Cytochrome P450: The Active Oxidant and Its Spectrum

Detection of a Kinetically Competent Compound-I Intermediate in the Vancomycin Biosynthetic Enzyme OxyB

Cytochrome P450 enzymes are abundantly encoded in microbial genomes. Their reactions have two general outcomes, one involving oxygen insertion via a canonical "oxygen rebound" mechanism and a second that diverts from this pathway and leads to a wide array of products, notably intramolecular oxidative cross-links. The antibiotic of-last-resort, vancomycin, contains three such cross-links, which are crucial for biological activity and are installed by the P450 enzymes OxyB, OxyA, and OxyC. The mechanisms of these enzymes have remained elusive in part because of the difficulty in spectroscopically capturing transient intermediates. Using stopped-flow UV/visible absorption and rapid freeze-quench electron paramagnetic resonance spectroscopies, we show that OxyB generates the highly reactive compound-I intermediate, which can react with a model vancomycin peptide substrate in a kinetically competent fashion to generate product. Our results have implications for the mechanism of OxyB and are in line with the notion that oxygen rebound and oxidative cross-links share early steps in their catalytic cycles.

Decomposition of 2,4-dihalophenols by dehaloperoxidase activity and spontaneous reaction with hydrogen peroxide

The enzyme dehaloperoxidase (DHP) found in the marine worm Amphitrite ornata is capable of enzymatic peroxidation of 2,4-dichlorophenol (DCP) and 2,4-dibromophenol (DBP). There is also at least one parallel oxidative pathway and the major products 2-chloro-1,4-benzoquinone (2-ClQ) and 2-bromo-1,4-benzoquinone (2-BrQ) undergo aspontaneous secondary hydroxylation reaction. The oxidation and hydroxylation reactions have been monitored by UV-visible spectroscopy, High Performance Liquid Chromatography (HPLC), and mass spectrometry. Evidence from time-resolved UV-visible spectroscopy suggests that the hydroxylations of 2-ClQ and 2-BrQ in the presence of hydrogen peroxide (H2O2) are non-enzymatic spontaneous processes approximately ∼10 and ∼ 5 times slower, respectively, than the enzymatic oxidation of DCP or DBP by DHP in identical solvent conditions. The products 2-ClQ and 2-BrQ have λmaxat 255 nm and 260 nm, respectively. Both substrates, DCP and DBP, react to form a parallel product peaked at 240 nm on the same time scale as the formation of 2-ClQ and 2-BrQ. The 240 nm band is not associated with the hydroxylation process, nor is it attributable to the catechol 3,5-dihalobenzene-1,3-diol observed by mass spectrometry. One possible explanation is that muconic acid is formed as a decomposition product, which could follow decomposition either the catechol or hydroxyquinone. These reactions give a more complete understanding of the biodegradation of xenobiotics by the multi-functional hemoglobin, DHP, in Amphitrite ornata. SYNOPSIS: The decomposition of 2,4-dihalophenols catalyzed by dehaloperoxidase was studied by UV-visible spectroscopy, High Performance Liquid Chromatography and Liquid Chromatography-Mass Spectrometry. Spectroscopic evidence suggests two major products, which we propose are 2-halo-1,4-benzoquinone and 2-halomuconic acid. These complementary techniques give a high-level view of the degradation of xenobiotics in marine ecosystems.

Capturing a bis-Fe(IV) State in Methylosinus trichosporium OB3b MbnH

The diheme bacterial cytochrome c peroxidase (bCcP)/MauG superfamily is a diverse set of enzymes that remains largely uncharacterized. One recently discovered member, MbnH, converts a tryptophan residue in its substrate protein, MbnP, to kynurenine. Here we show that upon reaction with H₂O₂, MbnH forms a bis-Fe(IV) intermediate, a state previously detected in just two other enzymes, MauG and BthA. Using absorption, Mössbauer, and electron paramagnetic resonance (EPR) spectroscopies coupled with kinetic analysis, we characterized the bis-Fe(IV) state of MbnH and determined that this intermediate decays back to the diferric state in the absence of MbnP substrate. In the absence of MbnP substrate, MbnH can also detoxify H₂O₂ to prevent oxidative self damage, unlike MauG, which has long been viewed as the prototype for bis-Fe(IV) forming enzymes. MbnH performs a different reaction from MauG, while the role of BthA remains unclear. All three enzymes can form a bis-Fe(IV) intermediate but within distinct kinetic regimes. The study of MbnH significantly expands our knowledge of enzymes that form this species. Computational and structural analyses indicate that electron transfer between the two heme groups in MbnH and between MbnH and the target tryptophan in MbnP likely occurs via a hole-hopping mechanism involving intervening tryptophan residues. These findings set the stage for discovery of additional functional and mechanistic diversity within the bCcP/MauG superfamily.

