The interaction of a homologous series of hydrocarbons with hepatic cytochrome P-450. Molecular orbital-derived electronic and structural parameters influencing the haemoprotein spin state

Molecular orbital-generated QSARs in a homologous series of alkoxyresorufins and studies of their interactive docking with P450s

1. Molecular and electronic structural parameters have been determined, by molecular orbital (MO) calculations, for a homologous series of 8 alkoxyresorufins (methoxy- to octoxy-). 2. Quantitative structure-activity relationships (QSARs) between these structural parameters and the rates of metabolism of the alkoxyresorufins in hepatic microsomes from the 3-methylcholanthrene (MC)-, and phenobarbital (PB)-pretreated mouse, and the beta-naphthoflavone (beta NF)-pretreated rat have been established. 3. The most significant single relationship is between beta NF-induction of cytochrome P4501 (CYP1A) and the total nucleophilic superdelocalizability (sigma SN) for the eight compounds in the series. 4. For double regressions, the electronic charge on the alkoxy oxygen, Q(O), or alpha-carbon Q(C), is important when combined with the hydrophobic substituent constant (pi). 5. These findings indicate that the rates of metabolism of these alkoxyresorufins are dependent upon their ability to cross cellular membranes, to fit the relevant CYP1A binding site, and on their ability to accept electrons from a donor nucleophilic species. 6. A different set of parameters correlated with CYP2B activity, namely, parameters of overall shape, which indicates that the way in which the alkoxyresorufins fit the CYP2B site, determines their differences in specificity. 7. Computer graphic interactive docking studies of the alkoxyresorufins with their affinity-specific cytochromes P450, namely, methoxy- with CYP1A2; ethoxy- with CYP1A1; pentoxy- with CYP2B1; and benzyloxy- with CYP3A, have also been undertaken to show the specific interactions of the alkoxyresorufins with the binding sites of the individual P450s.

Inhibition of rat hepatic aryl hydrocarbon hydroxylase activity by a series of 7-hydroxy coumarins: QSAR studies

1. Molecular orbital calculations, by the Modified Intermediate Neglect of Differential Overlap (MINDO/3) method, of a series of twenty-five 8-acyl-7-hydroxy coumarins show that the inhibition of aryl hydrocarbon hydroxylase (AHH) activities (cytochrome P4501, CYP1 activity, primarily CYP1A1) for 23 of these compounds is related to their structural parameters. The two remaining compounds are the only chlorinated derivatives; these are inactive towards the AHH system and were excluded from the quantitative structure-activity relationship (QSAR) analysis. 2. The results of multiple regression analyses show that AHH activity is dependent on the energy of the highest occupied molecular orbital, E(HOMO), in a single variable expression for the 23 compounds. However, a three-variable expression involving superdelocalizabilities provides a more significant correlation with biological activity. 3. The inactivity of the two chlorinated derivatives can be rationalized in terms of their low degree of molecular planarity, as estimated by the area/depth2 parameter, which presumably precludes them from interaction with CYP1.

Interaction of a series of nitriles with the alcohol-inducible isoform of P450: computer analysis of structure-activity relationships

1. Structural studies are reported on a series of 20 nitriles of varying rates of P4502E-mediated oxidative metabolism. 2. Parameters of molecular and electronic structure have been calculated for the generation of quantitative structure-activity relationships (QSARs) with the rates of oxidative metabolism of the nitriles, and with their acute toxicity. 3. Correlations between molecular polarizability, excitation energy and biological activity are presented as a result of QSAR analysis.

Correlation between site specificity and electrophilic frontier values in the metabolic hydroxylation of biphenyl, di-aromatic and CYP2D6 substrates: a molecular modelling study

1. A series of biphenyl, di-aromatic and CYP2D6 substrates known to undergo metabolic aromatic hydroxylation was derived from the literature, several animal species were represented. 2. Molecular orbital calculations were performed on the substrates using the AM1 semi-empirical force field and the electrophilic frontier values (f(E)) plotted for each available aromatic site. 3. A qualitative correlation was observed between the sites of oxidation and high f(E) values, suggesting the role of frontier orbitals in the metabolic hydroxylation of these substrates. 4. The mechanistic implications for the involvement of frontier orbitals in aromatic hydroxylation are discussed. It is proposed that electron abstraction occurs in the region of high electron density to form a radical cation. Hydrogen abstraction by Fe++O- then occurs followed by oxygen rebound. 5. The method can be helpful in indicating regio-specificity in the metabolic hydroxylation of bi-phenyls, related di-aromatic compounds and possibly CYP2D6 aromatic substrates.

