Regioselectivity of cytochrome P-450 catalyzed hydroxylation of fluorobenzenes predicted by calculated frontier orbital substrate characteristics

Identification of New Hepatic Metabolites of Miconazole by Biological and Electrochemical Methods Using Ultra-High-Performance Liquid Chromatography Combined with High-Resolution Mass Spectrometry

The main objective of this study was to investigate the metabolism of miconazole, an azole antifungal drug. Miconazole was subjected to incubation with human liver microsomes (HLM) to mimic phase I metabolism reactions for the first time. Employing a combination of an HLM assay and UHPLC-HRMS analysis enabled the identification of seven metabolites of miconazole, undescribed so far. Throughout the incubation with HLM, miconazole underwent biotransformation reactions including hydroxylation of the benzene ring and oxidation of the imidazole moiety, along with its subsequent degradation. Additionally, based on the obtained results, screen-printed electrodes (SPEs) were optimized to simulate the same biotransformation reactions, by the use of a simple, fast, and cheap electrochemical method. The potential toxicity of the identified metabolites was assessed using various in silico models.

Mechanism of Selective Aromatic Hydroxylation in the Metabolic Transformation of Paclitaxel Catalyzed by Human CYP3A4

Paclitaxel (PTX) is heralded as one of the most successful natural-product drugs for the treatment of refractory cancers. In humans, the hepatic metabolic transformation of PTX is primarily mediated by two cytochrome P450 enzymes (P450s): CYP3A4 and CYP2C8. The impact of P450 metabolism on the anticancer effectiveness of PTX is significant. However, the precise mechanism underlying selective P450-catalyzed reactions in PTX metabolism remains elusive. To address this knowledge gap, we conducted molecular docking and molecular dynamics simulations using multiple crystal structures of CYP3A4, which originally contained other ligands. These methods enabled us to determine the most plausible binding structure of PTX within the enzyme. By further employing hybrid quantum mechanics and molecular mechanics calculations, we successfully identified two primary pathways for the reaction between compound I (Cpd I) of CYP3A4 and PTX. One of these pathways involves the formation of an epoxide, while the other proceeds through a ketone intermediate.

Computational Investigation of the Bisphenolic Drug Metabolism by Cytochrome P450: What Factors Favor Intramolecular Phenol Coupling

Intramolecular phenol coupling reactions of alkaloids can lead to active metabolites catalyzed by the mammalian cytochrome P450 enzyme (P450); however, the mechanistic knowledge of such an "unusual" process is lacking. This work performs density functional theory computations to reveal the P450-mediated metabolic pathway leading from R-reticuline to the morphine precursor salutaridine by exploring possible intramolecular phenol coupling mechanisms involving diradical coupling, radical addition, and electron transfer. The computed results show that the outer-sphere electron transfer with a high barrier (>20.0 kcal/mol) is unlikely to happen. However, for inter-sphere intramolecular phenol coupling, it reveals that intramolecular phenol coupling of R-reticuline proceeds via the diradical mechanism consecutively by compound I and protonated compound II of P450 rather than the radical addition mechanism. The existence of a much higher radical rebound barrier than that of H-abstraction in the quartet high-spin state can endow the R-reticuline phenoxy radical with a sufficient lifetime to enable intramolecular phenol coupling, while the H-abstraction/radical rebound mode with a negligible rebound barrier leading to phenol hydroxylation can only happen in the doublet low-spin state. Therefore, the ratio [coupling]/[hydroxylation] can be approximately reflected by the relative yield of the high-spin and low-spin H-abstraction by P450, which thus can provide a theoretical ratio of 16:1 for R-reticuline, which is in accordance with previous experimental results. Especially, the high rebound barrier of the phenoxy radical derived from the weak electron-donating ability of the phenoxy radical is revealed as an intrinsic nature. Therefore, the revealed intramolecular phenol coupling mechanism can be potentially extended to several other bisphenolic drugs to infer groups of unexpected metabolites in organisms.

Development of [18F]ICMT-11 for Imaging Caspase-3/7 Activity during Therapy-Induced Apoptosis

Insufficient apoptosis is a recognised hallmark of cancer. A strategy to quantitatively measure apoptosis in vivo would be of immense value in both drug discovery and routine patient management. The first irreversible step in the apoptosis cascade is activation of the "executioner" caspase-3 enzyme to commence cleavage of key structural proteins. One strategy to measure caspase-3 activity is Positron Emission Tomography using isatin-5-sulfonamide radiotracers. One such radiotracer is [18F]ICMT-11, which has progressed to clinical application. This review summarises the design and development process for [18F]ICMT-11, suggesting potential avenues for further innovation.

Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins

As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.

Selectivity of C-H versus C-F Bond Oxygenation by Homo- and Heterometallic Fe4 , Fe3 Mn, and Mn4 Clusters

A series of tetranuclear [LM3 (HFArPz)3 OM'][OTf]2 (M, M'=Fe or Mn) clusters that displays 3-(2-fluorophenyl)pyrazolate (HFArPz) as bridging ligand is reported. With these complexes, manganese was demonstrated to facilitate C(sp2 )-F bond oxygenation via a putative terminal metal-oxo species. Moreover, the presence of both ortho C(sp2 )-H and C(sp2 )-F bonds in proximity of the apical metal center provided an opportunity to investigate the selectivity of intramolecular C(sp2 )-X bond oxygenation (X=H or F) in these isostructural compounds. With iron as the apical metal center, (M'=Fe) C(sp2 )-F bond oxygenation occur almost exclusively, whereas with manganese (M'=Mn), the opposite reactivity is preferred.

Biotransformation of fluorophenyl pyridine carboxylic acids by the model fungus Cunninghamella elegans

1. Fluorine plays a key role in the design of new drugs and recent FDA approvals included two fluorinated drugs, tedizolid phosphate and vorapaxar, both of which contain the fluorophenyl pyridyl moiety. 2. To investigate the likely phase-I (oxidative) metabolic fate of this group, various fluorinated phenyl pyridine carboxylic acids were incubated with the fungus Cunninghamella elegans, which is an established model of mammalian drug metabolism. 3. ¹⁹F NMR spectroscopy established the degree of biotransformation, which varied depending on the position of fluorine substitution, and gas chromatography-mass spectrometry (GC-MS) identified alcohols and hydroxylated carboxylic acids as metabolites. The hydroxylated metabolites were further structurally characterised by nuclear magnetic resonance spectroscopy (NMR), which demonstrated that hydroxylation occurred on the 4' position; fluorine in that position blocked the hydroxylation. 4. The fluorophenyl pyridine carboxylic acids were not biotransformed by rat liver microsomes and this was a consequence of inhibitory action, and thus, the fungal model was crucial in obtaining metabolites to establish the mechanism of catabolism.

Arene activation by a nonheme iron(III)-hydroperoxo complex: pathways leading to phenol and ketone products

Iron(III)-hydroperoxo complexes are found in various nonheme iron enzymes as catalytic cycle intermediates; however, little is known on their catalytic properties. The recent work of Banse and co-workers on a biomimetic nonheme iron(III)-hydroperoxo complex provided evidence of its involvement in reactivity with arenes. This contrasts the behavior of heme iron(III)-hydroperoxo complexes that are known to be sluggish oxidants. To gain insight into the reaction mechanism of the biomimetic iron(III)-hydroperoxo complex with arenes, we performed a computational (density functional theory) study. The calculations show that iron(III)-hydroperoxo reacts with substrates via low free energies of activation that should be accessible at room temperature. Moreover, a dominant ketone reaction product is observed as primary products rather than the thermodynamically more stable phenols. These product distributions are analyzed and the calculations show that charge interaction between the iron(III)-hydroxo group and the substrate in the intermediate state pushes the transferring proton to the meta-carbon atom of the substrate and guides the selectivity of ketone formation. These studies show that the relative ratio of ketone versus phenol as primary products can be affected by external interactions of the oxidant with the substrate. Moreover, iron(III)-hydroperoxo complexes are shown to selectively give ketone products, whereas iron(IV)-oxo complexes will react with arenes to form phenols instead.

Detoxification of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) by cytochrome P450 enzymes: A theoretical investigation