Anaerobic Infrared Spectroelectrochemical Methods for Studying Oxygen-Sensitive [FeFe] Hydrogenases

[FeFe] hydrogenases comprise an important class of H₂ evolving enzymes; however, these proteins are often oxygen sensitive and require anaerobic environments for characterization. Understanding the electrochemical relationships between various active and inactive states of these enzymes is instrumental in uncovering the reaction mechanisms of the complex six-iron active center of [FeFe] hydrogenases called H-cluster. Since states of the H-cluster exhibit distinct fingerprint-like spectra in the mid-IR range, IR spectroelectrochemical experiments provide a powerful methodological framework for this goal. This chapter describes protocols for performing Fourier-transform infrared (FTIR) spectroelectrochemical experiments on [FeFe] hydrogenases under anaerobic conditions. Topics included experimental design, data acquisition, and data analysis.

Endocrine-disrupting metabolic activation of 2-nitrofluorene catalyzed by human cytochrome P450 1A1: A QM/MM approach

Nitropolycyclic aromatic hydrocarbons (NPAHs) present one of the most important airborne pollutants. Recent studies have shown that one of the most abundant NPAHs, 2-Nitrofluorene (NF), was supposed to be converted to endocrine-disrupting metabolites by cytochrome P450 1A1 (CYP1A1) in human cells. However, the mechanism is still largely unexplored. Here the metabolic activation and transformation mechanism of NF catalyzed by CYP1A1 were systematically studied with the aid of Molecular Dynamics, Density Functional Theory and Quantum Mechanics/Molecular Mechanics techniques. We evidence that CYP1A1 can activate NF through two elementary processes: (i) electrophilic addition (12.4 kcal·mol-1) or hydrogen abstraction (38.2 kcal·mol-1) and (ii) epoxidation (5.9 and 8.7 kcal·mol-1) or NIH shift (12.5 and 14.9 kcal·mol-1) or proton shuttle (12.1 kcal·mol-1). Electrophilic addition was found to be the rate-determining step while epoxidation rather than NIH shift or proton shuttle is the more feasible pathway after electrophilic addition. Metabolites 6,7-epoxide-2-nitrofluorene and 7,8-epoxide-2-nitrofluorene were identified as the major epoxidation products. Epoxides are unstable and easy to react with hydrated hydrogen ions and hydroxyls to produce endocrine disrupter 7-hydroxy-2-nitrofluorene. Toxic analysis shows that some of the metabolites are more toxic to model aquatic organisms (e.g. Green algea) than NF. Binding affinity analysis to human sex hormone binding globulin reveals that NF metabolites all have endocrine-disrupting potential. This study provides a comprehensive understanding on the biotransformation process of NF and may aid future studies on various NPAHs activation catalyzed by human P450 enzyme.

Hidden Complexity in the Mechanism of the Autoreduction of Myoglobin Compound II

The non-native oxidation of horse heart myoglobin with hydrogen peroxide produces compound II which autoreduces by utilizing an internal oxidation site. Here, we utilize full UV-visible time-dependent kinetics with global kinetic singular value decomposition analysis to explore the mechanism and uncover more detail about the high-valent heme spectral features. By varying the hydrogen peroxide and myoglobin concentration, we were able to uncover more detailed spectra of myoglobin compound II and the autoreduction rate under several different pH conditions. The compound II spectra demonstrate pH-dependent features with an inflection point around pH 5.7 ± 0.1. The rate of autoreduction of compound II, k 2, increases with lower pH with a half-power proton dependence and no indication of a pK a > 3.9 ± 0.2, indicating that the autoreduction is still dependent on the protonation of the ferryl oxo species. The k 2 also demonstrates both hydrogen peroxide and myoglobin dependency. At myoglobin concentrations greater than 6.6 μM, the k 2 is myoglobin-independent, but for lower concentrations, a pH-sensitive concentration dependence is seen.

Exploring hitherto uninvestigated reactions of the fatty acid peroxygenase CYP152A1: catalase reaction and Compound I formation

CYP152A1 (cytochrome P450_BSβ) is a fatty acid peroxygenase, which specifically catalyses the oxidation of long-chain fatty acids using hydrogen peroxide as an oxidant. We have found that CYP152A1 possesses catalase activity, which competes with the hydroxylation of long-chain fatty acids, the oxidation of non-native substrates, and haem degradation. Using hydrogen peroxide, Compound I of CYP152A1 could not be observed, due to its swift decomposition via catalase activity, where Compound I reacts with another molecule of hydrogen peroxide to form O₂. In contrast, a clear spectral change indicative of Compound I formation was observed when mCPBA was employed as the oxidant. This work presents valuable insights into an important role for the catalase activity of CYP152A1 in avoiding enzyme deactivation when no substrate is available for oxidation.

Nitrene transfers mediated by natural and artificial iron enzymes

Amines are ubiquitous in biology and pharmacy. As a consequence, introducing N functionalities in organic molecules is attracting strong continuous interest. The past decade has witnessed the emergence of very efficient and selective catalytic systems achieving this goal thanks to engineered hemoproteins. In this review, we examine how these enzymes have been engineered focusing rather on the rationale behind it than the methodology employed. These studies are put in perspective with respect to in vitro and in vivo nitrene transfer processes performed by cytochromes P450. An emphasis is put on mechanistic aspects which are confronted to current molecular knowledge of these reactions. Forthcoming developments are delineated.

