In silico repurposing inhibition specificities 3C-like Protease SARS-CoV-2 by Quinic Acid, Gluconic Acid, and Ferulic Acid of Coffee pulp
DOI:
https://doi.org/10.36733/medicamento.v8i2.3971Keywords:
3CL Protease, Ferulic acid, corona virus, coffee pulp, quinic acid, gluconic acidAbstract
This study aims to explore the chemical compounds of the coffee pulp as an anti-covid-19 (anti-3C-like protease). In silico modeling was carried out by structure retrieval, protein preparation, and docking simulation. Specific Grid docking was used for ligands – protein interacting by using Molegro Virtual Docker 5, followed by visualizing Discovery studio version 21.1.1. Compounds contained in coffee pulp, quinic acid, gluconic acid, and ferulic acid separately bind to the same amino acid residues of 3CL Protease or each other. Furthermore, three compounds inhibited 3CLPro activity by catalytic site blocking of 3CLPro, indicating that coffee compounds have potential as molecular therapeutic materials for the coronavirus by inhibiting SARS-CoV-2 genome replication.
References
Ameca, G.M., Cerrilla, M.E.O., Córdoba, P.Z., Cruz, A.D., Hernández, M.S. and Haro, J.H., 2018. Chemical composition and antioxidant capacity of coffee pulp. Ciência e Agrotecnologia, 42(3), pp.307–313. https://doi.org/10.1590/1413-70542018423000818.
Arellano-González, M.A., Ramírez-Coronel, M.A., Torres-Mancera, M.T., Pérez-Morales, G.G. and Saucedo-Castañeda, G., 2011. Antioxidant Activity of Fermented and Nonfermented Coffee (Coffea arabica) Pulp Extracts. Food Technology and Biotechnology, 49(3), p.5.
Bahun, M., Jukić, M., Oblak, D., Kranjc, L., Bajc, G., Butala, M., Bozovičar, K., Bratkovič, T., Podlipnik, Č. and Poklar Ulrih, N., 2022. Inhibition of the SARS-CoV-2 3CL(pro) main protease by plant polyphenols. Food chemistry, 373(Pt B), pp.131594–131594. https://doi.org/10.1016/j.foodchem.2021.131594.
Bare, Y., Kuki, A.D., Rophi, A.H. and Candrakirana, G., 2019. Prediksi Asam Kuinat Sebagai Anti-Inflamasi Terhadap COX-2 Secara Virtual Virtual Prediction of Quinic Acid As Anti-Inflammation of COX-2. Biota: Jurnal Ilmu-Ilmu Hayati, 4(3), pp.124–129. https://doi.org/10.24002/biota.v4i3.2516.
Bare, Y., Sari, D.R.T., Mogi, M.C. and Nurak, M.M.D., 2022a. Senyawa Fucodiphlorethol Dan Phloroglucinol Alga Coklat Sebagai Inhibitor Lipase Secara In Silico. Florea: Jurnal Biologi dan Pembelajarannya, 9(1), p.7. https://doi.org/10.25273/florea.v9i1.11743.
Bare, Y., Sari, D.R.T., Ujiana, W.O., Ra’o, P.Y.S. and Pada, K., 2022b. Repurposing Of 6-Paradol as an Alternative Herbal Medicine For Alzheimer Disease. Medical Sains : Jurnal Ilmiah Kefarmasian, 7(2), pp.1–8. https://doi.org/10.37874/ms.v7i2.289.
Bare, Y., Timba, F.N.S., Nurak, M.M.D. and Mogi, M.C., 2022c. Eksplorasi Senyawa Kulit Kopi sebagai Anti Covid-19 Melalui Penghambatan 3C-Like Protease. JURNAL PENDIDIKAN MIPA, 12(2), pp.127–133. https://doi.org/10.37630/jpm.v12i2.563.
Bare, Y., Timba, F.N.S., Putra, S.H.J., Nirmalasari, M.A.Y., Sari, D.R.T. and Taek, M.M., 2022d. Kajian Senyawa Hexose dan Malic Acid Sebagai Inhibitor Papain Like Protease (PLPro) CORONA VIRUS. JURNAL BIOSENSE, 05(01), p.10. https://doi.org/10.36526/biosense.v5i01.1997.
