Cytochrome P450 and biological hydroxylation reactions

Enantioselective bioaccumulation, biotransformation and spatial distribution of chiral fungicide difenoconazole in earthworms (Eisenia fetida)

The enantioselective environmental behavior of difenoconazole, a widely utilized triazole fungicide commonly detected in agricultural soils, has yet to be comprehensively explored within the earthworm-soil system. To address this research gap, we investigated the bioaccumulation and elimination kinetics, degradation pathways, biotransformation mechanisms, spatial distribution, and toxicity of chiral difenoconazole. The four stereoisomers of difenoconazole were baseline separated and analyzed using SFC-MS/MS. Pronounced enantioselectivity was observed during the uptake phase, with earthworms exhibiting a preference for (2R,4R)-difenoconazole and (2R,4S)-difenoconazole. A total of five transformation products (TPs) were detected and identified using UHPLC-QTOF/MS in the earthworm-soil system. Four of the TPs were detected in both earthworm and soil, and one TP was produced only in eaerthwroms. Hydrolysis and hydroxylation were the primary transformation pathways of difenoconazole in both earthworms and soil. Furthermore, a chiral TP, 3-chloro, 4-hydroxy difenoconazole, was generated with significant enantioselectivity, and molecular docking results indicate the greater catalytic bioactivity of (2R,4R)- and (2R,4S)-difenoconazole, leading to the preferential formation of their corresponding hydroxylated TPs. Furthermore, Mass Spectrometry Imaging (MSI) was applied for the first time to explore the spatial distribution of difenoconazole and the TPs in earthworms, and the "secretory zone" was found to be the dominant region to uptake and biodegrade difenoconazole. ECOSAR predictions highlighted the potentially hazardous impact of most difenoconazole TPs on aquatic ecosystems. These findings are important for understanding the environmental fate of difenoconazole, evaluating environmental risks, and offering valuable insights for guiding scientific bioremediation efforts.

Modulation of Metabolic Detoxification Pathways Using Foods and Food-Derived Components: A Scientific Review with Clinical Application

Research into human biotransformation and elimination systems continues to evolve. Various clinical and in vivo studies have been undertaken to evaluate the effects of foods and food-derived components on the activity of detoxification pathways, including phase I cytochrome P450 enzymes, phase II conjugation enzymes, Nrf2 signaling, and metallothionein. This review summarizes the research in this area to date, highlighting the potential for foods and nutrients to support and/or modulate detoxification functions. Clinical applications to alter detoxification pathway activity and improve patient outcomes are considered, drawing on the growing understanding of the relationship between detoxification functions and different disease states, genetic polymorphisms, and drug-nutrient interactions. Some caution is recommended, however, due to the limitations of current research as well as indications that many nutrients exert biphasic, dose-dependent effects and that genetic polymorphisms may alter outcomes. A whole-foods approach may, therefore, be prudent.

Oxidation of cyclohexane using a novel RuO2–zeolite nanocomposite catalyst

We report the synthesis, using an organic-template-free hydrothermal crystallization method, and catalysis of a new type of nanocomposite material, 1.3 nm-sized RuO2 particles confined in faujasite zeolite. The zeolite-confined RuO2 composites were fully characterized with X-ray powder diffraction, Ru K-edge X-ray absorption, and high-resolution transmission electron microscopy. XRD and X-ray fluorescence analysis indicate that the framework is faujasite zeolite with a Si:Al ratio of 1.25. Ru K-edge X-ray absorption near-edge structures indicate that the ruthenium species in the zeolite is Ru(IV) with nearest-neighbor octahedral environments similar to hydrous RuO2, i.e., distorted "RuO6". The k2-weighted extended X-ray absorption fine structure indicates that the Ru(IV) species anchored in the zeolite likely form amorphous RuO2 with a 2D-chain structure, in which RuO6 units are connected together by two shared oxygen atoms. TEM shows that the particle size of RuO2 encapsulated inside the supercages of FAU is about 1.3 nm. The RuO2–FAU composites display significant catalytic activity in the oxidation of cyclohexane with tBHP under mild (room temperature and 1 atm (1 atm [Formula: see text] 101.325 kPa)) conditions. The ketone and alcohol concentration can be as high as 0.26 mol L–1 in 5 h with 48% peroxide efficiency. The catalyst is stable and reusable. Possible oxidation mechanisms are also discussed.Key words: nanocomposite, ruthenium oxide, catalysis, oxidation, zeolite.

