Molecular Docking: Bioactive Compounds in Indramayu Mango (Mangifera indica L.) Peel Waste as NS5B Hepatitis C Virus (HCV) Inhibitor
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Background: Hepatitis C is caused by hepatitis C virus (HCV) infection. HCV infection is one of the biggest causes of chronic liver disease. About 60-80% of patients with acute hepatitis C will develop chronic hepatitis C. Objective: This study aimed to analyze the potential of mango peel compounds as HCV NS5B inhibitors. Methods: The methods in this study are ligand preparation, physicochemical and pharmacokinetic predictions, protein structure preparation, molecular docking, data analysis, and visualization. Results: The results showed that the test ligands had binding free energies close to the reference ligands, namely Mangiferin -7.862 kcal/mol and respectively D-(+)-Maltose -6.453 kcal/mol, Dibutyl – phthalate -6.326 kcal/mol, bis-β-D-fructofuranose 1,2':2,3'-dianhydride -6.249 kcal/mol, 16-Heptadecyne-1,2,4-triol -5.476 kcal/mol, 3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid -5,360 kcal/mol, Trigonelline -4.905 kcal/mol, Hexitol -4.552 kcal/mol, α-Glucoheptitol -4.403 kcal/mol. All the test ligands bind the NS5B active site with hydrogen bonds. Furthermore, the ligand-receptor complex has a dissociation constant value and hydrogen bond length. Conclusion: The results showed that Mangiferin was the most potential ligand in inhibiting NS5B HCV of all the test ligands used.
Ali, N. S. M., Salleh, A. B., Leow, T. C., Abd Rahman, R. N. Z. R., & Ali, M. S. M. (2020). The Influence of Calcium toward Order/Disorder Conformation of Repeat-in-Toxin (RTX) Structure of Family I.3 Lipase from Pseudomonas fluorescens AMS8. Toxins, 12(9), 579. https://doi.org/10.3390/toxins12090579
Biovia, D. S. (2017). BIOVIA Discovery Studio Visualizer (p. 936).
Boyce, S. E., Tirunagari, N., Niedziela-Majka, A., Perry, J., Wong, M., Kan, E., Lagpacan, L., Barauskas, O., Hung, M., Fenaux, M., Appleby, T., Watkins, W. J., Schmitz, U., & Sakowicz, R. (2014). Structural and Regulatory Elements of HCV NS5B Polymerase-β-loop and C-terminal tail - Are Required for Activity of Allosteric Thumb Site II Inhibitors. PLoS ONE, 9(1), 1–12. https://doi.org/10.1371/journal.pone.0084808
Bukh, J. (2016). The History of Hepatitis C virus (HCV): Basic Research Reveals Unique Features in Phylogeny, Evolution and The Viral Life Cycle with New Perspectives for Epidemic Control. Journal of Hepatology, 65(1), S2–S21. https://doi.org/10.1016/j.jhep.2016.07.035
Castro, R., Perazzo, H., Grinsztejn, B., Veloso, V. G., & Hyde, C. (2015). Chronic Hepatitis C: An Overview of Evidence on Epidemiology and Management from a Brazilian Perspective. International Journal of Hepatology. https://doi.org/10.1155/2015/852968
Damayanti, S., Khonsa, K., & Amelia, T. (2021). Antiviral Activity and Toxicity Prediction of Compounds Contained in Figs (Ficus carica L.) by In Silico Method. Indonesian Journal of Pharmaceutical Science and Technology, 8(1), 21–33.
Faridah, Mumpuni, E., & Yunanto, Y. I. (2019). Analisis In-Silico Senyawa Kimia dalam Teh Hijau yang Bekerja pada Aktivator (PPAR-γ) sebagai Antiobesitas. Jurnal Ilmu Kefarmasian Indonesia, 17(2), 251–254.
Fida, S., Dewi, A. R., & Damayanti, D. S. (2021). Studi In Silico Senyawa Aktif Daun Sirsak (Annona muricata L.) pada Aldose Reductase dan Glutathione Reductase untuk Menghambat Katarak Diabetik. Jurnal Kedokteran Komunitas, 9(2), 1–14.
