Vol 66 No 1 (2021): Journal of the Chilean Chemical Society
Original Research Papers
Minor composition compounds of Algerian herbal medicines as inhibitors of SARS-CoV-2 main protease: Molecular Docking and ADMET properties prediction
Published
February 9, 2021
Keywords
- COVID-19, SARS-CoV-2, Algerian herbal, Natural compounds, Piperitol, ADMET, Molecular Docking.
How to Cite
YABRIR, B. (2021). Minor composition compounds of Algerian herbal medicines as inhibitors of SARS-CoV-2 main protease: Molecular Docking and ADMET properties prediction. Journal of the Chilean Chemical Society, 66(1), 5067-5074. Retrieved from https://jcchems.com/index.php/JCCHEMS/article/view/1597
Copyright (c) 2021 SChQ
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
Abstract
The identification of drugs against the new coronavirus (SARS-CoV-2) is an important requirement. Natural products are substances that serve as sources of beneficial chemical molecules for the development of effective therapies. In this study, 187 natural compounds from Algerian herbal medicines were docked in the active site of SARS-CoV-2 main protease. The result indicates that Piperitol, Warfarin, cis-calamenen-10-ol and α-Cadinene are the structures with best affinity in the binding site of the studied enzyme and all of them respect the conditions mentioned in Lipinski’s rule and have acceptable ADMET proprieties; so, these compounds could have more potent antiviral treatment of COVID-19 than the studied compounds, and they have important pharmacokinetic properties and bioavailability.
References
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[46] Bendif, H. Caractérisation phytochimique et détermination des activités biologiques in vitro des extraits actifs de quelques Lamiaceae: Ajuga iva (L.) Schreb., Teucrium polium L., Thymus munbyanus subsp. coloratus (Boiss. & Reut.) Greuter & Burdet et Rosmarinus eriocalyx Jord &. [dissertation]. ENS Kouba Algeria; (2017).
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[53] Melissa, R. Pitman and Ian Menz, R. in Applied Mycology and Biotechnology, D. K. Arora, R. M. Berka, G. B. Singh eds. Elsevier B. V. Netherlands, 2006; pp.37-59
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[55] Belhassan, A., Zaki, H., Aouidate, A., et al. Interactions between (4Z)-hex-4-en-1-ol and 2-methylbutyl 2-methylbutanoate with olfactory receptors using computational methods. Mor J Chem. (2019); 7(1):028-035.
[56] Hakmi, M., Bouricha, E.M., Kandoussi, I., et al. Repurposing of known anti-virals as potential inhibitors for SARS-CoV-2 main protease using molecular docking analysis. Bioinformation. (2020); 16(4):301-306.
[57] Jalkute, C.B., Barage, S.H., Dhanavade, M.J.. Identification of Angiotensin Converting Enzyme Inhibitor: An in Silico Perspective. Int J Pept Res Ther. (2015); 21: 107–115.
[58] Pires, D.E.V., Blundell, T.L., Ascher, D.B.. pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures. J Med Chem. (2015); 58(9):4066-4072.
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[60] Zhao, Y.H., Abraham, M.H., Le, J., et al. Rate-Limited Steps of Human Oral Absorption and QSAR Studies. (2002); 19:1446-1457.
[61] Belhassan, A., Chtita, S., Zaki, H., et al. Molecular docking analysis of N-substituted oseltamivir derivatives with the SARS-Cov-2 main protease. Bioinformation. (2020); 16:404-408.
[2] Wang, N., Shi, X., Jiang, L. et al. Structure of MERS-CoV spike receptor-binding domain complexed with human receptor DPP4. Cell Res. (2013); 23(8):986-993.
