Tania Widjaja, Arif Nur Muhammad Ansori, Viol Dhea Kharisma, Irvan Faizal, Yulanda Antonius, Joko Pebrianto Trinugroho, 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
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. Death from Ebola is mainly caused by multi-organ failure due to internal bleeding and fluid loss. Another Ebola outbreak spiked this February 2021, suggesting the low effectiveness of the previous vaccines used. Zaire Ebola virus (EBOV) is known to be the species highly involved in the recent outbreak with a high mortality rate. This study is carried out to design a B-cell epitope Ebola vaccine based on the conserved region of Zaire EBOV glycoprotein. Reverse vaccinology and immunoinformatics approaches are used in this study. Samples of Zaire EBOV glycoprotein sequences were retrieved from GenBank, NCBI. The 3D modeling was done using the SWISS-MODEL web server and PyMol software. Phylogenetic tree analysis was also done using MEGA X. B-cell epitope prediction was done by BepiPred 2.0 and Emini Surface Accessibility using the IEDB web server. Epitopes were selected based on their 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 the pET-24a(+) expression vector. This study revealed that peptides “LEIKKPD,” “TGFGTNETEYLF,” “PYFGPAA,” “PYFGPA,” and “KLSSTNQL” are the best candidate for the B-cell epitope vaccine. Phylogenetic tree and 3D modeling successfully showed the genetic and structural differences of Zaire EBOV GP originating from various countries. In silico cloning was also done using the pET28a(+) expression vector to design a clone vector map for the next vaccine development phase. © 2023 by Indonesian Journal of Pharmacy (IJP).
Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jl. Jend. Sudirman No.51, RW.4, Karet Semanggi, Jakarta, 12930, Indonesia; Doctoral Program in Veterinary Science, Faculty of Veterinary Medicine, Universitas Airlangga, Faculty of Venetery Medicine, Universitas Airlangga, Jl. Mulyorejo, Kec. Mulyorejo, East Java, Surabaya, 60115, Indonesia; Computational Virology Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia Foundation, Jl. Swadaya Barat No.24, Gresik, 61171, Indonesia; Center of Technology of Pharmaceutical and Medicinal, Agency for the Assessment and Application of Technology (BPPT), Jakarta, Indonesia; Faculty of Biotechnology, University of Surabaya, Baratajaya, Gubeng, Surabaya, 60284, Indonesia; Bioinformatics and Data Science Research Center, Bina Nusantara University, Jakarta, Jalan Kebon Jeruk Raya No. 27, Jakarta, 11530, Indonesia; Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Jl. Veteran, Jawa Timur, Malang, 65145, Indonesia; Center for Biotechnology of Animal Reproduction, South Ural State Agrarian University, Troitsk, 13 Gagarin St., Troitsk, 457100, Russian Federation; Department of Infectious Diseases, South Ural State Agrarian University, Troitsk, 13 Gagarin St., Troitsk, 457100, Russian Federation; 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; Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, Chakrata Rd, Prem Nagar, Uttarakhand, Dehradun, 248007, India; Department of Chemistry, Mississippi State University, Mississippi State, 39762-9573, MS, United States; 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; Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Negeri Padang, Jalan Prof. Dr. Hamka, Air Tawar Padang, Sumatera Barat, Padang, Indonesia
