B-Cell Conserved Epitope Screening and In Silico Cloning of Envelope Glycoprotein from Ebola Virus (EBOV) For Vaccine Candidate Construction

Tania  Widjaja; Arif Ansori; Viol Dhea  Kharisma; Irvan  Faizal; Yulanda  Antonius; Joko Pebrianto  Trinugroh; Rasyadan Taufiq Probojati; Muhammad Hermawan  Widyananda; Pavel  Burkov; Pavel  Scherbakov; Vera  Gribkova; Natalia  Nikolaeva; Natalia  Vasilievich; Vikash  Jakhmola; Md. Emdad  Ullah; Arli Aditya  Parikesit; Rahadian Zainul

doi:10.22146/ijp.4197

Tania Widjaja Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jl. Jend. Sudirman No.51, RW.4, Karet Semanggi, 12930, Jakarta, Indonesia
Arif Ansori Universitas Airlangga
Viol Dhea Kharisma Computational Virology Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia Foundation, Jl. Swadaya Barat No.24, 61171 Gresik, Indonesia
Irvan Faizal Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jl. Jend. Sudirman No.51, RW.4, Karet Semanggi, 12930, Jakarta, Indonesia; Center of Technology of Pharmaceutical and Medicinal, Agency for the Assessment and Application of Technology (BPPT), Jakarta, Indonesia.
Yulanda Antonius Faculty of Biotechnology, University of Surabaya, Baratajaya, Gubeng, 60284 Surabaya, Indonesia.
Joko Pebrianto Trinugroh Bioinformatics and Data Science Research Center, Bina Nusantara University, Jakarta, Jalan Kebon Jeruk Raya No. 27, Jakarta 11530 Indonesia
Rasyadan Taufiq Probojati Computational Virology Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia Foundation, Jl. Swadaya Barat No.24, 61171 Gresik, Indonesia
Muhammad Hermawan Widyananda Computational Virology Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia Foundation, Jl. Swadaya Barat No.24, 61171 Gresik, Indonesia; Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Jl. Veteran, Malang, Jawa Timur 65145 Indonesia
Pavel Burkov Center for Biotechnology of Animal Reproduction, South Ural State Agrarian University, Troitsk, Russian Federation, 13 Gagarin St., 457100 Troitsk, Russia
Pavel Scherbakov Department of Infectious Diseases, South Ural State Agrarian University, Troitsk, Russian Federation, 13 Gagarin St., 457100 Troitsk, Russia
Vera Gribkova Institute of Technology of Food Production and Technological Management, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), Moscow, Russian Federation
Natalia Nikolaeva Institute of Technology of Food Production and Technological Management, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), Moscow, Russian Federation
Natalia Vasilievich Institute of Technology of Food Production and Technological Management, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), Moscow, Russian Federation
Vikash Jakhmola Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, Chakrata Rd, Prem Nagar, Dehradun, Uttarakhand 248007, India
Md. Emdad Ullah Department of Chemistry, Mississippi State University, Mississippi State, MS 39762-9573, United States
Arli Aditya Parikesit Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Jl. Pulomas Barat No.Kav. 88, RT.4/RW.9, Kayu Putih, Kec. Pulo Gadung, Kota Jakarta Timur, Daerah Khusus Ibukota Jakarta 13210 Indonesia
Rahadian Zainul

Keywords: Vaccinology, B-Cell Epitope, Immunoinformatic, Ebola Virus

Abstract

Ebola virus (EBOV) is a type of RNA virus from the family of Filoviridae. The 2014-2016 Ebola outbreak in African countries Guinea, Liberia and Sierra Leone has a total of 28,616 cases and 11,310 deaths. People suffering from Ebola disease reported to have symptoms such as fever, body aches, diarrhea and internal and external bleeding. Death from Ebola is mostly caused by multi-organ failure due to internal bleeding and fluid loss. Another Ebola outbreak has spiked this February 2021, suggesting low effectivity of the previous vaccines used. Zaire Ebola virus (EBOV) is known to be the species highly involved on the recent outbreak with a high mortality rate. This study is carried out to design B-cell epitope Ebola vaccine based on the conserved region of Zaire EBOV glycoprotein. Reverse vaccinology and immunoinformatic approaches are used in this study. Samples of Zaire EBOV glycoprotein sequences were retrieved from GenBank, NCBI. The 3D modelling was done by using SWISS-MODEL web server and PyMol software. Phylogenetic tree analysis was also done by using MEGA X. B-cell epitope prediction was done by BepiPred 2.0 and Emini Surface Accessibility using IEDB web server. Epitopes were selected based on its conservancy by comparing the sequences with the MEGA X alignment result. Antigenicity, allergenicity and toxicity properties of the peptides were predicted using VaxiJen 2.0, AllerTOP 2.0 and ToxinPred web servers. In silico cloning was done as the final step using pET-24a(+) expression vector. This study revealed that peptide “LEIKKPD”, “TGFGTNETEYLF”, “PYFGPAA”, “PYFGPA”, and “KLSSTNQL” are the best candidate of B-cell epitope vaccine. Phylogenetic tree and 3D modelling successfully showed the genetic and structural differences of Zaire EBOV GP originating from various countries. In silico cloning was also done using pET28a(+) expression vector to design clone vector map to be used for the next phase of vaccine development.

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