Karamunting screening as an antifungal using the In Silico method targeting N-myristoyltransferase
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Feb 28, 2023
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Abstract
Karamunting has been empirically used by the community in overcoming itching disorders due to fungi. Therefore the purpose of this study was to screen in silico the content of Karamunting against N-myristoyltranseferase protein. The method used in this study was In Silico screening using PLANTS docking and the materials used were thirteen compounds contained in Karamunting. The results of this study are docking scores from -123.628 to -77.3801 and residues that have similarities with native ligands when interacting with N-myristoyltransferase, namely one to three amino acids, the predicted value using PASSonline ranges from 0.101 to 0.583. The conclusion of this study was obtained three compounds that have the potential as antifungals with the N-myristoyltransferase inhibitor mechanism, these compounds are α-tocopherol-quinone; α-tocopherol A; blumeatin.
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How to Cite
Hadi, S. and Nastiti, K. (2023) “Karamunting screening as an antifungal using the In Silico method targeting N-myristoyltransferase”, Science Midwifery, 10(6), pp. 4481-4487. doi: 10.35335/midwifery.v10i6.1134.
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ChemAxon. (2016). ChemAxon - Software Solutions and Services for Chemistry and Biology. In MarvinSketch, Version 16.10.31. https://chemaxon.com/
Chen, S.-N., Friesen, J. B., Webster, D., Nikolic, D., van Breemen, R. B., Wang, Z. J., Fong, H. H. S., Farnsworth, N. R., & Pauli, G. F. (2011). Phytoconstituents from Vitex agnus-castus fruits. Fitoterapia, 82(4), 528–533. https://doi.org/https://doi.org/10.1016/j.fitote.2010.12.003
Dipahayu, D., Soeratri, W., & Agil, M. (2014). Formulasi Krim Antioksidan Ekstrak Etanol Daun Ubi Jalar Ungu (Ipomoea Batatas (L.) Lamk) Sebagai Anti Aging. Pharmaceutical Sciences and Research, 3(1), 166–179. https://doi.org/https://scholarhub.ui.ac.id/psr/vol1/iss3/3/
Galli, F., Bonomini, M., Bartolini, D., Zatini, L., Reboldi, G., Marcantonini, G., Gentile, G., Sirolli, V., & Di Pietro, N. (2022). Vitamin E (Alpha-Tocopherol) Metabolism and Nutrition in Chronic Kidney Disease. In Antioxidants (Vol. 11, Issue 5). https://doi.org/10.3390/antiox11050989
Jeenkeawpieam, J. (2012). Antifungal activity and molecular identification of endophytic fungi from the angiosperm Rhodomyrtus tomentosa. AFRICAN JOURNAL OF BIOTECHNOLOGY, 11. https://doi.org/10.5897/AJB11.3962
Joffry, S. M., Yob, N. J., Rofiee, M. S., Affandi, M. M. R. M. M., Suhaili, Z., Othman, F., Akim, A. M., Desa, M. N. M., & Zakaria, Z. A. (2012). Melastoma malabathricum (L.) Smith Ethnomedicinal Uses, Chemical Constituents, and Pharmacological Properties: A Review. Evidence-Based Complementary and Alternative Medicine, 2012, 258434. https://doi.org/10.1155/2012/258434
Kao, Y.-Y., Chuang, T.-F., Chao, S.-H., Yang, J.-H., Lin, Y.-C., & Huang, H.-Y. (2013). Evaluation of the Antioxidant and Melanogenesis Inhibitory Properties of Pracparatum Mungo (Lu-Do Huang). Journal of Traditional and Complementary Medicine, 3(3), 163–170. https://doi.org/https://doi.org/10.4103/2225-4110.113443
