The Study of Potential Antiviral Compounds from Indonesian Medicinal Plants as Anti-COVID-19 with Molecular Docking Approach
DOI:
https://doi.org/10.33084/jmd.v1i1.2307Keywords:
Anti-COVID-19, Docking, Indonesia, Medicinal plantsAbstract
Corona Virus Disease 2019 (COVID-19) is a new strain of coronavirus called SARS-CoV-2, which was identified in Wuhan, China, in December 2019. The rapid transmission of COVID-19 from human to human forced researchers to find a potent drug by setting aside the time-consuming traditional method in drug development. The molecular docking approach is one a reliable method to screening compound from chemical drug or by finding a compound from Indonesian herbal plants. The present study aimed to assess the potency of compounds from five medicinal plants as potential inhibitors of PLpro and 3CLpro from SARS-CoV-2 using molecular study. The molecular docking was performed using Protein-Ligand Ant System (PLANTS) to analyze the potential compounds by the docking score. Remdesivir triphosphate was used as a standard for the comparison of the test compounds. The docking score obtained from the docking of PLpro with native ligand, remdesivir triphosphate, curcumin, demethoxycurcumin, bisdemethoxycurcumin, luteolin, apigenin, quercetin, kaempferol, formononetin-7-O-glucuronide, andrographolide, and neoandrographolide were -111.441, -103.827, -103.609, -102.363, -100.27, -79.6655, -78.6901, -80.9337, -79.4686, -82.1124, -79.1789, and -97.2452, respectively. Meanwhile, docking score with 3CLpro for the same ligand were -64.0074, -86.1811, -81.428, -87.1625, -78.2899, -73.4345, -70.3368, -71.5539, -68.4321, -72.0154, -75.9777, and -93.7746. The docking score data suggest that curcumin was the most potential as a PLpro inhibitor, while neoandrographolide was the best as a 3CLpro inhibitor.
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References
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30. Saleh MSM, Kamisah Y. Potential Medicinal Plants for the Treatment of Dengue Fever and Severe Acute Respiratory Syndrome-Coronavirus. Biomolecules. 2020;11(1):42. doi:10.3390/biom11010042
2. Frediansyah A, Nainu F, Dhama K, Mudatsir M, Harapan H. Remdesivir and its antiviral activity against COVID-19: A systematic review. Clin Epidemiol Glob Health. 2021;9:123-7. doi:10.1016/j.cegh.2020.07.011
3. Malin JJ, Suárez I, Priesner V, Fätkenheuer G, Rybniker J. Remdesivir against COVID-19 and Other Viral Diseases. Clin Microbiol Rev. 2020;34(1):e00162-20. doi:10.1128/cmr.00162-20
4. Nguyen HL, Thai NQ, Truong DT, Li MS. Remdesivir Strongly Binds to Both RNA-Dependent RNA Polymerase and Main Protease of SARS-CoV-2: Evidence from Molecular Simulations. J Phys Chem B. 2020;124(50):11337-48. doi:10.1021/acs.jpcb.0c07312
5. Bailly C, Vergoten G. Glycyrrhizin: An alternative drug for the treatment of COVID-19 infection and the associated respiratory syndrome? Pharmacol Ther. 2020;214:107618. doi:10.1016/j.pharmthera.2020.107618
6. Lin X, Li X, Lin X. A Review on Applications of Computational Methods in Drug Screening and Design. Molecules. 2020;25(6):1375. doi:10.3390/molecules25061375
7. Batool M, Ahmad B, Choi S. A Structure-Based Drug Discovery Paradigm. Int J Mol Sci. 2019;20(11):2783. doi:10.3390/ijms20112783
8. Attique SA, Hassan M, Usman M, Atif RM, Mahboob S, Al-Ghanim KA, et al. A Molecular Docking Approach to Evaluate the Pharmacological Properties of Natural and Synthetic Treatment Candidates for Use against Hypertension. Int J Environ Res Public Health. 2019;16(6):923. doi:10.3390/ijerph16060923
9. Badan Pengawas Obat dan Makanan Republik Indonesia. Pedoman Penggunaan Herbal dan Suplemen Kesehatan dalam Menghadapi COVID-19 di Indonesia. Jakarta: Badan Pengawas Obat dan Makanan Republik Indonesia; 2020.
