Author(s): Hendyco Pratama, Nur Imaniati Sumantri, Siti Fauziyah Rahman, Viol Dhea Kharisma, Arif Nur Muhammad Ansori


DOI: 10.52711/0974-360X.2023.00752   

Address: Hendyco Pratama1, Nur Imaniati Sumantri1*, Siti Fauziyah Rahman1, Viol Dhea Kharisma2,3, Arif Nur Muhammad Ansori4,5,6
1Department of Electrical Engineering, Faculty of Engineering, Universitas Indonesia, Depok, Indonesia.
2Computational Virology Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia Foundation, Gresik, Indonesia.
3Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia.
4Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia.
5European Virus Bioinformatics Center, Jena, Germany.
6Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India.
*Corresponding Author

Published In:   Volume - 16,      Issue - 10,     Year - 2023

Coronavirus disease 2019, also known as COVID-19, is a respiratory disease. Symptoms of COVID-19 include fever, dry cough, inflammation of the throat area, loss of smell, and even breathing difficulty. COVID-19 is caused by SARS-CoV-2 infection, a virus that is a member of the coronavirus family. The SARS-CoV-2 structure consists of S (spike), M (membrane), E (envelope), and N (nucleocapsid) protein. Two SARS-CoV-2 variants, namely alpha (B.1.1.7) and beta (B.1.351) variants are considered a variant of concern (VoC) due to their increased infectivity. It has been reported that the vaccine's efficacy against these two variants decreased. The purpose of this study is to compare epitopes from S and N proteins of alpha and beta variants to find the most suitable vaccine candidate through reverse vaccinology. In this study, physicochemical properties, antigenicity, and epitope prediction, as well as molecular docking of the epitope and B cell receptor, 5IFH, were done. The result suggested that the epitope from S protein was more suitable as a vaccine candidate. S protein epitope has a lower global energy value which means that it can bind to 5IFH more spontaneously compared to N protein epitopes. The most suitable vaccine candidate for the alpha variant is Pep_B, with a global energy value of -48.77 kcal/mol, and Pep_F, for the beta variant, with a global energy value of -61.61 kcal/mol. These results would recommend the epitopes to be used in further COVID-19 vaccine development.

Cite this article:
Hendyco Pratama, Nur Imaniati Sumantri, Siti Fauziyah Rahman, Viol Dhea Kharisma, Arif Nur Muhammad Ansori. Epitope-based Vaccine Design from Alpha and Beta Variant of SARS-CoV-2: An Immunoinformatics Approach. Research Journal of Pharmacy and Technology 2023; 16(10):4617-5. doi: 10.52711/0974-360X.2023.00752

Hendyco Pratama, Nur Imaniati Sumantri, Siti Fauziyah Rahman, Viol Dhea Kharisma, Arif Nur Muhammad Ansori. Epitope-based Vaccine Design from Alpha and Beta Variant of SARS-CoV-2: An Immunoinformatics Approach. Research Journal of Pharmacy and Technology 2023; 16(10):4617-5. doi: 10.52711/0974-360X.2023.00752   Available on:

