Sodium periodate, sodium chloride, organic hydroperoxides, and H2O2 as hydroxylating agents in steroid hydroxylation reactions catalyzed by partially purified cytochrome P-450

Emerging Strategies for Modifying Cytochrome P450 Monooxygenases into Peroxizymes

ConspectusCytochrome P450 monooxygenase is a versatile oxidizing enzyme with great potential in synthetic chemistry and biology. However, the dependence of its catalytic function on the nicotinamide cofactor NAD(P)H and redox partner proteins limits the practical catalytic application of P450 in vitro. An alternative to expensive cofactors is low-cost H2O2, which can be used directly to exploit the catalytic potential of P450s. However, the peroxide shunt pathway is generally inefficient at driving P450 catalysis compared to normal NAD(P)H-dependent activity. Over the last few decades, the scientific community has made continuous efforts to use directed evolution or site-directed mutagenesis to modify P450 monooxygenases into their peroxizyme modes─peroxygenase and peroxidase. Despite significant progress, obtaining efficient P450 peroxizymes remains a huge challenge. Here, we summarize our efforts to modulate peroxizyme activity in P450 monooxygenases and exploit their catalytic applications in challenging selective C-H oxidation, oxygenation, and oxyfunctionalization over the past seven years. We first developed a dual-functional small molecule (DFSM) strategy for transforming P450BM3 monooxygenase into peroxygenase. In this strategy, the typical DFSM, such as N-(ω-imidazolyl)-hexanoyl-l-phenylalanine (Im-C6-Phe), binds to the P450BM3 protein with an anchoring group at one end and plays a general acid-base catalytic role in the activation of H2O2 with an imidazolyl group at the other end. Compared with the O-O homolysis mechanism in the absence of DFSM, the addition of DFSM efficiently enables the heterolytic O-O cleavage of the adduct Fe-O-OH, thus being favored for the formation of active species compound I, which has been demonstrated by combining crystallographic and theoretical calculations. Furthermore, protein engineering showed the unique catalytic performance of DFSM-facilitated P450 peroxygenase for the highly difficult selective oxidation of C-H bonds. This catalytic performance was demonstrated during the chemoselective hydroxylation of gaseous alkanes, regioselective O-demethylation of aryl ethers, highly (R)-enantioselective epoxidation of styrene, and regio- and enantiomerically diverse hydroxylation of alkylbenzenes. Second, we demonstrated that DFSM-facilitated P450BM3 peroxygenase could be effectively switched to an efficient peroxidase mode through mechanism-guided protein engineering of redox-sensitive residues. Utilizing the peroxidase function of P450 enabled the direct nitration of unsaturated hydrocarbons including phenols, aromatic amines, and styrene derivatives, which was not only the P450-catalyzed direct nitration of phenols and aromatic amines for the first time but also the first example of the direct biological nitration of olefins. Finally, we report an H2O2 tunnel engineering strategy to enable peroxygenase activity in several different P450 monooxygenases for the first time, providing a general approach for accessing engineered P450 peroxygenases. In this Account, we highlight the emerging strategies we have developed for producing practical P450 peroxizyme biocatalysts. Although the DFSM strategy is primarily applied to P450BM3 to date, both strategies of redox-sensitive residue engineering and H2O2 tunnel engineering show great potential to extend to other P450s. These strategies have expanded the scope of applications of P450 chemistry and catalysis. Additionally, they provide a unique solution to the challenging selective oxidation of inert C-H bonds in synthetic chemistry.

A Unique P450 Peroxygenase System Facilitated by a Dual-Functional Small Molecule: Concept, Application, and Perspective

Cytochrome P450 monooxygenases (P450s) are promising versatile oxidative biocatalysts. However, the practical use of P450s in vitro is limited by their dependence on the co-enzyme NAD(P)H and the complex electron transport system. Using H₂O₂ simplifies the catalytic cycle of P450s; however, most P450s are inactive in the presence of H₂O₂. By mimicking the molecular structure and catalytic mechanism of natural peroxygenases and peroxidases, an artificial P450 peroxygenase system has been designed with the assistance of a dual-functional small molecule (DFSM). DFSMs, such as N-(ω-imidazolyl fatty acyl)-l-amino acids, use an acyl amino acid as an anchoring group to bind the enzyme, and the imidazolyl group at the other end functions as a general acid-base catalyst in the activation of H₂O₂. In combination with protein engineering, the DFSM-facilitated P450 peroxygenase system has been used in various oxidation reactions of non-native substrates, such as alkene epoxidation, thioanisole sulfoxidation, and alkanes and aromatic hydroxylation, which showed unique activities and selectivity. Moreover, the DFSM-facilitated P450 peroxygenase system can switch to the peroxidase mode by mechanism-guided protein engineering. In this short review, the design, mechanism, evolution, application, and perspective of these novel non-natural P450 peroxygenases for the oxidation of non-native substrates are discussed.