Bitencourt-Ferreira, G. and de Azevedo, W.F.J., 2019. Molegro Virtual Docker for Docking. Methods in molecular biology (Clifton, N.J.), 2053, pp.149–167. https://doi.org/10.1007/978-1-4939-9752-7_10.
Duangjai, A., Suphrom, N., Wungrath, J., Ontawong, A., Nuengchamnong, N. and Yosboonruang, A., 2016. Comparison of antioxidant, antimicrobial activities and chemical profiles of three coffee (Coffea arabica L.) pulp aqueous extracts. Integrative Medicine Research, 5(4), pp.324–331. https://doi.org/10.1016/j.imr.2016.09.001.
Elzupir, A.O., 2020. Inhibition of SARS-CoV-2 main protease 3CLpro by means of α-ketoamide and pyridone-containing pharmaceuticals using in silico molecular docking. Journal of Molecular Structure, 1222, p.128878. https://doi.org/10.1016/j.molstruc.2020.128878.
Farah, A. and Donangelo, C.M., 2006. Phenolic compounds in coffee. Brazilian Journal of Plant Physiology, 18(1), pp.23–36. https://doi.org/10.1590/S1677-04202006000100003.
Gottstein, V., Bernhardt, M., Dilger, E., Keller, J., Breitling-Utzmann, C.M., Schwarz, S., Kuballa, T., Lachenmeier, D.W. and Bunzel, M., 2021. Coffee Silver Skin: Chemical Characterization with Special Consideration of Dietary Fiber and Heat-Induced Contaminants. Foods, 10(8), p.1705. https://doi.org/10.3390/foods10081705.
Inbathamizh, L. and Padmini, E., 2013. QUINIC ACID AS A POTENT DRUG CANDIDATE FOR PROSTATE CANCER – A COMPARATIVE PHARMACOKINETIC APPROACH. 6(4), p.7. https://doi.org/10.1111/cbdd.12498.
Jo, S., Kim, S., Shin, D.H. and Kim, M.S., 2020b. Inhibition of SARS-CoV 3CL protease by flavonoids. Journal of Enzyme Inhibition and Medicinal Chemistry, 35(1), pp.145–151. https://doi.org/10.1080/14756366.2019.1690480.
Lee, C.-C., Kuo, C.-J., Ko, T.-P., Hsu, M.-F., Tsui, Y.-C., Chang, S.-C., Yang, S., Chen, S.-J., Chen, H.-C., Hsu, M.-C., Shih, S.-R., Liang, P.-H. and Wang, A.H.-J., 2009. Structural Basis of Inhibition Specificities of 3C and 3C-like Proteases by Zinc-coordinating and Peptidomimetic Compounds. Journal of Biological Chemistry, 284(12), pp.7646–7655. https://doi.org/10.1074/jbc.M807947200.
Lele, M.N.E., Ahmad, N.I. and Bare, Y., 2022. Molecular Interaction Analysis of Homodihydrocapsaicin as COX-2 Inhibitor. Spizaetus: Jurnal Biologi dan Pendidikan Biologi, 3(2), p.36. https://doi.org/10.55241/spibio.v3i2.63.
Murthy, P.S. and Madhava Naidu, M., 2012. Sustainable management of coffee industry by-products and value addition—A review. Resources, Conservation and Recycling, 66, pp.45–58. https://doi.org/10.1016/j.resconrec.2012.06.005.
Nurak, M.M.D., Lute, M.A., Eci, M.N. and Bare, Y., 2022. Potential of Sechium edule as Hypertensive Therapy: In Silico Study. Spizaetus: Jurnal Biologi dan Pendidikan Biologi, 3(2), p.10. https://doi.org/10.55241/spibio.v3i2.60.
Ujiana, W.O., Meak, L.E.C., Hiko, M.F. and Bare, Y., 2022. Potential of Triterpenoid Compounds in Sauropus androgynus L Merr as In Silico Inhibitor of Obesity. Spizaetus: Jurnal Biologi dan Pendidikan Biologi, 3(2), p.43. https://doi.org/10.55241/spibio.v3i2.64.
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