteins. Journal of Pharmacy & Pharmacognosy Research. 2021; 9(4): 484-496
16. Prahasanti C, Nugraha AP, Kharisma VD, et al. A bioinformatic approach of hydroxyapatite and polymethylmethacrylate composite exploration as dental implant biomaterial. Journal of Pharmacy & Pharmacognosy Research. 2021; 9(5): 746-754
17. Luqman A, Kharisma VD, Ruiz RA, et al. In Silico and in Vitro Study of Trace Amines (TA) and Dopamine (DOP) Interaction with Human Alpha 1-Adrenergic Receptor and the Bacterial Adrenergic Receptor QseC. Cellular physiology and biochemistry. International journal of experimental cellular physiology, biochemistry, and pharmacology. 2020; 54(5): 888–898
18. Purnama ER and Kharisma VD. Epitope mapping of capsid protein L1 from human papillomavirus to development cervical cancer vaccine through computational study. Journal of Physics: Conference Series. 2018; 1108(1): 012096
19. Ansori ANM, Kharisma VD, Antonius Y, et al. Immunobioinformatics analysis and phylogenetic tree construction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Indonesia: spike glycoprotein gene. J Tekno Lab. 2020; 9(1): 13-20
20. Adianingsih OR and Kharisma VD. Study of B cell epitope conserved region of the Zika virus envelope glycoprotein to develop multi-strain vaccine. J Appl Pharm Scie. 2019; 9(01): 098-103
21. Doytchinova IA and Flower DR. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC bioinformatics. 2007; 8(4)
22. Pan W, Chen DS, Lu YJ, et al. Bioinformatic prediction of the epitopes of Echinococcus granulosus antigen 5. Biomedical reports. 2017; 6(2): 181–187
23. Wilen CB, Tilton JC, Doms RW. HIV: cell binding and entry. Cold Spring Harbor perspectives in medicine. 2012; 2(8): a006866