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All Journal MEDIA KONSERVASI Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Majalah Geografi Indonesia Journal of Indonesian Tourism and Development Studies Journal of Tropical Biodiversity and Biotechnology JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA Jurnal Biodjati Jurnal Riset Biologi dan Aplikasinya Bioinformatics and Biomedical Research Journal Jurnal Sylva Lestari
Septiadi, Luhur
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Decision Sciences, Operations Research & Management Earth & Planetary Sciences Education Energy Engineering Environmental Science Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Social Sciences

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Journal : bioinformatics and biomedical research journal

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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.
Co-Authors Achmad, Caesar Rasendria Agung S. Kurnianto Agung Sih Kurnianto Aini, Quratul Alfaruqi, Nuri Thobibatus Shofia AMIR HAMIDY Aninnas, Afina Arief Darmawan Arifianto, Adityas Assiddiqy, Miftah Farid Berry Fakhry Hanifa Devi, Sandra Rafika Dewi, Nilasari Didik Wahyudi Dzakiyyaa, Ruwaida Erfanda, Muhammad Prayogi Fadhilah, Muhamad Aslam Fathoni, M Firdaus, Firman Firizki, Dinda Tinalanisari Hamidah, Wanda Haq, Mochammad Nur Izzul Kharisma, Viol Dhea Luchman Hakim Magvira, Nur Laila Muhammad Asmuni Hasyim Muhammad Fathoni, Muhammad Muhammad Rizqi Mukhtadin Mulyono, Rizki Mujahidin Nadhori, Qoyin Nanang Tri Haryadi Nia Kurniawan Nuning Nurcahyani Nurrofik, Agus Pamungkas, A. S. P. Rachman, Rhesma Sylvia Rijalullah, Muhammad Asyraf Rudi Hilmanto Santoso, Trio Setya, Yudha Sholikah, Ummi Suparno, Kelik Surya, Rikha Aryanie Syafrudin Syafrudin Utoyo, Laji Zen, Tresa Variyani