International Journal of Molecular Biotechnological Research Original Research

Using Multitarget Molecular Docking to Examine the Antiviral Potential of Clerodendrum Phlomidis against Measles

  1. Sampriya Raj Department of Biotechnology, NMAM Institute of Technology, Nitte, Karkala, Udupi
  2. Samiksha Bhor Department of Bioinformatics, Bionome, Bengaluru

Abstract

Objective: Measles, a viral disease caused by a member of the Paramyxoviridae virus family, is highly contagious and characterized by a respiratory illness and a maculopapular rash on the skin. Children are the main victims of the illness. In the context of drug development, this study investigates the efficacy of phytocompounds derived from Clerodendrum phlomidis against the target protein of the measles virus. Methods: The 7SKS protein was retrieved from the Protein Data Bank (PDB) database. Molecular docking studies were conducted systematically using PyRx and BIOVIA Discovery Studio Visualizer to assess the binding affinities of phytocompounds to the target protein. To evaluate the pharmacological properties of the phytocompounds, Swiss-ADME and ADMET lab were employed. Results: The docking results indicate that among the phytocompounds tested, Pectolinarin, beta-sitosterol, Clerodendrin A, Clerodin, Clerosterol, Daucosterol, Scutellarein, and Sterol exhibited the highest binding affinities to the target protein. However, based on the ADMET profile and drug-likeness prediction analysis, Clerodin and Scutellarein were found to have drug-like properties among the eight compounds evaluated. Conclusions: The results of this study indicate that Clerodin and Scutellarein possess specific binding affinity and therefore may be effective against the matrix protein. As such, these phytocompounds hold potential for use in therapeutic strategies against measles disease

Keywords

References (47)