[3] Kaul, D. An overview of coronaviruses including the SARS-2 coronavirus-Molecular biology, epidemiology and clinical implications. Curr. Med. Res. Pract. (2020);10: 54-64
[4] Balkhair, A.A. COVID-19 Pandemic: A New Chapter in the History of Infectious Diseases. Oman Med. J. (2020); Vol. 35, No. 2: e123
[5] Gorbalenya, A. E., Baker, S.C., Baric, R.S. et al. Severe acute respiratory syndrome-related coronavirus — the species and its viruses, a statement of the Coronavirus Study Group. Preprint at bioRxiv. (2020);
[6] Peng, M. Outbreak of COVID-19: An emerging global pandemic threat. Biomed. Pharmacother. (2020) ;129: 110499
[7] Wu, D., Wu, T., Liu, Q., et al. The SARS-CoV-2 outbreak: What we know. Int. J. Infecect. Dis. (2020); 94:44–48.
[8] Chauhan, S. Comprehensive review of coronavirus disease 2019 (COVID-19). Biomed. J. (2020); 43(4): 334-340.
[9] Juan A. Siordia Jr., J.A. Epidemiology and clinical features of COVID-19: A review of current literature. J. Clin Virol. (2020); 127: 104357
[10] Sohrabi, C., Alsafi, Z., O'Neill N. et al. World Health Organization declares global emergency: A review of the 2019 novel coronavirus (COVID-19). Int. J. Surg. (2020); 76: 71–76
[11] Lee D.Y.W, Li, Q.Y., Liu, J., Efferth T. Traditional Chinese herbal medicine at the forefront battle against COVID-19: Clinical experience and scientific basis. Phytomed. (2020).
[12] Palacios Cruz, M., Santos E., Velázquez Cervantes, M.A. COVID-19, a worldwide public health emergency. Rev. Clin. Esp. (2020).
[13] Kwon, S., Lee, W, Jin, C., Jang, I., Jung, W-S., Moon, S-K., Cho, S-K. Could herbal medicine (Soshihotang) be a new treatment option for COVID-19? a narrative review. Integr. Med. Res. (2020); 9(3), 100480.
[14] Huang, F., Li, Y., Leung, E. L-H. et al. A review of therapeutic agents and Chinese herbal medicines against SARSCOV-2 (COVID-19). Pharmacol. Res. (2020) 158, 1049292
[15] Leung, E.-L. H., Pan, H. D., Huang, Y. F. et al., The Scientific Foundation of Chinese Herbal Medicine against COVID-19, Eng.
[16] Luo, L., Jiang, J., Wang, C. et al. Analysis on herbal medicines utilized for treatment of COVID-19. Acta Pharm. Sin. B (2020); 10(17): 1192-1204.
[17] Ang, L., Lee, H.W., Choi, J.Y. et al. Herbal medicine and pattern identification for treating COVID-19: a rapid review of guidelines. Integr. Med. Res. (2020); 9: 100407
[18] Ang, L., Lee, H.W., Kim A. et al. Herbal medicine for the management of COVID-19 during the medical observation period: A review of guidelines. Integr. Med. Res. (2020); 9: 100465
[19] Panyod, S., Ho, C-T., Sheen, L-Y. Dietary therapy and herbal medicine for COVID-19 prevention: A review and perspective. J. Trad. Compl. Med. (2020) ; 10(4): 420-427.
[20] Baildya, N., Ghosh, N.N., Chattopadhyay, A.P. Inhibitory activity of hydroxychloroquine on COVID-19 main protease: An insight from MD-simulation studies. J. Mol. Struct. (2020); 1219:128595.
[21] Marmor, M.F., Kellner, U., Lai, T.Y., et al. Recommendations on screening for chloroquine and hydroxychloroquine retinopathy (2016 revision). Ophthalmol. (2016); 123:1386–1394
[22] Xian, Y., Zhang, J., Bian, Z. et al. Bioactive natural compounds against human coronaviruses: a review and perspective. Acta Pharm. Sin. B (2020); 10(7):1163-1174
[23] McKeea, D.L., Sternberg, A., Stange, U. et al. Candidate drugs against SARS-CoV-2 and COVID-19. Pharmacol. Res. (2020) ;157: 104859
[24] Kouznetsov, V.V. COVID-19 treatment: Much research and testing, but far, few magic bullets against SARS-CoV-2 coronavirus. Eur. J. Med. Chem. (2020); 203: 112647
[25] Abderrahim, A., Belhamel, K., Chalchat, J-C., et al. Chemical composition of the essential oil from Artemisia arborescens L. growing wild in Algeria. Rec Nat Prod. (2010); 4:87-90.
