Cytochrome P450 compound I: capture, characterization, and C-H bond activation kinetics

Investigating the Active Oxidants Involved in Cytochrome P450 Catalyzed Sulfoxidation Reactions

Cytochrome P450 (CYP) heme-thiolate monooxygenases catalyze the hydroxylation of the C-H bonds of organic molecules. This reaction is initiated by a ferryl-oxo heme radical cation (Cpd I). These enzymes can also catalyze sulfoxidation reactions and the ferric-hydroperoxy complex (Cpd 0) and the Fe(III)-H₂ O₂ complex have been proposed as alternative oxidants for this transformation. To investigate this, the oxidation of 4-alkylthiobenzoic acids and 4-methoxybenzoic acid by the CYP199A4 enzyme from Rhodopseudomonas palustris HaA2 was compared using both monooxygenase and peroxygenase pathways. By examining mutants at the mechanistically important, conserved acid alcohol-pair (D251N, T252A and T252E) the relative amounts of the reactive intermediates that would form in these reactions were disturbed. Substrate binding and X-ray crystal structures helped to understand changes in the activity and enabled an attempt to evaluate whether multiple oxidants can participate in these reactions. In peroxygenase reactions the T252E mutant had higher activity towards sulfoxidation than O-demethylation but in the monooxygenase reactions with the WT enzyme the activity of both reactions was similar. The peroxygenase activity of the T252A mutant was greater for sulfoxidation reactions than the WT enzyme, which is the reverse of the activity changes observed for O-demethylation. The monooxygenase activity and coupling efficiency of sulfoxidation and oxidative demethylation were reduced by similar degrees with the T252A mutant. These observations infer that while Cpd I is required for O-dealkylation, another oxidant may contribute to sulfoxidation. Based on the activity of the CYP199A4 mutants it is proposed that this is the Fe(III)-H₂ O₂ complex which would be more abundant in the peroxide-driven reactions.

Characterization of Reaction Intermediates Involved in the Water Oxidation Reaction of a Molecular Cobalt Complex

Molecular cobalt(III) complexes of bis-amidate-bis-alkoxide ligands, (Me₄N)[Co^III(L₁)] (1) and (Me₄N)[Co^III(L₂)] (2), are synthesized and assessed through a range of characterization techniques. Electrocatalytic water oxidation activity of the Co complexes in a 0.1 M phosphate buffer solution revealed a ligand-centered 2e^-/1H⁺ transfer event at 0.99 V followed by catalytic water oxidation (WO) at an onset overpotential of 450 mV. By contrast, 2 reveals a ligand-based oxidation event at 0.9 V and a WO onset overpotential of 430 mV. Constant potential electrolysis study and rinse test experiments confirm the homogeneous nature of the Co complexes during WO. The mechanistic investigation further shows a pH-dependent change in the reaction pathway. On the one hand, below pH 7.5, two consecutive ligand-based oxidation events result in the formation of a Co^III(L^2-)(OH) species, which, followed by a proton-coupled electron transfer reaction, generates a Co^IV(L^2-)(O) species that undergoes water nucleophilic attack to form the O-O bond. On the other hand, at higher pH, two ligand-based oxidation processes merge together and result in the formation of a Co^III(L^2-)(OH) complex, which reacts with OH^- to yield the O-O bond. The ligand-coordinated reaction intermediates involved in the WO reaction are thoroughly studied through an array of spectroscopic techniques, including UV-vis absorption spectroscopy, electron paramagnetic resonance, and X-ray absorption spectroscopy. A mononuclear Co^III(OH) complex supported by the one-electron oxidized ligand, [Co^III(L^3-)(OH)]^-, a formal Co^IV(OH) complex, has been characterized, and the compound was shown to participate in the hydroxide rebound reaction, which is a functional mimic of Compound II of Cytochrome P450.