10. Jena AB, Kanungo N, Nayak V, Chainy GBN, Dandapat J. Catechin and curcumin interact with S protein of SARS-CoV2 and ACE2 of human cell membrane: insights from computational studies. Sci Rep. 2021;11(1):2043. doi:10.1038/s41598-021-81462-7
11. Gupta S, Singh AK, Kushwaha PP, Prajapati KS, Shuaib M, Senapati S, et al. Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies. J Biomol Struct Dyn. 2020:1-12. doi:10.1080/07391102.2020.1776157
12. Park JY, Yuk HJ, Ryu HW, Lim SH, Kim KS, Park KH, et al. Evaluation of polyphenols from Broussonetia papyrifera as coronavirus protease inhibitors. J Enzyme Inhib Med Chem. 2017;32(1):504-15. doi:10.1080/14756366.2016.1265519
13. Jo S, Kim S, Shin DH, Kim MS. Inhibition of SARS-CoV 3CL protease by flavonoids. J Enzyme Inhib Med Chem. 2020;35(1):145-51. doi:10.1080/14756366.2019.1690480
14. Murugan NA, Pandian CJ, Jeyakanthan J. Computational investigation on Andrographis paniculata phytochemicals to evaluate their potency against SARS-CoV-2 in comparison to known antiviral compounds in drug trials. J Biomol Struct Dyn. 2020:1-12. doi:10.1080/07391102.2020.1777901
15. Tsai SC, Lu CC, Bau DT, Chiu YJ, Yen YT, Hsu YM, et al. Approaches towards fighting the COVID‑19 pandemic (Review). 2021; Int J Mol Med. 47(1):3-22. doi:10.3892/ijmm.2020.4794
16. Naqvi AAT, Fatima K, Mohammad T, Fatima U, Singh IK, Singh A, et al. Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach. Biochim Biophys Acta Mol Basis Dis. 2020;1866(10):165878. doi:10.1016/j.bbadis.2020.165878
17. Shin D, Mukherjee R, Grewe D, Bojkova D, Baek K, Bhattacharya A, et al. Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature. 2020;587(7835):657-62. doi:10.1038/s41586-020-2601-5
18. Wang R, Stephen P, Tao Y, Zhang W, Lin SX. Human endeavor for anti-SARS-CoV-2 pharmacotherapy: A major strategy to fight the pandemic. Biomed Pharmacother. 2021;137:111232. doi:10.1016/j.biopha.2021.111232
19. Douangamath A, Fearon D, Gerhtz P, Krojer T, Lukacik P, Owen CD, et al. Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease. Nat Commun. 2020;11(1):5047. doi:10.1038/s41467-020-18709-w
20. Purnomo H, Jenie UA, Nugroho AE, Pranowo HD. In silico and in vivo qualitative relationships of para-aminophenol analogues. Int J Pharm Clin Res. 2016;8(Suppl 5):367-71.
21. Castro-Alvarez A, Costa AM, Vilarrasa J. The Performance of Several Docking Programs at Reproducing Protein–Macrolide-Like Crystal Structures. Molecules. 2017;22(1):136. doi:10.3390/molecules22010136
22. Meng XY, Zhang HX, Mezei M, Cui M. Molecular Docking: A powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des. 2011;7(2):146-57. doi:10.2174/157340911795677602
23. Laksmiani NPL, Larasanty LPF, Santika AAGJ, Prayoga PAA, Dewi AAIK, Dewi NPAK. Active Compounds Activity from the Medicinal Plants Against SARS-CoV-2 using in Silico Assay. Biomed Pharmacol J. 2020;13(2):873-81. doi:10.13005/bpj/1953
24. Sharma A, Goyal S, Yadav AK, Kumar P, Gupta L. In-silico screening of plant-derived antivirals against main protease, 3CLpro and endoribonuclease, NSP15 proteins of SARS-CoV-2. J Biomol Struct Dyn. 2020:1-15. doi:10.1080/07391102.2020.1808077
25. Moghadamtousi SZ, Kadir HA, Hassandarvish P, Tajik H, Abubakar S, Zandi K. A review on antibacterial, antiviral, and antifungal activity of curcumin. Biomed Res Int. 2014;2014:186864. doi:10.1155/2014/186864
26. Wen CC, Kuo YH, Jan JT, Liang PH, Wang SY, Liu HG, et al. Specific plant terpenoids and lignoids possess potent antiviral activities against severe acute respiratory syndrome coronavirus. J Med Chem. 2007;50(17):4087-95. doi:10.1021/jm070295s
27. Puttaswamy H, Gowtham HG, Ojha MD, Yadav A, Choudhir G, Raguraman V, et al. In silico studies evidenced the role of structurally diverse plant secondary metabolites in reducing SARS-CoV-2 pathogenesis. Sci Rep. 2020;10(1):20584. doi:10.1038/s41598-020-77602-0
28. Okhuarobo A, Falodun JE, Erharuyi O, Imieje V, Falodun A, Langer P. Harnessing the medicinal properties of Andrographis paniculata for diseases and beyond: a review of its phytochemistry and pharmacology. Asian Pac J Trop Dis. 2014;4(3):213-22. doi:10.1016/S2222-1808(14)60509-0
29. Enmozhi SK, Raja K, Sebastine I, Joseph J. Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach. J Biomol Struct Dyn. 2020:1-7. doi:10.1080/07391102.2020.1760136
30. Saleh MSM, Kamisah Y. Potential Medicinal Plants for the Treatment of Dengue Fever and Severe Acute Respiratory Syndrome-Coronavirus. Biomolecules. 2020;11(1):42. doi:10.3390/biom11010042
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Published
2021-06-30
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Rizma BRP, Ananto AD, Sunarwidhi AL. The Study of Potential Antiviral Compounds from Indonesian Medicinal Plants as Anti-COVID-19 with Molecular Docking Approach. J Mol Docking [Internet]. 2021Jun.30 [cited 2024Nov.15];1(1):32-9. Available from: https://journal.umpr.ac.id/index.php/jmd/article/view/2307
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