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All Journal Makara Journal of Science Genbinesia Journal of Biology
Dian, Farida Aryani
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Health Professions Immunology & microbiology

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Molecular Simulation of B-Cell Epitope Mapping from Nipah Virus Attachment Protein to Construct Peptide-Based Vaccine Candidate: A Reverse Vaccinology Approach Kharisma, Viol Dhea; Dian, Farida Aryani; Burkov, Pavel; Scherbakov, Pavel; Derkho, Marina; Sepiashvili, Ekaterina; Sucipto, Teguh Hari; Parikesit, Arli Aditya; Murtadlo, Ahmad Affan Ali; Jakhmola, Vikash; Zainul, Rahadian
Makara Journal of Science Vol. 27, No. 2
Publisher : UI Scholars Hub

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Abstract

There are no specific drugs or vaccines for Nipah virus (NiV), which is a new Paramyxovirus that infects swine and humans. This study was conducted to investigate B-cell epitope mapping of the NiV attachment glycoprotein and to construct peptide-based vaccine candidates using the reverse vaccinology approach. To generate the linear B-cell epitope, the NiV isolates were extractad from GenBank, NCBI, using the IEDB web server; peptide modeling was conducted using PEP-FOLD3; docking was conducted using PatchDock and FireDock; and in silico cloning was designed using SnapGene. Various peptides were successfully identified from the NiV attachment glycoprotein based on B-cell epitope prediction, allergenicity prediction, similarity prediction, and toxicity prediction. An in silico cloning design of the pET plasmic was also developed. The peptide “RFENTTSDKGKIPSKVIKSYYGTMDIKKINEGLLD” (1G peptide) is predicted to be a potential candidate for the NiV vaccine as it has several good vaccine characteristics. It increases the immune response of B cells through activation, differentiation into plasma cells, the formation of memory cells, and it may increase IgM/IgG antibody titres for viral neutralization. However, the results of this study should be further verified through in vivo and in vitro analyses
Vaccine construction for human papilloma virus (HPV) type 16 and 18 Infection using in silico approach to combat cervical cancer Dharmawan, Muhammad Alsyifaa; Ansori, Arif Nur Muhammad; Dian, Farida Aryani; Probojati, Rasyadan Taufiq; Tamam, Muhammad Badrut; Kharisma, Viol Dhea
Genbinesia Journal of Biology Vol. 1 No. 1 (2021): November 2021
Publisher : Generasi Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55655/genbinesia.v1i1.3

Abstract

Human papillomavirus (HPV) is a virus that causes infection on the surface of the skin and has the potential to cause cervical cancer. This viral infection is characterized by the growth of warts on the skin in various areas of the body, such as the arms, legs, mouth, and genital area. Because the virus can endanger health, it is necessary to design an HPV vaccine to overcome this problem. In this study, we performed a study characterization of HPV types 16 and 18 sequences to obtain immunogenic epitopes retrieved from the National Center for Biotechnology Information (NCBI) web server. Then, epitope prediction was performed using the immune epitope database (IEDB) web server and selected to get the best vaccine candidate for HPV types 16 and 18. We recommend 16P1 as an epitope-based peptide vaccine candidate for HPV type 16 and 18P4 for type 18. Both vaccine candidates are antigenic, non-allergenic, and non-toxic. The 16P1 and 18P4 have the lowest global energy values ​​among the other candidates. However, further research is needed to be able to develop the best vaccine (in vitro and in vivo experiments).
Co-Authors Adi Sofyan Ansori, Muhammad Arli Aditya Parikesit Burkov, Pavel Derkho, Marina Dharmawan, Muhammad Alsyifaa Jakhmola, Vikash Kharisma, Viol Dhea Murtadlo, Ahmad Affan Ali Rahadian Zainul Rasyadan Taufiq Probojati Scherbakov, Pavel Sepiashvili, Ekaterina Tamam, Muhammad Badrut Teguh Hari Sucipto, Teguh Hari