1.    Utami AT, Budiarti RPN. Honey as Miracle Therapy for Covid-19: Literature Study. Bali Medical Journal. 2022; 11(3): 1207–1211. DOI: 10.15562/bmj.v11i3.3542
2.    Lee KW, Gew LT, Siau CS, Peh SC, Chia YC, Yacob S, Chan NN, Seow VK, Ooi PB. COVID-19 vaccine hesitancy and its associated factors in Malaysia. PLoS One. 2022; 17(9): e0266925. doi: 10.1371/journal.pone.0266925.
3.    Ansori ANM, Kharisma VD, Fadholly A, Tacharina MR, Antonius Y, Parikesit AA. Severe Acute Respiratory Syndrome Coronavirus-2 Emergence and Its Treatment with Alternative Medicines: A Review. Research Journal of Pharmacy and Technology. 2021; 14(10):5551-7. DOI: 10.52711/0974-360X.2021.00967
4.    Ansori AN, Kharisma VD, Parikesit AA, Dian FA, Probojati RT, Rebezov M, Scherbakov P, Burkov P, Zhdanova G, Mikhalev A, Antonius Y, Pratama MRF, Sumantri NI, Sucipto TH, Zainul R. Bioactive Compounds from Mangosteen (Garcinia mangostana L.) as an Antiviral Agent via Dual Inhibitor Mechanism against SARS-CoV- 2: An In Silico Approach. Phcog J. 2022; 14(1): 85-90. DOI: 10.5530/pj.2022.14.12
5.    Reviono, Muhammad F, Maharestri KZ, Hanif I, Sukmagautama C, Apriningsih H, Hananto AZA, Harsini. Efficacy of therapeutic plasma exchange and convalescent plasma therapy in moderate-to-severe COVID-19 patients. Bali Medical Journal. 2022; 11(3): 1369–1374. DOI: 10.15562/bmj.v11i3.3493
6.    Rahman FF, Haris F. COVID-19 emergency response in Southeast Asian region: A bibliographic analysis using VOSviewer software. Bali Medical Journal. 2022; 11(3): 1656–1659. DOI: 10.15562/bmj.v11i3.3758
7.    Kharisma VD, Agatha A, Ansori ANM, Widyananda MH, Rizky WC, Dings TGA, Derkho M, Lykasova I, Antonius Y, Rosadi I, Zainul R. Herbal combination from Moringa oleifera Lam. and Curcuma longa L. as SARS-CoV-2 antiviral via dual inhibitor pathway: A viroinformatics approach. J Pharm Pharmacogn Res. 2022; 10(1): 138-146. DOI: 10.56499/jppres21.1174_10.1.138
8.    Aldino M, Maulani R, Probojati R, Dhea Karisma V, Ansori ANM, Parikesit AA. Potential Vaccine Targets for COVID-19 and Phylogenetic Analysis Based on the Nucleocapsid Phosphoprotein of Indonesian SARS-CoV-2 Isolates. Indonesian Journal of Pharmacy. 2021; 32(3): 328-337. DOI: 10.22146/ijp.1497
9.    Wong CY, Tham JS, Foo CN, Leng Ng F, Shahar S, Zahary MN, Ismail MN, Tan CS, Hoh BP, Kumar SV, Lim YM. Factors influencing COVID-19 vaccination intention among university students: A cross-sectional study in Malaysia. Biosafety and Health. 2022.
10.    Antonius Y, Ongko J, Hardjo PH. Identification of potential activity of volatile compounds derived from pogostemon Cablin benth as antiviral of SARS-CoV-2. Int J App Pharm. 2023; 15(1): 93-97.
11.    Hsieh PP, Kristian H, Permana AAJM, Wongsodiharjo M, Nugraheni PA, Charisti P, Diarsvitri W. The clinical pictures of COVID-19 pediatric patients in dr. R. Soedarsono Regional General Hospital, Pasuruan, East Java, Indonesia. Bali Medical Journal. 2022; 11(1): 460–465. DOI: 10.15562/bmj.v11i1.3046
12.    Jena M, Kumar V, Kancharla S, et al. Reverse vaccinology approach towards the in-silico multi-epitope vaccine development against SARS-CoV-2. F1000. Research. 2021; 10: 1-14.
13.    Gupta E, et al. Identification of potential vaccine candidates against SARS-CoV-2.JMIR Bioinform Biotech.2020;35(2) 10.2196/32401
14.    Sarkar B, Ullah MA, Johora FT, et al. Immunoinformatics-guided designing of epitope-based subunit vaccines against the SARS Coronavirus-2 (SARS-CoV-2). Immunobiology. 2020; 225(3):
15.    Walls AC, Park YJ, Tortorici MA, et al. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Gylcoprotein.Cell. 2020; 181(2):
16.    Public Health England. Investigation of SARS-CoV-2 Variants of Concern in England: Technical Briefing 6.2020
17.    Ahmed SF, Quadeer AA, and McKay MR. Preliminary identification of potential vaccine targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies. Viruses. 2020; 12(3).
18.    Tamura K, Stecher G, and Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution. 2021; 38:
19.    National Center for Biotechnology Information (NCBI). Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information. 1988.
20.    Waterhouse A, Bertoni M, Biepert S, et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018; 46.
21.    Khuluq H, Yusuf PA, Perwitasari DA. A bibliometric analysis of coronavirus disease (COVID-19) mortality rate. Bali Medical Journal. 2022; 11(2): 579–586. DOI: 10.15562/bmj.v11i2.3423
22.    Gasteiger E, Hoogland CG, Gattiker A, et al. Protein Identification and Analysis Tools on the ExPaSy Server. John M. Walker: The Proteomics Protocols Handbook. 2005.
23.    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
24.    Dimitrov I, Flower DR, and Doytchinova I. AllerTOP - a server for in silico prediction of allergens. BMC Bioinformatics. 2013; 26:
25.    Lamiable A, et al.PEP-FOLD3: Faster de novo structure prediction for linear peptides in solution and in complex. Nucleic Acids Res.2016;44.
26.    Minici C, et al. Crystal Structure of the BCR Fab fragment from subset #2 case