Enzyme Kinetics of Oxidative Metabolism-Cytochromes P450

The cytochrome P450 enzymes (CYPs) are the most important enzymes in the oxidative metabolism of hydrophobic drugs and other foreign compounds (xenobiotics). The versatility of these enzymes results in some unusual kinetic properties, stemming from the simultaneous interaction of multiple substrates with the CYP active site. Often, the CYPs display kinetics that deviate from standard hyperbolic saturation or inhibition kinetics. Non-Michaelis-Menten or "atypical" saturation kinetics include sigmoidal, biphasic, and substrate inhibition kinetics (see Chapter 2 ). Interactions between substrates include competitive inhibition, noncompetitive inhibition, mixed inhibition, partial inhibition, activation, and activation followed by inhibition (see Chapters 4 and 6 ). Models and equations that can result in these kinetic profiles will be presented and discussed.

Shallow Distance Dependence for Proton-Coupled Tyrosine Oxidation in Oligoproline Peptides

We have explored the kinetic effect of increasing electron transfer (ET) distance in a biomimetic, proton-coupled electron-transfer (PCET) system. Biological ET often occurs simultaneously with proton transfer (PT) in order to avoid the high-energy, charged intermediates resulting from the stepwise transfer of protons and electrons. These concerted proton-electron-transfer (CPET) reactions are implicated in numerous biological ET pathways. In many cases, PT is coupled to long-range ET. While many studies have shown that the rate of ET is sensitive to the distance between the electron donor and acceptor, extensions to biological CPET reactions are sparse. The possibility of a unique ET distance dependence for CPET reactions deserves further exploration, as this could have implications for how we understand biological ET. We therefore explored the ET distance dependence for the CPET oxidation of tyrosine in a model system. We prepared a series of metallopeptides with a tyrosine separated from a Ru(bpy)32+ complex by an oligoproline bridge of increasing length. Rate constants for intramolecular tyrosine oxidation were measured using the flash-quench transient absorption technique in aqueous solutions. The rate constants for tyrosine oxidation decreased by 125-fold with three added proline residues between tyrosine and the oxidant. By comparison, related intramolecular ET rate constants in very similar constructs were reported to decrease by 4-5 orders of magnitude over the same number of prolines. The observed shallow distance dependence for tyrosine oxidation is proposed to originate in part from the requirement for stronger oxidants, leading to a smaller hole-transfer effective tunneling barrier height. The shallow distance dependence observed here and extensions to distance-dependent CPET reactions have potential implications for long-range charge transfers.

Inorganic reaction mechanisms. A personal journey

This review covers highlights of the work performed in the van Eldik group on inorganic reaction mechanisms over the past two decades in the form of a personal journey. Topics that are covered include, from NO to HNO chemistry, peroxide activation in model porphyrin and enzymatic systems, the wonder-world of Ru^III(edta) chemistry, redox chemistry of Ru(iii) complexes, Ru(ii) polypyridyl complexes and their application, relevant physicochemical properties and reaction mechanisms in ionic liquids, and mechanistic insight from computational chemistry. In each of these sections, typical examples of mechanistic studies are presented in reference to related work reported in the literature.

Hole Hopping through Cytochrome P450

High-potential iron-oxo species are intermediates in the catalytic cycles of oxygenase enzymes. They can cause heme degradation and irreversible oxidation of nearby amino acids. We have proposed that there are protective mechanisms in which hole hopping from oxidized hemes through tryptophan/tyrosine chains generates a surface-exposed amino-acid oxidant that could be rapidly disarmed by reaction with cellular reductants. In investigations of cytochrome P450_BM3, we identified Trp96 as a critical residue that could play such a protective role. This Trp is cation-π paired with Arg398 in 81% of mammalian P450s. Here we report on the effect of the Trp/Arg cation-π interaction on Trp96 formal potentials as well as on electronic coupling strengths between Trp96 and the heme both for wild type cytochrome P450 and selected mutants. Mutation of Arg398 to His, which decreases the Trp96 formal potential, increases Trp-heme electronic coupling; however, surprisingly, the rate of phototriggered electron transfer from a Ru-sensitizer (through Trp96) to the P450_BM3 heme was unaffected by the Arg398His mutation. We conclude that Trp96 has moved away from Arg398, suggesting that the protective mechanism for P450s with this Trp-Arg pair is conformationally gated.

Cytochrome P450 119 Compounds I Formed by Chemical Oxidation and Photooxidation Are the Same Species

Compound I from cytochrome P450 119 prepared by the photooxidation method involving peroxynitrite oxidation of the resting enzyme to Compound II followed by photooxidation to Compound I was compared to Compound I generated by m-chloroperoxybenzoic acid (MCPBA) oxidation of the resting enzyme. The two methods gave the same UV/Visible spectra, the same products from oxidations of lauric acid and palmitic acid and their (ω-2,ω-2,ω-3,ω-3)-tetradeuterated analogues, and the same kinetics for oxidations of lauric acid and caprylic acid. The experimental identities between the transients produced by the two methods leave no doubt that the same Compound I species is formed by the two methods.

