Development of SARS-CoV-2 Inhibitors Using Molecular Docking Study with Different Coronavirus Spike Protein and ACE2
DOI:
https://doi.org/10.33084/jmd.v1i1.2212Keywords:
Molecular Docking, ADME, ACE2 Receptor, Spike protein, PhytochemicalsAbstract
The novel coronavirus SARS-CoV-2 is an acute respiratory tract infection that emerged in Wuhan city, China. The spike protein of coronaviruses is the main driving force for host cell recognition and is responsible for binding to the ACE2 receptor on the host cell and mediates the fusion of host and viral membranes. Recognizing compounds that could form a complex with the spike protein (S-protein) potently could inhibit SARS-CoV-2 infections. The software was used to survey 300 plant natural compounds or derivatives for their binding ability with the SARS-CoV-2 S-protein. The docking score for ligands towards each protein was calculated to estimate the binding free energy. Four compounds showed a strong ability to bind with the S-protein (neohesperidin, quercetin 3-O-rutinoside-7-O-glucoside, 14-ketostypodiol diacetate, and hydroxypropyl methylcellulose) and used to predict its docking model and binding regions. The highest predicted ligand/protein affinity was with quercetin 3-O-rutinoside-7-O-glucoside followed by neohesperidin. The four compounds were also tested against other related coronavirus and showed their binding ability to S-protein of the bat, SARS, and MERS coronavirus strains, indicating that they could bind and block the spike activities and subsequently prevent them infection of different coronaviruses. Molecular docking also showed the probability of the four ligands binding to the host cell receptor ACE2. The interaction residues and the binding energy for the complexes were identified. The strong binding ability of the four compounds to the S-protein and the ACE2 protein indicates that they might be used to develop therapeutics specific against SARS-CoV-2 and close related human coronaviruses.
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References
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16. Kaur SP, Gupta V. COVID-19 Vaccine: A comprehensive status report. Virus Res. 2020;288:198114. doi:10.1016/j.virusres.2020.198114
17. Wu C, Liu Y, Yang Y, Zhang P, Zhong W, Wang Y, et al. Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B. 2020;10(5):766-88. doi:10.1016/j.apsb.2020.02.008
18. Xian Y, Zhang J, Bian Z, Zhou H, Zhang Z, Lin Z, et al. Bioactive natural compounds against human coronaviruses: a review and perspective. Acta Pharm Sin B. 2020;10(7):1163-74. doi:10.1016/j.apsb.2020.06.002
19. Verma S, Twilley D, Esmear T, Oosthuizen CB, Reid AM, Nel M, et al. Anti-SARS-CoV Natural Products With the Potential to Inhibit SARS-CoV-2 (COVID-19). Front Pharmacol. 2020;11:561334. doi:10.3389/fphar.2020.561334
20. Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. J Comput Chem. 2010;31(2):455-61. doi:10.1002/jcc.21334
21. Yamashita F, Hashida M. In silico approaches for predicting ADME properties of drugs. Drug Metab Pharmacokinet. 2004;19(5):327-38. doi:10.2133/dmpk.19.327
22. Lionta E, Spyrou G, Vassilatis DK, Cournia Z. Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances. Curr Top Med Chem. 2014;14(16):1923-38. doi:10.2174/1568026614666140929124445
23. Pantsar T, Poso A. Binding Affinity via Docking: Fact and Fiction. Molecules. 2018;23(8):1899. doi:10.3390/molecules23081899
24. Herrera NG, Morano NC, Celikgil A, Georgiev GI, Malonis RJ, Lee JH, et al. Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis. ACS Omega. 2021;6(1):85-102. doi:10.1021/acsomega.0c03512
25. Robson B. COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance. Comput Biol Med. 2020;121:103749. doi:10.1016/j.compbiomed.2020.103749
26. Liu M, Wang T, Zhou Y, Zhao Y, Zhang Y, Li J. Potential Role of ACE2 in Coronavirus Disease 2019 (COVID-19) Prevention and Management. J Transl Int Med. 2020;8(1):9-19. doi:10.2478/jtim-2020-0003
27. Tang T, Bidon M, Jaimes JA, Whittaker GR, Daniel S. Coronavirus membrane fusion mechanism offers a potential target for antiviral development. Antiviral Res. 2020;178:104792. doi:10.1016/j.antiviral.2020.104792
28. Vishwakarma P, Yadav N, Rizvi ZA, Khan NA, Chiranjivi AK, Mani S, et al. Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein Based Novel Epitopes Induce Potent Immune Responses in vivo and Inhibit Viral Replication in vitro. Front Immunol. 2021;12:613045. doi:10.3389/fimmu.2021.613045