Two types of detoxification routes, N-demethylation to form 4-phenyl-1,2,3,6-tetrahydropyridine (PTP) and aromatic hydroxylation to generate 4-(4'-hydroxyphenyl)-1-methyl-1,2,3,6-tetrahydropyridine (MPTP-OH), for 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mediated by Compound I (Cpd I) of cytochrome P450 are investigated theoretically using hybrid density functional calculations. Quantum chemical results reveal that for the N-demethylation, the initial C-H bond activation is achieved via a hydrogen atom transfer (HAT) mechanism. This is followed by a subsequent O-rebound to yield the carbinolamine intermediate. Due to the nature of pericyclic reaction, the generated carbinolamine decomposes in a non-enzymatic aqueous environment with the assistance of water molecules, forming amine and hydrated formaldehyde. For the aromatic hydroxylation, an initial addition of Cpd I to the substrate occurs mainly through a side-on approach with a subsequent proton shuttle to form the phenol product. A comparison of the energy barriers for both routes indicates that the N-demethylation (7.5/5.7kcal/mol for the quartet/doublet state in solvent) is thermodynamically more favorable than the aromatic hydroxylation process (14.9/14.8kcal/mol for the quartet/doublet state in solvent). This trend is in good agreement with the experimental product distribution, viz., the N-demethylation product PTP is more than the aromatic hydroxylation product MPTP-OH. Taken together, these observations not only enrich our knowledge on the mechanistic details of the N-dealkylation and the aromatic hydroxylation by P450s, but also provide certain insights into the metabolism of other analogous toxins.

Understanding P450-mediated Bio-transformations into Epoxide and Phenolic Metabolites

Adverse drug reactions are commonly the result of cytochrome P450 enzymes (CYPs) converting the drugs into reactive metabolites. Thus, information about the CYP bioactivation of drugs would not only provide insight into metabolic stability, but also into the potential toxicity. For example, oxidation of phenyl rings may lead to either toxic epoxides or safer phenols. Herein, we demonstrate that the potential to form reactive metabolites is encoded primarily in the properties of the molecule to be oxidized. While the enzyme positions the molecule inside the binding pocket (selects the site of metabolism), the subsequent reaction is only dependent on the substrate itself. To test this hypothesis, we used this observation as a predictor of drug inherent toxicity. This approach was used to successfully identify the formation of reactive metabolites in over 100 drug molecules. These results provide a new perspective on the impact of functional groups on aromatic oxidation of drugs and their effects on toxicity.

Computational toxicological investigation on the mechanism and pathways of xenobiotics metabolized by cytochrome P450: a case of BDE-47

Understanding the transformation mechanism and products of xenobiotics catalyzed by cytochrome P450 enzymes (CYPs) is vital to risk assessment. By density functional theory computation with the B3LYP functional, we simulated the reaction of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) catalyzed by the active species of CYPs (Compound I). The enzymatic and aqueous environments were simulated by the polarizable continuum model. The results reveal that the addition of Compound I to BDE-47 is the rate-determining step. The addition of Compound I to the ipso and nonsubstituted C atoms forms tetrahedral σ-adducts that further transform into epoxides. Hydroxylation of the epoxides leads to hydroxylated polybrominated diphenyl ethers and 2,4-dibromophenol. The addition to the Br-substituted C2 and C4 atoms has a higher barrier than addition to the nonsubstituted C atoms, forming phenoxide and cyclohexadienone which subsequently undergo debromination/hydroxylation. A novel mechanism was identified in which the approach of Compound I to C2 led to formation of a phenoxide and an expelled Br(-) ion. The predicted products were consistent with the metabolites identified by others. As a first attempt to simulate the enzymatic transformation of a polycyclic compound, this study may enlighten a computational method to predict the biotransformation of xenobiotics catalyzed by CYPs.

Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450

Cytochrome P450 enzymes play key roles in the metabolism of the majority of drugs. Improved models for prediction of likely metabolites will contribute to drug development. In this work, two possible metabolic routes (aromatic carbon oxidation and O-demethylation) of dextromethorphan are compared using molecular dynamics (MD) simulations and density functional theory (DFT). The DFT results on a small active site model suggest that both reactions might occur competitively. Docking and MD studies of dextromethorphan in the active site of P450 2D6 show that the dextromethorphan is located close to heme oxygen in a geometry apparently consistent with competitive metabolism. In contrast, calculations of the reaction path in a large protein model [using a hybrid quantum mechanical-molecular mechanics (QM/MM) method] show a very strong preference for O-demethylation, in accordance with experimental results. The aromatic carbon oxidation reaction is predicted to have a high activation energy, due to the active site preventing formation of a favorable transition-state structure. Hence, the QM/MM calculations demonstrate a crucial role of many active site residues in determining reactivity of dextromethorphan in P450 2D6. Beyond substrate binding orientation and reactivity of Compound I, successful metabolite predictions must take into account the detailed mechanism of oxidation in the protein. These results demonstrate the potential of QM/MM methods to investigate specificity in drug metabolism.

