QM/MM Study of the Active Species of the Human Cytochrome P450 3A4, and the Influence Thereof of the Multiple Substrate Binding
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- 作者：Dan Fishelovitch ; Carina Hazan ; Hajime Hirao ; Haim J. Wolfson ; Ruth Nussinov ; Sason Shaik
- 刊名：Journal of Physical Chemistry B
- 出版年：2007
- 出版时间：December 13, 2007
- 年：2007
- 卷：111
- 期：49
- 页码：13822 - 13832
- 全文大小：522K
- 年卷期：v.111,no.49(December 13, 2007)
- ISSN：1520-5207
文摘
Cytochrome P450 3A4 is involved in the metabolism of 50% of all swallowed drugs. The enzyme functionsby means of a high-valent iron-oxo species, called compound I (Cpd I), which is formed after entrance ofthe substrate to the active site. We explored the features of Cpd I using hybrid quantum mechanical/molecularmechanical calculations on various models that are either substrate-free or containing one and two moleculesof diazepam as a substrate. Mössbauer parameters of Cpd I were computed. Our major finding shows thatwithout the substrate, Cpd I tends to elongate its Fe-S bond, localize the radical on the sulfur, and formhydrogen bonds with A305 and T309, which may hypothetically lead to Cpd I consumption by H-abstraction.However, the positioning of diazepam close to Cpd I, as enforced by the effector molecule, was found tostrengthen the NH···S interactions of the conserved I443 and G444 residues with the proximal cysteinateligand. These interactions are known to stabilize the Fe-S bond, and as such, the presence of the substrateleads to a shorter Fe-S bond and it prevents the localization of the radical on the sulfur. This diazepam-CpdI stabilization was manifested in the 1W0E conformer. The effector substrate did not influence Cpd I directlybut rather by positioning the active substrate close to Cpd I, thus displacing the hydrogen bonds with A305and T309, and thereby giving preference to substrate oxidation. It is hypothesized that these effects on CpdI, promoted by the restrained substrate, may be behind the special metabolic behavior observed in cases ofmultiple substrate binding (also called cooperative binding). This restraint constitutes a mechanism wherebysubstrates stabilize Cpd I sufficiently long to affect monooxygenation by P450s at the expense of Cpd Idestruction by the protein residues.