Gholam, G. M., Darmawan, N. I., Siregar, J. E., & Artika, I. M. (2022). Selected Polyphenols from Date (Phoenix dactylifera) as Anti-Virulence of Candida albicans Through Multiple Enzyme Targets. Biointerface Research in Applied Chemistry, 13(4), 386. https://doi.org/10.33263/BRIAC134.386
Gholam, G. M. (2022). Molecular docking of the bioactive compound Ocimum sanctum as an inhibitor of Sap 1 Candida albicans. Sasambo Journal of Pharmacy, 3(1), 18–24. https://doi.org/https://doi.org/10.29303/sjp.v6i1.264
Gholam, G. M., & Firdausy, I. A. (2022). Molecuar Docking Study of Natural Compounds from Red Betel (Piper crocatum Ruiz & Pav) as Inhibitor of Secreted Aspartic Proteinase 5 (Sap 5) in Candida albicans, 3(2), 97-104. https://doi.org/10.29303/sjp.v3i2.145
Imran, M., Arshad, M. S., Butt, M. S., Kwon, J. H., Arshad, M. U., & Sultan, M. T. (2017). Mangiferin: A Natural Miracle Bioactive Compound Against Lifestyle Related Disorders. Lipids in Health and Disease, 16(84), 1–17. https://doi.org/10.1186/s12944-017-0449-y
Komarudin, A. D. P., Purnama, M. F. G., Sari, A. Y., Izzati, A., Sahila, E. N. M. R., Hidayat, S., Apriliya, T. N., & Muchtaridi. (2021). Studi In Silico Senyawa Tanaman Nerium oleander terhadap STAT-3 pada Kanker Payudara. Jurnal Farmasi Udayana, 10(2), 149–155. https://doi.org/10.24843/jfu.2021.v10.i02.p07
Krieger, E., & Vriend, G. (2014). YASARA View - Molecular Graphics for All Devices - From Smartphones to Workstations. Bioinformatics, 30(20), 2981–2982. https://doi.org/10.1093/bioinformatics/btu426
Li, H. C., & Lo, S. Y. (2015). Hepatitis C Virus: Virology, Diagnosis and Treatment. World Journal of Hepatology, 7(10), 1377–1389. https://doi.org/10.4254/wjh.v7.i10.1377
Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings. Advanced Drug Delivery Reviews, 23, 3–25. https://doi.org/10.1016/S0169-409X(96)00423-1
Lipinski Rule of Five. (n.d.). Retrieved July 19, 2022, from http://www.scfbio-iitd.res.in/software/drugdesign/lipinski.jsp
Luthfia, M., Eryandini, A., Geraldi, D., Narita, C., Miftahul, C., Jannah, & Ambarsari, L. (2021). Potency of Bioactive Compounds in Indramayu Mango Peel Waste to Inhibit ACE2. Current Biochemistry, 8(2), 51–62.