Computation-Aided Engineering of Cytochrome P450 for the Production of Pravastatin

CYP105AS1 is a cytochrome P450 from Amycolatopsis orientalis that catalyzes monooxygenation of compactin to 6-epi-pravastatin. For fermentative production of the cholesterol-lowering drug pravastatin, the stereoselectivity of the enzyme needs to be inverted, which has been partially achieved by error-prone PCR mutagenesis and screening. In the current study, we report further optimization of the stereoselectivity by a computationally aided approach. Using the CoupledMoves protocol of Rosetta, a virtual library of mutants was designed to bind compactin in a pro-pravastatin orientation. By examining the frequency of occurrence of beneficial substitutions and rational inspection of their interactions, a small set of eight mutants was predicted to show the desired selectivity and these variants were tested experimentally. The best CYP105AS1 variant gave >99% stereoselective hydroxylation of compactin to pravastatin, with complete elimination of the unwanted 6-epi-pravastatin diastereomer. The enzyme-substrate complexes were also examined by ultrashort molecular dynamics simulations of 50 × 100 ps and 5 × 22 ns, which revealed that the frequency of occurrence of near-attack conformations agreed with the experimentally observed stereoselectivity. These results show that a combination of computational methods and rational inspection could improve CYP105AS1 stereoselectivity beyond what was obtained by directed evolution. Moreover, the work lays out a general in silico framework for specificity engineering of enzymes of known structure.

Exploring the Factors which Result in Cytochrome P450 Catalyzed Desaturation Versus Hydroxylation

The cytochrome P450 family of monooxygenase enzymes have essential biological roles involving the selective oxidation of carbon-hydrogen bonds. They can also catalyze other important metabolic reactions including desaturation to form alkenes. Currently the factors that control the partition between P450 hydroxylation and desaturation pathways are poorly defined. The CYP199A4 enzyme from the bacterium Rhodopseudomonas palustris HaA2 catalyzes the oxidation of 4-ethyl- and 4-isopropyl- benzoic acids with hydroxylation and desaturation occurring in significant quantities. Here we demonstrate that 4-cyclopropylbenzoic acid is regioselectively hydroxylated by CYP199A4 at the benzylic carbon. In contrast, the oxidation of 4-n-propylbenzoic acid by CYP199A4 results in three major metabolites: an alkene from desaturation and two hydroxylation products at the benzylic (Cα) and Cβ carbons in similar quantities. Extending the length of the alkyl substituent resulted in 4-n-butylbenzoic acid being oxidized at the benzylic position (45%) and desaturated (55%). In contrast, 4-isobutylbenzoic generated very little alkene (5%) but was hydroxylated at the benzylic position (54%) and at the tertiary Cβ position (41%). The oxidation of 4-n-propylbenzoic acid by the F298 V mutant of CYP199A4 occurred with no hydroxylation at Cβ and a significant increase in metabolites arising from desaturation (73%). The X-ray crystal structures of CYP199A4 with each substrate revealed that they bind in the active site with the alkyl substituent positioned over the heme. However, the longer alkylbenzoic acids were bound in a different conformation as was 4-n-propylbenzoic acid in the F298 V mutant. Overall, the changes in metabolite distribution could be ascribed to bond strength differences and the position of the alkyl group relative to the heme.

Computations reveal a crucial role of an aromatic dyad in the catalytic function of plant cytochrome P450 mint superfamily

Enzymes are highly specific for their native functions, however with advances in bioengineering tools such as directed evolution, several enzymes are being repurposed for the secondary function of contemporary significance(Khersonsky and Tawfik, 2010 [1]⁾. Due to the functional versatility, the Cytochrome P450 (CYP450) superfamily has become the ideal scaffold for such bioengineering. In the current study, using MD (molecular dynamics) simulations and hybrid QM/MM (Quantum mechanics/molecular mechanics) calculations, we have studied the mechanism of spontaneous emergence of a secondary function due to a single site mutation in two plant CYP450 enzymes from the mint family. The MD simulations of WT (wild type) CYP71D18 and CYP71D13 enzymes and their variants show a crucial gating mechanism by aromatic dyad formed by Phe121 and Phe363 which regulates the substrate recognition. The QM/MM calculations reveal that the hydroxylation reactions at C3 and C6 positions in WT CYP71D18 and CYP71D13 enzymes as well as their variants follow a hydrogen atom transfer (HAT) followed by a single electron transfer (SET) mechanism, which is different from the typical rebound mechanism shown by most of the CYP450 enzymes.