Isotope effects and intermediates in the reduction of NO by P450(NOR)

The mechanism of the heme-thiolate-dependent NADH-NO reductase (P450(NOR)) from Fusarium oxysporum was investigated by kinetic isotope effects including protio, [4S-2H]-, [4R-2H]-, [4,4(2)H(2)]-NADH and stopped-flow measurements. The respective kinetic isotope effects were measured at high NO concentrations and were found to be 1.7, 2.3 and 3.8 indicating a rate-limitation at the reduction step and a moderate stereoselectivity in binding of the cofactor NADH. In a different approach the kinetic isotope effects were determined directly for the reaction of the Fe(III)-NO complex with [4R-2H]- and [4S-2H]-NADH by stopped-flow spectroscopy. The resulting isotope effects were 2.7+/-0.4 for the R-form and 1.1+/-0.1 for the S-form. In addition the 444 nm intermediate could be chemically generated by addition of an ethanolic borohydride solution to the ferric-NO complex at -10 degrees C. In pulse radiolysis experiments a similar absorbing species could be observed when hydroxylamine radicals were generated in the presence of Fe (III) P450(NOR). Based on these results we postulate hydride transfer from NADH to the ferric P450-NO complex resulting in a ferric hydroxylamine-radical or ferryl hydroxylamine-complex and this step, as indicated by the kinetic isotope effects, to be rate-limiting at high concentrations of NO. However, at low concentrations of NO the decay of the 444 nm species becomes the rate-limiting step as envisaged by stopped-flow and optical kinetic measurements in a system in which NO was continuously generated. The last step in the catalytic cycle may proceed by a direct addition of the NO radical to the Fe-hydroxylamine complex or by electron transfer from the NO radical to the ferric-thiyl moiety in analogy to the postulated mechanisms of prostacyclin and thromboxane biosynthesis by the corresponding P450 enzymes. The latter process of electron transfer could then constitute a common step in all heme-thiolate catalyzed reactions.

Theoretical study of the electrostatic and steric effects on the spectroscopic characteristics of the metal-ligand unit of heme proteins. 2. C-O vibrational frequencies, 17O isotropic chemical shifts, and nuclear quadrupole coupling constants

The quantum chemical calculations, vibronic theory of activation, and London-Pople approach are used to study the dependence of the C-O vibrational frequency, 17O isotropic chemical shift, and nuclear quadrupole coupling constant on the distortion of the porphyrin ring and geometry of the CO coordination, changes in the iron-carbon and iron-imidazole distances, magnitude of the iron displacement out of the porphyrin plane, and presence of the charged groups in the heme environment. It is shown that only the electrostatic interactions can cause the variation of all these parameters experimentally observed in different heme proteins, and the heme distortions could modulate this variation. The correlations between the theoretically calculated parameters are shown to be close to the experimentally observed ones. The study of the effect of the electric field of the distal histidine shows that the presence of the four C-O vibrational bands in the infrared absorption spectra of the carbon monoxide complexes of different myoglobins and hemoglobins can be caused by the different orientations of the different tautomeric forms of the distal histidine. The dependence of the 17O isotropic chemical shift and nuclear quadrupole coupling constant on pH and the distal histidine substitution can be also explained from the same point of view.