Tuning the Geometric and Electronic Structure of Synthetic High-Valent Heme Iron(IV)-Oxo Models in the Presence of a Lewis Acid and Various Axial Ligands

High-valent ferryl species (e.g., (Por)FeIV═O, Cmpd-II) are observed or proposed key oxidizing intermediates in the catalytic cycles of heme-containing enzymes (P-450s, peroxidases, catalases, and cytochrome c oxidase) involved in biological respiration and oxidative metabolism. Herein, various axially ligated iron(IV)-oxo complexes were prepared to examine the influence of the identity of the base. These were generated by addition of various axial ligands (1,5-dicyclohexylimidazole (DCHIm), a tethered-imidazole system, and sodium derivatives of 3,5-dimethoxyphenolate and imidazolate). Characterization was carried out via UV-vis, electron paramagnetic resonance (EPR), 57Fe Mössbauer, Fe X-ray absorption (XAS), and 54/57Fe resonance Raman (rR) spectroscopies to confirm their formation and compare the axial ligand perturbation on the electronic and geometric structures of these heme iron(IV)-oxo species. Mössbauer studies confirmed that the axially ligated derivatives were iron(IV) and six-coordinate complexes. XAS and 54/57Fe rR data correlated with slight elongation of the iron-oxo bond with increasing donation from the axial ligands. The first reported synthetic H-bonded iron(IV)-oxo heme systems were made in the presence of the protic Lewis acid, 2,6-lutidinium triflate (LutH+), with (or without) DCHIm. Mössbauer, rR, and XAS spectroscopic data indicated the formation of molecular Lewis acid ferryl adducts (rather than full protonation). The reduction potentials of these novel Lewis acid adducts were bracketed through addition of outer-sphere reductants. The oxidizing capabilities of the ferryl species with or without Lewis acid vary drastically; addition of LutH+ to F8Cmpd-II (F8 = tetrakis(2,6-difluorophenyl)porphyrinate) increased its reduction potential by more than 890 mV, experimentally confirming that H-bonding interactions can increase the reactivity of ferryl species.

Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function

Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.

Privileged Role of Thiolate as the Axial Ligand in Hydrogen Atom Transfer Reactions by Oxoiron(IV) Complexes in Shaping the Potential Energy Surface and Inducing Significant H-Atom Tunneling

An H/D kinetic isotope effect (KIE) of 80 is found at -20 °C for the oxidation of 9,10-dihydroanthracene by [Fe^IV(O)(TMCS)]⁺, a complex supported by the tetramethylcyclam (TMC) macrocycle with a tethered thiolate. This KIE value approaches that previously predicted by DFT calculations. Other [Fe^IV(O)(TMC)(anion)] complexes exhibit values of 20, suggesting that the thiolate ligand of [Fe^IV(O)(TMCS)]⁺ plays a unique role in facilitating tunneling. Calculations show that tunneling is most enhanced (a) when the bond asymmetry between C-H bond breaking and O-H bond formation in the transition state is minimized, and (b) when the electrostatic interactions in the O---H---C moiety are maximal. These two factors-which peak for the best electron donor, the thiolate ligand-afford a slim and narrow barrier through which the H-atom can tunnel most effectively.

Control of C-H Bond Activation by Mo-Oxo Complexes: pKa or Bond Dissociation Free Energy (BDFE)?

A density functional theory (DFT) study (BMK/6-31+G(d)) was initiated to investigate the activation of benzylic carbon-hydrogen bonds by a molybdenum-oxo complex with a potentially redox noninnocent supporting ligand-a simple mimic of the active species of the enzyme ethylbenzene dehydrogenase (EBDH)-through deprotonation (C-H bond heterolysis) or hydrogen atom abstraction (C-H bond homolysis) routes. Activation free-energy barriers for neutral and anionic Mo-oxo complexes were high, but lower for anionic complexes than neutral complexes. Interesting trends as a function of substituents were observed that indicated significant H^δ+ character in the transition states (TS), which was further supported by the preference for [2 + 2] addition over HAA for most complexes. Hence, it was hypothesized that C-H activation by these EBDH mimics is controlled more by the pK_a than by the bond dissociation free energy of the C-H bond being activated. Therefore, the results suggest promising pathways for designing more efficient and selective catalysts for hydrocarbon oxidation based on EBDH active-site mimics.

Use of bioconjugation with cytochrome P450 enzymes

Bioconjugation, defined as chemical modification of biomolecules, is widely employed in biological and biophysical studies. It can expand functional diversity and enable applications ranging from biocatalysis, biosensing and even therapy. This review summarizes how chemical modifications of cytochrome P450 enzymes (P450s or CYPs) have contributed to improving our understanding of these enzymes. Genetic modifications of P450s have also proven very useful but are not covered in this review. Bioconjugation has served to gain structural information and investigate the mechanism of P450s via photoaffinity labeling, mechanism-based inhibition (MBI) and fluorescence studies. P450 surface acetylation and protein cross-linking have contributed to the investigation of protein complexes formation involving P450 and its redox partner or other P450 enzymes. Finally, covalent immobilization on polymer surfaces or electrodes has benefited the areas of biocatalysis and biosensor design. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.