Kinetics of chromium(V)-oxo and chromium(IV)-oxo porphyrins: Reactivity and mechanism for sulfoxidation reactions

In this work, chromium(IV)-oxo porphyrins [Cr^IV(Por)(O)] (2) (Por = porphyrin) were produced either by oxidation of [Cr^III(Por)Cl] (1) with iodobenzene diacetate or visible light photolysis of porphyrin‑chromium(III) chlorates. Subsequent oxidation of 2 with silver perchlorate gave chromium(V)-oxo porphyrins [Cr^V(Por)(O)](ClO₄) (3) in three porphyrin ligands, including 5,10,15,20-tetramesitylporphyrin(TMP, a), 5,10,15,20-tetrakis(2,6-difluorophenyl)porphyrin(TDFPP, b), and 5,10,15,20-tetrakis(pentafluorophenyl)porphyrin (TPFPP, c). Complexes 2 and 3 reacted with thioanisoles to produce the corresponding sulfoxides, and their kinetics of sulfoxidation reactions with a series of aryl methyl sulfides(thioanisoles) were studied in organic solutions. Chromium(V)-oxo porphyrins are several orders of magnitudes more reactive than chromium(IV)-oxo species, and representative second-order rate constants (k_ox) for the oxidation of thioansole are (0.40 ± 0.01) M^-1 s^-1 (3a), and (2.82 ± 0.20) × 10² M^-1 s^-1 (3b), and (2.20 ± 0.01) × 10³ M^-1 s^-1 (3c). The order of reactivity for 2 and 3 follows TPFPP > TDFPP > TMP, in agreement with the electrophilic nature of metal-oxo complexes. Hammett analyses indicate significant charge transfer in the transition states for oxidation of para-substituted thioanisoles by [Cr^V(Por)(O)]⁺. The ρ⁺ constants are -1.69 for 3a, -2.63 for 3b, and - 2.89 for 3c, respectively, mirror values found previously for related metal-oxo species. A mechanism involving the electrophilic attack of the Cr^V-oxo at sulfides to form a sulfur cation intermediate in the rate-determining step is suggested. Competition studies with chromium(III) porphyrin chloride and PhI(OAc)₂ gave relative rate constants for oxidations of competing thioanisoles that closely match ratios of absolute rate constants from chromium(V)-oxo species, which are true oxidants under catalytic conditions.

Mechanism of Melatonin Metabolism by CYP1A1: What Determines the Bifurcation Pathways of Hydroxylation versus Deformylation?

Melatonin, a widely applied cosmetic active ingredient, has a variety of uses as a skin protector through antioxidant and anti-inflammatory functions as well as giving the body UV-induced defenses and immune system support. In the body, melatonin is synthesized from a tryptophan amino acid in a cascade of reactions, but as melatonin is toxic at high concentrations, it is metabolized in the human skin by the cytochrome P450 enzymes. The P450s are diverse heme-based mono-oxygenases that catalyze oxygen atom-transfer processes that trigger metabolism and detoxification reactions in the body. In the catalytic cycle of the P450s, a short-lived high-valent iron(IV)-oxo heme cation radical is formed that has been proposed to be the active oxidant. How and why it activates melatonin in the human body and what the origin of the product distributions is, are unknown. This encouraged us to do a detailed computational study on a typical human P450 isozyme, namely CYP1A1. We initially did a series of molecular dynamics simulations with substrate docked into several orientations. These simulations reveal a number of stable substrate-bound positions in the active site, which may lead to differences in substrate activation channels. Using tunneling analysis on the full protein structures, we show that two of the four binding conformations lead to open substrate-binding pockets. As a result, in these open pockets, the substrate is not tightly bound and can escape back into the solution. In the closed conformations, in contrast, the substrate is mainly oriented with the methoxy group pointing toward the heme, although under a different angle. We then created large quantum cluster models of the enzyme and focused on the chemical reaction mechanisms for melatonin activation, leading to competitive O-demethylation and C⁶-aromatic hydroxylation pathways. The calculations show that active site positioning determines the product distributions, but the bond that is activated is not necessarily closest to the heme in the enzyme-substrate complex. As such, the docking and molecular dynamics positioning of the substrate versus oxidant can give misleading predictions on product distributions. In particular, in quantum mechanics cluster model I, we observe that through a tight hydrogen bonding network, a preferential 6-hydroxylation of melatonin is obtained. However, O-demethylation becomes possible in alternative substrate-binding orientations that have the C⁶-aromatic ring position shielded. Finally, we investigated enzymatic and non-enzymatic O-demethylation processes and show that the hydrogen bonding network in the substrate-binding pocket can assist and perform this step prior to product release from the enzyme.