Diverse reactions catalyzed by cytochrome P450 and biosynthesis of steroid hormone

Steroid hormones modulate numerous physiological processes in various higher organisms. Research on the physiology, biosynthesis, and metabolic degradation of steroid hormones is crucial for developing drugs, agrochemicals, and anthelmintics. Most steroid hormone biosynthetic pathways, excluding those in insects, have been elucidated, and the roles of several cytochrome P450s (CYPs, P450s), heme (iron protoporphyrin IX)-containing monooxygenases, have been identified. Specifically, P450s of the animal steroid hormone biosynthetic pathways and their three dimensional structures and reaction mechanisms have been extensively studied; however, the mechanisms of several uncommon P450 reactions involved in animal steroid hormone biosynthesis and structures and reaction mechanisms of various P450s involved in plant and insect steroid hormone biosynthesis remain unclear. Recently, we determined the crystal structure of P450 responsible for the first and rate-determining step in brassinosteroids biosynthesis and clarified the regio- and stereo-selectivity in the hydroxylation reaction mechanism. In this review, we have outlined the general catalytic cycle, reaction mechanism, and structure of P450s. Additionally, we have described the recent advances in research on the reaction mechanisms of steroid hormone biosynthesis-related P450s, some of which catalyze unusual P450 reactions including C–C bond cleavage reactions by utilizing either a heme–peroxo anion species or compound I as an active oxidizing species. This review article is an extended version of the Japanese article, Structure and mechanism of cytochrome P450s involved in steroid hormone biosynthesis, published in SEIBUTSU BUTSURI Vol. 61, p. 189–191 (2021).

Oxygen Surrogate Systems for Supporting Human Drug-Metabolizing Cytochrome P450 Enzymes

Oxygen surrogates (OSs) have been used to support cytochrome P450 (P450) enzymes for diverse purposes in drug metabolism research, including reaction phenotyping, mechanistic and inhibition studies, studies of redox partner interactions, and to avoid the need for NADPH or a redox partner. They also have been used in engineering P450s for more cost-effective, NADPH-independent biocatalysis. However, despite their broad application, little is known of the preference of individual P450s for different OSs or the substrate dependence of OS-supported activity. Furthermore, the biocatalytic potential of OSs other than cumene hydroperoxide (CuOOH) and hydrogen peroxide (H₂O₂) is yet to be explored. Here, we investigated the ability of the major human drug-metabolizing P450s, namely CYP3A4, CYP2C9, CYP2C19, CYP2D6, and CYP1A2, to use the following OSs: H₂O₂, tert-butyl hydroperoxide (tert-BuOOH), CuOOH, (diacetoxyiodo)benzene, and bis(trifluoroacetoxy)iodobenzene. Overall, CuOOH and tert-BuOOH were found to be the most effective at supporting these P450s. However, the ability of P450s to be supported by OSs effectively was also found to be highly dependent on the substrate used. This suggests that the choice of OS should be tailored to both the P450 and the substrate under investigation, underscoring the need to employ screening methods that reflect the activity toward the substrate of interest to the end application. SIGNIFICANCE STATEMENT: Cytochrome P450 (P450) enzymes can be supported by different oxygen surrogates (OSs), avoiding the need for a redox partner and costly NADPH. However, few data exist comparing relative activity with different OSs and substrates. This study shows that the choice of OS used to support the major drug-metabolizing P450s influences their relative activity and regioselectivity in a substrate-specific fashion and provides a model for the more efficient use of P450s for metabolite biosynthesis.

The relationships between cytochromes P450 and H2O2: Production, reaction, and inhibition

In this review we address the relationship between cytochromes P450 (P450) and H2O2. This association can affect biology in three distinct ways. First, P450s produce H2O2 as a byproduct either during catalysis or when no substrate is present. This reaction, known as uncoupling, releases reactive oxygen species that may have implications in disease. Second, H2O2 is used as an oxygen-donating co-substrate in peroxygenase and peroxidase reactions catalyzed by P450s. This activity has proven to be important mainly in reactions involving prokaryotic P450s, and investigators have harnessed this reaction with the aim of adaptation for industrial use. Third, H2O2-dependent inhibition of human P450s has been studied in our laboratory, demonstrating heme destruction and also the inactivating oxidation of the heme-thiolate ligand to a sulfenic acid (-SOH). This reversible oxidative modification of P450s may have implications in the prevention of uncoupling and may give new insights into the oxidative regulation of these enzymes. Research has elucidated many of the chemical mechanisms involved in the relationship between P450 and H2O2, but the application to biology is difficult to evaluate. Further studies are needed reveal both the harmful and protective natures of reactive oxygen species in an organismal context.

A new look at the role of thiolate ligation in cytochrome P450

Protonated ferryl (or iron(IV)hydroxide) intermediates have been characterized in several thiolate-ligated heme proteins that are known to catalyze C-H bond activation. The basicity of the ferryl intermediates in these species has been proposed to play a critical role in facilitating this chemistry, allowing hydrogen abstraction at reduction potentials below those that would otherwise lead to oxidative degradation of the enzyme. In this contribution, we discuss the events that led to the assignment and characterization of the unusual iron(IV)hydroxide species, highlighting experiments that provided a quantitative measure of the ferryl basicity, the iron(IV)hydroxide pKa. We then turn to the importance of the iron(IV)hydroxide state, presenting a new way of looking at the role of thiolate ligation in these systems.

