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All Journal Jurnal Teknologi Laboratorium Bioinformatics and Biomedical Research Journal Makara Journal of Science
Kharisma, Viol Dhea
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Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Education Engineering Other

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Immunobioinformatics analysis and phylogenetic tree construction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Indonesia: spike glycoprotein gene Ansori, Arif Nur Muhammad; Kharisma, Viol Dhea; Antonius, Yulanda; Tacharina, Martia Rani; Rantam, Fedik Abdul
Jurnal Teknologi Laboratorium Vol 9 No 1 (2020): 2020 (1): Special Edition "COVID-19"
Publisher : POLTEKKES KEMENKES YOGYAKARTA

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (986.383 KB) | DOI: 10.29238/teknolabjournal.v9i1.221

Abstract

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread worldwide and as a result, the World Health Organization (WHO) declared it a pandemic. At present, there are no approved vaccines against SARS-CoV-2. Therefore, the aim of this study was to predict epitope-based vaccines using bioinformatics approaches and phylogenetic tree construction of SARS-CoV-2 against the backdrop of the COVID-19 pandemic. In this study, we employed 27 isolates of SARS-CoV-2 spike glycoprotein genes retrieved from GenBank® (National Center for Biotechnology Information, USA) and the GISAID EpiCoV™ Database (Germany). We analyzed the candidate epitopes using the Immune Epitope Database and Analysis Resource. Furthermore, we performed a protective antigen prediction with VaxiJen 2.0. Data for B-cell epitope prediction, protective antigen prediction, and the underlying phylogenetic tree of SARS-CoV-2 were obtained in this research. Therefore, these data could be used to design an epitope-based vaccine against SARS-CoV-2. However, the advanced study is recommended for confirmation (in vitro and in vivo).
The In Silico Analysis and Identification of Possible Inhibitor of H5N1 Virus: Compounds Analysis and Identification of Possible Neuraminidase Inhibitors Syafrudin, Syafrudin; Septiadi, Luhur; Alfaruqi, Nuri Thobibatus Shofia; Wahyudi, Didik; Kharisma, Viol Dhea
Bioinformatics and Biomedical Research Journal Vol. 1 No. 2 (2018): Volume 1 Issue 2
Publisher : Future Science

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Abstract

Fingerroot (Boesenbergia pandurata (Roxb.)) belongs to the family Zingiberaceae (Ginger). B. pandurata has pharmacological benefits such as neuroprotective, chemoprotective, anti-inflammatory, anti-angiogenic, antioxidant, an inhibitor of protease enzyme NS2B/NS3 dengue virus, Japanese encephalitis virus and swine flu virus (H1N1). This study aims to determine the most effective compounds from B. pandurata as neuraminidase inhibitors of H5N1 virus. The amino acid sequence for neuraminidase of avian influenza A virus subtype H5N1 of A/China/GD02/2006 was retrieved from protein sequence database at NCBI. Then, modeled by Swiss Model. Analyse of molecular docking was performed using PyRx and the interactions between neuraminidase inhibitors of H5N1 and B. pandurata active compound was analyzed by PyMol software and LigPlot+ software. From the 30 active compounds which have been docked, 4-hydroxypanduratin A, rubranine, boesenbergin B, boesenbergin A, 5,7-dimethoxyflavone, and tectochrysin had an equal or smaller free binding energy than control compound. 4-hydroxypanduratin A proved to be the most potent active compound as a neuraminidase inhibitor (NA 1) because it has the most negative binding energy and the same amino acid binding residue with the control compound. Therefore, 4-hydroxypanduratin A is predicted to be used as inhibitors of neuraminidase in the H5N1 virus.
Prediction of Novel Bioactive Compound from Zingiber officinale as Non-nucleoside Reverse Transcriptase Inhibitors (NNRTIs) of HIV-1 through Computational Study Kharisma, Viol Dhea; Septiadi, Luhur; Syafrudin, Syafrudin
Bioinformatics and Biomedical Research Journal Vol. 1 No. 2 (2018): Volume 1 Issue 2
Publisher : Future Science

