Conserved B-cell epitope identification of envelope glycoprotein (GP120) HIV-1 to develop multi-strain vaccine candidate through bioinformatics approach

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Viol Dhea Kharisma Arif Nur Muhammad Ansori https://orcid.org/0000-0002-1279-3904 Gabrielle Ann Villar Posa Wahyu Choirur Rizky Sofy Permana Arli Aditya Parikesit

Abstract

Acquired immune deficiency syndrome (AIDS) has been identified from US patients since 1981. AIDS is caused by infection with the human immunodeficiency virus type 1 (HIV-1) which is a retrovirus. HIV-1 gp120 can be recognized by the immune system because it is located outside the virion. The conserved region is identified in gp120, and it is recognized by an immune cell which then initiates specific immune responses, viral mutation escape, and increase vaccine protection coverage, a benefit derived from the conserved region-based vaccine design. However, previous researchers have little knowledge on this conserved region as a target for vaccine design. This paper explains how the conserved region of gp120 HIV-1 is a major target for vaccine design through a bioinformatics approach. The conserved region from gp120 was explored as a vaccine design target with a bioinformatics tool that consists of B-cell epitope mapping, vaccine properties, molecular docking, and dynamic simulation. The peptide vaccine candidate of B5 with the gp120 HIV-1 conserved region was found to provoke B-cell activation through a direct pathway, produce specific antibody, and increase protection from multi-strain viral infection.

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How to Cite
Kharisma, V., Ansori, A., Posa, G., Rizky, W., Permana, S., & Parikesit, A. (2021). Conserved B-cell epitope identification of envelope glycoprotein (GP120) HIV-1 to develop multi-strain vaccine candidate through bioinformatics approach. Jurnal Teknologi Laboratorium, 10(1), 06-13. https://doi.org/https://doi.org/10.29238/teknolabjournal.v10i1.274
Section
Virology