Novel 96-well quantitative bioelectrocatalytic analysis platform reveals highly efficient direct electrode regeneration of cytochrome P450 BM3 on indium tin oxide

Enzymes are the most effective catalysts for a broad range of difficult chemical reactions e.g. hydroxylation of non-activated C-H Bonds and stereoselective synthesis. Nevertheless, a lot of enzymes are not accessible for the biotechnological applications or industrial use. One reason is the prerequisite of expensive cofactors. In this context, we developed a bioelectrocatalytic analysis platform for the electrochemical and photonic quantification of the direct electron transfer from the electrode to redox enzymes and therefore, bypass the need of soluble cofactors that had to be continuously exchanged or regenerated. As reference enzyme, we chose cytochrome P450 BM3 that is restricted by NADPH dependence. We optimized the substrate spectrum for aromatic compounds by introduction of the triple mutation A74G/F87V/L188Q and established a sensitive fluorimetric product formation assay to monitor the enzymatic conversion of 7-ethoxycoumarine to 7-hydroxycoumarine. Gold and indium tin oxide electrodes were characterized with respect to surface morphology, charge-transfer resistance and P450 BM3 immobilization as well as activity. Using gold electrodes, no significant product formation by electrode mediated direct electron transfer could be detected. In contrast, P450 BM3 adsorbed on unmodified indium tin oxide electrodes revealed 36% activity by electrode mediated direct electron transfer in comparison to enzyme regeneration by NADPH. Since the reaction volumes are in the microliter range and upscaling of the measurement system is easily possible, our analysis platform is a useful tool for bioelectrocatalytic enzyme characterization and library screening based optimization for applications in the field of enzyme catalyzed chemical synthesis but also enzyme based fuel cells.

The Oxygen Dilemma: A Severe Challenge for the Application of Monooxygenases?

Monooxygenases are promising catalysts because they in principle enable the organic chemist to perform highly selective oxyfunctionalisation reactions that are otherwise difficult to achieve. For this, monooxygenases require reducing equivalents, to allow reductive activation of molecular oxygen at the enzymes' active sites. However, these reducing equivalents are often delivered to O2 either directly or via a reduced intermediate (uncoupling), yielding hazardous reactive oxygen species and wasting valuable reducing equivalents. The oxygen dilemma arises from monooxygenases' dependency on O2 and the undesired uncoupling reaction. With this contribution we hope to generate a general awareness of the oxygen dilemma and to discuss its nature and some promising solutions.

Involvement of Cytochrome P450 in Reactive Oxygen Species Formation and Cancer

This review examines the involvement of cytochrome P450 (CYP) enzymes in the formation of reactive oxygen species in biological systems and discusses the possible involvement of reactive oxygen species and CYP enzymes in cancer. Reactive oxygen species are formed in biological systems as byproducts of the reduction of molecular oxygen and include the superoxide radical anion (∙O2-), hydrogen peroxide (H2O2), hydroxyl radical (∙OH), hydroperoxyl radical (HOO∙), singlet oxygen ((1)O2), and peroxyl radical (ROO∙). Two endogenous sources of reactive oxygen species are the mammalian CYP-dependent microsomal electron transport system and the mitochondrial electron transport chain. CYP enzymes catalyze the oxygenation of an organic substrate and the simultaneous reduction of molecular oxygen. If the transfer of oxygen to a substrate is not tightly controlled, uncoupling occurs and leads to the formation of reactive oxygen species. Reactive oxygen species are capable of causing oxidative damage to cellular membranes and macromolecules that can lead to the development of human diseases such as cancer. In normal cells, intracellular levels of reactive oxygen species are maintained in balance with intracellular biochemical antioxidants to prevent cellular damage. Oxidative stress occurs when this critical balance is disrupted. Topics covered in this review include the role of reactive oxygen species in intracellular cell signaling and the relationship between CYP enzymes and cancer. Outlines of CYP expression in neoplastic tissues, CYP enzyme polymorphism and cancer risk, CYP enzymes in cancer therapy and the metabolic activation of chemical procarcinogens by CYP enzymes are also provided.

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.

High warfarin sensitivity in carriers of CYP2C9*35 is determined by the impaired interaction with P450 oxidoreductase

Cytochrome P450 2C9 (CYP2C9) metabolizes many clinically important drugs including warfarin and diclofenac. We have recently reported a new allelic variant, CYP2C9*35, found in a warfarin hypersensitive patient with Arg125Leu and Arg144Cys mutations. Here, we have investigated the molecular basis for the functional consequences of these polymorphic changes. CYP2C9.1 and CYP2C9-Arg144Cys expressed in human embryonic kidney 293 cells effectively metabolized both S-warfarin and diclofenac in NADPH-dependent reactions, whereas CYP2C9-Arg125Leu or CYP2C9.35 were catalytically silent. However, when NADPH was replaced by a direct electron donor to CYPs, cumene hydroperoxide, hereby bypassing the CYP oxidoreductase (POR), all variant enzymes were active, indicating unproductive interactions between CYP2C9.35 and POR. In silico analysis revealed a decrease of the electrostatic potential of CYP2C9-Arg125Leu-POR interacting surface and the loss of stabilizing salt bridges between these proteins. In conclusion, our data strongly suggest that the Arg125Leu mutation in CYP2C9.35 prevents CYP2C9-POR interactions resulting in the absence of NADPH-dependent CYP2C9-catalyzed activity in vivo, thus influencing the warfarin sensitivity in the carriers of this allele.