Evidence for a 1-electron oxidation mechanism in N-dealkylation of N,N-dialkylanilines by cytochrome P450 2B1. Kinetic hydrogen isotope effects, linear free energy relationships, comparisons with horseradish peroxidase, and studies with oxygen surrogates

Many enzymes catalyze N-dealkylations of alkylamines, including cytochrome P450 (P450) and peroxidase enzymes. Peroxidases, exemplified by horseradish peroxidase (HRP), are generally accepted to catalyze N-dealkylations via 1-electron transfer processes. Several lines of evidence also support a 1-electron mechanism for many P450 reactions, although this view has been questioned in light of reported trends for kinetic hydrogen isotope effects for N-demethylation with a series of 4-substituted N,N-dimethylanilines. No continuous trend for an increase of isotope effects with the electronic parameters of para-substitution was seen for the P450 2B1-catalyzed reactions in this study. The larger value seen with the 4-nitro derivative is consistent with a shift in mechanism due to either a reversible electron transfer step preceding deprotonation or to a hydrogen atom abstraction mechanism. With HRP, the trend is to lower isotope effects with para electron-withdrawing substituents, due to an apparent shift in rate-limiting steps. Biomimetic model high-valent porphyrins showed reduction rates with variously 4-substituted N,N-dialkylanilines that were consistent with a positively charged intermediate; such relationships were not seen for anisole O-demethylation with P450 2B1. In contrast to the case with the NADPH-supported P450 reactions, high deuterium isotope effects ( approximately 7) were seen in the N-dealkylations supported by the oxygen surrogate iodosylbenzene. With iodosylbenzene, colored aminium radicals were observed in the oxidations of aminopyrine, N,N-dimethyl-4-aminothioanisole, and 4-methoxy-N,N-dimethylaniline. With the latter compound, a substantial intermolecular deuterium isotope effect was observed for N-demethylation. In the N-dealkylation of N-ethyl,N-methylaniline by P450 2B1 (NADPH-supported), the ratio of N-demethylation to N-deethylation was 16. Although it is probably possible for P450s to catalyze amine N-dealkylations via hydrogen atom abstraction when such a course is electronically or sterically favored, we interpret the evidence to favor a 1-electron pathway with N,N-dialkylamines with P450 2B1 as well as HRP and several biomimetic models.

Theoretical study of the distal-side steric and electrostatic effects on the vibrational characteristics of the FeCO unit of the carbonylheme proteins and their models

The vibronic theory of activation and quantum chemical intermediate neglect of differential overlap (INDO) calculations are used to study the activation of carbon monoxide (change of the C-O bond index and force field constant) by the imidazole complex with heme in dependence on the distortion of the porphyrin ring, geometry of the CO coordination, iron-carbon and iron-imidazole distances, iron displacement out of the porphyrin plane, and presence of the charged groups in the heme environment. It is shown that the main contribution to the CO activation stems from the change in the sigma donation from the 5 sigma CO orbital to iron, and back-bonding from the iron to the 2 pi orbital of CO. It follows from the results that none of the studied distortions can explain, by itself, the wide variation of the C-O vibrational frequency in the experimentally studied model compounds and heme proteins. To study the dependence of the properties of the FeCO unit on the presence of charged groups in the heme environment, the latter are simulated by the homogeneous electric field and point charges of different magnitude and location. The results show that charged groups can strongly affect the strength of the C-O bond and its vibrational frequency. It is found that the charges located on the distal side of the heme plane can affect the Fe-C and C-O bond indexes (and, consequently, the Fe-C and C-O vibrational frequencies), both in the same and in opposite directions, depending on their position. The theoretical results allow us to understand the peculiarities of the effect of charged groups on the properties of the FeCO unit both in heme proteins and in their model compounds.