Prediction of activation energies for aromatic oxidation by cytochrome P450

We have estimated the activation energy for aromatic oxidation by compound I in cytochrome P450 for a diverse set of 17 substrates using state-of-the-art density functional theory (B3LYP) with large basis sets. The activation energies vary from 60 to 87 kJ/mol. We then test if these results can be reproduced by computationally less demanding methods. The best methods (a B3LYP calculation of the activation energy of a methoxy-radical model or a partial least-squares model of the semiempirical AM1 bond dissociation energies and spin densities of the tetrahedral intermediate for both a hydroxyl-cation and a hydroxyl-radical model) give correlations with r(2) of 0.8 and mean absolute deviations of 3 kJ/mol. Finally, we apply these simpler methods on several sets of reactions for which experimental data are available and show that we can predict the reactive sites by combining calculations of the activation energies with the solvent-accessible surface area of each site.

Promises and pitfalls of quantitative structure-activity relationship approaches for predicting metabolism and toxicity

The description of quantitative structure-activity relationship (QSAR) models has been a topic for scientific research for more than 40 years and a topic within the regulatory framework for more than 20 years. At present, efforts on QSAR development are increasing because of their promise for supporting reduction, refinement, and/or replacement of animal toxicity experiments. However, their acceptance in risk assessment seems to require a more standardized and scientific underpinning of QSAR technology to avoid possible pitfalls. For this reason, guidelines for QSAR model development recently proposed by the Organization for Economic Cooperation and Development (OECD) [Organization for Economic Cooperation and Development (OECD) (2007) Guidance document on the validation of (quantitative) structure-activity relationships [(Q)SAR] models. OECD Environment Health and Safety Publications: Series on Testing and Assessment No. 69, Paris] are expected to help increase the acceptability of QSAR models for regulatory purposes. The guidelines recommend that QSAR models should be associated with (i) a defined end point, (ii) an unambiguous algorithm, (iii) a defined domain of applicability, (iv) appropriate measures of goodness-of-fit, robustness, and predictivity, and (v) a mechanistic interpretation, if possible [Organization for Economic Cooperation and Development (OECD) (2007) Guidance document on the validation of (quantitative) structure-activity relationships [(Q)SAR] models. The present perspective provides an overview of these guidelines for QSAR model development and their rationale, as well as the promises and pitfalls of using QSAR approaches and these guidelines for predicting metabolism and toxicity of new and existing chemicals.

Quantitative structure-activity relationship modeling of the toxicity of organothiophosphate pesticides to Daphnia magna and Cyprinus carpio

Within the REACH regulatory framework in the EU, quantitative structure-activity relationships (QSAR) models are expected to help reduce the number of animals used for experimental testing. The objective of this study was to develop QSAR models to describe the acute toxicity of organothiophosphate pesticides to aquatic organisms. Literature data sets for acute toxicity data of organothiophosphates to fish and one data set from experiments with 15 organothiophosphates on Daphniamagna performed in the present study were used to establish QSARs based on quantum mechanically derived molecular descriptors. The logarithm of the octanol/water partition coefficient, logK(ow,) the energy of the lowest unoccupied molecular orbital, E(lumo), and the energy of the highest occupied molecular orbital, E(homo) were used as descriptors. Additionally, it was investigated if toxicity data for the invertebrate D. magna could be used to build a QSAR model to predict toxicity to fish. Suitable QSAR models (0.80<r(2)<0.82) were derived to predict acute toxicity of organothiophosphates to fish (Cyprinus carpio) and the invertebrate (D. magna). Toxicity data for D. magna correlated well (r(2)=0.94) with toxicity data for C. carpio. This implies that by performing toxicity tests with D. magna, one can use our interspecies QSAR model to predict the acute toxicity of organothiophosphates to fish. The three QSAR models were validated either both internally and externally (D. magna) or internally only (carp and D. magna to carp). For each QSAR model, an applicability domain was defined based on the chemical structures and the ranges of the descriptor values of the training set compounds. From the 100196 European Inventory of Existing Commercial Chemical Substances (EINECS), 83 compounds were identified that fit the selection criteria for the QSAR models. For these compounds, using our QSAR models, one can obtain an indication of their toxicity without the need for additional experimental testing.