Constructing manmade enzymes for oxygen activation

Natural oxygenases catalyse the insertion of oxygen into an impressive array of organic substrates with exquisite efficiency, specificity and power unparalleled by current biomimetic catalysts. However, their true potential to provide tailor-made oxygenation catalysts remains largely untapped, perhaps a consequence of the evolutionary complexity imprinted into their three-dimensional structures through millennia of exposure to parallel selective pressures. In this perspective we describe how we may take inspiration from natural enzymes to design manmade oxygenase enzymes free from such complexity. We explore the differing chemistries accessed by natural oxygenases and outline a stepwise methodology whereby functional elements key to oxygenase catalysis are assembled within artificially designed protein scaffolds.

Indole peroxygenase activity of indoleamine 2,3-dioxygenase

The heme enzyme indoleamine 2,3-dioxygenase (IDO) was found to catalyze the oxidation of indole by H(2)O(2), with generation of 2- and 3-oxoindole as the major products. This reaction occurred in the absence of O(2) and reducing agents and was not inhibited by superoxide dismutase or hydroxyl radical scavengers, although it was strongly inhibited by L-Trp. The stoichiometry of the reaction indicated a one-to-one correspondence for the consumption of indole and H(2)O(2). The (18)O-labeling experiments indicated that the oxygen incorporated into the monooxygenated products was derived almost exclusively from H(2)(18)O(2), suggesting that electron transfer was coupled to the transfer of oxygen from a ferryl intermediate of IDO. These results demonstrate that IDO oxidizes indole by means of a previously unrecognized peroxygenase activity. We conclude that IDO inserts oxygen into indole in a reaction that is mechanistically analogous to the "peroxide shunt" pathway of cytochrome P450.

Recollection of the early years of the research on cytochrome P450

Since the publication of the first paper on "cytochrome P450" in 1962, the biochemical research on this novel hemoprotein expanded rapidly in the 1960s and the 1970s as its principal roles in various important metabolic processes including steroid hormone biosynthesis in the steroidogenic organs and drug metabolism in the liver were elucidated. Establishment of the purification procedures of microsomal and mitochondrial P450s in the middle of the 1970s together with the introduction of molecular biological techniques accelerated the remarkable expansion of the research on P450 in the following years. This review paper summarizes the important developments in the research on P450 in the early years, for about two decades from the beginning, together with my personal recollections.

Structural diversity of cytochrome P450 enzyme system

Cytochrome P450 enzyme system consists of P450 and its NAD(P)H-linked reductase or reducing system, and catalyses monooxygenation reactions. The most prevalent type in eukaryotic organisms is 'microsomes type', which consists of membrane-bound P450 and NADPH-P450 reductase. The second type is 'mitochondria type', in which P450 is bound to the inner membrane while the reducing system consisting of an NADPH-linked flavoprotein and a ferredoxin-type iron-sulphur protein is soluble in the matrix space. The third type is 'bacteria type', in which both P450 and the reducing system are soluble in the cytoplasm. In addition to these three types, several forms of P450-reductase fusion proteins have been found in prokaryotic organisms. On the other hand, some P450s catalyse the re-arrangement of the oxygen atoms in the substrate molecules that does not require the supply of reducing equivalents for the reaction. A peculiar P450, P450nor, receives electrons directly from NADH for the reduction of nitric oxide.

Cytochrome P450 125 (CYP125) catalyses C26-hydroxylation to initiate sterol side-chain degradation in Rhodococcus jostii RHA1

The cyp125 gene of Rhodococcus jostii RHA1 was previously found to be highly upregulated during growth on cholesterol and the orthologue in Mycobacterium tuberculosis (rv3545c) has been implicated in pathogenesis. Here we show that cyp125 is essential for R. jostii RHA1 to grow on 3-hydroxysterols such as cholesterol, but not on 3-oxo sterol derivatives, and that CYP125 performs an obligate first step in cholesterol degradation. The involvement of cyp125 in sterol side-chain degradation was confirmed by disrupting the homologous gene in Rhodococcus rhodochrous RG32, a strain that selectively degrades the cholesterol side-chain. The RG32 Omega cyp125 mutant failed to transform the side-chain of cholesterol, but degraded that of 5-cholestene-26-oic acid-3beta-ol, a cholesterol catabolite. Spectral analysis revealed that while purified ferric CYP125(RHA1) was < 10% in the low-spin state, cholesterol (K(D)(app) = 0.20 +/- 0.08 microM), 5 alpha-cholestanol (K(D)(app) = 0.15 +/- 0.03 microM) and 4-cholestene-3-one (K(D)(app) = 0.20 +/- 0.03 microM) further reduced the low spin character of the haem iron consistent with substrate binding. Our data indicate that CYP125 is involved in steroid C26-carboxylic acid formation, catalysing the oxidation of C26 either to the corresponding carboxylic acid or to an intermediate state.

Demonstration of a peroxide shunt in the tetrahydropterin-dependent aromatic amino acid monooxygenases

The nonheme iron enzyme phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase catalyze the hydroxylation of their aromatic amino acid substrates using a tetrahydropterin as the source of electrons. The hydroxylating intermediate is proposed to be an Fe(IV)O species. We report here that all three enzymes will catalyze hydroxylation reactions using H(2)O(2) in place of tetrahydropterin and oxygen, forming tyrosine and 3-hydroxyphenylalanine from phenylalanine, 4-HOCH(2)-phenylalanine from 4-CH(3)-phenylalanine, and hydroxycyclohexylalanine from 3-cyclohexylalanine. No peroxide-dependent reaction is seen with active site mutants of TyrH and PheH in which the stability or reactivity of the iron center is compromised. These results provide further support for an Fe(IV)O hydroxylating intermediate.

