Characterization in silico of bioactive compound in tea plant as a potentials inhibitor of SARS-CoV-2 Mpro

Mohamad Endy Yulianto; Ari Yuniastuti; Dadan Rohdiana; Vita Paramita; Hermawan Dwi Ariyanto; Rizka Amalia; Sutrisno Sutrisno; Indah Hartati; Shabri Shabri; Retno Dwi Nyamiati; Siti Rahmawati

Abstract

One of the screenings of the chemical structure that has the potential as an active major protease (Mpro) inhibitor in SARS-CoV-2 is bioactive compounds, such as oolonghomobisflavan-A, theaflavin-3-O-gallate, and theaflavin (TF). These bioactive compounds are main components of catechin oxidation, which contribute color, taste, and aroma to black tea. Enzymatic oxidation events in black tea processing have started at the beginning of the mill. In silico studies of active site Mpro as an inhibitor of SARS-CoV-2 were conducted using Protein Data Bank from a web platform. This analysis was carried out using the AutoDock Vina software integrated with PyRx 0.8. The molecular docking results were visualized in 3D and 2D with the BIOVIA Discovery Studio software with the result that amino acid residues and chemical bonds formed were visible, indicating the binding site of a target protein. The production of bioactive compounds through the tea fermentation process accelerated the oxidation rate of catechins into the contained bioactive compounds, which was analyzed using a spectrophotometer with a wavelength of 380 nm. Bioactive compound analysis used the response surface methodology. The results of docking the oolonghomobisflavan compound with Mpro indicated the highest binding affinity, namely −8.0 kcal/mol; however, the oolonghomobisflavan compound with Mpro did not show the same interaction as the control. On the contrary, for the docking of theaflavin-3’-Ogallate with Mpro, the binding affinity was −6.3 kcal/mol and showed the same interaction with the control, namely, LysA:137, where the compound formed hydrogen bonds, and analysis of the selected compound was carried out on the theaflavin-3’-O-gallate compound. The optimal operating conditions for the extraction process were at a flow rate of 17.65 l/minute with a fermentation time of 50 minutes, which produced a maximum theaflavin level of 0.938%.

Keyword: Tea bioactive compound theaflavin SARS-CoV-2.

Citation:

Yulianto ME, Yuniastuti A, Rohdiana D, Paramita VE, Aryanto HD, Amalia R, Sutrisno S, Hartati I, Shabri S, Nyamiati RD, Rahmawati S. Characterization in silico of bioactive compound in tea plant as a potentials inhibitor of SARSCoV-2 Mpro. J Appl Pharm Sci, 2022. Online First.

Copyright: © The Author(s). This is an open-access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Reference

Bhardwaj VK, Singh R, Sharma J, Rajendran V, Purohit R, Kumar S. Identification of bioactive molecules from tea plant as SARSCoV-2 main protease inhibitors. J Biomol Struct Dyn, 1-10.

Borman S. New QSAR techniques eyed for environmental assessments. Chem Eng News, 1990, 68(8):20-3. https://doi.org/10.1021/cen-v068n008.p020

Chamata Y, Watson KA, Jauregi P. Whey-derived peptides interactions with ACE by molecular docking as a potential predictive tool of natural ACE inhibitors. Int J Mol Sci, 2020; 21(3):1-14. https://doi.org/10.3390/ijms21030864

Chandini SK, Rao LJ, Subramanian R. Membrane clarification of black tea extracts. Food Bioprocess Technol, 2013; 6(8):1926-43. https://doi.org/10.1007/s11947-012-0847-0

Chen Y, Cai H, Pan J, Xiang N, Tien P, Ahola T, Guo D. Functional screen reveals SARS coronavirus nonstructural protein nsp14 as a novel cap N7 methyltransferase. Proc Natl Acad Sci USA; 106(9):3484-9. https://doi.org/10.1073/pnas.0808790106

Chen Y, Liu Q, Guo D. Emerging coronaviruses: genome structure, replication, and pathogenesis. J Med Virol, 2020; 92(4):418-23. https://doi.org/10.1002/jmv.25681

Ekins S, Mestres J, Testa B. In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling. Br J Pharmacol, 2007; 152(1):9-20. https://doi.org/10.1038/sj.bjp.0707305

Ghosh S, Chakraborty R, Chatterjee G, Raychaudhuri U. Study on fermentation conditions of palm juice vinegar by response surface methodology and development of a kinetic model. Brazilian J Chem Eng, 2012; 29(3):461-72. https://doi.org/10.1590/S0104-66322012000300003