Teratogenicity of phenylhydantoins in an in vitro system: molecular orbital-generated quantitative structure-toxicity relationships

1. The ability of 20 mono- and di-phenylhydantoin derivatives to inhibit differentiation of rat embryo mid-brain and limb bud cells in culture has been used as an index of the teratogenic hazard represented by these compounds. 2. Molecular orbital calculations on these compounds, using the MINDO-3 (modified intermediate neglect of differential overlap) and CNDO-2 (complete neglect of differential overlap) methods, were combined with indices of teratogenicity in the two cell types, to generate a coherent structure-toxicity relationship. 3. Teratogenicity correlated with frontier orbital electron density of the N1 hydantoin ring atom (HOMO-N1) in a sub-series of 12 monophenylhydantoins, whereas the corresponding toxicity for both mono- and di-phenylhydantoins related more to the molecular polarizability (alpha mol) of the molecule. 4. Furthermore the same structural parameter (alpha mol) exhibited a parallelism with log P values of these 20 compounds, indicating the importance of lipophilicity in the toxicity of these compounds. 5. Overall, the data emphasize the ability of electronic structural calculations to identify chemical descriptors of toxicity.

Molecular orbital studies of oxygen activation and mechanisms of cytochromes P-450-mediated oxidative metabolism of xenobiotics

Molecular dimensions and molecular orbital calculations of the electronic structures of 56 substrates, inhibitors and inducers of the cytochromes P-448 and other families of the cytochromes P-450 are reported. Substrates of the cytochromes P-448 are shown to be planar molecules with relatively large values of area/depth2, and to have electronic structures with relatively low values for delta E, the difference in energy between the frontier orbitals (E(LEMO)- E(HOMO)). Substrates of other families of the cytochromes P-450 are globular molecules, with relatively low values of area/depth2 and relatively high values of delta E. Molecular orbital calculations of the active oxygen species, singlet oxygen and superoxy anion, have also been made. Singlet oxygen is a poor electron donor (low values of E(HOMO)) but a good electron acceptor (low values of E(LEMO)), whereas superoxy anion is a good electron donor and a poor electron acceptor. Cytochrome P-448 substrates, which are good electron donors, would preferentially accept singlet oxygen, a good electron acceptor; substrates of the other families of cytochrome P-450, which are less effective electron donors, would preferentially accept superoxy anion, a good electron donor, although substrates of both cytochromes P-448 and other P-450s may accept both species of active oxygen. Together with recent published evidence, these data provide a greater understanding of the mode of activation of oxygen by the various families of the cytochromes P-450, and to the insertion of active oxygen into the substrates. Mechanisms are proposed for the oxygenation of substrates, namely, epoxidation involving singlet oxygen and hydroxylation by superoxy anion. Finally, a detailed explanation of the cytochrome P-450 cycle is discussed, and mechanisms of the different types of oxidative metabolism are presented.

Molecular orbital calculations and quantitative structure-activity relationships for some polyaromatic hydrocarbons

1. Correlations between biological activity and electronic structure for 7 polyaromatic hydrocarbons are reported. 2. Molecular orbital (MO) calculations by the MINDO/3 method indicate that the hydrophobic parameter, log P (the logarithm of the octanol/water partition coefficient) exhibits a parallelism with total electrophilic superdelocalizability, and a similar relationship is shown with protein binding. 3. Inhibition of dimethylnitrosamine (DMN) demethylase activity is linearly related to total nucleophilic superdelocalizability, and other correlations are shown with mutagenicity and benzo[a]pyrene hydroxylase (AHH) activity.

Quantitative structure-activity relationships in a series of alcohols exhibiting inhibition of cytochrome P-450-mediated aniline hydroxylation

The results of Molecular Orbital (MO) calculations by the MINDO/3 method are reported, together with the results of multiple regression analysis of electronic and structural parameters with inhibition of aniline hydroxylation by a series of 22 alcohols. The most significant correlations show the relationships between molecular length, frontier electron density of the alpha-carbon and hydroxyl oxygen, nucleophilic superdelocalizability of the hydroxyl hydrogen, energy of the highest occupied MO and biological activity involving binding to microsomal cytochromes P-450. Using the data of Cohen and Mannering (Mol. Pharmacol., 9 (1973) 383), Testa, (Chem.-Biol. Interact., 34 (1981) 287) has shown that the inhibition of aniline hydroxylation by a series of alcohols can be related to their electronic structure and hydrophobicity (measured by log P, the octanol-water partition coefficient). The mode of binding and effect on spin-state equilibria in cytochrome P-450 by alcohols has been elucidated by Testa, whereas an alternative hypothesis based on connectivity correlations has been reported by Sabljic and Sabljic (Mol. Pharmacol., 23 (1983) 213). The present work shows that the biological response can be explained by calculated electronic structure and molecular shape parameters. Also, one compound (the only tertiary alcohol) from the original set that was not included in Testa's calculations and analysis, is included in this work and its activity successfully calculated. The latter authors, Sabljic and Sabljic, were led to exclude the data for this compound and one other (phenyl methanol) in order to achieve a good correlation with their calculated parameters of molecular structure.