Modulation of redox potential and alteration in reactivity via the peroxide shunt pathway by mutation of cytochrome P450 around the proximal heme ligand

In the thermophilic cytochrome P450 from the thermoacidophilic crenarchaeon Sulfolobus tokodaii strain 7 (P450st), a phenylalanine residue at position 310 and an alanine residue at position 320 are located close to the heme thiolate ligand, Cys317. Single site-directed mutants F310A and A320Q and double mutant F310A/A320Q have been constructed. All mutant enzymes as well as wild-type (WT) P450st were expressed at high levels. The substitution of F310 with Ala and of A320 with Gln induced shifts in redox potential and blue shifts in Soret absorption of ferrous-CO forms, while spectral characterization showed that in the resting state, the mutants almost retained the structural integrity of the active site. The redox potential of the heme varied as follows: -481 mV (WT), -477 mV (A320Q), -453 mV (F310A), and -450 mV (F310A/A320Q). The trend in the Soret band of the ferrous-CO form was as follows: 450 nm (WT) < 449 nm (A320Q) < 446 nm (F310A) < 444 nm (F310A/A320Q). These results established that the reduction potential and electron density on the heme iron are modulated by the Phe310 and Ala320 residues in P450st. The electron density on the heme decreases in the following order: WT > A320Q > F310A > F310A/A320Q. The electron density on the heme iron infers an essential role in P450 activity. The decrease in electron density interferes with the formation of a high-valent oxo-ferryl species called Compound I. However, steady-state turnover rates of styrene epoxidation with H2O2 show the following trend: WT approximately equal to A320Q < F310A approximately equal to F310A/A320Q. The shunt pathway which can provide the two electrons and oxygen required for a P450 reaction instead of NAD(P)H and dioxygen can rule out the first and second heme reduction in the catalytic process. Because the electron density on the heme iron might be deeply involved in the k cat values in this system, the intermediate Compound 0 which is the precursor species of Compound I mainly appears to participate dominantly in epoxidation with H2O2.

Formation of the Active Species of Cytochrome P450 by Using Iodosylbenzene: A Case for Spin-Selective Reactivity

The generation of the active species for the enzyme cytochrome P450 by using the highly versatile oxygen surrogate iodosylbenzene (PhIO) often produces different results compared with the native route, in which the active species is generated through O(2) uptake and reduction by NADPH. One of these differences that is addressed here is the deuterium kinetic isotope effect (KIE) jump observed during N-dealkylation of N,N-dimethylaniline (DMA) by P450, when the reaction conditions change from the native to the PhIO route. The paper presents a theoretical analysis targeted to elucidate the mechanism of the reaction of PhIO with heme, to form the high-valent iron-oxo species Compound I (Cpd I), and define the origins of the KIE jump in the reaction of Cpd I with DMA. It is concluded that the likely origin of the KIE jump is the spin-selective chemistry of the enzyme cytochrome P450 under different preparation procedures. In the native route, the reaction proceeds via the doublet spin state of Cpd I and leads to a low KIE value. PhIO, however, diverts the reaction to the quartet spin state of Cpd I, which leads to the observed high KIE values. The KIE jump is reproduced here experimentally for the dealkylation of N,N-dimethyl-4-(methylthio)aniline, by using intra-molecular KIE measurements that avoid kinetic complexities. The effect of PhIO is compared with N,N-dimethylaniline-N-oxide (DMAO), which acts both as the oxygen donor and the substrate and leads to the same KIE values as the native route.

Mechanistic study of iron(III) [tetrakis(pentafluorophenyl)porphyrin triflate (F(20)TPP)Fe(OTf) catalyzed cyclooctene epoxidation by hydrogen peroxide

We have recently proposed a mechanism for the epoxidation of cyclooctene by H2O2 catalyzed by iron(III) [tetrakis(pentafluorophenyl)]porphyrin chloride, (F20TPP)FeCl, in solvent containing methanol [Stephenson, N. A.; Bell, A.T. Inorg. Chem. 2006, 45, 2758-2766]. In that study, we found that catalysis did not occur unless (F20TPP)FeCl first dissociated, a process facilitated by the solvation of the Cl- anion by methanol and the coordination of methanol to the (F20TPP)Fe+ cation. Methanol as well as other alcohols was also found to facilitate the heterolytic cleavage of the O-O bond of H2O2 coordinated to the (F20TPP)Fe+ cation via a generalized acid mechanism. In the present study, we have shown that catalytic activity of the (F20TPP)Fe+ cation can be achieved in aprotic solvent by displacing the tightly bound chloride anion with a weakly bound triflate anion. By working in an aprotic solvent, acetonitrile, it was possible to determine the rate of heterolytic O-O bond cleavage in coordinated H2O2 unaffected by the interaction of the peroxide with methanol. A mechanism is proposed for this system and is shown to be valid over a range of reaction conditions. The mechanisms for cyclooctene epoxidation and H2O2 decomposition for the aprotic and protic solvent systems are similar with the only difference being the mechanism of proton-transfer prior to heterolytic cleavage of the oxygen-oxygen bond of coordinated hydrogen peroxide. Comparison of the rate parameters indicates that the utilization of hydrogen peroxide for cyclooctene epoxidation is higher in a protic solvent than in an aprotic solvent and results in a smaller extent of porphyrin degradation due to free radical attack. It was also shown that water can coordinate to the iron porphyrin cation in aprotic systems resulting in catalyst deactivation; this effect was not observed when methanol was present, since methanol was found to displace all of the coordinated water.