Hernandez MA, Rathinavelu A. Basic pharmacology: understanding drug actions and reactions. 1st edition, CRC Press, Routledge, UK, 2017. https://doi.org/10.1201/9781315272672 Kanbarkar N, Mishra S. Matrix metalloproteinase inhibitors identified from Camellia sinensis for COVID-19 prophylaxis: an in silico approach. Adv Tradit Med, 2021; 21(1):173-88. https://doi.org/10.1007/s13596-020-00508-9

Khanal P, Dey YN, Patil R, Chikhale R, Wanjari MM, Gurav SS, Patil BM, Srivastava B, Gaidhani SN. Combination of system biology to probe the anti-viral activity of andrographolide and its derivative against COVID-19. RSC Adv, 2021; 11(9. https://doi.org/10.1039/D0RA10529E

Kumar A, Choudhir G, Shukla SK, Sharma M, Tyagi P, Bhushan A, Rathore M. Identification of phytochemical inhibitors against main protease of COVID-19 using molecular modeling approaches. J Biomol Struct Dyn, 2020; 1-11. https://doi.org/10.21203/rs.3.rs-31210/v1

Lung J, Lin YS, Yang YH, Chou YL, Shu LH, Cheng YC, Liu HT, Wu CY. (2020). The potential chemical structure of anti-SARS-CoV-2 RNA-dependent RNA polymerase. J Med Virol, 2020; 92(6):693-97. https://doi.org/10.1002/jmv.25761

Peretto G, Sala S, Caforio ALP Acute myocardial injury, MINOCA, or myocarditis? Improving characterization of coronavirusassociated myocardial involvement. Eur Heart J, 2020; 41(22):2124-5. https://doi.org/10.1093/eurheartj/ehaa396

Saputri KE, Fakhmi N, Kusumaningtyas E, Priyatama D, Santoso B. Docking molekular potensi anti diabetes melitus tipe 2 turunan zerumbon sebagai inhibitor aldosa reduktase dengan Autodock-Vina. Chim Natura Acta, 2016; 4(1):16. https://doi.org/10.24198/cna.v4.n1.10443

Shabri S, Maulana H. Synthesis and isolation of theaflavin from fresh tea leaves as bioactive ingredient of antioxidant supplements. Jurnal Penelitian Teh Dan Kina, 2017; 20(1):1. https://doi.org/10.22302/pptk.jur.jptk.v20i1.120

Syahputra G, Ambarsari L, Sumaryada T. Simulasi docking kurkumin enol, bismetoksikurkumin dan analognya sebagai inhibitor enzim12-pipoksigenase. Jurnal Biofisika, 2014; 10(1):55-67.

Tahir ul Qamar M, Alqahtani SM, Alamri MA, Chen LL. Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. J Pharm Anal, 2020; 10(4):313-9 https://doi.org/10.1016/j.jpha.2020.03.009

Tang X, Wu C, Li X, Song Y, Yao X, Wu X, Dung Y, Zhang H, Wang Y, Qian Z, Cui J, Lu J. On the origin and continuing evolution of SARS-CoV-2. Nat Sci Rev, 2020; 7(6):1012-23. Available via https://academic. oup.com/nsr/advance-article-abstract/doi/10.1093/nsr/nwaa036/5775463. https://doi.org/10.1093/nsr/nwaa036

Tao W, Zhou Z, Zhao B, Wei T. Simultaneous determination of eight catechins and four theaflavins in green, black and oolong tea using new HPLC-MS-MS method. J Pharm Biomed Anal, 2016; 131:140-5. https://doi.org/10.1016/j.jpba.2016.08.020

Wu CH, Hong BH, Ho CT, Yen GC. Targeting cancer stem cells in breast cancer: Potential anticancer properties of 6-shogaol and pterostilbene. J Agric Food Chem, 2015; 63(9):2432-41. https://doi.org/10.1021/acs.jafc.5b00002

Yulianto ME, Paramita V, Hartati I, Amalia R. Response surface methodology of pressurized liquid water extraction of curcumin from curcuma domestica val. Rasayan J Chem, 2018; 11(4):1564-71. https://doi.org/10.31788/RJC.2018.1141990

Zhang J, Cui H, Jiang H, Fang L, Wang W, Su W, Xiong C. Rapid determination of theaflavins by HPLC with a new monolithic column. Czech J Food Sci, 2019; 37(2):112-9. https://doi.org/10.17221/213/2018-CJFS

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