Korb, O., Stützle, T., & Exner, T. E. (2009). Empirical scoring functions for advanced Protein-Ligand docking with PLANTS. Journal of Chemical Information and Modeling, 49(1), 84–96. https://doi.org/10.1021/ci800298z
Lagunin, A., Stepanchikova, A., Filimonov, D., & Poroikov, V. (2000). PASS: prediction of activity spectra for biologically active substances. Bioinformatics (Oxford, England), 16(8), 747–748. https://doi.org/10.1093/bioinformatics/16.8.747
Niah, R., & Baharsyah, R. N. (2018). Potensi Ekstrak Daun Tanaman Karamunting (Melastoma Malabathricum L.) di Daerah Kalimantan sebagai Antibakteri Staphylococcus Aureus. Jurnal Ilmiah Manuntung, 4(1), 36–30. https://doi.org/https://doi.org/10.51352/jim.v4i1.138
Nichols, C., Ng, J., Keshu, A., Kelly, G., Conte, M. R., Marber, M. S., Fraternali, F., & De Nicola, G. F. (2020). Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1β-IL1R and p38α-TAB1 Complexes. Journal of Medicinal Chemistry, 63(14), 7559–7568. https://doi.org/10.1021/acs.jmedchem.0c00403
Pradityo, T., Santoso, N., Ervizal, A., & Zuhud, M. (2016). Etnobotani di Kebun Tembawang Suku Dayak Iban, Desa Sungai Mawang, Kalimantan Barat. Media Konservasi, 21(2), 183–198. https://doi.org/https://doi.org/10.29244/medkon.21.2.183- 198
Rodríguez, E., Arqués, J. L., Rodríguez, R., Nuñez, M., Medina, M., Talarico, T. L., Casas, I. A., Chung, T. C., Dobrogosz, W. J., Axelsson, L., Lindgren, S. E., Dobrogosz, W. J., Kerkeni, L., Ruano, P., Delgado, L. L., Picco, S., Villegas, L., Tonelli, F., Merlo, M., … Masuelli, M. (1989). Protein-Protein and Protein-Ligand Docking. Intech, 32(tourism), 137–144. https://www.intechopen.com/books/advanced-biometric-technologies/liveness-detection-in-biometrics
Sogabe, S., Masubuchi, M., Sakata, K., Fukami, T. A., Morikami, K., Shiratori, Y., Ebiike, H., Kawasaki, K., Aoki, Y., Shimma, N., D’Arcy, A., Winkler, F. K., Banner, D. W., & Ohtsuka, T. (2002). Crystal structures of Candida albicans N-myristoyltransferase with two distinct inhibitors. Chemistry & Biology, 9(10), 1119–1128. https://doi.org/10.1016/s1074-5521(02)00240-5
Systèmes, D. (2020). Free Download: BIOVIA Discovery Studio Visualizer - Dassault Systèmes. https://discover.3ds.com/discovery-studio-visualizer-download#_ga=2.4935860.685747970.1587999055-a5d1c1c0-3176-11e9-a86f-e302515d21c8
Uzzaman, M., Chowdhury, M., & Hossen, M. (2019). Thermochemical, Molecular docking and ADMET studies of Aspirin metabolites. Frontiers in Drug, Chemistry and Clinical Research, 2. https://doi.org/10.15761/FDCCR.1000130
Xu, S. B., Chen, W. F., Liang, H. Q., Lin, Y. C., Deng, Y. J., & Long, K. H. (1993). [Protective action of blumeatin against experimental liver injuries]. Zhongguo yao li xue bao = Acta pharmacologica Sinica, 14(4), 376–378.
Zakaria, Z. A., Rofiee, M. S., Mohamed, A. M., Teh, L. K., & Salleh, M. Z. (2011). In vitro antiproliferative and antioxidant activities and total phenolic contents of the extracts of Melastoma malabathricum leaves. Journal of Acupuncture and Meridian Studies, 4(4), 248–256. https://doi.org/10.1016/j.jams.2011.09.016
Zhang, L.-B., Ji, J., Lei, C., Wang, H.-Y., Zhao, Q.-S., & Hou, A.-J. (2012). Isoprenylated flavonoid and adipogenesis-promoting constituents of Dodonaea viscosa. Journal of Natural Products, 75(4), 699–706. https://doi.org/10.1021/np2009797