Theoretical Studies On The Important Proteins Of P450 Enzymes

Today,along with the development of the improvement of computer information technology and the correlative theories, the molecular simulations of protein have been an important research field in biology science. By using the molecular mechanics, molecular dynamics and molecular docking, the three dimensions (3D) structures and the interactions between receptors and substrates can be obtained. On basis of these, the obtained outcomes can give some explanations of the experimental appearance and provide the theoretical instruction for the ligands design of the particular protein and the advancement of the new medicine for the related diseases. In my thesis, molecular simulation dynamics and molecular docking were used to study two cytochrome P450s. The main results are summarized as follows:1. Molecular dynamics for CYP2A13 and molecular docking of the substratesThe human cytochrome P450 2A13 (CYP2A13), is a functional member of CYP2A gene subfamily. CYP2A13 is predominantly expressed in the respiratory, with the highest level in the nasal mucosa, followed by the trachea and lung. CYP2A13 also detected in a number of human tissues, including brain, mammary gland, prostate, testis and uterus. It plays an important role in catalyzing the metabolism of many environmental chemicals and several tobacco-specific carcinogens. CYP2A13 also functions in the activation of several other procarcinogens and the metabolism of toxins. Alkoxyresorufin O-dealkylase activities, including methoxyresorufin O-demethylase, ethoxyresorufin O-deethylase, and benzyloxyresorufinO-debenzylase (BROD) activities are well-known typical catalytic markers for a variety of CYP enzymes, and thus have a great potential to elucidate the CYP induction by chemical exposure. Recently, it was reported that CYP2A13 can catalyze the metabolic activations of ethoxyresorufin O-deethylation, and methoxyresorufin O-demethylase.With the energy minimization and molecular dynamics methods, the 3D structure of CYP2A13 was refined. The docking study of three alkoxyresorufin O-dealkylase is performed on the basis of the 3D structure and active site of CYP2A13. A relative larger moiety at the oxidation site can induce the conformational changes in the active site residues of CYP2A13 and make the binding of ligand with CYP2A13 more favorable. We can conjecture that CYP2A13 should have the ability to metabolize the isopropoxyresorufin and the intrinsic clearance of O-dealkylation would be higher. The docking results provide explanations for the remarkable difference and offer further experimental studies of structure-function relationship in CYP2A13.2. Molecular dynamics for CYP2B6 and molecular docking of the substratesHuman CYP2B6 has been thought to be an important function in drug metabolism, and it is widely expressed in kidney, liver, lung, intestine, uterine endometrium, bronchoalveolar macrophages, peripheral blood lymphocytes and brain. It involved in oxidative metabolism of a wide variety of endogenous and exogenous compounds. CYP2B6 is the only functional member of human CYP2B family and is regarded as an enzyme for xenobiotic such as pesticide. More recent publications cite an estimate of the CYP2B6 contribution to drug metabolism at about 8%, and involve in many endogenous hormone and eatables metabolism. CYP2B6 can be inhibited and induced by many drugs and the genetic polymorphisms have been found. The factors of race, gender and age affect the expression and activity of CYP2B6.Propofol is a short-acting anesthetic commonly used in clinical practice. The approximately 40% oxidation of propofol via ring hydroxylation is catalyzed by cytochrome P450. Efavirenz, a first generation non-nucleoside reverse transcriptase inhibitor of HIV-1, is one of the preferred components of the first line treatment regimen of HIV infection worldwide. It is used as the first generation non-nucleoside reverse transcriptase inhibitor and is used as a component of first-line antiretroviral therapy. Bupropion is a typical antidepressant and antismoking agent, and it can be used demethlated adrenaline, dopamine inhibitor and antismoking agent. Mephobarbital (5-ethyl-1-methyl-5-phenylbarbituric acid) has been used in the treatment of epilepsy since the 1930s and it is a chiral compound that is commercially available as a racemate of R-mephobarbital. CYP2B6 participates in the oxidative metabolism of several important clinically drugs and these activities are specific.With the docking study of propofol, propofol analog, bupropion, efavirenz and mephobarbital, we obtained the intimate interaction of CYP2B6 with substrates. The docked results showed that propofol analog enters into the active site easier. Residues Glu301, Thr302, Leu363 and Val 477 could be the most important residues on the basis of the computational results. These results will offer further information for new drug based on 3D structure of human CYP2B6.