Article Sidebar

Download
PDF

Main Article Content

Abstract

The severe form of respiratory disease (COVID-19), caused by SARS-COV-2 virus, has evolved into a pandemic is the defining global health crisis of our time and greatest challenge we have faced since second World War. Hence, the current situation demands an immediate need to explore all the possible therapeutic strategies that can be control spread of the diseases. We identified potent COVID-19 Mpro inhibitors based on molecular docking studies on 24 known antiviral natural compounds, which are from medicinal plants and marine sponges. The results revealed that 15 potential COVID-19 main protease inhibitors have been identified among the 24 natural compounds of plants and marine origin. The result further revealed that the selected natural products that has lower free binding energy is Halituline (-8.41 Kcal/mol). As these active compounds were extensively validated by molecular docking, the chance that at least few of these compounds could be bioactive is excellent.

Keywords

COVID-19 SARS-CoV-2 Docking Binding energy Natural product

Article Details

How to Cite
Sadhasivam, G. (2020). Molecular Docking Studies of Some Natural Products Against SARS-CoV-2 Main Protease: Potential Therapeutic Agents for COVID-19. Asian Journal of Organic & Medicinal Chemistry, 5(3), 254–264. https://doi.org/10.14233/ajomc.2020.AJOMC-P288
Download Citation
Endnote/Zotero/Mendeley (RIS)
BibTeX