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Abstract

Human immunodeficiency virus 1 (HIV-1) is one of the viruses of that causes AIDS in humans and disease outbreaks in this modern era. Reverse transcriptase (RT) enzyme though to be the functional enzyme that play a role on the HIV-1 virus replication. Bioactive compounds contained on Ginger (Zingiber officinale) is known to inhibit viral replication. This study aims to determine the alternative bioactive compounds contained on Ginger (Zingiber officinale) as as a non-nucleoside reverse transcriptase (NNRTIs) HIV-1 inhibitors through computational study. The reverse transcriptase (RT) enzyme model was retrieved from protein sequence database (PDB) and validated with Ramachandran Plot and the compound contained on Ginger was retrieved from database. Analysis of molecular docking, performed using PyRx and the interactions between Reverse Transcriptase (RT) enzyme of HIV-1 virus and Zingiber officinale active compound was analyzed by PyMol and LigPlot+, also the drug-likeness molecule properties with The Lipinski Rule’s of Five. From 24 active compound which have been docked, ?-sitosterol proven to be the most potential bioactive compound as inhibitors of Reverse Transcriptase (RT) enzyme because it has more negative binding energy and the same amino acid residue with the control. Therefore, ?-sitosterol is predicted to be used as non-nucleoside reverse transcriptase (NNRTIs) HIV-1 inhibitors.
Conserved B-cell epitope identification of envelope glycoprotein (GP120) HIV-1 to develop multi-strain vaccine candidate through bioinformatics approach Kharisma, Viol Dhea; Ansori, Arif Nur Muhammad; Posa, Gabrielle Ann Villar; Rizky, Wahyu Choirur; Permana, Sofy; Parikesit, Arli Aditya
Jurnal Teknologi Laboratorium Vol 10 No 1 (2021): inpress
Publisher : POLTEKKES KEMENKES YOGYAKARTA

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29238/teknolabjournal.v10i1.274

Abstract

Acquired immune deficiency syndrome (AIDS) has been identified from US patients since 1981. AIDS is caused by infection with the human immunodeficiency virus type 1 (HIV-1) which is a retrovirus. HIV-1 gp120 can be recognized by the immune system because it is located outside the virion. The conserved region is identified in gp120, and it is recognized by an immune cell which then initiates specific immune responses, viral mutation escape, and increase vaccine protection coverage, a benefit derived from the conserved region-based vaccine design. However, previous researchers have little knowledge on this conserved region as a target for vaccine design. This paper explains how the conserved region of gp120 HIV-1 is a major target for vaccine design through a bioinformatics approach. The conserved region from gp120 was explored as a vaccine design target with a bioinformatics tool that consists of B-cell epitope mapping, vaccine properties, molecular docking, and dynamic simulation. The peptide vaccine candidate of B5 with the gp120 HIV-1 conserved region was found to provoke B-cell activation through a direct pathway, produce specific antibody, and increase protection from multi-strain viral infection.
COVID-19 In Silico Drug with Zingiber officinale Natural Product Compound Library Targeting the Mpro Protein Wijaya, Renadya Maulani; Hafidzhah, Muhammad Aldino; Kharisma, Viol Dhea; Ansori, Arif Nur Muhammad; Parikesit, Arli Aditya
Makara Journal of Science Vol. 25, No. 3
Publisher : UI Scholars Hub

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Abstract

Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a worldwide pandemic. Ginger (Zingiber officinale) is a rhizome, which is commonly used for culinary and medicinal purposes. In Indonesia, ginger is taken as traditional medicine by processing it into a drink known as jamu. The present study aimed to assess and evaluate the bioactive compounds in ginger that can be used in drug design for treating COVID-19. The crystal structure of the SARS-CoV-2 main protease (Mpro) was generated from a protein sequence database, i.e., Protein Data Bank, and the bioactive compounds in ginger were derived from the existing compounds library. Mpro is involved in polyprotein synthesis, including viral maturation and nonstructural protein gluing, making it a potential antiviral target. Furthermore, the bioactive compounds in ginger were analyzed using Lipinski’s rule of five to determine their drug-like molecular properties. Moreover, molecular docking analysis was conducted using the Python Prescription 0.8 (Virtual Screening Tool) software, and the interaction between SARS-CoV-2 Mpro and the bioactive compounds in ginger was extensively examined using the PyMOL software. Out all of the 16 bioactive compounds that were docked successfully, 4-gingerol, which has the lowest binding energy against SARS-CoV-2 Mpro, as per the virtual screening results, was proven to have the most potential as a viral inhibitor of SARS-CoV-2
Co-Authors Alfaruqi, Nuri Thobibatus Shofia Antonius, Yulanda Arif Nur Muhammad Ansori Arli Aditya Parikesit Didik Wahyudi Fedik Abdul Rantam Hafidzhah, Muhammad Aldino Posa, Gabrielle Ann Villar Rizky, Wahyu Choirur Septiadi, Luhur Sofy Permana Syafrudin Syafrudin Tacharina, Martia Rani Wijaya, Renadya Maulani