References

1. Douek DC, Roederer M, Koup RA. Emerging concepts in the immunopathogenesis of AIDS. Annu Rev Med. 2009;60:471-484. doi:10.1146/annurev.med.60.041807.123549
2. Acharya P, Lusvarghi S, Bewley CA, Kwong PD. HIV-1 gp120 as a therapeutic target: Navigating a moving labyrinth. Expert Opin Ther Targets. 2016;19(6):765-783. doi:10.1517/14728222.2015.1010513.HIV-1
3. Cuevas JM, Geller R, Garijo R, López-Aldeguer J, Sanjuán R. Extremely high mutation rate of HIV-1 in vivo. PLoS Biol. 2015;13(9):1-19. doi:10.1371/journal.pbio.1002251
4. Campbell-Yesufu OT, Gandhi RT. Update on human immunodeficiency virus (HIV)-2 infection. Clin Infect Dis. 2011;52(6):780-787. doi:10.1093/cid/ciq248
5. Castley A, Sawleshwarkar S, Varma R, et al. A national study of the molecular epidemiology of HIV-1 in. PLoS One. 2017;12(5):1-17. doi:10.1371/journal.pone.0170601
6. Gao Y, McKay PF, Mann JFS. Advances in HIV-1 vaccine development. Viruses. 2018;10(4):1-26. doi:10.3390/v10040167
7. Zahroh H, Ma’rup A, Tambunan USF, Parikesit AA. Immunoinformatics approach in designing epitopebased vaccine against meningitis-inducing bacteria (Streptococcus pneumoniae,Neisseria meningitidis,and Haemophilus influenzae type b). Drug Target Insights. 2016;10:19-29. doi:10.4137/DTI.S38458
8. Adianingsih OR, Kharisma VD. Study of B cell epitope conserved region of the Zika virus envelope glycoprotein to develop multi-strain vaccine. J Appl Pharm Sci. 2019;9(1):98-103. doi:10.7324/JAPS.2019.90114
9. Ansori ANM, Kharisma VD, Nugraha AP. Phylogenetic and pathotypic characterization of avian paramyxovirus serotype 1 (APMV-1) in Indonesia. Biochem Cell Arch. 2020;20(August):3023-3027. doi:10.35124/bca.2020.20.S1.3023
10. Bienert S, Waterhouse A, De Beer TAP, et al. The SWISS-MODEL Repository-new features and functionality. Nucleic Acids Res. 2017;45(D1):D313-D319. doi:10.1093/nar/gkw1132
11. Maxwell PI, Popelier PLA. Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective. J Comput Chem. 2017;38(29):2459-2474. doi:10.1002/jcc.24904
12. Jespersen MC, Peters B, Nielsen M, Marcatili P. BepiPred-2.0: Improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res. 2017;45(W1):W24-W29. doi:10.1093/nar/gkx346
13. Kharisma VD, Ansori ANM. Construction of epitope-based peptide vaccine against SARS-CoV-2: Immunoinformatics study. J Pure Appl Microbiol. 2020;14(Suppl1):999-1005. doi:10.22207/JPAM.14.SPL1.38
14. Porter KA, Xia B, Beglov D, et al. ClusPro PeptiDock: Efficient global docking of peptide recognition motifs using FFT. Bioinformatics. 2017;33(20):3299-3301. doi:10.1093/bioinformatics/btx216
15. Fahmi M, Kharisma VD, Ansori ANM, Ito M. Retrieval and Investigation of Data on SARS-CoV-2 and COVID-19 Using Bioinformatics Approach. In: Advances in Experimental Medicine and Biology. Springer, Cham; 2021:839-857. doi:10.1007/978-3-030-63761-3_47
16. Rigsby RE, Parker AB. Using the PyMOL application to reinforce visual understanding of protein structure. Biochem Mol Biol Educ. 2016;44(5):433-437. doi:10.1002/bmb.20966
17. Liu X, Shi Y, Deng Y, Dai R. Using molecular docking analysis to discovery Dregea sinensis Hemsl. potential mechanism of anticancer, antidepression, and immunoregulation. Pharmacogn Mag. 2017;13(51):358-362. doi:10.4103/pm.pm_384_16
18. Kuriata A, Gierut AM, Oleniecki T, et al. CABS-flex 2.0: A web server for fast simulations of flexibility of protein structures. Nucleic Acids Res. 2018;46(W1):W338-W343. doi:10.1093/nar/gky356
19. Desormeaux A, Coutu M, Medjahed H, et al. The Highly Conserved Layer-3 Component of the HIV-1 gp120 Inner Domain Is Critical for CD4-Required Conformational Transitions. J Virol. 2013;87(5):2549-2562. doi:10.1128/jvi.03104-12
20. Dorgham K, Pietrancosta N, Affoune A, et al. Reverse immunology approach to define a new HIV-gp41-Neutralizing epitope. J Immunol Res. 2019;2019:1-13. doi:10.1155/2019/9804584
21. Kreer C, Gruell H, Mora T, Walczak AM, Klein F. Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies. Vaccines. 2020;8(13):1-19. doi:10.3390/vaccines8010013
22. Ali M, Pandey RK, Khatoon N, Narula A, Mishra A, Prajapati VK. Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection. Sci Rep. 2017;7(9232):1-13. doi:10.1038/s41598-017-09199-w
23. Gupta S, Kapoor P, Chaudhary K, Gautam A, Kumar R, Raghava GPS. In Silico Approach for Predicting Toxicity of Peptides and Proteins. PLoS One. 2013;8(9):1-10. doi:10.1371/journal.pone.0073957
24. Yadav S, Pandey SK, Singh VK, Goel Y, Kumar A, Singh SM. Molecular docking studies of 3-bromopyruvate and its derivatives to metabolic regulatory enzymes: Implication in designing of novel anticancer therapeutic strategies. PLoS One. 2017;12(5):1-15. doi:10.1371/journal.pone.0176403
25. Grdadolnik J, Merzel F, Avbelj F. Origin of hydrophobicity and enhanced water hydrogen bond strength near purely hydrophobic solutes. Proc Natl Acad Sci U S A. 2017;114(2):322-327. doi:10.1073/pnas.1612480114
26. Wu P, Chaudret R, Hu X, Yang W. Noncovalent interaction analysis in fluctuating environments. J Chem Theory Comput. 2013;9(5):2226-2234. doi:10.1021/ct4001087
27. Yam-Puc JC, Toellner KM, Zhang L, Zhang Y. Role of B-cell receptors for B-cell development and antigen-induced differentiation. F1000Research. 2018;7:1-9. doi:10.12688/f1000research.13567.1
28. Su Z, Wu Y. Computational studies of protein-protein dissociation by statistical potential and coarse-grained simulations: A case study on interactions between colicin E9 endonuclease and immunity proteins. Phys Chem Chem Phys. 2019;21(5):2463-2471. doi:10.1039/c8cp05644g