A Combination of "Push Effect" Strategy with "Triple-Phase-Boundary Engineering" on Iron Porphyrin-Based MOFs: Enhanced Selectivity and Activity for Oxygen Reduction

Herein, the "push effect" strategy combined with "triple-phase-boundary" (TPB) engineering was innovatively employed to target the single Fe-N₄ sites in an iron porphyrin-based metal-organic framework, with axially coordinated 4-octylpyridine groups on Fe-N₄ (named as PCN-224 (Fe)-1). The amphiphilic 4-octylpyridine groups donate sufficient electrons toward Fe-N₄ by the Fe-N(pyridine) coordination bond and simultaneously provide effective TBP reactive sites by the hydrophobic octyl terminals, resulting in enhanced ORR activity of the PCN-224 (Fe)-1 in hydrophobic octyl terminals, with an E_1/2 of 0.81 V and complete 4-electron selectivity. Furthermore, TPB engineering is utilized to construct the PCN-224 (Fe)-1-based Zn-air battery with a maximum power density of 98 mW cm^-2, demonstrating great practical application potential for molecule-based ORR catalysts. Meanwhile, the "push effect" mechanism on ORR is revealed by electron paramagnetic resonance, in situ UV-vis spectroelectrochemical analysis, and density functional theory.

Engineering medicinal plant-derived CYPs: a promising strategy for production of high-valued secondary metabolites

Cytochorme P450s (CYPs) play a critical role in the catalysis of secondary metabolite biosynthetic pathways. For their commercial use, various strategies for metabolic pathway engineering using CYP as a potential target have been explored. Plants produce a vast diversity of secondary metabolites which are being used to treat various ailments and diseases. Some of these metabolites are difficult to obtain in large quantities limiting their industrial use. Cytochrome P450 enzymes (CYPs) are important catalysts in the biosynthesis of highly valued secondary metabolites, and are found in all domains of life. With the development of high-throughput sequencing and high-resolution mass spectrometry, new biosynthetic pathways and associated CYPs are being identified. In this review, we present CYPs identified from medicinal plants as a potential game changer in the metabolic engineering of secondary metabolic pathways. We present the achievements made so far in enhancing the production of important bioactivities through pathway engineering, giving some popular examples. At last, current challenges and possible strategies to overcome the limitations associated with CYP engineering to enhance the biosynthesis of target secondary metabolites are also highlighted.

Caught in the act: Monitoring OO bond cleavage in Acylperoxoferric cytochrome P450cam to form compound I in real time

While monitoring the reaction of ferric cytochrome P450cam (Cyp101) with substituted peroxybenzoic acids using rapid-scanning, stopped-flow (RSSF) spectroscopy, an intermediate appears en route to formation of the high-valent moiety known as Compound I [Fe(IV)=O/porphyrin radical cation] that is thought to be the key catalytic species for O-atom transfer to substrate. We have previously suggested (Spolitak, T., Dawson, J.H., Ballou, D.P., J. Biol. Chem.2005, 280, 20,300-20,309) that this species is an acylperoxo-ferric heme adduct that subsequently undergoes OO bond cleavage to generate Compound I. Singular value decomposition analysis of the RSSF data for formation of this intermediate shows that the energy of its Soret absorption peak is sensitive to the electron donor properties of the aryl substituents on the peracid. A linear Hammett correlation plot is seen for the energy of the Soret absorption peak vs. the Hammett σ constant. This correlation requires that the aryl substituents remain as part of the ligand bound to the heme iron, providing direct evidence that the adduct is indeed a ferric acylperoxo derivative. Linear Hammett correlation plots are also seen for both the rate of formation of the intermediate as well as for its conversion to Compound I. It is proposed that the electron donating/withdrawing properties of the aryl-bound substituents affect the electrophilic nature for binding substrate, changing the observed rate of formation for the acylperoxo intermediate, as well as the propensity and stability of the substituted benzoic acid to serve as the leaving group during OO bond cleavage yielding Compound I.

