Cytochrome P-450 Catalyzed Insecticide Metabolism. Prediction of Regio- and Stereoselectivity in the Primer Metabolism of Carbofuran:  A Theoretical Study

Abstract

The molecular mechanism of carbofuran metabolism was investigated by molecular modeling using the energy-minimized active site of cytochrome P-450 cam . A feasible binding conformation of carbofuran was subjected to Monte Carlo (MC) conformational search and molecular dynamics (MD) simulation in the active site to obtain the global minimum of the enzyme-substrate complex. For exploring its conformational space, MC was found to be more effective than simple MD. Enzyme-substrate interactions were examined in detail in all low-energy states. Distances between the active ferryl oxygen of the central heme unit and the reactive centers of carbofuran involved in oxidative metabolism were monitored. H-bonding interaction between the carbamate group of carbofuran and the Tyr96-OH group, as well as the steric effects of Val247 and Val295, were found to be crucial for the orientation of carbofuran. The preferred formation of 3-hydroxycarbofuran, the major primer metabolite, could be rationalized by the model. The configuration at the C3 atom was predicted to be S in accordance with the stereospecificity reported for the natural substrate.

Cytochrome P450 in Silico: An Integrative Modeling Approach

“…24,25,86,131,133,135 QM calculations of the rate-limiting H-atom abstraction step of C-H hydroxylation reactions of the enzyme, based on conformations from MD simulations, could describe additional details of product formation and supported a two-state abstraction and oxygen rebound mechanism of the CYP monooxygenase activity. [24][25][26] CYP102 (BM3), the second CYP to be crystallized, spurred much MD and homology modeling work. The ligand-bound and ligand-free conformations differ considerably, and these differences revealed the existence of a substrate access and product exit channel.…”

Cytochrome P450 Catalyzed Nitric Oxide Synthesis: A Theoretical Study

“…Electrostatic treatment involved a distance dependent dielectric constant (ε = 4) (26) and atomic charges for all protein atoms obtained from the original AMBER* force field. For heme we used published parameters (27). Atomic charges for heme atoms were obtained from scaled HF6-31G + * calculations (28).…”

“…In our recent studies (27,(29)(30)(31) we demonstrated that Monte Carlo conformational analysis is an effective tool in docking calculations. The combined conformational search used in these docking calculations involves the variation of the internal degrees of freedom of the substrate and the binding site (rotatable bonds) as well as the external degrees of freedom of the ligand (relative translations and rotations) relative to the binding site.…”

“…revealed that MC conformational analysis applied for proteins can be more effective than conventional MD simulations (27). Low energy binding modes of arginine were therefore obtained using this new MC docking methodology.…”

Oxidative Activation and Degradation of Organophosphorus Pesticides Mediated by Iron Porphyrins

“…4) In order to examine the mode of action of P450-catalyzed oxidation at a molecular level, Keserü et al have applied computational methods including molecular orbital (MO) calculations and molecular dynamic simulations to the carbofuran-P450cam complex utilizing the three-dimensional structure of the enzyme. 5) Either hydrogen bonding or steric constraint imposed by the polypeptide backbone was found to highly control the oxidation of carbofuran near the active site and the major metabolic hydroxylation at the 3-position was correctly elucidated. Another approach has been to use synthetic metalloporphyrins as a model of P450 especially in the field of drug metabolism.…”