Design, synthesis, and biological characterization of a caspase 3/7 selective isatin labeled with 2-[18F]fluoroethylazide

Imaging of programmed cell death (apoptosis) is important in the assessment of therapeutic response in oncology and for diagnosis in cardiac and neurodegenerative disorders. The executioner caspases 3 and 7 ultimately effect cellular death, thus providing selective molecular targets for in vivo quantification of apoptosis. To realize this potential, we aimed to develop 18F-labeled isatin sulfonamides with high metabolic stability and moderate lipophilicity while retaining selectivity and affinity for caspase 3/7. A small library of isatins modified with fluorinated aromatic groups and heterocycles was synthesized. A lead compound incorporating 2'-fluoroethyl-1,2,3-triazole was identified with subnanomolar affinity for caspase 3. "Click labeling" provided the 18F-labeled tracer in 65 +/- 6% decay-corrected radiochemical yield from 2-[18F]fluoroethylazide. The compound showed high stability in vivo with rapid uptake and elimination in healthy tissues and tumor. The novel 18F-labeled isatin is a candidate radiotracer for further preclinical evaluation for imaging of apoptosis.

SPORCalc: A development of a database analysis that provides putative metabolic enzyme reactions for ligand-based drug design

Understanding both the enzyme reactions that contribute to intermediate metabolism and the biochemical fate of candidate therapeutic and toxic agents are essential for drug design. Traditional metabolic databases indicate whether reactions have been observed but do not provide the likelihoods of reactions occurring, for example those of mixed function oxygenases and oxidases, during phase I metabolism. The desire for more quantitative predictions motivated the development of the recently introduced Substrate Product Occurrence Ratio Calculator (SPORCalc) that identifies metabolically labile atom positions in candidate compounds. This paper describes a further development and provides a clearer explanation of SPORCalc for the computational pharmacology, medicinal chemistry and drug design communities interested in metabolic prediction of xenobiotics using chemical databases of biotransformations. Examples of reaction centre detection in Metabolite are described followed by a demonstration of almokalant, an anti-arrhythmic agent, undergoing phase I metabolism. In general, occurrence ratio (OR) values are calculated throughout a compound and its transformed metabolites to give propensity (p) values at each atom position. The OR values from substrates and products in the database are essential for addition and elimination reactions. For almokalant, the resulting p values ranged from 10(-1) to 10(-5) and their order of magnitude reflected the known and experimentally observed metabolites. SPORCalc depends entirely on the level of detail from isoform- or species-specific reaction classes in Metabolite. Labile atom positions (sites of metabolism) are identified in both the candidate compound and its metabolites. In general, the likelihood of one enzyme isoform-dependent reaction occurring relative to another and the putative metabolic routes from different isoforms can be investigated. SPORCalc can be developed further to include suitable three-dimensional, structure-activity and physiochemical information.

Human cytochrome p450 family 4 enzymes: function, genetic variation and regulation

The microsomal cytochrome P450 (CYP) family 4 monooxygenases are the major fatty acid omega-hydroxylases. These enzymes remove excess free fatty acids to prevent lipotoxicity, catabolize leukotrienes and prostanoids, and also produce bioactive metabolites from arachidonic acid omega-hydroxylation. In addition to endogenous substrates, recent evidence indicates that CYP4 monooxygenases can also metabolize xenobiotics, including therapeutic drugs. This review focuses on human CYP4 enzymes and updates current knowledge concerning catalytic activity profiles, genetic variation and regulation of expression. Comparative differences between the human and rodent CYP4 enzymes regarding catalytic function and conditional expression are also discussed.

Molecular orbital studies on brominated diphenyl ethers. Part II--reactivity and quantitative structure-activity (property) relationships

Polybrominated diphenyl ethers (PBDEs) are widely used as flame retardants and are increasingly turning up in the environment. Their structural similarities to polychlorinated biphenyls and thyroid hormones suggest they may be a risk to human health. The present study examines the reactivity of brominated diphenyl ethers (BDEs) on the basis of the electronic structures as calculated by semiempirical AM1 self-consistent field molecular orbital (SCF-MO) method. Frontier orbital energies were used to elucidate the reactivity of BDEs in electrophilic, nucleophilic and photolytic reactions. From an examination of the frontier electron densities, the regioselectivity, or orientation, of metabolic reactions of BDEs was predicted. Furthermore, satisfactory quantitative structure-activity (property) relationship (QSAR and QSPR) models were derived to calculate gas chromatographic and ultraviolet spectral properties and luciferase induction activities from the AM1-computed electronic parameters.

