title: Emergence of hydrogen bonds from molecular dynamics simulation of substituted N-phenylthiourea-catechol oxidase complex.
abstract: A series of N-phenylthiourea derivatives was built starting from the X-ray structure in the molecular mechanics framework and the interaction profile in the complex with the catechol oxidase was traced using molecular dynamics simulation. The results showed that the geometry and interactions between ligand and receptor were highly related to the position of the substituted side chains of phenyl moiety. At the end of molecular dynamics run, a concentrated multicenter hydrogen bond was created between the substituted ligand and receptor. The conformation of the ligand itself were also restricted in the receptor pocket. Furthermore, the simulation time of 50 ns were found to be long enough to explore the relevant conformational space and the stationary behavior of the molecular dynamic could be observed.
authors.affiliation: College of Pharmacy, Chungnam National University, Daejeon, 34134, Korea. parki@cnu.ac.kr.
authors.forename: Kyung-Lae
authors.identifier: http://orcid.org/0000-0003-2340-2291
authors.initials: KL
authors.lastname: Park
mesh_terms: D004156:Catechol Oxidase / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation / Q000639:trends; D010670:Phenylthiourea / Q000737:chemistry* / Q000378:metabolism
chemical_list: D010670:Phenylthiourea; D004156:Catechol Oxidase
keywords: Catechol oxidase; Hydrogen bond; Molecular dynamics; Molecular mechanics