In Silico Identification of Flavonoids from Corriandrum sativum Seeds against Coronavirus Covid-19 Main Protease
Molecular docking analysis is routinely used in modern drug research to understand and predict the relationship between a drug molecule and a target protein from a microbe. The entry and replication of pathogens in host cells can be prevented by drugs identified in this way. The coronavirus disease associated with SARS-CoV-2, COVID-19, has become today's most infectious and lethal pandemic disease in the world. Burgeoning in the absence of any particular vaccine or therapeutic agent against SARS-CoV-2.The situation urges the need for appropriate medications to treat patients infected with the virus. Consequently, the study focus on evaluate the therapeutic potential of flavonoids present in Corriandrum sativum seeds that could serve as suitable remedies for COVID19.We analyzed the binding affinity of four flavonoids were screened against Mpro protein of SARS-CoV-2 by PyRx Virtual Screening tool and also results are validated with Lig-Plot Plus. Lopinavir shows binding affinity of -8.3 Kcal/mol and exhibit stable, strong interaction with active site of COVID19 main protease. Besides flavonoids, Rutin found to have the highest binding affinity compared to Lopinavir with the Mpro protease, followed by Chlorogenic acid, Quercetin and Caffeic acid. The present study concludes that Rutin present in the integrant of seeds shows the highest potentiality for acting as in inhibitor of main protease enzyme. Further, characterization of the amino acid residues comprising the viral binding site and the nature of the hydrogen bonding involved in the ligand receptor interaction shows significant findings with Rutin binding to the MPro protein at amino acid. The amino acid acid present in active sites of Mpro protease responsible for virus pathogenicity. The findings of the present study need in vivo experiments to prove the utility of Rutin compounds and further use in making Corriandrum sativum seeds as anti-SARS-CoV-2 product in near future.
Keywords: Corriandrum sativum seeds,Novel Coronavirus, SARS-CoV2, COVID-19, Protease, Molecular Docking.
2. WHO Coronavirus Disease (COVID-19) Dashboard | WHO Coronavirus Disease (COVID-19) Dashboard [Internet]. [cited 2021 Jan 21]. Available from: https://covid19.who.int/
3. Jin Y, Yang H, Ji W, Wu W, Chen S, Zhang W, et al. Virology, epidemiology, pathogenesis, and control of covid-19 [Internet]. Vol. 12, Viruses. MDPI AG; 2020 [cited 2021 Jan 20]. Available from: https://pubmed.ncbi.nlm.nih.gov/32230900/
4. Kaushik S, Kaushik S, Sharma Y, Kumar R, Yadav JP. The Indian perspective of COVID-19 outbreak [Internet]. Vol. 31, VirusDisease. Springer; 2020 [cited 2021 Jan 20]. p. 146–53. Available from: https://pubmed.ncbi.nlm.nih.gov/32368570/
5. Dashraath P, Wong JLJ, Lim MXK, Lim LM, Li S, Biswas A, et al. Coronavirus disease 2019 (COVID-19) pandemic and pregnancy. Am J Obstet Gynecol [Internet]. 2020 Jun 1 [cited 2021 Jan 20];222(6):521–31. Available from: https://pubmed.ncbi.nlm.nih.gov/32217113/
6. Li G, De Clercq E. Therapeutic options for the 2019 novel coronavirus (2019-nCoV) [Internet]. Vol. 19, Nature reviews. Drug discovery. NLM (Medline); 2020 [cited 2021 Jan 21]. p. 149–50. Available from: https://pubmed.ncbi.nlm.nih.gov/32127666/
7. Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y, et al. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature [Internet]. 2020 Jun 11 [cited 2021 Jan 21];582(7811):289–93. Available from: https://pubmed.ncbi.nlm.nih.gov/32272481/
8. Kumar S, Pandey AK. Chemistry and biological activities of flavonoids: An overview [Internet]. Vol. 2013, The Scientific World Journal. ScientificWorld Ltd.; 2013 [cited 2021 Jan 21]. Available from: https://pubmed.ncbi.nlm.nih.gov/24470791/
9. Adem S, Eyupoglu V, Sarfraz I, Rasul A, Ali M. Identification of Potent COVID-19 Main Protease (Mpro) Inhibitors from Natural Polyphenols: An in Silico Strategy Unveils a Hope against CORONA [Internet]. Preprints; 2020 [cited 2021 Jan 21]. Available from: https://doi.org/10.20944/preprints202003.0333.v1