NMR studies of recombinant cytochrome P450cam mutants

In the active center of cytochrome P450cam, Thr-252 is one of the conserved amino acid residues in the cytochrome P450 superfamily and plays a key role in the hydroxylation of camphor. T252A mutant, in which Thr-252 is replaced by alanine, consumed O2 at a rate comparable to that of the wild-type enzyme, whereas the amount of exo-5-hydroxycamphor formed was less than 10% of that formed by the wild-typed enzyme and H2O2 is the main product in the hydroxylation reaction. H2O2 was also yielded by the valine mutant and the consumption rate of O2 was much lower than that for the wild-type enzyme (Imai et al (1989) Proc Natl Acad Sci USA 86, 7823-7827). On the basis of the 1H- and 15N-NMR spectra, it was revealed that the anionic nature of the axial thiolate and the heme-environmental structures were substantially affected in the absence of d-camphor by the amino acid substitution at 252 Thr. In T252A mutant, however, the binding of camphor reduced these conformational alterations in the heme vicinity, probably due to the formation of interactions between camphor and enzyme. On the other hand, T252V mutant still exhibited large reduction of the anionic nature of the axial ligand in the presence of d-camphor and structural changes around heme were also enhanced, since the affinity of the valine mutant to d-camphor was low. These results imply that the hydrophobic and/or steric effects of the valine residue at 252 interfere with interactions around heme and camphor binding sites, which corresponds to the larger functional defects for T252V mutant.

An efficient mimic of cytochrome P-450 from a zeolite-encaged iron complex in a polymer membrane

Many attempts have been made to mimic the catalytic oxidative properties of the enzyme cytochrome P-450. For homogeneous systems the mechanisms of oxidation can be readily determined but proper mimicry of the protein environment is difficult to achieve. Heterogeneous mimics have been designed that use organometallic complexes encapsulated in the supercages of zeolites, which enables control of selectivity and inhibition of auto-oxidation. But these systems do not show any mechanistic analogy with the enzymatic process, and the oxidation rates tend to be low. Here we report a composite catalytic system that achieves realistic mimicry of cytochrome P-450 as well as catalytic turnover rates that make the system industrially viable. Our catalyst incorporates iron phthalocyanine complexes encapsulated in crystals of zeolite Y, which are in turn embedded in a polydimethylsiloxane membrane. The polymer acts as a mimic of the phospholipid membrane in which cytochrome P-450 resides, acting as an interface between two immiscible phases and avoiding the need for solvents or phase-transfer agents. This system oxidizes alkanes at room temperature at rates comparable to those of the enzyme. The observation of a large kinetic isotope effect and the preferential oxidation of tertiary C-H bonds suggest close mechanistic similarities to the enzymatic process.

Inhibitor-induced conformational change in cytochrome P-450CAM

The X-ray crystal structures of cytochrome P-450CAM complexed with both enantiomers of a chiral, multifunctional inhibitor have been refined to R-factors of 21.0% [(+)-enantiomer] and 19.6% [(-)-enantiomer] at approximately 2.1-A resolution. Binding of either enantiomer, both considerably larger than the natural substrate camphor, results in similar, dramatic structural changes in the enzyme. In contrast to all previous P-450CAM crystallographic structures, the Tyr96 side chain is not pointing "down" toward the heme but is rather directed "up" into the proposed substrate access channel. This conformational change is accompanied by the displacement of the Phe193 side chain out into the solvent at the enzyme surface. These changes are consistent with the assignment of this region of the enzyme as the access channel [Poulos et al. (1986) Biochemistry 25, 5314-5322] and suggest that several aromatic residues lining the channel may be involved in substrate recognition and channeling to the active site. The cation usually observed coordinated to the Tyr96 carbonyl oxygen is missing in the presence of the (+)-enantiomer but is present with the (-)-enantiomer. The Phe87 side chain, located near the inhibitor binding site, adopts different orientations depending upon which enantiomer is bound. Finally, electron density reveals that although the inhibitor enantiomers were dichlorinated as provided, when bound to P-450CAM the chlorine atoms are present at only 0-20% occupancy, probably reflecting selective binding of impurities in the samples. Coordinates of these inhibited P-450CAM complexes have been deposited in the Brookhaven Protein Data Bank [Bernstein et al. (1977) J. Mol. Biol. 112, 535-542].