Permata, E. I., & Khoirunnisa, Y. (2020). Efek Mangiferin dalam Mengatasi Masalah Kesehatan. Jurnal Penelitian Perawat Profesional, 2(1), 31–38. https://doi.org/10.37287/jppp.v2i1.38
Pires, D. E. V, Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures. Journal of Medicinal Chemistry, 58, 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
Rabaan, A. A., Al-Ahmed, S. H., Bazzi, A. M., Alfouzan, W. A., Alsuliman, S. A., Aldrazi, F. A., & Haque, S. (2020). Overview of Hepatitis C Infection, Molecular Biology, and New Treatment. Journal of Infection and Public Health, 13(5), 773–783. https://doi.org/10.1016/j.jiph.2019.11.015
Sabariegos, R., Albentosa-González, L., Palmero, B., Clemente-Casares, P., Ramírez, E., García-Crespo, C., Gallego, I., de Ávila, A. I., Perales, C., Domingo, E., & Mas, A. (2021). Akt Phosphorylation of Hepatitis C Virus NS5B Regulates Polymerase Activity and Hepatitis C Virus Infection. Frontiers in Microbiology, 12, 3043. https://doi.org/10.3389/fmicb.2021.754664
Shakya, A. K. (2019). Natural Phytochemicals: Potential Anti-HCV Targets In Silico Approach. Journal of Applied Pharmaceutical Science, 9(8), 94–100. https://doi.org/10.7324/JAPS.2019.90813
Singh, D. (2016). Defining Desirable Natural Product Derived Anticancer Drug Space: Optimization of Molecular Physicochemical Properties and ADMET Attributes. ADMET and DMPK, 4(2), 98–113. https://doi.org/10.5599/admet.4.2.291
Srivastava, S., Shree, P., Pandey, H., & Tripathi, Y. B. (2018). Incretin Hormones Receptor Signaling Plays The Key Role in Antidiabetic Potential of PTY-2 Against STZ-induced Pancreatitis. Biomedicine & Pharmacotherapy, 97, 330–338. https://doi.org/10.1016/j.biopha.2017.10.071
Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving The Speed and Accuracy of Docking With a New Scoring Function, Efficient Optimization and Multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334.AutoDock
Uzzaman, M., Chowdhury, K., & Hossen, M. B. (2019). Thermochemical , molecular docking and ADMET studies of aspirin metabolites. 2, 1–5. https://doi.org/10.15761/FDCCR.1000130
Uzzaman, M., Hasan, M. K., Mahmud, S., Yousuf, A., Islam, S., Uddin, M. N., & Barua, A. (2021). Physicochemical, Spectral, Molecular Docking and ADMET Studies of Bisphenol Analogues; A Computational Approach. Informatics in Medicine Unlocked, 25, 100706. https://doi.org/10.1016/j.imu.2021.100706
Velázquez, F., Venkatraman, S., Lesburg, C. A., Rosenblum, S. B., Kozlowski, J. A., & Njoroge, F. G. (2012). Synthesis of New 4,5-Dihydrofuranoindoles and Their Evaluation as HCV NS5B Polymerase Inhibitors. Organic Letters, 14(2), 556–559.
Venkatachalam, K. V, & Ettrich, R. H. (2021). Role of Aspartic Acid Residues D87 and D89 in APS Kinase Domain of Human with Phosphatases/Kinases. Biochemistry and Biophysics Reports, 28, 101155. https://doi.org/10.1016/j.bbrep.2021.101155
Wei, Y., Li, J., Qing, J., Huang, M., Wu, M., Gao, F., Li, D., Hong, Z., Kong, L., Huang, W., & Lin, J. (2016). Discovery of Novel Hepatitis C Virus NS5B Polymerase Inhibitors by Combining Random Forest, Multiple e-Pharmacophore Modeling and Docking. PLoS ONE, 11(2), 1–25. https://doi.org/10.1371/journal.pone.0148181
Weni, M., Safithri, M., & Seno, D. S. H. (2020). Molecular Docking of Active Compounds Piper crocatum on The Alpha-Glucosidase Enzyme as Antidiabetic. Indonesian Journal of Pharmaceutical Science and Technology, 7(2), 64–72.
WHO. (2021). Hepatitis C. World Health Organization. https://www.who.int/news-room/fact-sheets/detail/hepatitis-c
Zaelani, B. F. D., Safithri, M., & Andrianto, D. (2021). Molecular Docking of Red Betel (Piper crocatum Ruiz & Pav) Bioactive Compounds as HMG-CoA Reductase Inhibitor. 24(3), 101–107. https://doi.org/10.14710/jksa.24.3.101-107
Zahra, H., Haridas, R. B., Gholam, G. M., & Setiawan, A. G. (2022). Aktivitas Antiulseratif Berbagai Tanaman Herbal dan Prospek Masa Depan Sebagai Tanaman Budidaya. Jurnal Sains Dan Kesehatan, 4(3), 343–353. https://doi.org/10.25026/jsk.v4i3.1046
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