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http://dx.doi.org/10.17480/psk.2016.60.2.78

The Interaction of Phenylthiourea Derivatives as Catechol Oxidase Inhibitors by Molecular Mechanics Simulation  

Park, Kyung Lae (Department of Pharmaceutics, College of Pharmacy, Chungnam National University)
Publication Information
YAKHAK HOEJI / v.60, no.2, 2016 , pp. 78-84 More about this Journal
Abstract
N-Phenylthiourea derivatives and catechol oxidase receptor complex was studied using molecular mechanics method. The starting structure was adopted from the protein databank and the calculation of energy minimization and molecular dynamics was performed with AMBER package. The molecular dynamics showed that the simulation time span of 20 ns was long enough to observe the interaction profile and stationary ligand-receptor configuration in the complex. The conformation of the ligand was related to the interaction to the receptor and the efficacy was also interpreted in this context.
Keywords
metalloprotein; catechol oxidase; molecular mechanics; ligand-receptor complex;
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1 Lennard-Jones, J. E. : On the determination of molecular fields. Proc. R. Soc. Lond. 106, 463 (1924).   DOI
2 Ramachandran, G. N., Ramakrishnan, C. and Sasisekharan, V. : Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7, 95 (1963).   DOI
3 Ando, H., Kondoh, H., Ichihashi, M. and Hearing, V. J. : Approaches to identify inhibitors of melanin biosynthesis via the quality control of tyrosinase. J. Inves. Dermatol. 127, 751 (2007).   DOI
4 Wang, J., Cieplak, P. and Kollman, P. A. : How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21, 1049 (2000).   DOI
5 Karlin, K. D. : Metalloenzymes, structural motifs, and inorganic models. Science 261, 701 (1993).   DOI
6 Kim, Y. J. and Uyama, H. : Tyrosinase inhibitors from natural and synthetic sources: structure, inhibition mechanism and perspective for the future. Cell. Mol. Life Sci. 62, 1707 (2005).   DOI
7 Klabunde, T., Eicken, C., Sacchettini, J. C. and Krebs, B. : Crystal structure of a plant catechol oxidase containing a dicopper center. Nat. Struct. Biol. 5, 1084 (1998).   DOI
8 Thanigaimalai, P., Hoang, T. A. L., Lee, K. C., Bang, S. C., Sharma, V. K., Yun, C. Y., Roh, E., Hwang, B. Y., Kim, Y. and Jung, S. H. : Design and synthesis of novel hydroxyalkylaminomethylchromones for their IL-5 inhibitory activity. Bioorg. Med. Chem. 18, 4625 (2010).   DOI
9 Case, D. A., Darden, T. A., Cheatham III, T. E., Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Walker, R. C., Zhang, W., Merz, K. M., Roberts, B., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Kollosvary, I., Wong, K. F., Paesani, F., Vanicek, J., Liu, J., Wu, X., Brozell, S. R., Steinbrecher, T., Goehlke, H., Cai, Q., Ye, X., Wang, J., Hsieh, M.-J., Cui, G., Roe, D. R., Mathews, D. H., Seetin, M. G., Sagui, C., Babin, V., Luchko, T., Gusarov, S., Kovalenko, A. and Kollman, P. A. : AMBER12. University of California, San Francisco (2012).
10 Park, K. L. : Modeling partial atomic charge of organic molecule and mutated amino acid in a protein-ligand complex for molecular mechanics simulation. Bull. Korean Chem. Soc. 34, 299 (2013).   DOI
11 Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. and Klein, M. L. : Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926 (1983).   DOI
12 Jakalian, A., Bush, B. L., Jack, D. B. and Bayly, C. I. : Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method. J. Comput. Chem. 21, 132 (2000).   DOI
13 Wang, J., Wolf, R. M., Caldwell, J. W., Kollamn, P. A. and Case, D. A. : Development and testing of a general amber force field. J. Comput. Chem. 25, 1157 (2004).   DOI
14 van Gunsteren, W. F., Berendsen, H. J. C., Colonna, F., Perahia, D., Hollenberg, J. P. and Lellouch, D. : On searching neighbors in computer simulations of macromolecular systems. J. Comput. Chem. 5, 272 (1984).   DOI
15 van Gunsteren, W. F. and Berendsen, H. J. C. : Computer simulation as a tool for tracing the conformational differences between proteins in solution and in the crystalline state. J. Mol. Biol. 176, 559 (1984).   DOI
16 van Gunsteren, W. F. and Karplus, M. : A method for constrained energy minimization of macromolecules. J. Comput. Chem. 1, 266 (1980).   DOI
17 Fletcher, R. and Reeves, C. M. : Function minimization by conjugate gradients. Comput. J. 7, 149 (1964).   DOI
18 van Gunsteren, W. F. : Computer Simulation of Biomolecular Systems (Ed.: van Gunsteren, W. F., Weiner, P. K. and Wilkinson, A. J.), ESCOM, Leiden, 1993, Vol. 2, p. 8.
19 Ryckaert, J. P., Ciccotti, G. and Berendsen, H. J. C. : Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327 (1977).   DOI