Synthesis, structure and spectroscopic properties of two models for the active site of the oxygenated state of cytochrome P450 [corrected]

Two dioxygen adducts of thiolato-iron(II) porphyrins, [K(222)][Fe(TPpivP)(SC6HF4)(O2)] 1a and [Na(18c.6)][Fe(TPpivP)(SC6HF4)(O2)] 2 were synthesized by reaction of O2 with five-coordinate, high-spin, cryptated alkali metal thiolato-iron(II) 'picket fence' porphyrinate. They were characterized by visible and infrared spectroscopy: lambda max (log epsilon) = 360 nm (4), 427 nm (4.69), 560 nm (3.69), 610 nm (3.40) for both compounds; v(16O-16O) = 1139 cm-1 in chlorobenzene and fluorobenzene for 1a and 2. Single crystals of composition [K(222)][Fe(TPpivP)(SC6HF4)(O2)].[K(222)](SC6HF4)(C 6H5Cl)(H2O) 1b were obtained by diffusion of pentane/xylene mixtures into chlorobenzene solutions of 1a at -5 degrees C. Single crystals of composition [Na(18c.6)][Fe(TPpivP)(SC6HF4)(O2)] were obtained by slow diffusion of pentane into benzene solutions of 2. Structures of 1b and 2 were studied at 20 degrees C (1b) and -100 degrees C (1b and 2). 1b: space group P2(1)/c (monoclinic), a = 16.806(5) A (1.6806 nm), b = 14.331(4) A (1.4331 nm), c = 52.000(15) A (5.2000 nm), beta = 92.95(2) degrees, V = 12.507 A3 (12.507 nm3), Z = 4, Dcal = 1.28 g.cm-3 (t = 20 degrees C). The final R1 factor was 0.085 for 5238 reflections having I greater than 3 sigma(I). 2: space group P2(1)/c (monoclinic), a = 13.107(3) A (1.3107 nm), b = 27.055(4) A (2.7055 nm), c = 25.029(4) A (2.5029 nm), beta = 96.84(2) degrees, V = 8812 A3 (8.812 nm3), Z = 4, Dcal = 1.18 g.cm-3 (t = -100 degrees C). The final R1 factor was 0.088 for 6587 reflections having I greater than 3 sigma(I). The iron atom is, in both compounds, bonded to the four porphyrinato nitrogens (Np), the sulfur atom of the axial thiolate and one oxygen atom of the axially end-on bonded dioxygen molecule. The average Fe-Np distance found in 1b [1.994(4) A, 0.1994 nm] is not significantly different from that found in 2 [1.993(3) A, 0.1993 nm]. The Fe-S bond length is 2.367(3) A (0.2367 nm) in 1b and 2.365(2) A (0.2365 nm) in 2. The Fe-O1 distances with the oxygen atom of O2 bonded to iron are respectively 1.837(9) A (0.1837 nm) and 1.850(4) A (0.1850 nm). The end-on bonded O2 molecule is disordered in both complexes 1b and 2.(ABSTRACT TRUNCATED AT 400 WORDS)

The role of physiological oxygen partial pressures in lipid peroxidation. Theoretical considerations and experimental evidence

The oxidative breakdown of membrane lipids, i.e. lipid peroxidation, is considered to be decisively involved in a number of toxicological and pathological processes including liver injury caused by iron overload and halogenated alkanes such as CCl4. Within the physiological oxygen partial pressure (PO2) range, i.e. at PO2 between 1 and 100 mmHg, lipid peroxidation depends on O2 in a complex manner. For instance, CCl4-induced lipid peroxidation exhibits a distinct maximum at PO2 of around 7 mmHg, and iron-induced lipid peroxidation shows marked differences in its O2 dependence between an early lag phase and a later phase of self-accelerating propagation. The O2 dependence of lipid peroxidation is either determined by the O2 dependence of initiation or the O2 dependence of propagation. Factors decisive for this are presented and the underlying alterations in the pattern of the peroxidation-related reactions delineated.