[26] Apostolico, I., Aliberti, L., Caputo, L., et al. Chemical composition, antibacterial and phytotoxic activities of Peganum harmala seed essential oils from five different localities in Northern Africa. Molecules. (2016); 21:1235.
[27] Dob, T., Berramdane, T., Chelgoum, C. Chemical composition of essential oil of Pinus halepensis Miller growing in Algeria. Comptes Rendus Chim. (2005); 8:1939-1945.
[28] Ourzeddine, W., Fadel, H., Mechehoud, Y., et al. Chemical Composition and Antioxidant Activity of the Fruit Essential Oil of Zizyphus lotus (L.) Desf. (Rhamnaceae). (2017); 9(2):228-232.
[29] Laouer, H., Yabrir, B., Djeridane, A., et al. Composition, antioxidant and antimicrobial activities of the essential oil of Marrubium deserti. Nat Prod Commun. (2009); 4(8):1133-1138.
[30] Benayache, S., Benayache, F., Benyahia, S., et al. Leaf Oils of some Eucalyptus Species Growing in Algeria. J Essent Oil Res. (2001); 13:210-213.
[31] Yabrir, B. Essential Oil of Marrubium vulgare: Chemical Composition and Biological Activities. A Review. Nat Prod Sci. (2019); 25:81–91.
[32] Dob, T., Dahmane, D., Chelghoum, C. Essential Oil Composition of Juniperus Oxycedrus. Growing in Algeria. Pharm Biol. (2006); 44:1–6.
[33] Benabdallah, F.Z., Kouamé, R.O., El Bentchikou, M., et al. Études ethnobotanique, phytochimique et valorisation de l’activité antimicrobienne des feuilles et de l’oléorésine du pistachier de l’atlas (Pistacia atlantica Desf.). Phytothérapie. (2017); 15:222-229.
[34] Lograda, T., Chaker, A.N., Chalard, P., et al. Chemical composition and antimicrobial activity of essential oil of Genista numidica Spach. and G. saharae Coss et Dur. Asian J Plant Sci. (2009); 8:495-499.
[35] Boutaghane, N., Kabouche, A., Touzani, R., et al. GC/MS Analysis and Analgesic Effect of the Essential Oil of Matricaria pubescens from Algeria. Nat Prod Commun. (2011); 6(2):1251-252.
[36] Halla, N., Heleno, S.A., Costa, P., et al. Chemical profile and bioactive properties of the essential oil isolated from Ammodaucus leucotrichus fruits growing in Sahara and its evaluation as a cosmeceutical ingredient. Ind Crops Prod. (2018); 119:249-254.
[37] Chouitah, O. The essential oil of Algerian Ephedra alata subsp. alenda and its antimicrobial properties. J New Biol Rep. (2019); 8(3): 190-193.
[38] Chouitah, O. Chemical Composition and Antimicrobial Activities of the Essential Oil from Glycyrrhiza glabra Leaves. J Essent Oil-Bear Plants. (2011); 14(3):284-288.
[39] Berka-Zougali, B., Ferhat, M-A., Hassani, A., et al. Comparative Study of Essential Oils Extracted from Algerian Myrtus communis L. Leaves Using Microwaves and Hydrodistillation. Int J Mol Sci. (2012); 13:4673–95.
[40] Achoub, H., Zaiter, L., Benayache, F., et al. Chemical Composition of the Essential Oil of Aerial Parts of Thymus ciliatus (Desf.). Acta Sci Nat. (2019); 6:62–70.
[41] Benabed, H.K., Gourine, N., Ouinten, M., et al. Chemical Composition, Antioxidant and Antimicrobial Activities of the Essential Oils of Three Algerian Lamiaceae Species. Curr Nutr Food Sci. (2017); 13:97–109.