Mechanism and structure–reactivity relationships for aromatic hydroxylation by cytochrome P450

Cytochrome P450 enzymes play a central role in drug metabolism, and models of their mechanism could contribute significantly to pharmaceutical research and development of new drugs. The mechanism of cytochrome P450 mediated hydroxylation of aromatics and the effects of substituents on reactivity have been investigated using B3LYP density functional theory computations in a realistic porphyrin model system. Two different orientations of substrate approach for addition of Compound I to benzene, and also possible subsequent rearrangement pathways have been explored. The rate-limiting Compound I addition to an aromatic carbon atom proceeds on the doublet potential energy surface via a transition state with mixed radical and cationic character. Subsequent formation of epoxide, ketone and phenol products is shown to occur with low barriers, especially starting from a cation-like rather than a radical-like tetrahedral adduct of Compound I with benzene. Effects of ring substituents were explored by calculating the activation barriers for Compound I addition in the meta and para-position for a range of monosubstituted benzenes and for more complex polysubstituted benzenes. Two structure-reactivity relationships including 8 and 10 different substituted benzenes have been determined using (i) experimentally derived Hammett sigma-constants and (ii) a theoretical scale based on bond dissociation energies of hydroxyl adducts of the substrates, respectively. In both cases a dual-parameter approach that employs a combination of radical and cationic electronic descriptors gave good relationships with correlation coefficients R2 of 0.96 and 0.82, respectively. These relationships can be extended to predict the reactivity of other substituted aromatics, and thus can potentially be used in predictive drug metabolism models.

Reductive deamination as a new step in the anaerobic microbial degradation of halogenated anilines

In this paper we report the isolation and characterization of an anaerobic enrichment culture as well as of a Rhodococcus sp. strain 2 capable of degrading 3,4-dihaloanilines under nitrate reducing conditions. Using mass spectrometry several of the intermediates formed in the process of 3,4-dichloroaniline conversion were identified. Most interesting is the observation of reductive deamination and the formation of 1,2-dichlorobenzene as one of the intermediates. Using 19F NMR and fluorinated 3,4-dihaloaniline model substrates it was corroborated that reductive deamination of the anilines to give dihalobenzene intermediates represents a new initial step in the anaerobic microbial degradation of these halogenated anilines.

Computer-modeling-based QSARs for analyzing experimental data on biotransformation and toxicity

Over the past decades the description of quantitative structure-activity relationships (QSARs) has been undertaken in order to find predictive models and/or mechanistic explanations for chemical as well as biological activities. This includes QSAR studies in toxicology. In an approach beyond the classical QSAR approaches, attempts have been made to define parameters for the QSAR studies on the basis of quantum mechanical computer calculations. The conversion of relatively small xenobiotics within the active sites of biotransformation enzymes can be expected to follow the general rules of chemistry. This makes the description of QSARs on the basis of only one parameter, chosen on the basis of insight in the mechanism, feasible. In contrast, toxicological endpoints can very often be the result of more than one physico-chemical interaction of the compound with the model system of interest. Therefore the description of quantitative structure-toxicity relationships often does not follow a one-descriptor mechanistic approach but starts from the other end, describing QSARs by multi-parameter approaches. The present paper focuses on the possibilities and restrictions of using computer-based QSAR modeling for analyzing experimental toxicological data, with emphasis on examples from the field of biotransformation and toxicity.

Porphyrin-Fe(III)-hydroperoxide and porphyrin-Fe(III)-peroxide anion as catalytic intermediates in cytochrome P450-catalyzed hydroxylation reactions: a molecular orbital study

The hydroxylation of fluorobenzene and aniline, catalyzed by the porphyrin-Fe(III)-peroxide anion with either a cysteinate- or a histidyl-type of axial ligand as well as the hydroxylation of fluorobenzene, catalyzed by porphyrin-Fe(III)-hydroperoxide with a cysteinate-type of axial ligand as catalytic intermediates, have been investigated by electronic structure calculations in local spin-density approximation. Non-repulsive potential curves are, in contrast with porphyrin-Fe(III)-hydroperoxide, obtained only in the case of porphyrin-Fe(III)-peroxide anion as catalytic intermediate. The mutual substrate-porphyrin orientation with a dihedral angle between the plane of the substrate and the porphyrin plane of 45 degrees is more favorable compared with the parallel orientation between these two planes. This orientation differs for the case of fluorobenzene hydroxylation from the corresponding one calculated by us with the ferryl-oxo-pi-cation radical complex as a catalytic intermediate. The calculated reaction profiles show also the effectiveness of the histidyl-type coordinated porphyrin-Fe(III)-peroxide involved in P450 type of hydroxylation reactions. The calculations demonstrate the predominant role of the O1-O2 moiety of the porphyrin-Fe(III)-peroxide anion in the hydroxylation process of the substrates. The results indicate that the porphyrin-Fe(III)-peroxide anion is an effective catalytic species in hydroxylation reactions. In all the studied cases irrespective of the substrate and the nature of the axial ligand, the potential curves reach minimum at approximately 130-140 pm, expressing the length of an aromatic C-O bond.

