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Syafrudin Syafrudin
Environmental Engineering Department, Faculty Of Engineering, Diponegoro University Semarang
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Journal : Bioinformatics and Biomedical Research Journal

 1 
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 . Widayat A'yun, Husnul Karimah Qurrata A, Sadhu Adwitya A. Stevie Erga Abdullah, Nabil Izza Achmad Hufad Agung Wardana Agus Hartoko Alfaruqi, Nuri Thobibatus Shofia Alvin, Arya Alam Anastasya, Windy Divaci Andy Riski Pratama Anik Sarminingsih, Anik Arieyanti Dwi Astuti, Arieyanti Dwi Arifmiboy, Arifmiboy Astri Purnama Dewi Astuti, Farida Afriani Badrus Zaman Bagus Sujiwo Bambang Pujianto Bambang Riyanto Baskoro Lokahita Bella Nasila D Budi Prasetyo Samadikun Budianto, Tri Hendrawan Budiharjo, M. Arief Budiyono Budiyono Confera, Akbar Nugroho Darul Ilmi Denok Ambun Suri Dian Eni Sunarni Didik Wahyudi Dinah Husniah Fauzia Rahmiyati Yazid Fauziyah, Fita Firmansyah, Anton Fuadah, Tsani Tsamrotul Ganjar Samudro Ganjar Samudro H. Bunga Natalia Hadiyanto Hadiyanto Harusda, Dadhan Haryono S. Huboyo Haryono Setyo Huboyo Hayat, Nurul Henny Juliani, Henny Hernoni Septiani, Hernoni I Ketut Suada Iin Novitasari Ika Bagus Priyambada Imam Hanafi Indah Susilowati Indriyani Indriyani Inri Natalia Inri Natalia Iqbal Syaichurrozi Irawan Wisnu Wardhana Irwansyah Irwansyah Iswantir M Julian Marfal Karsam Karsam Khalish, Alif Akram Kharisma, Viol Dhea Kismartini Kismartini Larasati, Dyanung Latifa , Nurrahmi Latifa, Maysa Lucy Amena Sembiring M. Agung Wibowo M. Agung Wibowo Mahmud Mahmud Maman Fathurrohman, Maman Matin, Hashfi Hawali Abdul Mochamad Arief Budihardjo Mochtar Hadiwidodo Muhajirin, Muhajirin Muhiddinur Kamal Muktiono Waspodo Mulyati Mulyati NEVIATY PUTRI ZAMANI Nurandani Hardyanti Nurhasanah Nurhasanah Nurmaesyarah, Nurmaesyarah Nurul Awaliah Nurul Renaningtias, Nurul Paranita, Debbie Yuliana Purwanto Purwanto Putri, Soraya Annisa Rafiuddin, Rafiuddin Ramadan, Bimastyaji Surya Ratih Pujiastuti Rizki Tri Andrianingsih Rozita, Putri Rudy Kurniawan S. Suripin Sadhu Adwitya A Sani, Muhammad Thariq Sejati, Anang Wahyu Septiadi, Luhur Setiabudi Bambang Setyorini, Rita Agus Silviana Silviana Siswati, Muji SITI RACHMAWATI Sri Eko Wahyuni Sri Sumiyati Sriyana Sriyana Subhan, Ega Saiful Sudarno Sudarno Sudarwanto, Anang Suherman, Suherman Sulardjaka Sulardjaka Sumiati Sumiati Sutrisno, Sutrisno Suyadi, Andri Utami, Khurnia Tri Vitus Dwi Yunianto Budi Ismadi Wahyuni, Retno Hari Wati, Hessy Rahma Wati, Salmi Wedra Aprison Wicaksono, Vinsensius Priyo Winardi Dwi Nugraha Winardi Dwi Nugraha Yulius Yulius Yuliyanti yuliyanti Yusa Eko Saputro, Yusa Eko Zailani Zailani Zainal Abidin Arief ZAMAN, Badrus Zulhanudin, Al Farick Zulkifli Zulkifli