Reaction Intermediates and Molecular Mechanism of Peroxynitrite Activation by NO Synthases

The activation of the peroxynitrite anion (PN) by hemoproteins, which leads to its detoxification or, on the contrary to the enhancement of its cytotoxic activity, is a reaction of physiological importance that is still poorly understood. It has been known for some years that the reaction of hemoproteins, notably cytochrome P450, with PN leads to the buildup of an intermediate species with a Soret band at ∼435 nm (I435). The nature of this intermediate is, however, debated. On the one hand, I435 has been presented as a compound II species that can be photoactivated to compound I. A competing alternative involves the assignment of I435 to a ferric-nitrosyl species. Similar to cytochromes P450, the buildup of I435 occurs in nitric oxide synthases (NOSs) upon their reaction with excess PN. Interestingly, the NOS isoforms vary in their capacity to detoxify/activate PN, although they all show the buildup of I435. To better understand PN activation/detoxification by heme proteins, a definitive assignment of I435 is needed. Here we used a combination of fine kinetic analysis under specific conditions (pH, PN concentrations, and PN/NOSs ratios) to probe the formation of I435. These studies revealed that I435 is not formed upon homolytic cleavage of the O-O bond of PN, but instead arises from side reactions associated with excess PN. Characterization of I435 by resonance Raman spectroscopy allowed its identification as a ferric iron-nitrosyl complex. Our study indicates that the model used so far to depict PN interactions with hemo-thiolate proteins, i.e., leading to the formation and accumulation of compound II, needs to be reconsidered.

N-H Bond Dissociation Enthalpies and Facile H Atom Transfers for Early Intermediates of Fe-N2 and Fe-CN Reductions

Fe-mediated biological nitrogen fixation is thought to proceed via either a sequence of proton and electron transfer steps, concerted H atom transfer steps, or some combination thereof. Regardless of the specifics and whether the intimate mechanism for N2-to-NH3 conversion involves a distal pathway, an alternating pathway, or some hybrid of these limiting scenarios, Fe-NxHy intermediates are implicated that feature reactive N-H bonds. Thermodynamic knowledge of the N-H bond strengths of such species is scant, and is especially difficult to obtain for the most reactive early stage candidate intermediates (e.g., Fe-N═NH, Fe═N-NH2, Fe-NH═NH). Such knowledge is essential to considering various mechanistic hypotheses for biological (and synthetic) nitrogen fixation and to the rational design of improved synthetic N2 fixation catalysts. We recently reported several reactive complexes derived from the direct protonation of Fe-N2 and Fe-CN species at the terminal N atom (e.g., Fe═N-NH2, Fe-C≡NH, Fe≡C-NH2). These same Fe-N2 and Fe-CN systems are functionally active for N2-to-NH3 and CN-to-CH4/NH3 conversion, respectively, when subjected to protons and electrons, and hence provide an excellent opportunity for obtaining meaningful N-H bond strength data. We report here a combined synthetic, structural, and spectroscopic/analytic study to estimate the N-H bond strengths of several species of interest. We assess the reactivity profiles of species featuring reactive N-H bonds and estimate their homolytic N-H bond enthalpies (BDEN-H) via redox and acidity titrations. Very low N-H bond dissociation enthalpies, ranging from 65 (Fe-C≡NH) to ≤37 kcal/mol (Fe-N═NH), are determined. The collective data presented herein provide insight into the facile reactivity profiles of early stage protonated Fe-N2 and Fe-CN species.

Idiosyncratic Drug-Induced Liver Injury (IDILI): Potential Mechanisms and Predictive Assays

Idiosyncratic drug-induced liver injury (IDILI) is a significant source of drug recall and acute liver failure (ALF) in the United States. While current drug development processes emphasize general toxicity and drug metabolizing enzyme- (DME-) mediated toxicity, it has been challenging to develop comprehensive models for assessing complete idiosyncratic potential. In this review, we describe the enzymes and proteins that contain polymorphisms believed to contribute to IDILI, including ones that affect phase I and phase II metabolism, antioxidant enzymes, drug transporters, inflammation, and human leukocyte antigen (HLA). We then describe the various assays that have been developed to detect individual reactions focusing on each of the mechanisms described in the background. Finally, we examine current trends in developing comprehensive models for examining these mechanisms. There is an urgent need to develop a panel of multiparametric assays for diagnosing individual toxicity potential.

Spectroscopic and Kinetic Evidence for the Crucial Role of Compound 0 in the P450cam -Catalyzed Hydroxylation of Camphor by Hydrogen Peroxide

The hydroperoxo iron(III) intermediate P450cam Fe(III) -OOH, being the true Compound 0 (Cpd 0) involved in the natural catalytic cycle of P450cam , could be transiently observed in the peroxo-shunt oxidation of the substrate-free enzyme by hydrogen peroxide under mild basic conditions and low temperature. The prolonged lifetime of Cpd 0 enabled us to kinetically examine the formation and reactivity of P450cam Fe(III) -OOH species as a function of varying reaction conditions, such as pH, and concentration of H2 O2 , camphor, and potassium ions. The mechanism of hydrogen peroxide binding to the substrate-free form of P450cam differs completely from that observed for other heme proteins possessing the distal histidine as a general acid-base catalyst and is mainly governed by the ability of H2 O2 to undergo deprotonation at the hydroxo ligand coordinated to the iron(III) center under conditions of pH≥p${K{{{\rm P450}\hfill \atop {\rm a}\hfill}}}$. Notably, no spectroscopic evidence for the formation of either Cpd I or Cpd II as products of heterolytic or homolytic OO bond cleavage, respectively, in Cpd 0 could be observed under the selected reaction conditions. The kinetic data obtained from the reactivity studies involving (1R)-camphor, provide, for the first time, experimental evidence for the catalytic activity of the P450Fe(III) -OOH intermediate in the oxidation of the natural substrate of P450cam .