Identification of fluoropyrogallols as new intermediates in biotransformation of monofluorophenols in Rhodococcus opacus 1cp

The transformation of monofluorophenols by whole cells of Rhodococcus opacus 1cp was investigated, with special emphasis on the nature of hydroxylated intermediates formed. Thin-layer chromatography, mass spectrum analysis, and (19)F nuclear magnetic resonance demonstrated the formation of fluorocatechol and trihydroxyfluorobenzene derivatives from each of three monofluorophenols. The (19)F chemical shifts and proton-coupled splitting patterns of the fluorine resonances of the trihydroxyfluorobenzene products established that the trihydroxylated aromatic metabolites contained hydroxyl substituents on three adjacent carbon atoms. Thus, formation of 1,2, 3-trihydroxy-4-fluorobenzene (4-fluoropyrogallol) from 2-fluorophenol and formation of 1,2,3-trihydroxy-5-fluorobenzene (5-fluoropyrogallol) from 3-fluorophenol and 4-fluorophenol were observed. These results indicate the involvement of fluoropyrogallols as previously unidentified metabolites in the biotransformation of monofluorophenols in R. opacus 1cp.

TEAC antioxidant activity of 4-hydroxybenzoates

The influence of pH, intrinsic electron donating capacity, and intrinsic hydrogen atom donating capacity on the antioxidant potential of series of hydroxy and fluorine substituted 4-hydroxybenzoates was investigated experimentally and also on the basis of computer calculations. The pH-dependent behavior of the compounds in the TEAC assay revealed different antioxidant behavior of the nondissociated monoanionic form and the deprotonated dianionic form of the 4-hydroxybenzoates. Upon deprotonation the radical scavenging ability of the 4-hydroxybenzoates increases significantly. For mechanistic comparison a series of fluorobenzoates was synthesized and included in the studies. The fluorine substituents were shown to affect the proton and electron donating abilities of 4-hydroxybenzoate in the same way as hydroxyl substituents. In contrast, the fluorine substituents influenced the TEAC value and the hydrogen atom donating capacity of 4-hydroxybenzoate in a way different from the hydroxyl moieties. Comparison of these experimental data to computer-calculated characteristics indicates that the antioxidant behavior of the monoanionic forms of the 4-hydroxybenzoates is not determined by the tendency of the molecule to donate an electron, but by its ability to donate a hydrogen atom. Altogether, the results explain qualitatively and quantitatively how the number and position of OH moieties affect the antioxidant behavior of 4-hydroxybenzoates.

Quantitative structure activity relationships for the electron transfer reactions of Anabaena PCC 7119 ferredoxin-NADP+ oxidoreductase with nitrobenzene and nitrobenzimidazolone derivatives: mechanistic implications

The steady state single electron reduction of polynitroaromatics by ferredoxin-NADP+ oxidoreductase (EC 1.18.1.2) from cyanobacterium Anabaena PCC 7119 has been studied and quantitative structure activity relationships are described. The solubility of the polynitroaromatics as well as their reactivity towards ferredoxin-NADP+ oxidoreductase are markedly higher than those for previously studied mononitroaromatics and this enabled the independent measurement of the kinetic parameters-k(cat) and Km. Interestingly, the natural logarithm of the bimolecular rate constant, k(cat)/Km, and also the natural logarithm of k(cat) correlate with the calculated energy of the lowest unoccupied molecular orbital of the polynitroaromatic substrates. The minimal kinetic model in line with these quantitative structure activity relationships is a ping-pong mechanism which includes substrate binding equilibria in the second half reaction.