[42] Messara, Y., Fernane, F., Meddour, R. Chemical composition, antibacterial, and antifungal activities of the essential oil of Thymus numidicus Poiret from Algeria. Phytothérapie (2018); 16(3): 163-168.
[43] Hadj Khelifa, L., Brada, M., Brahmi, F., et al. Chemical composition and antioxidant activity of essential oil of Ocimum basilicum leaves from the northern region of Algeria. J Herb Med. (2012); 1:53-58.
[44] Brada, M., Khelifa, L.H., Achour, D., et al. Essential oil composition of Ocimum basilicum L. and Ocimum gratissimum L. from Algeria. J Essent Oil Bear Plants. (2011); 14:810-814.
[45] Bendif, H., Boudjeniba, M., Miara, M.D., et al. Essential Oil of Thymus munbyanus subsp. coloratus from Algeria: Chemotypification and in vitro Biological Activities. Chem Biodivers. (2017) ; 14(3).
[46] Bendif, H. Caractérisation phytochimique et détermination des activités biologiques in vitro des extraits actifs de quelques Lamiaceae: Ajuga iva (L.) Schreb., Teucrium polium L., Thymus munbyanus subsp. coloratus (Boiss. & Reut.) Greuter & Burdet et Rosmarinus eriocalyx Jord &. [dissertation]. ENS Kouba Algeria; (2017).
[47] Quezel, P., Santa, S. Nouvelle Flore de l’Algérie et des régions désertiques méridionales. Paris : CNRS ; (1963).
[48] IUCN International Union for Conservation of Nature. A guide to medicinal plants in north Africa. Malaga, Spain: IUCN Center for Mediterranean Cooperation; (2005).
[49] Pence, H.E., Williams, A. ChemSpider: An Online Chemical Information Resource. J Chem Educ. (2010); 87:1123-1224.
[50] Protein Data Bank PDB. http://www.rcsb.org
[51] Trott, O., Olson, A.J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. (2010); 31:455-61.
[52] Hunter, C.A., Lawson, K.R., Perkins, J., Urch, C.J. Aromatic interactions. J Chem Soc Perkin Trans 2. (2001); 0:651-669.
[53] Melissa, R. Pitman and Ian Menz, R. in Applied Mycology and Biotechnology, D. K. Arora, R. M. Berka, G. B. Singh eds. Elsevier B. V. Netherlands, 2006; pp.37-59
[54] Dassault Systèmes BIOVIA Discovery Studio Modeling Environment. Release 2017 Dassault Systèmes (2016).
[55] Belhassan, A., Zaki, H., Aouidate, A., et al. Interactions between (4Z)-hex-4-en-1-ol and 2-methylbutyl 2-methylbutanoate with olfactory receptors using computational methods. Mor J Chem. (2019); 7(1):028-035.
[56] Hakmi, M., Bouricha, E.M., Kandoussi, I., et al. Repurposing of known anti-virals as potential inhibitors for SARS-CoV-2 main protease using molecular docking analysis. Bioinformation. (2020); 16(4):301-306.
[57] Jalkute, C.B., Barage, S.H., Dhanavade, M.J.. Identification of Angiotensin Converting Enzyme Inhibitor: An in Silico Perspective. Int J Pept Res Ther. (2015); 21: 107–115.
[58] Pires, D.E.V., Blundell, T.L., Ascher, D.B.. pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures. J Med Chem. (2015); 58(9):4066-4072.
[59] Daina, A., Michielin, O., Zoete, V. Swiss ADME : a free web tool to evaluate pharmacokinetics , drug- likeness and medicinal chemistry friendliness of small molecules. Nat Publ Group. (2017); 1-13.
[60] Zhao, Y.H., Abraham, M.H., Le, J., et al. Rate-Limited Steps of Human Oral Absorption and QSAR Studies. (2002); 19:1446-1457.
[61] Belhassan, A., Chtita, S., Zaki, H., et al. Molecular docking analysis of N-substituted oseltamivir derivatives with the SARS-Cov-2 main protease. Bioinformation. (2020); 16:404-408.