29. Huang Y, Yang C, Xu XF, Xu W, Liu SW. Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19. Acta Pharmacol Sin. 2020;41(9):1141-9. doi:10.1038/s41401-020-0485-4
30. Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al. Addendum: A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;588(7836):E6. doi:10.1038/s41586-020-2951-z
31. Ge XY, Wang N, Zhang W, Hu B, Li B, Zhang YZ, et al. Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft. Virol Sin. 2016;31(1):31-40. doi:10.1007/s12250-016-3713-9
32. Zhu Z, Lian X, Su X, Wu W, Marraro GA, Zeng Y. From SARS and MERS to COVID-19: a brief summary and comparison of severe acute respiratory infections caused by three highly pathogenic human coronaviruses. Respir Res. 2020;21(1):224. doi:10.1186/s12931-020-01479-w
33. Zheng J. SARS-CoV-2: an Emerging Coronavirus that Causes a Global Threat. Int J Biol Sci. 2020;16(10):1678-85. doi:10.7150/ijbs.45053
34. Pandey P, Rane JS, Chatterjee A, Kumar A, Khan R, Prakash A, et al. Targeting SARS-CoV-2 spike protein of COVID-19 with naturally occurring phytochemicals: an in silico study for drug development. J Biomol Struct Dyn. 2020:1-11. doi:10.1080/07391102.2020.1796811
35. Hiremath S, Kumar HDV, Nandan M, Mantesh M, Shankarappa KS, Venkataravanappa V, et al. In silico docking analysis revealed the potential of phytochemicals present in Phyllanthus amarus and Andrographis paniculata, used in Ayurveda medicine in inhibiting SARS-CoV-2. 3 Biotech. 2021;11(2):44. doi:10.1007/s13205-020-02578-7
36. Vincent S, Arokiyaraj S, Saravanan M, Dhanraj M. Molecular Docking Studies on the Anti-viral Effects of Compounds from Kabasura Kudineer on SARS-CoV-2 3CLpro. Front Mol Biosci. 2020;7:613401. doi:10.3389/fmolb.2020.613401
37. Abubakar AR, Haque M. Preparation of Medicinal Plants: Basic Extraction and Fractionation Procedures for Experimental Purposes. J Pharm Bioallied Sci. 2020;12(1):1-10. doi:10.4103/jpbs.JPBS_175_19
38. Pereira DM, Cheel J, Areche C, San-Martin A, Rovirosa J, Silva LR, et al. Anti-Proliferative Activity of Meroditerpenoids Isolated from the Brown Alga Stypopodium flabelliforme against Several Cancer Cell Lines. Mar Drugs. 2011;9(5):852-62. doi:10.3390/md9050852
39. Vedpal, Jayaram U, Wadhwani A, Dhanabal SP. Isolation and characterization of flavonoids from the roots of medicinal plant Tadehagi triquetrum (L.) H.Ohashi. Nat Pod Res. 2020;34(13):1913-8. doi:10.1080/14786419.2018.1561679
40. Ju WT, Kwon OC, Kim HB, Sung GB, Kim HW, Kim YS. Qualitative and quantitative analysis of flavonoids from 12 species of Korean mulberry leaves. J Food Sci Technol. 2018;55(5):1789-96. doi:10.1007/s13197-018-3093-2
41. Qamar MTU, Alqahtani SM, Alamri MA, Chen LL. Structural basis of SARS-CoV-2 3CL pro and anti-COVID-19 drug discovery from medicinal plants. J Pharm Anal. 2020;10(4):313-9. doi:10.1016/j.jpha.2020.03.009
42. Bhowmik D, Nandi R, Prakash A, Kumar D. Evaluation of flavonoids as 2019-nCoV cell entry inhibitor through molecular docking and pharmacological analysis. Heliyon. 2021;7(3):e06515. doi:10.1016/j.heliyon.2021.e06515
43. Tutunchi H, Naeini F, Ostadrahimi A, Hosseinzadeh‐Attar MJ. Naringenin, a flavanone with antiviral and anti‐inflammatory effects: A promising treatment strategy against COVID‐19. Phytother Res. 2020:[Epub ahead of print. doi:10.1002/ptr.6781
44. Basu A, Sarkar A, Maulik U. Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2. Sci Rep. 2020;10:17699. doi:10.1038/s41598-020-74715-4
45. Maginnis MS. Virus–Receptor Interactions: The Key to Cellular Invasion. J Mol Biol. 2018;430(17):2590-611. doi:10.1016/j.jmb.2018.06.024
46. Schwede T. Protein Modelling: What Happened to the “Protein Structure Gap”? Structure. 2013;21(9):1531-40. doi:10.1016/j.str.2013.08.007
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2021-06-30
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Shamkh IM, Pratiwi D. Development of SARS-CoV-2 Inhibitors Using Molecular Docking Study with Different Coronavirus Spike Protein and ACE2. J Mol Docking [Internet]. 2021Jun.30 [cited 2024Nov.15];1(1):1-14. Available from: https://journal.umpr.ac.id/index.php/jmd/article/view/2212
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