X-ray structure analysis of the cholesterol 25- and 20-hydroperoxides, the elusive primary sidechain autoxidation products of cholesterol

The systematic X-ray structure analyses of the primary cholesterol sidechain autoxidation products cholesterol 25- and 20β(S)-hydroperoxide are presented and compared to cholesterol and 25-hydroxycholesterol. Intermolecular interactions in crystal structures of the molecules are revealed through Hirshfeld surface analysis and fingerprint plots. The magnitude of energy frameworks is presented by combining efficient calculations of intermolecular interaction energies with novel graphical representation.

Serial Femtosecond Crystallography Reveals the Role of Water in the One- or Two-Electron Redox Chemistry of Compound I in the Catalytic Cycle of the B-Type Dye-Decolorizing Peroxidase DtpB

Controlling the reactivity of high-valent Fe(IV)–O catalytic intermediates, Compounds I and II, generated in heme enzymes upon reaction with dioxygen or hydrogen peroxide, is important for function. It has been hypothesized that the presence (wet) or absence (dry) of distal heme pocket water molecules can influence whether Compound I undergoes sequential one-electron additions or a concerted two-electron reduction. To test this hypothesis, we investigate the role of water in the heme distal pocket of a dye-decolorizing peroxidase utilizing a combination of serial femtosecond crystallography and rapid kinetic studies. In a dry distal heme site, Compound I reduction proceeds through a mechanism in which Compound II concentration is low. This reaction shows a strong deuterium isotope effect, indicating that reduction is coupled to proton uptake. The resulting protonated Compound II (Fe(IV)–OH) rapidly reduces to the ferric state, giving the appearance of a two-electron transfer process. In a wet site, reduction of Compound I is faster, has no deuterium effect, and yields highly populated Compound II, which is subsequently reduced to the ferric form. This work provides a definitive experimental test of the hypothesis advanced in the literature that relates sequential or concerted electron transfer to Compound I in wet or dry distal heme sites.

17O Electron Nuclear Double Resonance Analysis of Compound I: Inverse Correlation between Oxygen Spin Population and Electron Donation

Although the activation of inert C-H bonds by metal-oxo complexes has been widely studied, important questions remain, particularly regarding the role of oxygen spin population (i.e., unpaired electrons on the oxo ligand) in facilitating C-H bond cleavage. In order to shed light on this issue, we have utilized ¹⁷O electron nuclear double resonance spectroscopy to measure the oxygen spin populations of three compound I intermediates in heme enzymes with different reactivities toward C-H bonds: chloroperoxidase, cytochrome P450, and a selenolate (selenocysteinyl)-ligated cytochrome P450. The experimental data suggest an inverse correlation between oxygen spin population and electron donation from the axial ligand. We have explored the implications of this result using a Hückel-type molecular orbital model and constrained density functional theory calculations. These investigations have allowed us to examine the relationship between oxygen spin population, oxygen charge, electron donation from the axial ligand, and reactivity.

Distinct effects of form selective cytochrome P450 inhibitors on cytochrome P450-mediated monooxygenase and hydrogen peroxide generating NADPH oxidase

A characteristic of cytochrome P450 (CYP) enzymes is their ability to generate H₂O₂, either directly or indirectly via superoxide anion, a reaction referred to as "NADPH oxidase" activity. H₂O₂ production by CYPs can lead to the accumulation of cytotoxic reactive oxygen species which can compromise cellular functioning and contribute to tissue injury. Herein we determined if form selective CYP inhibitors could distinguish between the activities of the monooxygenase and NADPH oxidase activities of rat recombinant CYP1A2, CYP2E1, CYP3A1 and CYP3A2 and CYP1A1/2-enriched β-naphthoflavone-induced rat liver microsomes, CYP2E1-enriched isoniazide-induced rat liver microsomes and CYP3A subfamily-enriched dexamethasone-induced rat liver microsomes. In the presence of 7,8-benzoflavone (2.0 μM) for CYP1A2 and 4-methylpyrazole (32 μM) or DMSO (16 mM) for CYP2E1, monooxygenase activity was blocked without affecting NADPH oxidase activity for both the recombinant enzymes and microsomal preparations. Ketoconazole (1.0 μM), a form selective inhibitor for CYP3A subfamily enzymes, completely inhibited monooxygenase activity of rat recombinant CYP3A1/3A2 and CYP3A subfamily in rat liver microsomes; it also partially inhibited NADPH oxidase activity. 7,8-benzoflavone is a type I ligand, which competes with substrate binding, while 4-methylpyrazole and DMSO are type II heme binding ligands. Interactions of heme with these type II ligands was not sufficient to interfere with oxygen activation, which is required for NADPH oxidase activity. Ketoconazole, a type II ligand known to bind multiple sites on CYP3A subfamily enzymes in close proximity to heme, also interfered, at least in part, with oxygen activation. These data indicate that form specific inhibitors can be used to distinguish between monooxygenase reactions and H₂O₂ generating NADPH oxidase of CYP1A2 and CYP2E1. Mechanisms by which ketoconazole inhibits CYP3A NADPH oxidase remain to be determined.