Non-enzymatic regeneration of nicotinamide and flavin cofactors for monooxygenase catalysis

Biocatalytic oxygenation chemistry is a rapidly evolving field in which monooxygenases are the tools of choice. Monooxygenases catalyze many industrially important synthetic transformations; however, their use in preparative applications is hampered by their intrinsic requirement for reducing equivalents. As a result, non-enzymatic strategies--where the reducing equivalents are introduced directly into the catalytic cycle--are being developed to supersede the well-established enzymatic NAD(P)H regeneration systems currently in use. In this review we summarize and evaluate recent achievements in this area.

Mechanistic studies on the metabolic scission of thiazolidinedione derivatives to acyclic thiols

Thiazolidinedione (TZD) derivatives have been reported to undergo metabolic activation of the TZD ring to produce reactive intermediates. In the case of troglitazone, it was proposed that a P450-mediated S-oxidation leads to TZD ring scission and the formation of a sulfenic acid intermediate, which may be trapped as a GSH conjugate. In the present study, we employed a model compound {denoted MRL-A, (+/-)-5-[(2,4-dioxothiazolidin-5-yl)methyl]-2-methoxy-N-[[(4-trifluoromethoxy)phenyl]methyl]benzamide} to investigate the mechanism of TZD ring scission. When MRL-A was incubated with monkey liver microsomes (or recombinant P450 3A4 and NADPH-P450 reductase) in the presence of NADPH and oxygen, the major products of TZD ring scission were the free thiol metabolite (M2) and its dimer (M3). Furthermore, a GSH conjugate of M2 (M4) also was formed when the incubation mixture was supplemented with GSH. Experiments with isolated M2 suggested that this metabolite was unstable and underwent spontaneous autooxidation to M3. A qualitatively similar metabolite profile was observed when MRL-A was incubated with recombinant P450 3A4 and cumene hydroperoxide. Because an oxygen atom is transferred to MRL-A under these conditions, these data suggested that S-oxidation alone may result in TZD ring scission and formation of M2 via a sulfenic acid intermediate. Also, because the latter incubation mixture did not contain any reducing agents, the formation of M2 may have occurred due to disproportionation of the sulfenic acid. When NADPH was added to the incubation mixture containing P450 3A4 and cumene hydroperoxide, the formation of M3 increased, suggesting that the sulfenic acid was reduced to M2 by NADPH and subsequently underwent dimerization to yield M3 (vide supra). When NADPH was replaced by GSH, the formation of M4 increased, consistent with reduction of the sulfenic acid by GSH. In summary, these results suggest that the TZD ring in MRL-A is activated by an initial P450-mediated S-oxidation step followed by spontaneous scission of the TZD ring to a putative sulfenic acid intermediate; the latter species then undergoes reduction to the free thiol by GSH, NADPH, and/or disproportionation. Finally, the thiol may dimerize to the corresponding disulfide or, in the presence of S-adenosylmethionine, form the stable S-methyl derivative.

High-throughput screening for stability and inhibitory activity of compounds toward cytochrome P450-mediated metabolism

With the advent of combinatorial chemistry and high-throughput screening technology, thousands of molecules can now be rapidly synthesized and screened for biological activity against large numbers of protein targets, greatly increasing the speed with which lead compounds are identified during the early stages of drug discovery. However, rapid optimization of parameters that determine whether a high-affinity ligand or a potent inhibitor will become a successful drug remains a challenge in improving the efficiency of the drug discovery process. Parameters that define absorption, distribution, metabolism, and excretion properties of drug candidates are important determinants of therapeutic efficacy, and thus should be optimized during early stages of drug discovery. Although the speed with which drugs are screened for properties such as absorption, cytochrome P450 (CYP) inhibition, and metabolic stability has increased over the past several years, the screening rate/capacity is still several orders of magnitude lower than those for high-throughput methods used in lead identification, resulting in a bottleneck in the drug discovery process. This review discusses current methods used in the in vitro screening of drugs for their stability toward CYP-mediated oxidative metabolism. This is a critical screen in the drug discovery process because metabolism by CYP represents an important clearance mechanism for the vast majority of compounds, thus affecting their oral bioavailability and/or duration of action.

