GPCRs
Possible dynamic anchor points in a benzoxazinone derivative-human oxytocin receptor system - a molecular docking and dynamics calculation
Balázs Jójárt, Árpád Márki
Abstract In this study, we performed a molecular docking and dynamics simulation for a benzoxazinone-human oxytocin receptor system to determine the possible hydrophobic and electrostatic interaction points in the dynamic complex. After the homology modeling, the ligand was docked into the putative active using AutoDock 3.05. After the application of energetic and structural filters, the complexes obtained were further refined with a simulated annealing protocol (AMBER8) to remove steric clashes. Three complexes were selected for subjection to the solecular dynamics simulation (5 ns), and the results on the occurrence of average anchor points showed a stable complex between the benzoxazinone derivative and the receptor. The complex could be used as a good starting point for further analysis with site-directed mutagenesis, or further computational research.
Journal of Molecular Modeling 2007, 13(1): 1-10.
Theoretical Investigation of the Activation Mechanism of the Human Histamine H4 Receptor - An Explicit Membrane Molecular Dynamics Simulation Study
Balázs Jójárt1,2, Róbert Kiss3,4, Béla Viskolcz1 , György M. Keserű4,5
1 Department of Chemistry and Chemical Informatics, Faculty of Education, University of Szeged, Boldogasszony sgt. 6., H-6725, Szeged, Hungary
2 Department of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, Eötvös u. 6., H-6720, Szeged, Hungary
3 Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes Endre u. 9., H-1092, Budapest, Hungary
4 Gedeon Richter Plc, Gyömrői út 19-21., H-1103, Budapest, Hungary
5 Department of General and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4., H-1111, Budapest, Hungary
Submitted to Journal of Chemical Information and Modelling.
Abstract In this study, we performed a molecular docking and dynamics simulation for a benzoxazinone-human oxytocin receptor system to determine the possible hydrophobic and electrostatic interaction points in the dynamic complex. After the homology modeling, the ligand was docked into the putative active using AutoDock 3.05. After the application of energetic and structural filters, the complexes obtained were further refined with a simulated annealing protocol (AMBER8) to remove steric clashes. Three complexes were selected for subjection to the solecular dynamics simulation (5 ns), and the results on the occurrence of average anchor points showed a stable complex between the benzoxazinone derivative and the receptor. The complex could be used as a good starting point for further analysis with site-directed mutagenesis, or further computational research.