Biological activity of kencur (Kaempferia galanga L.) against SARS-CoV-2 main protease
In silico study
Keywords:Bioinformatics, COVID-19, Kaempferia galanga L., Kencur, SARS-CoV-2
COVID-19 is a syndrome affecting pulmonary function but rather in serious conditions leads to death. Kencur (Kaempferia galanga L.) is a type of rhizome plant in Indonesia that is used as an herbal medicine called Jamu because it is believed to be able to cure various types of diseases. One of which is for anti-virus. The goal of this study was to see how effective the compounds in kencur are against COVID-19 with a molecular docking strategy. Kencur biological activities were obtained from the library and the design of the Acute Respiratory Syndrome Main protease (Mpro) has been gained from the protein data bank website. In addition, the biological activities in kencur were examined utilizing Lipinski's five-point concept was used to evaluate their substance molecular characteristics. Molecular docking analysis was performed with the PyRx Virtual Screening Tool software. The PyRx program was used for molecular docking simulation. While, the Discovery Studio Visualizer program was used to visualize the interaction between SARS-CoV-2 (Mpro) and the pharmacologically active metabolites in kencur. The docking evaluation on three antiviral substances revealed that Quercetin had the lowest binding energy when bound with Mpro and thus had the greatest potential as a viral inhibitor.
Ansori, A. N. M., Kharisma, V. D., Muttaqin, S. S., Antonius, Y., & Parikesit, A. A. (2020). Genetic variant of SARS-CoV-2 isolates in Indonesia: Spike glycoprotein gene. Journal of Pure and Applied Microbiology, 14(1), 971-978.
Chen, X., Chen, Y., Yin, Z., Wang, R., Hu, H., Liang, X., He, C., Yin, L., Ye, G., Zou, Y., Li, L., Tang, H., Jia, R., & Song, X. (2021). Kaempferol inhibits pseudorabies virus replication in vitro through regulation of MAPKs and NF-?B signaling pathways. Journal of Integrative Agriculture 20, 2227–2239.
Cherrak, S. A., Merzouk, H., & Mokhtari-Soulimane, N. (2020). Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies. PLoS One, 15(10), e0240653.
Choy, Y. B., & Prausnitz, M. R. (2011). The rule of five for non-oral routes of drug delivery: ophthalmic, inhalation and transdermal. Pharmaceutical research, 28(5), 943-948.
Davis, A. M., & Teague, S. J. (1999). Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis. Angewandte Chemie International Edition, 38(6), 736-749.
Earlia, N., Suhendra, R., Amin, M., Prakoeswa, C. R. S., & Idroes, R. (2019). GC/MS analysis of fatty acids on pliek u oil and its pharmacological study by molecular docking to filaggrin as a drug candidate in atopic dermatitis treatment. The Scientific World Journal, 2019.
Ghersi, D., & Sanchez, R. (2009). Improving accuracy and efficiency of blind protein?ligand docking by focusing on predicted binding sites. Proteins: Structure, Function, and Bioinformatics, 74(2), 417-424.
Gu, Y. Y., Zhang, M., Cen, H., Wu, Y. F., Lu, Z., Lu, F., ... & Lan, H. Y. (2021). Quercetin as a potential treatment for COVID-19-induced acute kidney injury: Based on network pharmacology and molecular docking study. PloS one, 16(1), e0245209.
Jamroz, M., Kolinski, A., & Kmiecik, S. (2013). CABS-flex: server for fast simulation of protein structure fluctuations. Nucleic acids research, 41(W1), W427-W431.
Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., ... & Yang, H. (2020). Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289-293.
Kandeel, M., & Al-Nazawi, M. (2020). Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease. Life sciences, 251, 117627. https://doi.org/10.1016/j.lfs.2020.117627
Kharisma, V. D., Agatha, A., Ansori, A. N. M., Widyananda, M. H., Rizky, W. C., Dings, T. G. A., ... & Zainul, R. (2021). Herbal combination from Moringa oleifera Lam. and Curcuma longa L. as SARS-CoV-2 antiviral via dual inhibitor pathway: A viroinformatics approach. Journal of Pharmacy & Pharmacognosy Research, 10(1), 138-146.