References

  1. L. van der Hoek, Human coronaviruses: What do They Cause?, Antivir. Ther., 12, 651 (2007).
  2. C. Geller, M. Varbanov and R.E. Duval, Human Coronaviruses: Insights into Environmental Resistance and Its Influence on the Development of New Antiseptic Strategies, Viruses, 4, 3044 (2012); https://doi.org/10.3390/v4113044
  3. P. Mukherjee, P. Desai, L. Ross, E.L. White and M.A. Avery, Structure-Based Virtual Screening Against SARS-3CLpro to Identify Novel Non-peptidic Hits, Bioorg. Med. Chem., 16, 4138 (2008); https://doi.org/10.1016/j.bmc.2008.01.011
  4. L.L. Chen, J. Li, C. Luo, H. Liu, W.J. Xu, G. Chen, O.W. Liew, W.L. Zhu, C.M. Puah, X. Shen and H.L. Jiang, Binding Interaction of Quercetin-3-b-galactoside and Its Synthetic Derivatives with SARS-CoV 3CLpro: Structure-Activity Relationship Studies Reveal Salient Pharmacophore Features, Bioorg. Med. Chem., 14, 8295 (2006); https://doi.org/10.1016/j.bmc.2006.09.014
  5. J.F. Chan, K.S. Li, K.K. To, V.C. Cheng, H. Chen and K.Y. Yuen, Is the Discovery of the Novel Human Betacoronavirus 2c EMC/2012 (HCoV-EMC) the Beginning of Another SARS-Like Pandemic, J. Infect., 65, 477 (2012); https://doi.org/10.1016/j.jinf.2012.10.002
  6. D. Paraskevis, E.G. Kostaki, G. Magiorkinis, G. Panayiotakopoulos, G. Sourvinos and S. Tsiodras, Full-Genome Evolutionary Analysis of the Novel Coronavirus (2019-nCoV) Rejects the Hypothesis of Emergence as a Result of a Recent Recombination Event, Infect. Genet. Evol., 79, 104212 (2020); https://doi.org/10.1016/j.meegid.2020.104212
  7. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports
  8. P. Ruwali, N. Rai, N. Kumar and P. Goutam, Antiviral Potential of Medicinal Plants: An Overview, Int. Res. J. Pharm., 4, 8 (2013); https://doi.org/10.7897/2230-8407.04603
  9. C.D. Owen, P. Lukacik, C.M. Strain-Damerell, A. Douangamath, A.J. Powell, D. Fearon, J. Brandao-Neto, A.D. Crawshaw, D. Aragao, M. Williams, R. Flaig, D. Hall, K. McAauley, D.I. Stuart, F. Von Delft and M.A. Walsh, COVID-19 Main Protease with Unliganded Active Site (2020).
  10. S.M.D. Rizvi, S. Shakil and M. Haneef, A Simple Click by Click Protocol to Perform Docking: AutoDock 4.2 Made Easy for Non-Bioinformaticians, Excli J., 12, 831 (2013).
  11. C.A. Lipinski, F. Lombardo, B.W. Dominy and P.J. Feeney, Experi-mental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings, Adv. Drug Deliv. Rev., 64, 4 (2012); https://doi.org/10.1016/j.addr.2012.09.019
  12. T. Ganyani, C. Kremer, D. Chen, A. Torneri, C. Faes and J. Wallinga, Estimating the Generation Interval for COVID-19 based on Symptom Onset Data, medRxiv Preprint (2020); https://doi.org/10.1101/2020.03.05.20031815
  13. B. Liu and J. Zhou, SARS-CoV Protease Inhibitors Design using Virtual Screening Method from Natural Products Libraries, J. Comput. Chem., 26, 484 (2005); https://doi.org/10.1002/jcc.20186
  14. N. Ansari and F. Khodagholi, Natural Products as Promising Drug Candidates for the Treatment of Alzheimer’s Disease: Molecular Mechanism Aspect, Curr. Neuropharmacol., 11, 414 (2013); https://doi.org/10.2174/1570159X11311040005
  15. H. Kubinyi, Drug Research: Myths, Hype and Reality, Nat. Rev. Drug Discov., 2, 665 (2003); https://doi.org/10.1038/nrd1156
  16. P. Srinivasan, S. Vijayakumar, S. Kothandaraman and M. Palani, Anti-Diabetic Activity of Quercetin Extracted from Phyllanthus emblica L. Fruit: in silico and in vivo Approaches, J. Pharm. Anal., 8, 109 (2018); https://doi.org/10.1016/j.jpha.2017.10.005
  17. Y. Li, P.P. But and V.E. Ooi, ANtiviral Activity and Mode of Action of Caffeoylquinic Acids from Schefflera heptaphylla (L.) Frodin, Antiviral Res., 68, 1 (2005); https://doi.org/10.1016/j.antiviral.2005.06.004
  18. C. Prieto and J.M. Castro, Porcine Reproductive and Respiratory Syndrome Virus Infection in the Boar: A Review, Theriogenology, 63, 1 (2005); https://doi.org/10.1016/j.theriogenology.2004.03.018
  19. X.H. Nong, Y.F. Wang, X.Y. Zhang, M.P. Zhou, X.Y. Xu and S.H. Qi, Territrem and Butyrolactone Derivatives from a Marine-Derived Fungus Aspergillus Terreus, Mar. Drugs, 12, 6113 (2014); https://doi.org/10.3390/md12126113
  20. M.M. Parida, C. Upadhyay, G. Pandya and A.M. Jana, Inhibitory potential of Neem (Azadirachta indica Juss) Leaves on Dengue virus Type-2 Replication, J. Ethnopharmacol., 79, 273 (2002); https://doi.org/10.1016/S0378-8741(01)00395-6
  21. Z. Keivan, T.T. Boon, S.S. Teoh, F.W. Pooi and A. Sazaly, P02.158. Tai Chi Community Program is Effective in Reducing Elderly Fall-Related Hospital Utilization: A Prospective Observational Study, BMC Complement. Altern. Med., 12, 214 (2012); https://doi.org/10.1186/1472-6882-12-S1-P214
