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Jan 19, 2020
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Mar 7, 2020
Published
Mar 7, 2020
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Abstract

Nigella plant genus has potential as anti-HIV. One species of Nigella, Nigella sativa has been reported to have HIV-1 protease enzyme inhibitory activity. This research aims to determine the compounds of the Nigella genus that have activity as HIV-1 protease enzyme inhibitory activity through molecular docking method by Autodock Vina and to compare interaction stability through molecular dynamics simulations by AMBER. The metabolite of the Nigella genus was obtained from the KnapSack website, and enzyme model was obtained from the Protein Data Bank (3NU3). The results of molecular docking found the lowest affinity energy of Nigella compound is Nigellidine 4-O-sulfite (-13.4 kcal/mol). Meanwhile, the affinity energy of the ligand native (Amprenavir) was -12.1 kcal/mol. The lowest affinity energy of Nigellidine 4-O-sulfite might be predicted to have potency as an HIV-1 Protease inhibitor. Molecular dynamics simulation showed Root Mean Square Fluctuation (RMSF) value of Nigellidine 4-O-sulfite with the amino acid active site is 0.4064 Å for ASP:25 and 0.5667 Å for ASP: 125. Whereas RMSF ligand native with the amino acid active site, ASP: 25 is 0.3647 Å and ASP: 125 is 0.3639 Å. The higher RMSF value of Nigellidine 4-O-sulfite describes the lower interaction stability than the ligand native.

Keywords

Nigella Molecular Docking Molecular Dynamics Protease HIV-1

Article Details

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How to Cite
Zubair, M. S., Maulana, S., & Mukaddas, A. (2020). Penambatan Molekuler dan Simulasi Dinamika Molekuler Senyawa Dari Genus Nigella Terhadap Penghambatan Aktivitas Enzim Protease HIV-1: Molecular Docking and Molecular Dynamics Simulation of Compounds from Nigella Genus on Protease HIV-1 Enzyme Inhibitors. Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) (e-Journal), 6(1), 132 - 140. https://doi.org/10.22487/j24428744.2020.v6.i1.14982

References

  1. Chairunnisa, A., & Runadi, D. (2017). Aktivitas Kalkon terhadap Reseptor Esterogen β (Er-β) Sebagai Antikanker Payudara Secara In Vitro Dan In Silico: Review. Farmaka, 14, 1–8.
  2. Depkes RI. (2006). Pelayanan Kefarmasian untuk Orang Dengan HIV/AIDS (ODHA). Jakarta: Departemen Kesehatan Republik Indonesia.
  3. Ghosh, A. K., Osswald, H. L., & Prato, G. (2017). Recent Progress in the Development of HIV-1 Protease Inhibitors for the Treatment of HIV/AIDS, 59 (11), 5172–5208. https://doi.org/10.1021/acs.jmedchem.5b01697.Recent
  4. Kemenkes RI. (2014). Infodatin AIDS. Jakarta: Pusat Data dan Informasi Kementerian Kesehatan Republik Indonesia.
  5. Kemenkes RI. (2017). Laporan Perkembangan HIV-AIDS & Infeksi Menular Seksual (IMS) Triwulan IV Tahun 2017. Jakarta: Kementerian Kesehatan Republik Indonesia.
  6. Ko, G. M., Reddy, A. S., Kumar, S., Bailey, B. A., & Garg, R. (2011). Computational Analysis of HIV-1 Protease Protein Binding Pockets. J Chem Inf Model, 50 (10), 1759-1771. https://doi.org/10.1021/ci100200u.Computational
  7. Kufareva, I., & Abagyan, R. (2012). Methods of protein structure comparison. Methods Mol Biol, 857, 231–257. https://doi.org/10.1007/978-1-61779-588-6
  8. Kurapati, K. R. V, Atluri, V. S., Samikkannu, T., & Garcia, G. (2016). Natural Products as Anti-HIV Agents and Role in HIV-Associated Neurocognitive Disorders (HAND): A Brief Overview, 6, 1–14. https://doi.org/10.3389/fmicb.2015.01444
  9. Kusumoto, I. T., Nakabayashi, T., Kida, H., Miyashiro, H., Namba, T., & Shimotohno, K. (1995). Screening of Various Plant Extracts used in Ayurvedic Medicine for Inhibitory Effects on Human Immunodeficiency Virus Type 1 (HIV-1) Protease, 9, 180–184.
  10. Onifade, A. A., Jewell, A. P., & Adedeji, W. A. (2013). Nigella Sativa Concoction Induced Sustained Seroreversion in HIV Patient, 10, 332–335
  11. Pandey, D., Chouhan, U., & Verma, N. (2017). HIV Infection : A Review of their Inhibitors Progression. Biomedical & Pharmacology Journal, 10(2), 749–758.
  12. Ramadhan, A. (2018). Skrining Virtual Penghambat Enzim Xantin Oksidase (XO) dan Siklooksigenase-2 (COX-2) dari Senyawa Tanaman Kelor (Moringa oleifera Lam.). Skripsi. Universitas Tadulako, Palu.
  13. Rex, R. (2009). Quantification of structure / dynamics correlation of globular proteins. Bachelor-und Masterarbeiten. Georg-August-Universität Göttingen.
  14. Singh, S., Gupta, A. K., & Verma, A. (2013). Molecular Properties and Bioactivity score of the Aloe vera antioxidant compounds – in order to lead finding. Research Journal of Pharmaceutical, Biological and Chemical Sciences, 4(2), 876–881.
  15. Yilmaz, N. K., Swanstrom, R., & Schiffer, C. A. (2017). Improving Viral Protease Inhibitors to Counter Drug Resistance, 24 (7), 547–557. https://doi.org/10.1016/j.tim.2016.03.010
  16. Zubair, M. S., Anam, S., Khumaidi, A., Susanto, Y., Hidayat, M., & Ridhay, A. (2016). Molecular Docking Approach to Identify Potential Anticancer Compounds from Begonia (Begonia sp). Advances of Science and Technology for Society, 080005, 1–7. https://doi.org/10.1063/1.4958513.

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