Kocaadam, B., & ?anlier, N. (2017). Curcumin, an active component of turmeric (Curcuma longa), and its effects on health. Critical reviews in food science and nutrition, 57(13), 2889-2895.
Kumar, D., Singh, P., Jayaraj, A., Kumar, V., Kumari, K., Chandra, R., & Ramappa, V. K. (2020). Selective docking of pyranooxazoles against nsP2 of CHIKV eluted through isothermally and non?isothermally MD simulations. ChemistrySelect, 5(14), 4210-4220.
Liguori, N., Croce, R., Marrink, S. J., & Thallmair, S. (2020). Molecular dynamics simulations in photosynthesis. Photosynthesis research, 144(2), 273-295.
Mustafa, R. A., Hamid, A. A., Mohamed, S., & Bakar, F. A. (2010). Total phenolic compounds, flavonoids, and radical scavenging activity of 21 selected tropical plants. Journal of food science, 75(1), C28-C35.
Naik, V. R., Munikumar, M., Ramakrishna, U., Srujana, M., Goudar, G., Naresh, P., ... & Hemalatha, R. (2021). Remdesivir (GS-5734) as a therapeutic option of 2019-nCOV main protease–in silico approach. Journal of Biomolecular Structure and Dynamics, 39(13), 4701-4714.
Parikesit, A. A., & Nurdiansyah, R. (2020). Drug repurposing option for COVID-19 with structural bioinformatics of chemical interactions approach. Cermin Dunia Kedokteran, 47(3), 222-226.
Parikesit, A. A., & Nurdiansyah, R. (2021). Natural products repurposing of the H5N1-based lead compounds for the most fit inhibitors against 3C-like protease of SARS-CoV-2. J Pharm Pharmacogn Res, 9(5), 730-745.
Petit, J., Meurice, N., Kaiser, C., & Maggiora, G. (2012). Softening the rule of five—where to draw the line?. Bioorganic & medicinal chemistry, 20(18), 5343-5351. https://doi.org/10.1016/j.bmc.2011.11.064
Rizvi, S. M. D., Shakil, S., & Haneef, M. (2013). A simple click by click protocol to perform docking: AutoDock 4.2 made easy for non-bioinformaticians. EXCLI journal, 12, 831.
Saakre, M., Mathew, D., & Ravisankar, V. (2021). Perspectives on plant flavonoid quercetin-based drugs for novel SARS-CoV-2. Beni-Suef University Journal of Basic and Applied Sciences, 10(1), 1-13.
Shaghaghi, N. (2020). Molecular docking study of novel COVID-19 protease with low risk terpenoides compounds of plants.
Sharma, S., Sharma, A., & Gupta, U. (2021). Molecular Docking studies on the Anti-fungal activity of Allium sativum (Garlic) against Mucormycosis (black fungus) by BIOVIA discovery studio visualizer 21.1. 0.0. Annals of Antivirals and Antiretrovirals, 5(1), 028-032.
ul Qamar, M. T., Alqahtani, S. M., Alamri, M. A., & Chen, L. L. (2020). Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. Journal of pharmaceutical analysis, 10(4), 313-319. https://doi.org/10.1016/j.jpha.2020.03.009
Umesh, H. R., Ramesh, K. V., & Devaraju, K. S. (2020). Molecular docking studies of phytochemicals against trehalose–6–phosphate phosphatases of pathogenic microbes. Beni-Suef University Journal of Basic and Applied Sciences, 9(1), 1-14.
Wijaya, R. M., Hafidzhah, M. A., Kharisma, V. D., Ansori, A. N. M., & Parikesit, A. A. (2021). Covid-19 in silico drug with Zingiber officinale natural product compound library targeting the mpro protein. Makara Journal of Science, 25(3), 5.
Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., ... & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved ?-ketoamide inhibitors. Science, 368(6489), 409-412.
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