Radical Autoxidation and Autogenous O2 Evolution in Manganese−Porphyrin Catalyzed Alkane Oxidations with Chlorite

A manganese porphyrin catalyst employing chlorite (ClO(2)(-)) as a "shunt" oxidant displays remarkable activity in alkane oxidation, oxidizing cyclohexane to cyclohexanol and cyclohexanone with >800 turnover numbers. The ketone is apparently formed without the intermediacy of alcohol and accounts for an unusually large fraction of the product ( approximately 40%). Radical scavenging experiments indicate that the alkane oxidation mechanism involves both carbon-centered and oxygen-centered radicals. The carbon-radical trap CBrCl(3) completely suppresses cyclohexanone formation and reduces cyclohexanol turnovers, while the oxygen-radical trap Ph(2)NH inhibits all oxidation until it is consumed. These observations are indicative of an autoxidation mechanism, a scenario further supported by TEMPO inhibition and (18)O(2) incorporation into products. However, similar cyclohexane oxidation activity occurs when air is excluded. This is explained by mass spectrometric and volumetric measurements showing catalyst-dependent O(2) evolution from the reaction mixture. The catalytic disproportionation of ClO(2)(-) into Cl(-) and O(2) provides sufficient O(2) to support an autoxidation mechanism. A two-path oxidation scheme is proposed to explain all of the experimental observations. The first pathway involves manganese-porphyrin catalyzed decomposition of ClO(2)(-) into both O(2) and an unidentified radical initiator, leading to classical autoxidation chemistry providing equal amounts of cyclohexanol and cyclohexanone. The second pathway is a "rebound" oxygenation involving a high-valent manganese-oxo intermediate, accounting for the excess of alcohol over ketone. This system highlights the importance of mechanistic studies in catalytic oxidations with highly reactive oxidants, and it is unusual in its ability to sustain autoxidation even under apparent exclusion of O(2).

Electron transfer in natural and unnatural flavoporphyrins

The development of chemical models for enzymes and their chemical and physical studies constitutes an important area of research from a scientific as well as an industrial point of view. Covalently linked flavin and porphyrin (flavoporphyrins) have attracted attention due to their applications as chemical models for flavoproteins and related enzymes. In this review, the literature has been surveyed to provide a comprehensive coverage of the synthetic methodology and characterization techniques of various types of synthetic flavoporphyrins.

NADPH- and hydroperoxide-supported 17beta-estradiol hydroxylation catalyzed by a variant form (432L, 453S) of human cytochrome P450 1B1

Human cytochrome P450 1B1 (CYP1B1) catalyzes the hydroxylation of 17beta-estradiol (E(2)) at C-4, with a lesser activity at C-2. The E(2) 4-hydroxylase activity of human CYP1B1 was first observed in studies of MCF-7 breast cancer cells. Sequencing of polymerase chain reaction products revealed that CYP1B1 expressed in MCF-7 cells was not the previously characterized enzyme but a polymorphic form with leucine substituted for valine at position 432 and serine substituted for asparagine at position 453. To investigate the NADPH- and organic hydroperoxide-supported E(2) hydroxylase activities of the 432L, 453S form of human CYP1B1, the MCF-7 CYP1B1 cDNA was cloned and the enzyme was expressed in Sf9 insect cells. In microsomal assays supplemented with human NADPH:cytochrome P450 oxidoreductase, the expressed 432L, 453S form catalyzed NADPH-supported E(2) hydroxylation with a similar preference for 4-hydroxylation as the 432V, 453N form, with maximal rates of 1.97 and 0.37 nmol (min)(-1)(nmol cytochrome P450)(-1) for 4- and 2-hydroxylation, respectively. Cumeme hydroperoxide efficiently supported E(2) hydroxylation by both the 432V, 453N and 432L, 453S forms at several-fold higher rates than the NADPH-supported activities and with a lesser preference for E(2) 4- versus 2-hydroxylation (2:1). The hydroperoxide-supported activities of both forms were potently inhibited by the CYP1B1 inhibitor, 3,3',4, 4',5,5'-hexachlorobiphenyl. These results indicate that the 432V, 453N and 432L, 453S forms of CYP1B1 have similar catalytic properties for E(2) hydroxylation, and that human CYP1B1 is very efficient in catalyzing the hydroperoxide-dependent formation of catecholestrogens.

Laboratory evolution of peroxide-mediated cytochrome P450 hydroxylation

Enzyme-based chemical transformations typically proceed with high selectivity under mild conditions, and are becoming increasingly important in the pharmaceutical and chemical industries. Cytochrome P450 monooxygenases (P450s) constitute a large family of enzymes of particular interest in this regard. Their biological functions, such as detoxification of xenobiotics and steroidogenesis, are based on the ability to catalyse the insertion of oxygen into a wide variety of compounds. Such a catalytic transformation might find technological applications in areas ranging from gene therapy and environmental remediation to the selective synthesis of pharmaceuticals and chemicals. But relatively low turnover rates (particularly towards non-natural substrates), low stability and the need for electron-donating cofactors prohibit the practical use of P450s as isolated enzymes. Here we report the directed evolution of the P450 from Pseudomonas putida to create mutants that hydroxylate naphthalene in the absence of cofactors through the 'peroxide shunt' pathway with more than 20-fold higher activity than the native enzyme. We are able to screen efficiently for improved mutants by coexpressing them with horseradish peroxidase, which converts the products of the P450 reaction into fluorescent compounds amenable to digital imaging screening. This system should allow us to select and develop mono- and di-oxygenases into practically useful biocatalysts for the hydroxylation of a wide range of aromatic compounds.

