Main Article Content


Caffeic acid, a cathecol-containing phytochemical found in coffee, has been reported as a potent matrix metalloproteinase 9 (MMP9) inhibitor. The IC50 value of caffeic acid as MMP9 inhibitor could reach below 20 nM. The research presented in this article employed molecular dynamics simulations to unravel the atomic mechanism of the MMP9 inhibition by caffeic acid. Molecular dynamics simulations of MMP9 for 10 ns using YASARA-Structure were performed with and without caffeic acid as the studied ligand. The results showed that caffeic acid stabilized the stucture of the MMP9.


Metaloproteinase matriks 9 Asam kafeat Dinamika molekul YASARA-Structure

Article Details

Author Biography

Enade Perdana Istyastono, Universitas Sanata Dharma

Fakultas Farmasi, Universitas Sanata Dharma, Yogyakarta, Indonesia.

How to Cite
Istyastono, E. P. (2020). Studi Dinamika Molekul Stabilisasi Metaloproteinase Matriks 9 oleh Asam Kafeat: Molecular Dynamics Studies of Matrix Metalloprotenase-9 Stabilization by Caffeic Acid. Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) (e-Journal), 6(2).


  1. Antoni, C., Vera, L., Devel, L., Catalani, M. P., Czarny, B., Cassar-Lajeunesse, E., et al. (2013). Crystallization of bi-functional ligand protein complexes. J. Struct. Biol., 182(3), 246–254.
  2. Guariguata, L., Whiting, D. R., Hambleton, I., Beagley, J., Linnenkamp, U., & Shaw, J. E. (2014). Global estimates of diabetes prevalence for 2013 and projections for 2035. Diabetes Res. Clin. Pract., 103(2), 137–149.
  3. Hariono, M., Yuliani, S. H., Istyastono, E. P., Riswanto, F. D. O., & Adhipandito, C. F. (2018). Matrix metalloproteinase 9 (MMP9) in wound healing of diabetic foot ulcer: Molecular target and structure-based drug design. Wound Medicine, 22(September 2018), 1–13.
  4. Jin, U. H., Lee, J. Y., Kang, S. K., Kim, J. K., Park, W. H., Kim, J. G., et al. (2005). A phenolic compound, 5-caffeoylquinic acid (chlorogenic acid), is a new type and strong matrix metalloproteinase-9 inhibitor: Isolation and identification from methanol extract of Euonymus alatus. Life Sci., 77(22), 2760–2769.
  5. Jones, J. I., Nguyen, T. T., Peng, Z., & Chang, M. (2019). Targeting MMP-9 in Diabetic Foot Ulcers. Pharmaceuticals, 12(2), 79.
  6. Krieger, E., Koraimann, G., & Vriend, G. (2002). Increasing the precision of comparative models with YASARA NOVA - A self-parameterizing force field. Proteins, 47(3), 393–402.
  7. Krieger, E., & Vriend, G. (2015). New ways to boost molecular dynamics simulations. J. Comput. Chem., 36(13), 996–1007.
  8. Król, K., Gantner, M., Tatarak, A., & Hallmann, E. (2020). The content of polyphenols in coffee beans as roasting, origin and storage effect. Eur. Food Res. Technol., 246(1), 33–39.
  9. Liu, K., Watanabe, E., & Kokubo, H. (2017). Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations. J. Comput. Aided Mol. Des., 31(2), 201–211.
  10. Naidu, M.M., Sulochanamma, G., Sampathu, S. R., & Srinivas, P. (2008). Studies on extraction and antioxidant potential of green coffee. Food Chem., 107(1), 377–384.
  11. Park, W., Kim, S., & Kim, C. (2005). A new matrix metalloproteinase-9 inhibitor 3,4-dihydroxycinnamic acid (caffeic acid) from methanol extract of Euonymus alatus: Isolation and structure determination. Toxicology, 207(3), 383–390.
  12. Sargsyan, K., Grauffel, C., & Lim, C. (2017). How Molecular Size Impacts RMSD Applications in Molecular Dynamics Simulations. J. Chem. Theory Comput., 13(4), 1518–1524.
  13. Wang, T., & Ghalih, M. (2017). Evaluation of Grey Forecasting Method of Total Domestic Coffee Consumption in Indonesia. IJBER, 6(4), 67–72.
  14. Wicaksono, R. G., Hariono, M., & Istyastono, E. P. (2020). Molecular dynamics studies of full human matrix metalloproteinase 9 liganded with N-hydroxy-2-[(4-phenylphenyl)sulfonyl-propan-2-yloxyamino]acetamide. J. Pharm. Sci. Community, accepted.
  15. Yusuf, S., Okuwa, M., Irwan, M., Rassa, S., Laitung, B., Thalib, A., et al. (2016). Prevalence and Risk Factor of Diabetic Foot Ulcers in a Regional Hospital, Eastern Indonesia. Open J. Nurs., 6(1), 1–10.