CYP108N12 initiates p-cymene biodegradation in Rhodococcus globerulus

Rhodococcus globerulus (R. globerulus) isolated from soil beneath Eucalyptus sp. was found to live on the monoterpenes 1,8-cineole, p-cymene and (R)- and (S)-limonene as sole sources of carbon and energy. Previous metabolic studies revealed that R. globerulus is capable of living on 1,8-cineole, the main monoterpene component of eucalyptus essential oil through the activity of cytochrome P450_cin (CYP176A1) [1]. Genomic sequencing of R. globerulus revealed a novel putative cytochrome P450 (CYP108N12) that shares 48% sequence identity with CYP108A1 (P450_terp) from Pseudomonas sp., an α-terpineol hydroxylase. Given the sequence similarity between CYP108N12 and P450_terp, it was hypothesised that CYP108N12 may be responsible for initiating the biodegradation of a monoterpene structurally similar to α-terpineol such as (R)-limonene, (S)-limonene or p-cymene. Encoded within the operon containing CYP108N12 were two putative bacterial P450 redox partners and putative alcohol and aldehyde dehydrogenases, suggesting a complete catalytic system for activating these monoterpenes. Binding studies revealed that p-cymene and (R)- and (S)-limonene all bound tightly to CYP108N12 but α-terpineol did not. A catalytically active system was reconstituted using the non-native redox partner putidaredoxin and putidaredoxin reductase that act with CYP101A1 (P450_cam) from Pseudomonas. This reconstituted system catalysed the hydroxylation of p-cymene to 4-isopropylbenzyl alcohol, and (R)- and (S)-limonene to (R)- and (S)-perillyl alcohol, respectively. R. globerulus was successfully grown on solely p-cymene, (R)-limonene or (S)-limonene. CYP108N12 was detected when R. globerulus was grown on p-cymene, but not either limonene enantiomer. The native function of CYP108N12 is therefore proposed to be initiation of p-cymene biodegradation by methyl oxidation and is a potentially attractive biocatalyst capable of specific benzylic and allylic hydroxylation.

Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants

The cytochrome P450 monooxygenase (CYP) superfamily comprises hemethiolate enzymes that perform remarkable regio- and stereospecific oxidative chemistry. As such, CYPs are key agents for the structural and functional tailoring of triterpenoids, one of the largest classes of plant natural products with widespread applications in pharmaceuticals, food, cosmetics, and agricultural industries. In this review, we provide a full overview of 149 functionally characterised CYPs involved in the biosynthesis of triterpenoids and steroids in primary as well as in specialised metabolism. We describe the phylogenetic distribution of triterpenoid- and steroid-modifying CYPs across the plant CYPome, present a structure-based summary of their reactions, and highlight recent examples of particular interest to the field. Our review therefore provides a comprehensive up-to-date picture of CYPs involved in the biosynthesis of triterpenoids and steroids in plants as a starting point for future research.

