Evaluation of phenolic acids of Corylus avellana L. as potential SARS CoV-2 Main protease inhibitors

Year 2021, Volume: 14 Issue: 2, 492 - 509, 31.08.2021

Ali Acar

https://doi.org/10.18185/erzifbed.897348

Cited By: 1

Abstract

The novel human coronavirus, called SARS-CoV-2, first appeared in late 2019 in Wuhan, causing a respiratory disease termed COVID-19 in China and has been declared a pandemic worldwide. Although many different vaccine development studies against SARS-CoV-2 have reached the final stage, the protection that these vaccines will provide to society is not known for now, and therefore, effective antiviral drugs should be developed. In this study, the effects of the phenolic acids found in Corylus avellana L. on SARS-CoV-2 Main protease (Mpro) was investigated by molecular docking analysis. Also, the pharmacophore properties, biological properties, pharmacokinetics and drug-likeness properties of the compounds examined in the study were evaluated. Molecular docking of Mpro and phenolic acids was done with Autodock Vina. Many of the phenolic acids investigated in the study have interacted with the active site and catalytic residues of the Mpro. Drug similarity of phenolic acids interacting with MPro and each of the interacting compounds were found to be potential target inhibitors against SARS-CoV-2 Mpro and it was determined that its use would have limited or no side effect on the body.

Keywords

SARS-CoV-2, molecular docking, bioactivity, pharmacophore features, Corylus avellana L.

Potansiyel SARS CoV-2 Ana proteaz inhibitörleri olarak Corylus avellana L.'nin fenolik asitlerinin değerlendirilmesi

Abstract

SARS-CoV-2 adı verilen yeni insan koronavirüsü, ilk olarak 2019'un sonlarında Wuhan'da ortaya çıktığında Çin'de COVID-19 adlı bir solunum hastalığına neden oldu ve dünya çapında bir pandemi ilan edildi. SARS-CoV-2'ye karşı birçok farklı aşı geliştirme çalışması son aşamaya gelmiş olsa da bu aşıların topluma sağlayacağı koruma şimdilik bilinmemektedir ve bu nedenle etkili antiviral ilaçlar geliştirilmelidir. Bu çalışmada, Corylus avellana L.'de bulunan fenolik asitlerin SARS-CoV-2 ana proteaz (Mpro) üzerindeki etkileri moleküler yerleştirme analizi ile araştırılmıştır. Ayrıca çalışmada incelenen bileşiklerin farmakofor özellikleri, biyolojik özellikleri, farmakokinetikleri ve ilaca benzerlik özellikleri de değerlendirilmiştir. Mpro ve fenolik asitlerin moleküler yerleştirmesi Autodock Vina ile yapıldı. Çalışmada araştırılan fenolik asitlerin çoğu, Mpro'nun aktif bölgesi ve katalitik kalıntıları ile etkileşime girmiştir. MPro ile etkileşime giren fenolik asitlerin ilaç benzerliği ve etkileşen bileşiklerin her birinin SARS-CoV-2 Mpro'ya karşı potansiyel hedef inhibitörler olduğu bulundu ve kullanımının vücut üzerinde sınırlı veya hiçbir yan etkisi olmayacağı belirlendi.

Keywords

SARS-CoV-2, Moleküler yerleştirme, biyoaktivite, farmakofor özellikleri, corylus avellana L.