Antioxidant activities of carotenoids: quantitative relationships between theoretical calculations and experimental literature data

Quantitative structure activity relationships (QSARs) are described for the antioxidant activity of series of all-trans carotenoids. The antioxidant activity of the carotenoids is characterised by literature data for (i) their relative ability to scavenge the ABTS*+ radical cation, reflected by the so-called trolox equivalent antioxidant capacity (TEAC) value, (ii) their relative rate of oxidation by a range of free radicals, or (iii) their capacity to inhibit lipid peroxidation in multilamellar liposomes, leading to a decrease in formation of thiobarbituric acid reactive substances (TBARS). All these antioxidant values for radical scavenging action correlate quantitatively with computer-calculated ionisation potentials of the carotenoids. These correlations are observed both when the ionisation potential is calculated as the negative of the energy of the highest occupied molecular orbital (-E(HOMO)) of the molecule, or as the relative change in heat of formation (deltadeltaHF) upon the one-electron oxidation of the carotenoids. The calculations provide a theoretical assay able to characterise the intrinsic electron donating capacity of an antioxidant, in hydrophilic, hydrophobic or artificial membrane environment.

Molecular orbital study of porphyrin–substrate interactions in cytochrome P450 catalysed aromatic hydroxylation of substituted anilines

The reaction mechanism for the primary reaction step of the hydroxylation of 3-fluoro-6-methylaniline, attacked at different positions (oxygen attack across a C-C bond and direct attack at positions para and ortho with respect to the NH(2)-group) catalysed by a high-valent ferryl-oxo porphyrin a(2u)-cation complex with H(3)CS(-) as an axial ligand, has been investigated on the basis of electronic structure calculations in local spin-density approximation. Non-repulsive potential curves are obtained only in cases of direct attack at the para- and ortho-positions with respect to NH(2), but not for epoxide formation. Comparing the potential curves for the hydroxylation at the positions para and ortho to the NH(2)-group, an attack at the para-position is more likely. The relative orientation of the substrate towards the porphyrin is essentially determined by the interaction between the substituents of the substrate and the porphyrin. Consequently, different geometrical orientations of the substrate are obtained for hydroxylation at the para- and ortho-positions. In both cases of direct attack the substrate plane is not parallel to the porphyrin plane. The decisive role of sulphur in the hydroxylation is demonstrated by the participation of the S(3p)-orbitals in all molecular orbitals involved in the reaction.

Quantitative structure activity relationships for the conversion of nitrobenzimidazolones and nitrobenzimidazoles by DT-diaphorase: implications for the kinetic mechanism

Quantitative structure activity relationships (QSARs) for the conversion of nitrobenzimidazolones and nitrobenzimidazoles by rat liver DT-diaphorase (EC 1.6.99.2) are described. The parameter used for description of the QSARs is the energy of the lowest unoccupied molecular orbital (E(LUMO)) of the nitroaromatic compounds. Interestingly, correlations with E(LUMO) were observed for both the natural logarithm of kcat, but also for the natural logarithm of kcat/Km. The minimal kinetic model in line with these QSARs is a ping-pong mechanism that includes a substrate binding equilibrium in the second half reaction.

Epoxidation of olefins by cytochrome P450: evidence from site-specific mutagenesis for hydroperoxo-iron as an electrophilic oxidant

P450 cytochromes (P450) catalyze many types of oxidative reactions, including the conversion of olefinic substrates to epoxides by oxygen insertion. In some instances epoxidation leads to the formation of products of physiological importance from naturally occurring substrates, such as arachidonic acid, and to the toxicity, carcinogenicity, or teratogenicity of foreign compounds, including drugs. In the present mechanistic study, the rates of oxidation of model olefins were determined with N-terminal-truncated P450s 2B4 and 2E1 and their respective mutants in which the threonine believed to facilitate proton delivery to the active site was replaced by alanine. Styrene epoxidation, cyclohexene epoxidation and hydroxylation to give 1-cyclohexene-3-ol, and cis- or trans-butene epoxidation (without isomerization) and hydroxylation to give 2-butene-1-ol were all significantly decreased by the 2B4 T302A mutation. Reduced proton delivery in this mutant is believed to interfere with the activation of dioxygen to the oxenoid species, as shown earlier by decreased hydroxylation of several substrates and enhanced aldehyde deformylation via a presumed peroxo intermediate. Of particular interest, however, the T303A mutation of P450 2E1 resulted in enhanced epoxidation of all of the model olefins along with decreased allylic hydroxylation of cyclohexene and butene. These results and a comparison of the ratios of the rates of epoxidation and hydroxylation support the concept that two different species with electrophilic properties, hydroperoxo-iron (FeO2H)3+ and oxenoid-iron (FeO)3+, can effect olefin epoxidation. The ability of cytochrome P450 to use several different active oxidants generated from molecular oxygen may help account for the broad reaction specificity and variety of products formed by this versatile catalyst.