Cytochrome P450Blt Enables Versatile Peptide Cyclisation to Generate Histidine- and Tyrosine-Containing Crosslinked Tripeptide Building Blocks

We report our investigation of the utility of peptide crosslinking cytochrome P450 enzymes from biarylitide biosynthesis to generate a range of cyclic tripeptides from simple synthons. The crosslinked tripeptides produced by this P450 include both tyrosine-histidine (A-N-B) and tyrosine-tryptophan (A-O-B) crosslinked tripeptides, the latter a rare example of a phenolic crosslink to an indole moiety. Tripeptides are easily isolated following proteolytic removal of the leader peptide and can incorporate a wide range of amino acids in the residue inside the crosslinked tripeptide. Given the utility of peptide crosslinks in important natural products and the synthetic challenge that these can represent, P450 enzymes have the potential to play roles as important tools in the generation of high-value cyclic tripeptides for incorporation in synthesis, which can be yet further diversified using selective chemical techniques through specific handles contained within these tripeptides.

Depicting the proton relay network in human aromatase: New insights into the role of the alcohol-acid pair

Human aromatase is the cytochrome P450 catalyzing the conversion of androgens into estrogens in a three steps reaction essential to maintain steroid hormones balance. Here we report the capture and spectroscopic characterization of its compound I (Cpd I), the main reactive species in cytochromes P450. The typical spectroscopic transitions indicating the formation of Cpd I are detected within 0.8 s when mixing aromatase with meta-chloroperoxybenzoic acid. The estrogen product is obtained from the same reaction mixture, demonstrating the involvement of Cpd I in aromatization reaction. Site-directed mutagenesis is applied to the acid-alcohol pair D309 and T310 and to R192, predicted to be part of the proton relay network. Mutants D309N and R192Q do not lead to Cpd I with an associated loss of activity, confirming that these residues are involved in proton delivery for Cpd I generation. Cpd I is captured for T310A mutant and shows 2.9- and 4.4-fold faster rates of formation and decay, respectively, compared to wild-type (WT). However, its activity is lower than the WT and a larger amount of H2 O2 is produced during catalysis, indicating that T310 has an essential role in proton gating for generation of Cpd 0 and Cpd I and for their stabilization. The data provide new evidences on the role of threonine belonging to the conserved "acid-alcohol" pair and known to be crucial for oxygen activation in cytochromes P450.

Effect of Brшnsted Acid on the Reactivity and Selectivity of the Oxoiron(V) Intermediates in C-H and C=C Oxidation Reactions

The effect of HClO4 on the reactivity and selectivity of the catalyst systems 1,2/H2O2/AcOH, based on nonheme iron complexes of the PDP families, [(Me2OMePDP)FeIII(μ-OH)2FeIII(MeOMe2PDP)](OTf)4 (1) and [(NMe2PDP)FeIII(μ-OH)2FeIII(NMe2PDP](OTf)4 (2), toward oxidation of benzylideneacetone (bna), adamantane (ada), and (3aR)-(+)-sclareolide (S) has been studied. Adding HClO4 (2–10 equiv. vs. Fe) has been found to result in the simultaneous improvement of the observed catalytic efficiency (i.e., product yields) and the oxidation regio- or enantioselectivity. At the same time, HClO4 causes a threefold increase of the second-order rate constant for the reaction of the key oxygen-transferring intermediate [(Me2OMePDP)FeV=O(OAc)]2+ (1a), with cyclohexane at −70 °C. The effect of strong Brønsted acid on the catalytic reactivity is discussed in terms of the reversible protonation of the Fe=O moiety of the parent perferryl intermediates.

Enzyme-Mimicking Materials from Designed Self-Assembly of Lysine-Rich Peptides and G-Quadruplex DNA/Hemin DNAzyme: Charge Effect of the Key Residues on the Catalytic Functions

In enzymatic active sites, the essential functional groups are spatially arranged as a result of the enzyme three-dimensional folding, which leads to remarkable catalytic properties. We are inspired to self-assemble the polylysine peptides with guanine-rich DNA and hemin as cofactor to fabricate the peroxidase-mimicking catalytic nanomaterials. The DNA can fold into G-quadruplex to provide a supramolecular scaffold and a nucleobase for supporting and coordinating hemin, and the polylysine provides amine as distal groups to promote the H₂O₂ adsorption to the iron of hemin. The polylysine and DNA components synergistically accelerated the hemin-catalyzed reactions, and the complex containing ε-polylysine exhibited higher activity than α-polylysine. This activity difference is attributed to the higher pK_a value and more susceptible protonation of amine of ε-polylysine than α-polylysine. The ε-polylysine/DNA/hemin had similar coordination states of hemin and conformations of the components to α-polylysine/DNA/hemin but accelerated the formation of the intermediate compound I faster than α-polylysine. Theoretical simulation reveals that the unprotonated NH₂ behaved like a base catalyst, similar to His-42 residue in the natural heme pocket, while the protonated NH₃⁺ acted as an acid, which indicated that the base catalyst on the distal side of the hemin pocket is more active than the acid. This work provides an avenue to control the distribution of the catalytic residues in an enzyme-like active site and to understand the roles of the key residues of native enzymes.