References

• Aanouz, I., Belhassan, A., El-Khatabi, K., Lakhlifi, T., El-Ldrissi, M., Bouachrine, M. 2020. “Moroccan Medicinal plants as inhibitors against SARS-CoV-2 main protease: Computational investigations”, Journal of Biomolecular Structure and Dynamics, 1-9.
• Alasalvar, C., Shahidi, F., Liyanapathirana, C. M., Ohshima, T. 2003. “Turkish tombul hazelnut (Corylus avellana L.). 1. Compositional characteristics”, Journal of Agricultural and Food Chemistry, 51(13), 3790-3796.
• Arun, K. G., Sharanya, C. S., Abhithaj, J., Francis, D., Sadasivan, C. 2020. “Drug repurposing against SARS-CoV-2 using E-pharmacophore based virtual screening, molecular docking and molecular dynamics with main protease as the target”, Journal of Biomolecular Structure and Dynamics, 2020, 1-12.
• Bahaeddin, Z., Yans, A., Khodagholi, F., Hajimehdipoor, H., Sahranavard, S. 2017. “Hazelnut and neuroprotection: Improved memory and hindered anxiety in response to intra-hippocampal Aβ injection”, Nutritional Neuroscience, 20(6), 317-326.
• Banerjee, A., Kulcsar, K., Misra, V., Frieman, M., Mossman, K. 2019. “Bats and coronaviruses”, Viruses, 11(1), 41.
• Belouzard, S., Millet, J. K., Licitra, B. N., Whittaker, G. R. 2012. “Mechanisms of coronavirus cell entry mediated by the viral spike protein”, Viruses, 4(6), 1011-1033.
• Bourgonje, A. R., Abdulle, A. E., Timens, W., Hillebrands, J. L., Navis, G. J., Gordijn, S. J., Bolling, M.C., Dijkstra, G., Voors, A. A., Osterhaus, A. D. M. E., van der Voort, P. H. J., Mulder, D. J., van Goor, H. 2020. “Angiotensin‐converting enzyme 2 (ACE2), SARS‐CoV‐2 and the pathophysiology of coronavirus disease 2019 (COVID‐19)” The Journal of Pathology, 251(3), 228-248.
• Cappelli, G., Giovannini, D., Basso, A. L., Demurtas, O. C., Diretto, G., Santi, C., Girelli, G., Bacchetta, L., Mariani, F. 2018. “A Corylus avellana L. extract enhances human macrophage bactericidal response against Staphylococcus aureus by increasing the expression of anti-inflammatory and iron metabolism genes”, Journal of Functional Foods, 45, 499-511.
• 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.
• Daina, A., Michielin, O., Zoete, V. 2017. “SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules”, Scientific Reports, 7(1), 1-13.
• Di Renzo, L., Merra, G., Botta, R., Gualtieri, P., Manzo, A., Perrone, M. A., Mazza, M., Cascapera, S., De Lorenzo, A. 2017. “Post-prandial effects of hazelnut-enriched high fat meal on LDL oxidative status, oxidative and inflammatory gene expression of healthy subjects: a randomized trial”, European Review for Medical and Pharmacological Sciences, 21(7), 1610-26.
• Elfiky, A. A. 2020. “Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study”, Life Sciences, 253, 117592.
• Gorbalenya, A. E., Baker, S. C., Baric, R., Groot, R. J. D., Drosten, C., Gulyaeva, A. A., Haagmans, B. L., Lauber, C., Leontovich, A. M., Neuman, B. W., Penzar, D., Perlman, S., Poon, L. L. M., Samborskiy, D., Sidorov, I. A., Sola, I., Zieburh, J. 2020. “Severe acute respiratory syndrome-related coronavirus: The species and its viruses–a statement of the coronavirus study group”, BioRxiv, 2020, 1-20.
• Graham, R. L., Baric, R. S. 2010. “Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission”, Journal of Virology, 84(7), 3134-3146.
• Guex, N., Peitsch, M. C. 1997. “SWISS‐MODEL and the Swiss‐Pdb Viewer: an environment for comparative protein modeling”, Electrophoresis, 18(15), 2714-2723. Hegyi, A., Ziebuhr, J. 2002. “Conservation of substrate specificities among coronavirus main proteases”, Journal of General Virology, 83(3), 595-599.
• Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., Yang, X., Bai, F., Liu, H., Liu, X., Guddat, L. W., Xu, W., Xiao, G., Qin, C., Shi, Z., Jiang, H., Rao, Z., Yang, H. 2020. “Structure of M pro 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.
• Kornsteiner, M., Wagner, K. H., Elmadfa, I. 2006. “Tocopherols and total phenolics in 10 different nut types”, Food Chemistry, 98(2), 381-387.
• Kumar, Y., Singh, H., Patel, C. N. 2020. “In silico prediction of potential inhibitors for the main protease of SARS-CoV-2 using molecular docking and dynamics simulation based drug-repurposing”, Journal of Infection and Public Health, 13(9), 1210-1223.
• Lai, T. H., Tang, E. W., Chau, S. K., Fung, K. S., Li, K. K. 2020. “Stepping up infection control measures in ophthalmology during the novel coronavirus outbreak: an experience from Hong Kong”, Graefe’s Archive for Clinical and Experimental Ophthalmology, 258(5), 1049-1055.
• Lee, J., Worrall, L. J., Vuckovic, M., Rosell, F. I., Gentile, F., Ton, A. T., Caveney, N. A., Ban, F., Cherkasov, A., Paetzel, M., Strynadka, N. C. J. 2020. “Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site”, Nature Communications, 11(1), 1-9.
• Lipinski, C. A., Lombardo, F., Dominy, B. W., Feeney, P. J. 1997. “Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings”, Advanced Drug Delivery Reviews, 23(1-3), 3-25.
• Lu, H. 2020. “Drug treatment options for the 2019-new coronavirus (2019-nCoV)”, Bioscience Trends, 14(1), 69-71.
• Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Bi, Y., Ma, X., Zhan, F., Wang, L., Hu, T., Zhou, H., Hu, Z., Zhou, W., Zhao, L., Chen, J., Meng, Y., Wang, J., Lin, Y., Yuan, J., Xie, Z., Ma, J., Liu, W. J., Wang, D., Xu, W., Holmes, E. C., Gao, G. F., Wu, G., Chen, W., Shi, W., Tan, W. 2020. “Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding”, The Lancet, 395(10224), 565-574.
• Masullo, M., Montoro, P., Mari, A., Pizza, C., Piacente, S. 2015. “Medicinal plants in the treatment of women's disorders: Analytical strategies to assure quality, safety and efficacy”, Journal of Pharmaceutical and Biomedical Analysis, 113, 189-211.
• Mohanty, P., Bhatnagar, S. 2019. “In silico screening to identify inhibitors of growth factor receptor 2–focal adhesion kinase interaction for therapeutic treatment of pathological cardiac hypertrophy” Assay and Drug Development Technologies, 17(2), 58-67.
• Molinspiration, 2020, https://www.molinspiration.com/, Last Accessed Date: 10 Jan 2021.
• Mollica, A., Zengin, G., Stefanucci, A., Ferrante, C., Menghini, L., Orlando, G., Brunetti, L., Locatelli, M., Dimmito, M. P., Novellino, E., Wakeel, O. K., Ogundeji, M. O., Onaolapo, A. Y., Onaolapo, O. J. 2018. “Nutraceutical potential of Corylus avellana daily supplements for obesity and related dysmetabolism”, Journal of Functional Foods, 47, 562-574.
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., Olson, A. J. 2009. “AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility”, Journal of Computational Chemistry, 30(16), 2785-2791.
• Muralidharan, N., Sakthivel, R., Velmurugan, D., Gromiha, M. M. 2020. “Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19”, Journal of Biomolecular Structure and Dynamics, 2020, 1-6.
• O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., Hutchison, G. R. 2011. “Open Babel: An open chemical toolbox”, Journal of Cheminformatics, 3(1), 1-14.
• Parvez, A., Meshram, J., Tiwari, V., Sheik, J., Dongre, R., Youssoufi, M. H., Hadda, T. B. 2010. “Pharmacophores modeling in terms of prediction of theoretical physico-chemical properties and verification by experimental correlations of novel coumarin derivatives produced via Betti’s protocol”, European Journal of Medicinal Chemistry, 45(9), 4370-4378.
• Paules, C. I., Marston, H. D., Fauci, A. S. 2020. “Coronavirus infections—More than just the common cold”, Jama, 323(8), 707-708.
• Pelvan, E., Olgun, E. Ö., Karadağ, A., Alasalvar, C. 2018. “Phenolic profiles and antioxidant activity of Turkish Tombul hazelnut samples (natural, roasted, and roasted hazelnut skin)” Food Chemistry, 244, 102-108.
• Platteau, C., De Loose, M., De Meulenaer, B., Taverniers, I. 2011. “Quantitative detection of hazelnut (Corylus avellana) in cookies: ELISA versus real-time PCR”, Journal of Agricultural and Food Chemistry, 59(21), 11395-11402.
• Prosperini, S., Ghirardello, D., Scursatone, B., Gerbi, V., Zeppa, G. 2009. “Identification of soluble phenolic acids in hazelnut (Corylus avellana L.) kernel”, Acta Horticulturae, 845, 677-680.
• Rodríguez-Morales, A. J., MacGregor, K., Kanagarajah, S., Patel, D., Schlagenhauf, P. 2020. “Going global–Travel and the 2019 novel coronavirus”, Travel Medicine and Infectious Disease, 33, 101578.
• Rushforth, K. 1999. Trees of Britain and Europe. Harper Collins Publishers, London, UK.
• Sampangi-Ramaiah, M. H., Vishwakarma, R., Shaanker, R. U. 2020. “Molecular docking analysis of selected natural products from plants for inhibition of SARS-CoV-2 main protease”, Current Science, 118(7), 1087-1092.
• Shah, K., Mujwar, S., Gupta, J. K., Shrivastava, S. K., Mishra, P. 2019. “Molecular docking and in silico cogitation validate mefenamic acid prodrugs as human cyclooxygenase-2 inhibitor”, Assay and Drug Development Technologies, 17(6), 285-291.
• Tang, B., Bragazzi, N. L., Li, Q., Tang, S., Xiao, Y., Wu, J. (2020). “An updated estimation of the risk of transmission of the novel coronavirus (2019-nCov)”, Infectious Disease Modelling, 5, 248-255.
• Trott, O., Olson, A. J. 2010. “AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading”, Journal of Computational Chemistry, 31(2), 455-461.
• Vijayakumar, B. G., Ramesh, D., Joji, A., Kannan, T. 2020. “In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2”, European Journal of Pharmacology, 886, 173448.
• Xia, B., Kang, X. 2011. “Activation and maturation of SARS-CoV main protease”, Protein & Cell, 2(4), 282-290.
• Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., Hilgenfeld, R. 2020. “Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors”, Science, 368(6489), 409-412.
• Zhou, P., Yang, X. L., Wang, X. G., Hu, B., Zhang, L., Zhang, W., Si, H. R., Zhu, Y., Li, B., Huang, C. L., Chen, H. D., Chen, J., Luo, Y., Guo,, H., Jiang, R. D., Liu, M. Q. , Ying, C., Shen, X. R., Wang, X., Zheng, X. S., Zhao, K., Chen, Q. J., Deng, F., Liu, L. L., Yan, B., Zhan, F. X., Wang, Y. Y., Xiao, G. F., Shi, Z. L. 2020. “A pneumonia outbreak associated with a new coronavirus of probable bat origin”, Nature, 579(7798), 270-273.