27.    Micini C, et al. Distinct homotypic B-Cell receptor interactions shape the outcome of chronic lymphocytic leukaemia.Nat Commun.2017;8(15746)
28.    Duhovny D, Nussinov R, and Wolfson HJ. Efficient Unbound Docking of Rigid Molecules. Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI).
29.    Duhovny D, Inbar Y, and Nussinov R. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucl. Acids. Res. 2005;
30.    Andrusier N, Nussinov R, and Wolfson HJ.FireDock: Fast Interaction Refinement.Proteins. 2007; 69(1):
31.    Mashiach E, Schneidman-Duhovny D, Andrusier N, et al. FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res. 2008;
32.    Schrödinger, L., DeLano, W. PyMol. 2020.
33.    Zhao N, et al. Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China. Front.
34.    Forster P. et al. Phylogenetic network analysis of SARS-CoV-2 genomes. PNAS.2020;117(17):9241-9243.
35.    O'Toole A, et al. Tracking the internation spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 [version 1; peer review: 3 approved]. wellcome open res.2021;6(121)
36.    Guruprasad K, Reddy BVB, and Pandit MW.Correlation between stability of a protein and its dipeptide composition: A novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng. Des. Sel. 1990; 4(2):
37.    Chang KY and Yang JR. Analysis and Prediction of Highly Effective Antiviral Peptides Based on Random Forests. PLoS One. 2013; 8(8).
38.    Guan Y, Zhu Q, Huang D, et al. An equation to estimate the difference between theoretically predicted and SDS PAGE-displayed molecular weights for an acidic peptide. Sci. Rep. 2015; 5(13370):
39.    Heffron J and Mayer BK. Virus Isoelectric Point Estimation: Theories and Methods. Appl. Environ. Microbiol. 2021; 87(3):
40.    Moldoveanu SC and David V. Properties of Analytes and Matrices Determining HPLC Selection. Selection of the HPLC Method in Chemical Analysis.
41.    Novák P and Havlíček V. Protein Extraction and Precipitation. Proteomic Profiling and Analytical Chemistry.2016; 2:
42.    Panda S and Chandra G. Physicochemical characterization and functional analysis of some snake venom toxin proteins and related non-toxin proteins of other chordates. Bioinformation. 2012; 8(18):
43.    Zhang J and Tao A. Antigenicity, Immunogenicity, Allergenicity. Allergy Bioinformatics.
44.    Ikpeazu OV, Otuokere IE, and Igwe KK. Computational Characterization of the Binding Energy and Interactions between Trimethoprim and Dihydrofolate Reductases of Candida albicans, Staphylococcus aureus and Thermotoga Maritima. Acta Scientific Pharmaceutical Sciences. 2017; 1(3): 26-30.
45.    Hasegawa M. Thermodynamic Basis for Phase Diagrams. Treatise on Process Metallurgy2013;1: 527-556.
46.    Ferreira VP and Cortes C. The Complement System. Ref. Modul. Biomed. Sci. 2021.
47.    Mancardi D and Daëron M. Fc Receptors in Immune Responses. Ref. Modul. Biomed. Sci.2014.
48.    Dutta NK, Mazumdar K, and Gordy JT. The Nucleocapsid Protein of SARS–CoV-2: a Target for Vaccine Development. J. Virol. 2020; 94(13).
49.    Bai Z, Cao Y, Liu W, et al. The SARS-CoV-2 Nucleocapsid Protein and Its Role in Viral Structure, Biological Functions, and a Potential Target for Drug or Vaccine Mitigation. Viruses. 2021; 13(1115): 1-13.
50.    Chia LY, Kumar PV, Maki MAA, Ravichandran G, Thilagar S. A Review: The Antiviral Activity of Cyclic Peptides. Int J Pept Res Ther. 2023; 29(1): 7. doi: 10.1007/s10989-022-10478-y.
51.    Wijaya RM, Hafidzhah MA, Kharisma VD, Ansori ANM, Parikesit AP. COVID-19 In Silico Drug with Zingiber officinale Natural Product Compound Library Targeting the Mpro Protein. Makara J Sci. 2021; 25(3): 5. DOI: 10.7454/mss.v25i3.1244
52.    Nugrahaningsih DAA, Purnomo E, Siswanto, Reviono, Yasmina A, Prenggono MD, Fajari NM, Rudiansyah M, Harsini, Syarif RA, Sholikhah EN. Features of COVID-19 adult patients and the treatment in Indonesia: a retrospective cohort study. Bali Medical Journal. 2022; 11(1): 528–539. DOI: 10.15562/bmj.v11i1.2810
53.    Hanardi DDYP, Rochmawati E. Tracing management and epidemiological characteristics of close contact COVID-19 in primary health care. Bali Medical Journal. 2022; 11(3): 1614–1619. DOI: 10.15562/bmj.v11i3.3705
54.    Ansori ANM, Kharishma VD, Muttaqin SS, Antonius Y, Parikesit AA. Genetic Variant of SARS-CoV-2 Isolates in Indonesia: Spike Glycoprotein Gene. J Pure Appl Microbiol. 2020; 14: 971-978. DOI: 10.22207/JPAM.14.SPL1.35
55.    Kharisma VD, Ansori ANM. Construction of Epitope-Based Peptide Vaccine Against SARS-CoV-2: Immunoinformatics Study. J Pure Appl Microbiol. 2020; 14: 999-1005. DOI: 10.22207/JPAM.14.SPL1.38
56.    Santosa D, Sofro MAU, Retnaningsih R, Pangarsa EA, Setiawan B, Farhanah N, Kholis FN, Handoyo T, Rahardjo S, Nindhita LR, Puspitasari I, Naibaho RM, Kharismasari R, Kartiyani I, Yunarvika V, Rizky D, Suhartono S. Convalescent plasma as an adjunctive treatment for severe and critically ill COVID-19. Bali Medical Journal. 2021; 10(3): 851–859. DOI: 10.15562/bmj.v10i3.2590

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 

56th percentile
Powered by  Scopus

SCImago Journal & Country Rank

Recent Articles


Not Available