In Silico Screening of Traditional Herbal Medicine Derived Chemical Constituents for Possible Potential Inhibition against SARS-CoV-2


Affiliations

  • SRM College of Pharmacy, SRMIST, Department of Pharmaceutical Chemistry, Kancheepuram, Tamil Nadu, 603203, India
  • Parul Institute of Pharmacy & Research, Parul University, Department of Pharmacognosy and Phytochemistry, Waghodia, Gujarat, 391760, India
  • SRM College of Pharmacy, SRMIST, Dr APJ Abdul Kalam Research Lab, Kancheepuram, Tamil Nadu, 603203, India

Abstract

The outbreak of SARS-CoV-2 has initiated an exploration to find an efficient anti-viral agent. From the previous scientific studies of traditional herbal medicines like garlic, ginger, onion, turmeric, chilli, cinchona and pepper, 131 chemical constituents were identified. The filtered search of drug-like-molecules searched using Datawarrior resulted in 13 active constituents (apoquinine, catechin, cinchonidine, cinchonine, cuprediene, epicatechin, epiprocurcumenol, epiquinine, procurcumenol, quinidine, quinine, zedoaronediol, procurcumadiol) showed no mutagenic, carcinogenic or toxic properties. In silico study of these 13 compounds with the best binding affinity towards SARS-CoV-2 protease was carried out. The ligands were subjected to molecular docking using Autodock Vina. Epicatechin and apoquine showed highest binding affinity of -7 and -7.5kcal/mol while catechin and epicatechin showed four hydrogen bond interactions. It is interesting and worth noticing the interaction of GLU166 residue with the ligand in most of the constituents. The effectiveness of catechin and epicatechin as an antiviral agent could be tested against COVID-19.

Keywords

COVID-19, Catechin, Epicatechin, Data Warrior, Molecular Docking, Plant Products

Subject Discipline

Natural product

Full Text:

References

WHO. Naming the coronavirus disease (COVID-19) and the virus that causes it [Internet]. [cited 2020 Apr 8]. Available from: https://www.who.int/emergencies/ diseases/novel-coronavirus-2019/technical-guidance/ naming-the-coronavirus-disease-(covid-2019)-and-thevirusthat-causes-it.

Liu RP, Ge J De, Zhong Y, Zheng Q, Sun R. Traditional Chinese medicine for treatment of COVID-19 based on literature mining of targeting cytokine storm. Chinese Traditional and Herbal Drugs. 2020; 51(5):1096–105.

Li Y, Liu X, Guo L, Li J, Zhong D, Zhang Y, Clarke M, Jin R. Traditional Chinese herbal medicine for treating novel coronavirus (COVID-19) pneumonia: Protocol for a systematic review and meta-Analysis. Systematic Reviews. 2020; 9(1). https://doi.org/10.1186/s13643020-01343-4. PMid:32268923 PMCid:PMC7138957

Lerner K. SARS, MERS, and the Emergence of coronaviruses. Worldmark Global Health and Medicine Issues [Internet]. 2016. Available from:

Yan R, Zhang Y, Li Y, Xia L, Guo Y, Zhou Q. Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science. 2020; 367(6485):1444–8. https:// doi.org/10.1126/science.abb2762. PMid:32132184. PMC id:PMC7164635.

Ludwig S, Zarbock A. Coronaviruses and SARSCoV2: A Brief Overview. Anesthesia and Analgesia. 2020. https://doi.org/10.1213/ANE.0000000000004845. PMid:32243297. PMCid:PMC7173023

Wang X, Xu W, Hu G, Xia S, Sun Z, Liu Z, et al. SARSCoV2 infects T lymphocytes through its spike proteinmediated membrane fusion. Cellular and Molecular Immunology. 2020. https://doi.org/10.1038/s41423-0200424-9

Wang Q, Zhang Y, Wu L, Niu S, Song C, Zhang Z, et al. Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell. 2020. https://doi.org/10.1016/j.cell.2020.03.045. PMid:32275855 PMCid:PMC7144619

