Intvestgation Of Ligand Channels And Cooperativity Mechanism In Cytochrome P450s

The interactions between biomolecules are considered to be the basis of the lives and drug design. Molecular docking, molecular dynamics simulations and the calculation of binding free energy are used to illustrate the mechanisms of the protein-protein and protein-drug interactions. This thesis includes two parts:the possible ligand pathway in CYP2E1 and the mechanisms of ligand cooperativity in CYP2C9.In chapter 1, an overview of major experimental methods and possible ligand pathways in six typical P450 enzymes were presented. The arrangement of the whole thesis was also provided.In chapter 2, the possible channels of ligands in CYP2E1 were explored. Random acceleration molecular dynamics simulations combined with steered molecular dynamics and potentials of mean force calculations were performed to identify the possible unbinding pathways of ligands in CYP2E1. The results showed that channel 2c and 2a were most likely as the unbinding channels of ligands in CYP2E1. Residues Phe298 and Phe478 acted as the gate keeper during indazole unbinding along channels 2c and 2a, respectively. Previous site-directed mutagenesis experiments also supported these findings.In chapter 3, the mechanisms of ligand cooperativity in CYP2C9 were studied. The experiment results showed that phenytoin was medicated by the effector lansoprazole and the other two drugs (diclofenac and warfarin) were not influenced by lansoprazole. However, the detail mechanisms of this phenomenon have not been eludicated so far. In this study, reasonable structures generated by molecular docking were selected due to the distance between the metabolic site of the drug and heme. Then molecular dynamics simulations were carried out, RMSD and RMSF revealed that the effector lansoprazole stabilized the position of phenytoin in the active site, which was in agreement with the biological experiments. The hydrogen bond between G296 and drug was considered to be the key interaction according to the calculation of binding free energy.Chapter 4 is the summary of the whole thesis.