Characterizing the Intermediates Compound I and II in the Cytochrome P450 Catalytic Cycle with Nonlinear X-ray Spectroscopy: A Simulation Study

Cytochrome P450 enzymes are an important family of biocatalysts that oxidize chemically inert CH bonds. There are many unresolved questions regarding the catalytic reaction intermediates, in particular P450 Compound I (Cpd-I) and II (Cpd-II). By using simple molecular models, we simulate various X-ray spectroscopy signals, including X-ray absorption near-edge structure (XANES), resonant inelastic X-ray scattering (RIXS), and stimulated X-ray Raman spectroscopy (SXRS) of the low- and high-spin states of Cpd-I and II. Characteristic peak patterns are presented and connected to the corresponding electronic structures. These X-ray spectroscopy techniques are complementary to more conventional infrared and optical spectroscopy and they help to elucidate the evolving electronic structures of transient species along the reaction path.

Strong Inhibition of O-Atom Transfer Reactivity for Mn(IV)(O)(π-Radical-Cation)(Lewis Acid) versus Mn(V)(O) Porphyrinoid Complexes

The oxygen atom transfer (OAT) reactivity of two valence tautomers of a Mn(V)(O) porphyrinoid complex was compared. The OAT kinetics of Mn(V)(O)(TBP8Cz) (TBP8Cz = octakis(p-tert-butylphenyl)corrolazinato(3-)) reacting with a series of triarylphosphine (PAr3) substrates were monitored by stopped-flow UV-vis spectroscopy, and revealed second-order rate constants ranging from 16(1) to 1.43(6) × 10(4) M(-1) s(-1). Characterization of the OAT transition state analogues Mn(III)(OPPh3)(TBP8Cz) and Mn(III)(OP(o-tolyl)3)(TBP8Cz) was carried out by single-crystal X-ray diffraction (XRD). A valence tautomer of the closed-shell Mn(V)(O)(TBP8Cz) can be stabilized by the addition of Lewis and Brønsted acids, resulting in the open-shell Mn(IV)(O)(TBP8Cz(•+)):LA (LA = Zn(II), B(C6F5)3, H(+)) complexes. These Mn(IV)(O)(π-radical-cation) derivatives exhibit dramatically inhibited rates of OAT with the PAr3 substrates (k = 8.5(2) × 10(-3) - 8.7 M(-1) s(-1)), contrasting the previously observed rate increase of H-atom transfer (HAT) for Mn(IV)(O)(TBP8Cz(•+)):LA with phenols. A Hammett analysis showed that the OAT reactivity for Mn(IV)(O)(TBP8Cz(•+)):LA is influenced by the Lewis acid strength. Spectral redox titration of Mn(IV)(O)(TBP8Cz(•+)):Zn(II) gives Ered = 0.69 V vs SCE, which is nearly +700 mV above its valence tautomer Mn(V)(O)(TBP8Cz) (Ered = -0.05 V). These data suggest that the two-electron electrophilicity of the Mn(O) valence tautomers dominate OAT reactivity and do not follow the trend in one-electron redox potentials, which appear to dominate HAT reactivity. This study provides new fundamental insights regarding the relative OAT and HAT reactivity of valence tautomers such as M(V)(O)(porph) versus M(IV)(O)(porph(•+)) (M = Mn or Fe) found in heme enzymes.

Ferryl protonation in oxoiron(IV) porphyrins and its role in oxygen transfer

Ferryl porphyrins, P-Fe(IV)═O, are central reactive intermediates in the catalytic cycles of numerous heme proteins and a variety of model systems. There has been considerable interest in elucidating factors, such as terminal oxo basicity, that may control ferryl reactivity. Here, the sulfonated, water-soluble ferryl porphyrin complexes tetramesitylporphyrin, oxoFe(IV)TMPS (FeTMPS-II), its 2,6-dichlorophenyl analogue, oxoFe(IV)TDClPS (FeTDClPS-II), and two other analogues are shown to be protonated under turnover conditions to produce the corresponding bis-aqua-iron(III) porphyrin cation radicals. The results reveal a novel internal electromeric equilibrium, P-Fe(IV)═O ⇆ P(+)-Fe(III)(OH2)2. Reversible pKa values in the range of 4-6.3 have been measured for this process by pH-jump, UV-vis spectroscopy. Ferryl protonation has important ramifications for C-H bond cleavage reactions mediated by oxoiron(IV) porphyrin cation radicals in protic media. Both solvent O-H and substrate C-H deuterium kinetic isotope effects are observed for these reactions, indicating that hydrocarbon oxidation by these oxoiron(IV) porphyrin cation radicals occurs via a solvent proton-coupled hydrogen atom transfer from the substrate that has not been previously described. The effective FeO-H bond dissociation energies for FeTMPS-II and FeTDClPS-II were estimated from similar kinetic reactivities of the corresponding oxoFe(IV)TMPS(+) and oxoFe(IV)TDClPS(+) species to be ∼92-94 kcal/mol. Similar values were calculated from the two-proton P(+)-Fe(III)(OH2)2 pKa(obs) and the porphyrin oxidation potentials, despite a 230 mV range for the iron porphyrins examined. Thus, the iron porphyrin with the lower ring oxidation potential has a compensating higher basicity of the ferryl oxygen. The solvent-derived proton adds significantly to the driving force for C-H bond scission.