10. Ninfali P, Antonelli A, Magnani M, Scarpa ES. Antiviral properties of flavonoids and delivery strategies. Nutrients [Internet]. 2020 Sep 1 [cited 2021 Jan 21];12(9):1–19. Available from: https://pubmed.ncbi.nlm.nih.gov/32825564/
11. Wei JN, Liu ZH, Zhao YP, Zhao LL, Xue TK, Lan QK. Phytochemical and bioactive profile of Coriandrum sativum L. [Internet]. Vol. 286, Food Chemistry. Elsevier Ltd; 2019 [cited 2021 Jan 21]. p. 260–7. Available from: https://pubmed.ncbi.nlm.nih.gov/30827604/
12. Vo A. International Journal of Basic and Applied Sciences Reverse phase HPLC for the detection of flavonoids in the ethanolic extract of Coriandrum sativum L. seeds. Int J Basic Appl Sci [Internet]. 2012 [cited 2021 Jan 21];1(1):21–6. Available from: www.crdeep.org
13. Omrani M, Keshavarz M, Nejad Ebrahimi S, Mehrabi M, McGaw LJ, Ali Abdalla M, et al. Potential Natural Products Against Respiratory Viruses: A Perspective to Develop Anti-COVID-19 Medicines. Front Pharmacol [Internet]. 2021 Feb 17 [cited 2021 Mar 5];11:2115. Available from: https://www.frontiersin.org/articles/10.3389/fphar.2020.586993/full
14. Chhetri A, Chettri S, Rai P, Mishra DK, Sinha B, Brahman D. Synthesis, characterization and computational study on potential inhibitory action of novel azo imidazole derivatives against COVID-19 main protease (Mpro: 6LU7). J Mol Struct [Internet]. 2021 Feb 5 [cited 2021 Jan 22];1225. Available from: https://pubmed.ncbi.nlm.nih.gov/32963413/
15. Meng X-Y, Zhang H-X, Mezei M, Cui M. Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery. Curr Comput Aided-Drug Des [Internet]. 2012 Nov 11 [cited 2021 Jan 22];7(2):146–57. Available from: https://pubmed.ncbi.nlm.nih.gov/21534921/
16. Ferreira LG, Dos Santos RN, Oliva G, Andricopulo AD. Molecular docking and structure-based drug design strategies [Internet]. Vol. 20, Molecules. MDPI AG; 2015 [cited 2021 Jan 22]. p. 13384–421. Available from: https://pubmed.ncbi.nlm.nih.gov/26205061/
17. Khan T, Lawrence AJ, Azad I, Raza S, Khan AR. Molecular Docking Simulation with Special Reference to Flexible Docking Approach. JSM Chem [Internet]. 2018 [cited 2021 Jan 22];6(1):1053. Available from: http://zinc.docking.org/
18. O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An Open chemical toolbox. J Cheminform [Internet]. 2011 Oct [cited 2021 Jan 22];3(10). Available from: https://pubmed.ncbi.nlm.nih.gov/21982300/
19. Latha MS, Saddala MS. Molecular docking based screening of a simulated HIF-1 protein model for potential inhibitors. Bioinformation [Internet]. 2017 Nov 30 [cited 2021 Jan 22];13(11):388–93. Available from: https://pubmed.ncbi.nlm.nih.gov/29225432/
20. Dallakyan S, Olson AJ. Small-molecule library screening by docking with PyRx. Methods Mol Biol [Internet]. 2015 [cited 2021 Jan 22];1263:243–50. Available from: https://pubmed.ncbi.nlm.nih.gov/25618350/
21. Wallace AC, Laskowski RA, Thornton JM. Ligplot: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng Des Sel [Internet]. 1995 Feb [cited 2021 Jan 22];8(2):127–34. Available from: https://pubmed.ncbi.nlm.nih.gov/7630882/
22. Latha MS, Saddala MS. Molecular docking based screening of a simulated HIF-1 protein model for potential inhibitors. Bioinformation [Internet]. 2017 Nov 30 [cited 2021 Jan 23];13(11):388–93. Available from: https://pubmed.ncbi.nlm.nih.gov/29225432/
23. El-Saber Batiha G, Beshbishy AM, Ikram M, Mulla ZS, Abd El-Hack ME, Taha AE, et al. The pharmacological activity, biochemical properties, and pharmacokinetics of the major natural polyphenolic flavonoid: Quercetin [Internet]. Vol. 9, Foods. MDPI Multidisciplinary Digital Publishing Institute; 2020 [cited 2021 Jan 23]. Available from: /pmc/articles/PMC7143931/?report=abstract
24. Colunga Biancatelli RML, Berrill M, Catravas JD, Marik PE. Quercetin and Vitamin C: An Experimental, Synergistic Therapy for the Prevention and Treatment of SARS-CoV-2 Related Disease (COVID-19) [Internet]. Vol. 11, Frontiers in Immunology. Frontiers Media S.A.; 2020 [cited 2021 Jan 23]. p. 1451. Available from: /pmc/articles/PMC7318306/?report=abstract
25. Ganeshpurkar A, Saluja AK. The Pharmacological Potential of Rutin [Internet]. Vol. 25, Saudi Pharmaceutical Journal. Elsevier B.V.; 2017 [cited 2021 Jan 23]. p. 149–64. Available from: https://pubmed.ncbi.nlm.nih.gov/28344465/
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