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All Journal Genbinesia Journal of Biology
Dhea Kharisma, Viol
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Health Professions Immunology & microbiology

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A bioinformatics approach to design a novel epitope-based vaccine against Simian Immunodeficiency Virus (Retroviridae: Lentivirus) Dhea Kharisma, Viol; Ansori, Arif Nur Muhammad; Ullah, Md. Emdad; Dings, Tim Godefridus Antonius; Probojati, Rasyadan Taufiq; Fadholly, Amaq; Turista, Dora Dayu Rahma; Tacharina, Martia Rani; Zainul, Rahadian
Genbinesia Journal of Biology Vol. 2 No. 1 (2022): November 2022
Publisher : Generasi Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55655/genbinesia.v2i1.26

Abstract

Simian Immunodeficiency Viruses (SIV) have been found to naturally infect African nonhuman primates (NHP). This causative agents are important and one of the special interest as the root cause of the HIV/AIDS pandemic, one of the most threatening infectious diseases worldwide. The aim of this study was to design an epitope-based vaccine using bioinformatics approaches of the circulating SIV in Kenya, Africa. In this study, we used 17 partial SIV envelope glycoprotein genes retrieved from GenBank® (National Center for Biotechnology Information, USA). We analysed the candidate epitopes using the Immune Epitope Database and Analysis Resource. Then, we performed the protective antigens prediction usingVaxiJen. Interestingly, this study revealed the data of B cell epitope prediction, protective antigens prediction, and molecular phylogenetic of circulating SIV in Kenya, Africa. In sum, this study can be used to design a novel epitope-based vaccine against SIV. We suggest further studies to conduct confirmatory experiments (in vitro and in vivo).
A novel antiviral candidate from Moringa oleifera through dual targeting mechanism of SARS-CoV-2 protease: Computational Sscreening Listiyani, Priscilla; Dhea Kharisma, Viol
Genbinesia Journal of Biology Vol. 2 No. 2 (2023): March 2023
Publisher : Generasi Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55655/genbinesia.v2i2.32

Abstract

COVID-19 is triggered by SARS-CoV-2 which is related in a similar way to SARS-CoV and MERS-CoV. RdRp is an essential component of the virus in replication and transcription. RdRp triggers polymerase activity through binding to cofactors such as nsp7 and nsp8. Mpro plays an important role in viral protease activity for the assembly process. RdRp and Mpro can be used as targets to inhibit the replicative activity of SARS-CoV-2. Moringa oleifera is used by people around the world as a traditional medicine because it has antioxidant, anti-inflammatory, and antiviral properties. This study reveals the molecular mechanism of Moringa oleifera as an inhibitor of key proteins in SARS-CoV-2 replication through a computational approach. Additionally, the in silico method in this study consists of sample preparation in the database, druglikeness prediction, antiviral probability, virtual screening, chemical bond interaction, and 3D visualization. Moringa oleifera may have potential as an antiviral candidate through Ellagic Acid activity as a dual inhibitor through inhibition of SARS-CoV-2 replication and assembly. The candidate compound can generate weak bonding interactions such as hydrogen and hydrophobic to trigger binding stability at specific domains.
Molecular Mechanisms of Hepatitis C Virus (HCV) Triggering Normal Cell Transformation into Cancer: A Mini Review Dhea Kharisma, Viol; Sima, Putri Melati
Genbinesia Journal of Biology Vol. 2 No. 3 (2023): July 2023
Publisher : Generasi Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55655/genbinesia.v2i3.43

Abstract

Hepatitis C virus (HCV) infection has become a serious concern because it can trigger the severity of complications leading to hepatocellular carcinoma (HCC). HCV is a virus with single-stranded RNA (ssRNA) type genetic material, with virions composed of structural proteins such as glycoprotein, envelope, and core, then HCV also has nonstructural proteins such as NS3, NS4, NS4B, NS5A, NS5B. The development of HCV infection therapy has been carried out through direct-acting antiviral agents (DAAs) with the hope of achieving a reduction in mortality and HCC risk. However, these strategies cannot fully reduce the risk of HCC in patients who have recovered from HCV infection. This review briefly reviews several factors from the virus and host to trigger cellular transformation of hepatocytes into HCC. HCV infection can trigger the transformation of hepatocytes into cancer in the case of HCC influenced by two factors consisting of pro-oncogenic and growth factors. Pro-oncogenic of HCV initiates HCC through the release of ROS that triggers genetic mutations and upregulation of proliferation in hepatocytes, it allows internal cell factors to also work in the process of transformation into cancer such as increased growth factor activity for antiapoptotic response, survival, and proliferation to trigger increased severity of HCC.
Co-Authors Adi Sofyan Ansori, Muhammad Amaq Fadholly Dings, Tim Godefridus Antonius Listiyani, Priscilla Rahadian Zainul Rasyadan Taufiq Probojati Sima, Putri Melati Tacharina, Martia Rani Turista, Dora Dayu Rahma Ullah, Md. Emdad