Monooxygenase, peroxidase and peroxygenase properties and reaction mechanisms of cytochrome P450 enzymes

This review examines the monooxygenase, peroxidase and peroxygenase properties and reaction mechanisms of cytochrome P450 (CYP) enzymes in bacterial, archaeal and mammalian systems. CYP enzymes catalyze monooxygenation reactions by inserting one oxygen atom from O2 into an enormous number and variety of substrates. The catalytic versatility of CYP stems from its ability to functionalize unactivated carbon-hydrogen (C-H) bonds of substrates through monooxygenation. The oxidative prowess of CYP in catalyzing monooxygenation reactions is attributed primarily to a porphyrin π radical ferryl intermediate known as Compound I (CpdI) (Por•+FeIV=O), or its ferryl radical resonance form (FeIV-O•). CYP-mediated hydroxylations occur via a consensus H atom abstraction/oxygen rebound mechanism involving an initial abstraction by CpdI of a H atom from the substrate, generating a highly-reactive protonated Compound II (CpdII) intermediate (FeIV-OH) and a carbon-centered alkyl radical that rebounds onto the ferryl hydroxyl moiety to yield the hydroxylated substrate. CYP enzymes utilize hydroperoxides, peracids, perborate, percarbonate, periodate, chlorite, iodosobenzene and N-oxides as surrogate oxygen atom donors to oxygenate substrates via the shunt pathway in the absence of NAD(P)H/O2 and reduction-oxidation (redox) auxiliary proteins. It has been difficult to isolate the historically elusive CpdI intermediate in the native NAD(P)H/O2-supported monooxygenase pathway and to determine its precise electronic structure and kinetic and physicochemical properties because of its high reactivity, unstable nature (t½~2 ms) and short life cycle, prompting suggestions for participation in monooxygenation reactions of alternative CYP iron-oxygen intermediates such as the ferric-peroxo anion species (FeIII-OO-), ferric-hydroperoxo species (FeIII-OOH) and FeIII-(H2O2) complex.

Mechanistic insight into peroxo-shunt formation of biomimetic models for compound II, their reactivity toward organic substrates, and the influence of N-methylimidazole axial ligation

High-valent iron-oxo species have been invoked as reactive intermediates in catalytic cycles of heme and nonheme enzymes. The studies presented herein are devoted to the formation of compound II model complexes, with the application of a water soluble (TMPS)Fe(III)(OH) porphyrin ([meso-tetrakis(2,4,6-trimethyl-3-sulfonatophenyl)porphinato]iron(III) hydroxide) and hydrogen peroxide as oxidant, and their reactivity toward selected organic substrates. The kinetics of the reaction of H2O2 with (TMPS)Fe(III)(OH) was studied as a function of temperature and pressure. The negative values of the activation entropy and activation volume for the formation of (TMPS)Fe(IV)=O(OH) point to the overall associative nature of the process. A pH-dependence study on the formation of (TMPS)Fe(IV)=O(OH) revealed a very high reactivity of OOH(-) toward (TMPS)Fe(III)(OH) in comparison to H2O2. The influence of N-methylimidazole (N-MeIm) ligation on both the formation of iron(IV)-oxo species and their oxidising properties in the reactions with 4-methoxybenzyl alcohol or 4-methoxybenzaldehyde, was investigated in detail. Combined experimental and theoretical studies revealed that among the studied complexes, (TMPS)Fe(III)(H2O)(N-MeIm) is highly reactive toward H2O2 to form the iron(IV)-oxo species, (TMPS)Fe(IV)=O(N-MeIm). The latter species can also be formed in the reaction of (TMPS)Fe(III)(N-MeIm)2 with H2O2 or in the direct reaction of (TMPS)Fe(IV)=O(OH) with N-MeIm. Interestingly, the kinetic studies involving substrate oxidation by (TMPS)Fe(IV)=O(OH) and (TMPS)Fe(IV)=O(N-MeIm) do not display a pronounced effect of the N-MeIm axial ligand on the reactivity of the compound II mimic in comparison to the OH(-) substituted analogue. Similarly, DFT computations revealed that the presence of an axial ligand (OH(-) or N-MeIm) in the trans position to the oxo group in the iron(IV)-oxo species does not significantly affect the activation barriers calculated for C-H dehydrogenation of the selected organic substrates.