Spectral studies on structure-activity relationships of thromboxane synthase inhibitors

Thromboxane A2 synthase is a cytochrome P450-type enzyme and its interaction with imidazole or pyridine-based inhibitors could be studied by absolute and difference spectroscopy with the solubilized as well as the purified enzyme. Nitrogenous bases shift the 418-nm Soret absorption by 4-6 nm to the red and among them the best inhibitors of enzyme activity showed a stoichiometric binding to the enzyme. The structural and energetic prerequisites for such high binding affinities were primarily the liganding of the basic nitrogen to the hemin but also the attachment of a hydrophobic carboxylic side chain to the active site at an about 1 nm distance from the nitrogen. In addition, the side chain seemed to be oriented almost parallel to the plane of the heme. If this geometry was changed, a decrease in affinity was observed and if the ligand binding was sterically hindered, a spectral shift to a five-coordinated complex absorbing at 390 nm occurred. This is best explained by the displacement of an endogenous oxygen ligand, presumably water, from the sixth coordination position of the heme. From these results it can be concluded that the inhibitors mimic the binding of prostaglandin H2 (PGH2) with its carboxylic group at the carboxyl side chain and the endoperoxide oxygen atom at C9 as previously reported. The methyl side chain of PGH2 does not seem to play a role in the formation of the enzyme-substrate complex.

DNA breaks generated by the bleomycin-iron III complex in the presence of KHSO5, a single oxygen donor

KHSO5, a water soluble single oxygen donor, is shown to be capable of activating bleomycin-FeIII complex for DNA cleavage. DNA breaks mediated by bleomycin-FeIII in the presence of H2O2 or KHSO5 are compared and the P450-like activation of metallobleomycins is discussed.

Cytochrome P-450/pseudosubstrate interactions and the role of antioxidants in the adrenal cortex

The adrenal cortex is the site of the synthesis of the steroid hormones such as the glucocorticoid cortisol and the mineralocorticoid aldosterone. The pathway of biosynthesis of these steroids from cholesterol involves a sequence of transformations using cytochrome P-450 enzymes. The hypothesis presented here is that damage to cytochrome P-450 enzymes on interaction with certain steroids, synthesized by the adrenal cortex itself, may be of pathological and perhaps physiological importance. The interaction between cytochrome P-450 enzymes and these steroids, which act as pseudosubstrates, may form part of the pathogenesis of some steroidogenic enzyme deficiencies, with consequent overproduction of precursor steroids, leading to mineralocorticoid or androgen excess. This interaction is dependent on achieving high concentrations of the pseudosubstrate steroids in the adrenal cortex, which probably occurs as a result of the arrangement of the vasculature in the adrenal gland. High concentrations of steroids may be expected to accumulate in steroidogenic cells, both in culture and in vivo, and may have autoregulating effects. The high content of antioxidant compounds in the adrenal cortex, principally ascorbate, may serve to protect cytochrome P-450 enzymes from the damaging effects of oxygen radical species formed as a result of cytochrome P-450/pseudosubstrate interactions.

Base (O.-2, e-, or OH-)-induced autoxygenation of organic substrates: a model chemical system for cytochrome P-450-catalyzed monoxygenation and dehydrogenation by dioxygen

When catalytic quantities of superoxide ion (O.-2; or of electrons from electrolysis or of OH-) are introduced into a dry acetonitrile solution that contains excess substrate (RH), ambient air (O2), 1,2-diphenylhydrazine (PhNHNHPh), and iron(II), the substrate is rapidly and efficiently monoxygenated (e.g., triphenylphosphine----triphenylphosphine oxide, benzyl alcohol----benzaldehyde, diphenylsulfoxide----diphenylsulfone) or dehydrogenated (1,4-cyclohexadiene----benzene). The model consists of (i) an O2-activation segment that produces H2O2 from an O.-2-initiated autoxidation of disubstituted hydrazine (a model for reduced flavin), (formula; see text) and (ii) a H2O2-activation segment via the iron(II)-induced formation of ferryl ion (FeO2+), Fe(II) + H2O2----FeO2 + H2O, an effective monoxygenating agent: FeO2+ + RH----Fe(II) + ROH. The combination of i and ii provides a catalytic system for the autoxidation of organic substrates with reaction cycles that are similar to those for cytochrome P-450 monoxygenases.