  22. K. Hayashi, K. Minoda, Y. Nagaoka, T. Hayashi and S. Uesato, Antiviral Activity of Berberine and Related Compounds against Human Cytomegalovirus, Bioorg. Med. Chem. Lett., 17, 1562 (2007); https://doi.org/10.1016/j.bmcl.2006.12.085
  23. N.I. Pavlova, O.V. Savinova, S.N. Nikolaeva, E.I. Boreko and O.B. Flekhter, Antiviral Activity of Betulin, Betulinic and Betulonic Acids Against Some Enveloped and Non-enveloped Viruses, Fitoterapia, 74, 489 (2003); https://doi.org/10.1016/S0367-326X(03)00123-0
  24. M.J. Currens, R.J. Gulakowski, J.M. Mariner, R.A. Moran, R.W. Buckheit, K.R. Gustafson, J.B. McMahon and M.R. Boyd, Antiviral Activity and Mechanism of Action of Calanolide A against the Human Immuno-deficiency Virus Type-1, J. Pharmacol. Exp. Ther., 279, 645 (1996).
  25. J.H. Peter, Compounds with Anti-HIV Activity from Plants, Trans. Royal Soc. Trop. Med. Hyg., 90, 604 (1996); https://doi.org/10.1016/S0035-9203(96)90403-4
  26. B.-Q. Wang, Salvia miltiorrhiza: Chemical and Pharmacological Review of a Medicinal Plant, J. Med. Plants Res., 4, 2813 (2010).
  27. P.G. Canonico, W.L. Pannier, J.W. Huggins and K.L. Rienehart, Inhibition of RNA Viruses in vitro and in Rift Valley Fever-Infected Mice by Didemnins A and B, Antimicrob. Agents Chemother., 22, 696 (1982); https://doi.org/10.1128/AAC.22.4.696
  28. K. Yasukawa, Y. Ikeya, H. Mitsuhashi, M. Iwasaki, M. Aburada, S. Nakagawa, N. Takeuchi and M. Takido, Gomisin A Inhibits Tumor Promotion by 12-O-Tetra-decanoylphorbol-13-Acetate in Two-Stage Carcinogenesis in Mouse Skin, Oncology, 49, 68 (1992); https://doi.org/10.1159/000227014
  29. A.C. da Silva, J.M. Kratz, F.M. Farias, A.T. Henriques, J. dos Santos, R.M. Leonel, C. Lerner, B. Mothes, C.R.M. Barardi and C.M.O. Simões, In Vitro Antiviral Activity of Marine Sponges Collected Off Brazilian Coast, Biol. Pharm. Bull., 29, 135 (2006); https://doi.org/10.1248/bpb.29.135
  30. G. Poonam, Chemical Constituents of Haliclona: An Overview, J. Pharmacogn. Phytochem., 8, 823 (2019).
  31. A. Paredes, M. Alzuru, J. Mendez and M. Rodríguez-Ortega, Anti-Sindbis Activity of Flavanones Hesperetin and Naringenin, Biol. Pharm. Bull., 26, 108 (2003); https://doi.org/10.1248/bpb.26.108
  32. X. Xu, H. Xie, Y. Wang and X. Wei, A-Type Proanthocyanidins from Lychee Seeds and Their Antioxidant and Antiviral Activities, J. Agric. Food Chem., 58, 11667 (2010); https://doi.org/10.1021/jf1033202
  33. I.S. Abd-Elazem, H.S. Chen, R.B. Bates and R.C. Huang, Isolation of Two Highly Potent and Non-toxic Inhibitors of Human Immuno-deficiency Virus Type 1 (HIV-1) Integrase from Salvia miltiorrhiza, Antiviral Res., 55, 91 (2002); https://doi.org/10.1016/S0166-3542(02)00011-6
  34. P.L. Wang, L.F. Li, Q.Y. Wang, L.Q. Shang, P.Y. Shi and Z. Yin, Anti-Dengue-Virus Activity and Structure-Activity Relationship Studies of Lycorine Derivatives, ChemMedChem, 9, 1522 (2014); https://doi.org/10.1002/cmdc.201300505
  35. M. Aggarwal, G.P. Leser and R.A. Lamb, Repurposing Papaverine as an Antiviral Agent against Influenza Viruses and Paramyxoviruses, J. Virol., 94, 19 (2020); https://doi.org/10.1128/JVI.01888-19
  36. C.D. Andjelic, V. Planelles and L.R. Barrows, Characterizing the Anti-HIV Activity of Papuamide A, Mar. Drugs, 6, 528 (2008); https://doi.org/10.3390/md20080027
  37. A.D. Naik and A.R. Juvekar, Effects of Alkaloidal Extract of Phyllanthus niruri on HIV Replication, Indian J. Med. Sci., 57, 387 (2003).
  38. Y. Hwang, D. Rowley, D. Rhodes, J. Gertsch, W. Fenical and F. Bushman, Mechanism of Inhibition of a Poxvirus Topoisomerase by the Marine Natural Product Sansalvamide A, Mol. Pharmacol., 55, 1049 (1999); https://doi.org/10.1124/mol.55.6.1049
  39. S.Z. Moghadamtousi, S. Nikzad, H.A. Kadir, S. Abubakar and K. Zandi, Potential Antiviral Agents from Marine Fungi: An Overview, Mar. Drugs, 13, 4520 (2015); https://doi.org/10.3390/md13074520
  40. J.-N. Wang, C.-Y. Hou, Y.-L. Liu, L.-Z. Lin, R.R. Gil and G.A. Cordell, Swertifrancheside, An HIV-Reverse Transcriptase Inhibitor and the First Flavone-Xanthone Dimer, from Swertia franchetiana, J. Nat. Prod., 57, 211 (1994); https://doi.org/10.1021/np50104a003
  41. N. Sun, P. Sun, M. Yao, A. Khan, Y. Sun, K. Fan, W. Yin and H. Li, Autophagy Involved in Antiviral Activity of Sodium Tanshinone IIA Sulfonate against Porcine Reproductive and Respiratory Syndrome Virus Infection in vitro, Antivir. Ther., 24, 27 (2018); https://doi.org/10.3851/IMP3268
  42. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew and A.J. Olson, Automated Docking Using a Lamarckian Genetic Algorithm and An Empirical Binding Free Energy Function, J. Comput. Chem., 19, 1639 (1998); https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14<1639:: AID-JCC10>3.0.CO;2-B