Kaladhar SVGKD. Effects of drugs on spike glycoprotein of sars-cov 2 in control of covid-2019. International Journal of Advanced Research. 2020; 8(3):918–24. https://doi.org/10.21474/IJAR01/10706

Law S, Leung AW, Xu C. Severe Acute Respiratory Syndrome (SARS) and Coronavirus disease-2019 (COVID-19): From causes to preventions in Hong Kong. International Journal of Infectious Diseases. 2020; 94:156–63. https://doi.org/10.1016/j.ijid.2020.03.059. PMid:32251790 PMCid:PMC7195109

Giron CC, Laaksonen A, Silva FLB da. pbioRxiv. 2020;2020.04.05.026377.

Rut W, Groborz K, Zhang L, Sun X, Zmudzinski M, Hilgenfeld R, et al. Substrate specificity profiling of SARS-CoV-2 Mpro protease provides basis for antiCOVID-19 drug design. bioRxiv. 2020. https://doi.org/10.1101/2020.03.07.981928. PMid:32014497

Rabaan AA, Al-ahmed SH, Sah R, Tiwari R, Iqbal M, Patel SK, et al. SARS-CoV-2 / COVID-19 and advances in developing potential therapeutics and vaccines to counter this emerging pandemic virus - A Review. Preprints. 2020; 4:1–46. https://doi.org/10.20944/ preprints202004.0075.v1

Bharath EN, Manjula SN, Vijaychand A. In silico drug design-tool for overcoming the innovation deficit in the drug discovery process. International Journal of Pharmacy and Pharmaceutical Sciences. 2011; 3(2):8– 12.

Ang L, Lee HW, Choi JY, Zhang J, Soo Lee M. Herbal medicine and pattern identification for treating COVID-19: A rapid review of guidelines. Integrative Medicine Research. 2020; 9(2):100407. https://doi.org/10.1016/j.imr.2020.100407. PMid:32289016 PMCid: PMC7104236

Ferner RE, Aronson JK. Chloroquine and hydroxychloroquine in covid-19. The BMJ. 2020; 369. https://doi.org/10.1136/bmj.m1432. PMid:32269046

Atallah P, Wagener KB, Schulz MD. ADMET: The future revealed. Macromolecules. 2013. https://doi.org/10.1002/chin.201336195

López-López E, Naveja JJ, Medina-Franco JL. DataWarrior: An evaluation of the open-source drug discovery tool. Expert Opinion on Drug Discovery. 2019. https://doi.org/10.1080/17460441.2019.1581170.

PMid:30806519

Trott O, Olson AJ. Autodock vina: Improving the speed and accuracy of docking. Journal of Computational Chemistry. 2019; 31(2):455–61.

Lindstrom W, Morris GM, Weber C, Huey R. Using AutoDock for virtual screening. The Scripps Research Institue [Internet]. 2006.

Lin LT, Hsu WC, Lin CC. Antiviral natural products and herbal medicines. Journal of Traditional and Complementary Medicine. 2014; 4(1):24–35. https://doi.org/10.4103/2225-4110.124335. PMid:24872930 PMCid:PMC4032839

Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y, et al. Structure of Mpro from COVID-19 virus and discovery of its inhibitors. Nature. 2020. https://doi.org/10.1101/2020.02.26.964882

Lohidashan K, Rajan M, Ganesh A, Paul M, Jerin J. Pass and Swiss ADME collaborated in silico docking approach to the synthesis of certain pyrazoline spacer compounds for dihydrofolate reductase inhibition and antimalarial activity. Bangladesh Journal of Pharmacology. 2018; 13(1):23–9. https://doi.org/10.3329/bjp.v13i1.33625

Contrera JF. Validation of Toxtree and SciQSAR in silico predictive software using a publicly available benchmark mutagenicity database and their applicability for the qualification of impurities in pharmaceuticals. Regulatory Toxicology and Pharmacology. 2013; 67(2):285–93. https://doi.org/10.1016/j.yrtph.2013.08.008. PMid: 23969001


Refbacks

  • There are currently no refbacks.