Enzyme kinetics of oxidative metabolism: cytochromes P450

The cytochrome P450 enzymes (CYPs) are the most important enzymes in the oxidative metabolism of hydrophobic drugs and other foreign compounds (xenobiotics). The versatility of these enzymes results in some unusual kinetic properties, stemming from the simultaneous interaction of multiple substrates with the CYP active site. Often, the CYPs display kinetics that deviate from standard hyperbolic saturation or inhibition kinetics. Non-Michaelis-Menten or "atypical" saturation kinetics include sigmoidal, biphasic, and substrate inhibition kinetics (see Chapter 3 ). Interactions between substrates include competitive inhibition, noncompetitive inhibition, mixed inhibition, partial inhibition, activation, and activation followed by inhibition (see Chapter 4 ). Models and equations that can result in these kinetic profiles will be presented and discussed.

Kinetic solvent isotope effect in human P450 CYP17A1-mediated androgen formation: evidence for a reactive peroxoanion intermediate

Human steroid hormone biosynthesis is the result of a complex series of chemical transformations operating on cholesterol, with key steps mediated by members of the cytochrome P450 superfamily. In the formation of the male hormone dehydroepiandrosterone, pregnenolone is first hydroxylated by P450 CYP17A1 at the 17-carbon, followed a second round of catalysis by the same enzyme that cleaves the C17-C20 bond, releasing acetic acid and the 17-keto product. In order to explore the mechanism of this C-C "lyase" activity, we investigated the kinetic isotope effect on the steady-state turnover of Nanodisc-incorporated CYP17A1. Our experiments revealed the expected small positive (~1.3) isotope effect for the hydroxylase chemistry. However, a surprising result was the large inverse isotope effect (~0.39) observed for the C-C bond cleavage activity. These results strongly suggest that the P450 reactive intermediate involved in this latter step is an iron-bound ferric peroxoanion.

Reactive intermediates in cytochrome p450 catalysis

Recently, we reported the spectroscopic and kinetic characterizations of cytochrome P450 compound I in CYP119A1, effectively closing the catalytic cycle of cytochrome P450-mediated hydroxylations. In this minireview, we focus on the developments that made this breakthrough possible. We examine the importance of enzyme purification in the quest for reactive intermediates and report the preparation of compound I in a second P450 (P450ST). In an effort to bring clarity to the field, we also examine the validity of controversial reports claiming the production of P450 compound I through the use of peroxynitrite and laser flash photolysis.

EPR, resonance Raman, and DFT calculations on thiolate- and imidazole-bound iron(III) porphyrin complexes: role of the axial ligand in tuning the electronic structure

Iron(III) porphyrin complexes bearing covalently attached imidazole and thiolate axial ligands are investigated using resonance Raman, electron paramagnetic resonance, and cyclic voltammetry. The thiolate ligand stabilizes a low-spin ground state in solvent-bound six-coordinate species, weakens the Fe-N(pyr) bonds, and shifts the Fe(III/II) potential more negative by ~500 mV relative to an imidazole-bound species. Density functional theory calculations reproduce the experimental observation and indicate that the covalent charge donation from thiolate to iron reduces the Z(eff) on the iron. This increases the Fe(3d) orbital energies, which changes the bonding interaction present in these complexes significantly. In particular, the increase of the Fe(3d) energies activates an iron-to-porphyrin π*-back-bonding interaction not present in the imidazole-bound complex.

Detection and kinetic characterization of a highly reactive heme-thiolate peroxygenase compound I

The extracellular heme-thiolate peroxygenase from Agrocybe aegerita (AaeAPO) has been shown to hydroxylate alkanes and numerous other substrates using hydrogen peroxide as the terminal oxidant. We describe the kinetics of formation and decomposition of AaeAPO compound I upon its reaction with mCPBA. The UV-vis spectral features of AaeAPO-I (361, 694 nm) are similar to those of chloroperoxidase-I and the recently described cytochrome P450-I. The second-order rate constant for AaeAPO-I formation was 1.0 (±0.4) × 10(7) M(-1) s(-1) at pH 5.0, 4 °C. The relatively slow decomposition rate, 1.4 (±0.03) s(-1), allowed the measurement of its reactivity toward a panel of substrates. The observed rate constants, k2', spanned 5 orders of magnitude and correlated linearly with bond dissociation enthalpies (BDEs) of strong C-H bond substrates with a log k2' vs BDE slope of ∼0.4. However, the hydroxylation rate was insensitive to a C-H BDE below 90 kcal/mol, similar to the behavior of the tert-butoxyl radical. The shape and slope of the Brønsted-Evans-Polanyi plot indicate a symmetrical transition state for the stronger C-H bonds and suggest entropy control of the rate in an early transition state for weaker C-H bonds. The AaeAPO-II Fe(IV)O-H BDE was estimated to be ∼103 kcal/mol. All results support the formation of a highly reactive AaeAPO oxoiron(IV) porphyrin radical cation intermediate that is the active oxygen species in these hydroxylation reactions.