Peroxide-supported in-vitro cytochrome P450 activities in Haemonchus contortus

The potential for cytochrome P450 from Haemonchus contortus to operate in the oxygen-poor intestinal environment was investigated by examining the ability of the cytochrome to act in vitro as a peroxygenase in utilising cumene hydroperoxide for substrate oxidations not requiring molecular oxygen. Peroxygenase and NADPH-supported monooxygenase activities were measured in microsomes prepared from L3 and adult nematodes. Both cumene hydroperoxide- and NADPH-supported ethoxycoumarin O-deethylase and aldrin epoxidase activities were detected in larval microsomes. Adult microsomes showed low levels of cumene hydroperoxide-supported ethoxycoumarin O-deethylase, as well as NADPH- and cumene hydroperoxide-supported aldrin epoxidase activities. The use of inhibitors in ethoxycoumarin O-deethylase assays with larval microsomes indicated that the peroxygenase pathway does not proceed via ferrous cytochrome P450 (no inhibition by carbon monoxide), did not require molecular oxygen, and did not depend on electron flow from cytochrome P450 reductase. Larval activity was inhibited by typical cytochrome P450 inhibitors (piperonyl butoxide, SKF-525A, chloramphenicol, metyrapone, n-octylamine) and was unaffected by the peroxidase inhibitor salicylhydroxamic acid. In contrast, adult microsomal cumene hydroperoxide-supported ethoxycoumarin O-deethylase activity was significantly inhibited by both cytochrome P450 inhibitors and salicylhydroxamic acid. Adult microsomes also contained potassium ferrocyanide peroxidase activity utilising cumene hydroperoxide. This activity showed a similar pattern of inhibition by both cytochrome P450 and peroxidase inhibitors. Whilst the ability of larval H. contortus cytochrome P450 to act as a peroxygenase in vitro was demonstrated, the inhibition results with adult microsomes showing both cytochrome P450 and peroxidase activities require further investigation to clarify the nature of the adult microsomal cumene hydroperoxide-supported O-deethylase activity.

The structure of heme proteins Compounds I and II: some misconceptions

Many reactions catalyzed by heme proteins involve an oxidation of the heme to one or two equivalents above the ferric state. Such intermediates are often referred to as Compound II and Compound I, respectively. Several different notations are used in the literature to describe the chemical structures of these compounds, which has led to errors and misinterpretations. The main problems are: 1. For many biochemists the notations X - FeIV = O and X - Fe + = O are equivalent and are used interchangeably, whereas other biochemists interpret these notations to have quite different meanings. 2. It is inaccurate and misleading to illustrate the increased oxidation state of Compound I by just adding two positive charges to the structure. 3. The bond between the oxygen and iron is not a conventional double bond and illustrating it as such leads to misconceptions concerning its properties. 4. In several instances, including horseradish peroxidase Compound I, there is reason to doubt that the radical moiety of the porphyrin ring (or of the protein in other peroxidases) carries a positive charge. The purpose of this article is to promote the use of uniform, as well as chemically correct, formulae and equations in describing the structures and reactivities of Compounds I and II. To accomplish this, a new notation is proposed for the iron-oxygen bond in these compounds.

Photoaffinity labeling of cytochrome P4501A1 with azidocumene: identification of cumene hydroperoxide binding region

Cumene hydroperoxide can support cytochrome P450-catalyzed reactions in the absence of molecular oxygen, NADPH, and cytochrome P450-NADPH oxidoreductase. Its binding at the cytochrome P450 active site is governed by the structure of the cumene hydroperoxide binding region. In order to define the region of cytochrome P4501A1 at which cumene hydroperoxide binds, we prepared an analog of cumene hydroperoxide for use as a photoaffinity label. p-Azido-isopro-pylbenzene (azidocumene) and its tritiated derivative were photolyzed in water solution by uv light with a half-life of 29 s. The 7-ethoxycoumarin deethylatation catalyzed by P450 using the cumene hydroperoxide-supported system was strongly inhibited by the presence of the label. Covalent binding to the protein after photoactivation was blocked by 50% in the presence of cumene hydroperoxide. HPLC analysis after trypsin digestion of the labeled protein showed that [3H]-azidocumene was attached covalently to the peptide VDMTPAYGLTLK corresponding to residues 492-503 in the 1A1 sequence. The radioactivity level of this fraction was reduced by 50% when the labeling was carried out in the presence of cumene hydroperoxide. To confirm the identified region the labeled protein was cleaved by cyanogen bromide. HPLC separation of the CNBr digest showed two peaks with a high level of radioactivity. The SDS/Tricine PAGE analysis of the radioactive fraction with an elution time of 43 min revealed a 2.4-kDa peptide carrying a high level of covalently bound radioactivity. The N-terminal sequence identified the labeled peptide to be a fragment generated by CNBr corresponding to residues 494-512. The N-terminal sequence of the labeled peptide with elution time of 27 min, TLKH, matches amino acid residues 501-504 in the P4501A1 sequence. We can conclude that in the overlapping region of all three identified peptides, T501-L502-K503, is the site where azidocumene covalently binds to P4501A1. The sequence alignment of cytochrome P4501A1 with cytochrome P450102 predicts that this region might correspond to beta-sheet structure localized on the distal side of the heme ring near the I helix and the oxygen binding pocket. To our knowledge, this is the first report to localize the cumene hydroperoxide binding region in the cytochrome P450 active site.