  1. World Health Organization: WHO. (2023). Measles. www.who.int. https://www.who.int/news-room/fact-sheets/detail/measles
  2. Measles: Epidemiology and transmission. (n.d.). MediLib. https://www.medilib.ir/uptodate/
  3. Diane E. Griffin. Measles Vaccine. Viral Immunology. Mar 2018.86-95. Published in Volume: 31 Issue 2: March 1, 2018 Online Ahead of Print: December 19, 2017
  4. Kondamudi, N. P. (2022, December 23). Measles. StatPearls - NCBI Bookshelf. https://www.ncbi.nlm.nih.gov/books/NBK448068/
  5. Mina, M. J., Kula, T., Leng, Y., Li, M. Z., De Vries, R. D., Knip, M., Siljander, H., Rewers, M., Choy, D. F., Wilson, M., Larman, H. B., Nelson, A. M., Griffin, D. E., De Swart, R. L., & Elledge, S. J. (2019). Measles virus infection diminishes pre-existing antibodies that offer protection from other pathogens. Science, 366(6465), 599–606.
  6. Laksono, B. M., De Vries, R. D., McQuaid, S., Duprex, W. P., & De Swart, R. L. (2016). Measles Virus Host Invasion and Pathogenesis. Viruses, 8(8), 210.
  7. Mukherjee, P. K., Harwansh, R. K., Bahadur, S., Banerjee, S., Kar, A., Chanda, J., Biswas, S., Ahmmed, S. M., & Katiyar, C. (2017). Development of Ayurveda – Tradition to trend. Journal of Ethnopharmacology, 197, 10–24.
  8. Parasuraman, S., Thing, G. S., & Dhanaraj, S. A. (2014). Polyherbal formulation: Concept of ayurveda. Pharmacognosy reviews, 8(16), 73–80.
  9. Jameel, M. N., Ali, A., & Ali, M. K. (2017). Extraction and isolation of new compounds from traditional herbal medicine; Clerodendrum phlomidis Linn. Future Journal of Pharmaceutical Sciences, 3(2), 118–123
  10. Chauhan, M. (2019). Agnimantha / Clerodendrum Phlomidis. Planet Ayurveda. https://www.planetayurveda.com/library/agnimantha-clerodendrum-phlomidis/
  11. Chowdhary, Y. (2022). Chemical Composition of Clerodendrum Phlomidis: A Review. Asian Journal of Research In Pharmaceutical Sciences, 12(02), 133-136.
  12. Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-aided Molecular Design, 27(3), 221–234.
  13. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The protein data bank. Nucleic Acids Res 2000;28:235-42 Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, et al. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci 2018;27:293-315.
  14. Norris, M., Husby, M. L., Kiosses, W. B., Yin, J., Saxena, R., Rennick, L. J., Heiner, A., Harkins, S., Pokhrel, R., Schendel, S. L., Hastie, K. M., Landeras-Bueno, S., Salie, Z. L., Lee, B., Chapagain, P. P., Maisner, A., Duprex, W. P., Stahelin, R. V., & Saphire, E. O. (2022). Measles and Nipah virus assembly: Specific lipid binding drives matrix polymerization. Science Advances, 8(29).
  15. Ramachandran plot evaluation (n.d.). https://swift.cmbi.umcn.nl/servers/html/ramchk.html
  16. Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, et al. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci 2018;27:293-315
  17. PubChem. (n.d.). PubChem. PubChem. https://pubchem.ncbi.nlm.nih.gov/
  18. Mcconkey BJ, Sobolev V, Edelman M. The performance of current methods in ligand-protein docking. Curr Sci 2002;83:845-55.
  19. Morris GM, Lim-Wilby M. Molecular Docking. Methods in Molecular Biology. 2008:365-382. doi:10.1007/978-1-59745-177-2_19
  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;31:455-61.
  21. O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open babel: An open chemical toolbox. J Cheminform 2011;3:33.
  22. Biovia DS. Discovery Studio Modeling Environment. San Diego: Dassault Systemes; 2015. Available from: https://www.scirp. org/(S(351jmbntv- nsjt1aadkposzje))/reference/
  23. referencespapers. aspx?referenceid=2450411 [Last accessed on 2023 April 15].
  24. Gleichmann, N. (2023). What Is ADME? Drug Discovery From Technology Networks. https://www.technologynetworks.com/drug-discovery/articles/what-is-adme-336683
  25. 14.ADME and Toxicology | MoDRN. (n.d.). https://modrn.yale.edu/education/undergraduate-curriculum/modrn-u-modules/adme-and-toxicology
  26. Daina A, Michielin O, Zoete V. SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 2017;7:42717.
  27. Xiong G, Wu Z, Yi J, Fu L, Yang Z, Hsieh C, et al. ADMETlab 2.0: An integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Res 2021;49:W5-14.
  28. Daina A, Zoete V. A BOILED-Egg to predict gastrointestinal absorption and brain penetration of small molecules. ChemMedChem 2016;11:1117-21
  29. National Center for Biotechnology Information (2023). PubChem Compound Summary for CID 168849, Pectolinarin. Retrieved April 15, 2023 from https://pubchem.ncbi.nlm.nih.gov/
  30. compound/Pectolinarin.
  31. National Center for Biotechnology Information (2023). PubChem Compound Summary for CID 5281697, Scutellarein. Retrieved April 15, 2023 from https://pubchem.ncbi.nlm.nih.gov/
  32. compound/Scutellarein.
  33. National Center for Biotechnology Information (2023). PubChem Compound Summary for CID 442013, Clerodendrin A. Retrieved April 15, 2023 from https://pubchem.ncbi.nlm.nih.gov/
  34. compound/Clerodendrin-A.
  35. National Center for Biotechnology Information (2023). PubChem Compound Summary for CID 442014, Clerodin. Retrieved April 15, 2023 from https://pubchem.ncbi.nlm.nih.gov/
  36. compound/Clerodin.
  37. National Center for Biotechnology Information (2023). PubChem Compound Summary for CID 1107, Sterol. Retrieved April 15, 2023 from https://pubchem.ncbi.nlm.nih.gov/compound/Sterol.
  38. National Center for Biotechnology Information (2023). PubChem Compound Summary for CID 5283638, Clerosterol. Retrieved April 15, 2023 from https://pubchem.ncbi.nlm.nih.gov/
  39. compound/Clerosterol.
  40. National Center for Biotechnology Information (2023). PubChem Compound Summary for CID 222284, Beta-Sitosterol. Retrieved April 15, 2023 from https://pubchem.ncbi.nlm.nih.gov/
  41. compound/Beta-Sitosterol.
  42. National Center for Biotechnology Information (2023). PubChem Compound Summary for CID 5742590, Sitogluside. Retrieved April 15, 2023 from https://pubchem.ncbi.nlm.nih.gov/
  43. compound/Sitogluside.
  44. Kabra SK, Lodha R. Antibiotics for preventing complications in children with measles. Cochrane Database of Systematic Reviews. 2013;2013(8). doi:10.1002/14651858.cd001477.pub4
  45. Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, 31(2), 455–461.
  46. Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S., & Olson, A. J. (2016). Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nature protocols, 11(5), 905–919.
  47. van de Waterbeemd, H., & Gifford, E. (2003). ADMET in silico modelling: towards prediction paradise?. Nature reviews. Drug discovery, 2(3), 192–204