The Hyperporphyrin Concept: A Contemporary Perspective

The Gouterman four-orbital model conceptualizes porphyrin UV-visible spectra as dominated by four frontier molecular orbitals-two nearly degenerate HOMOs and two exactly degenerate LUMOS under D 4h symmetry. These are well separated from all the other molecular orbitals, and normal spectra involve transitions among these MOs. Unusual spectra occur when additional orbitals appear in this energy range, typically as a consequence of the central coordinated atom. For example, metals with empty d orbitals in a suitable energy range may lead to charge transfer from porphyrin (ligand) to metal, that is, so-called LMCT transitions. Metals with filled p or d orbitals may lead to charge transfer from metal to porphyrin, MLCT transitions. These cases lead to additional peaks and/or significant redshifts in the spectra and were classified as hyperporphyrins by Gouterman. Cases in which spectra are blueshifted were classified as hypsoporphyrins; they are common for relatively electronegative late transition metal porphyrins. Many of the same principles apply to porphyrin analogues, especially corroles. In this Perspective, we focus on two newer classes of hyperporphyrins: one reflecting substituent effects in protonated or deprotonated free-base tetraphenyporphyrins and the other reflecting "noninnocent" interactions between central metal ions and corroles. Hyperporphyrin effects on spectra can be dramatic, yet they can be generated by relatively simple changes and subtle structural variations, such as acid-base reactions or the selection of a central metal ion. These concepts suggest strategies for engineering porphyrin or porphyrinoid dyes for specific applications, especially those requiring far-red or near-infrared absorption or emission.

Binding of Dual-Function Hybridized MetalOrganic Capsules to Enzymes for Cascade Catalysis

The combination of chemo- and biocatalysis for multistep syntheses provides attractive advantages in terms of evolvability, promiscuity, and sustainability striving for desirable catalytic performance. Through the encapsulation of flavin analogues by both NADH and heme mimics codecorated heteroleptic metal-organic capsules, herein, we report a progressive host-guest strategy to imitate cytochrome P450s catalysis for cascade oxidative coupling catalysis. Besides the construction of stable dual-function metal-organic capsules and the modification of cofactor-decorated capsules at the domain of enzymes, this supramolecular strategy involves multistage directional electron flow, affording reactive ferric peroxide species for inducing oxygenation. Under light irradiation, the metal-organic capsule selectively converts stilbene to oxidative coupling products (including 2-oxo-1,2-diphenylethyl formate, 2-alkoxy-1,2-diphenylethanone) in tandem with enzymatic reactions respectively, at the domain of natural enzymes. The ingenious combination of capsules and enzymes with the in situ-regenerated capsule-loaded NADH cofactor promises non-native coupling reactions by forming regional cooperation and division. This abiotic-biotic conjugated host-guest strategy is conducive to the de novo creation of multifunctional components approaching active enzymatic sites for reinforced matter and energy transporting, demonstrating a key role of multicomponent supramolecular catalysts for one-pot integrated catalytic conversions.

Roles of cytochrome P450 enzymes in pharmacology and toxicology: Past, present, and future

The development of the cytochrome P450 (P450) field has been remarkable in the areas of pharmacology and toxicology, particularly in drug development. Today it is possible to use the knowledge base and relatively straightforward assays to make intelligent predictions about drug disposition prior to human dosing. Much is known about the structures, regulation, chemistry of catalysis, and the substrate and inhibitor specificity of human P450s. Many aspects of drug-drug interactions and side effects can be understood in terms of P450s. This knowledge has also been useful in pharmacy practice, as well as in the pharmaceutical industry and medical practice. However, there are still basic and practical questions to address regarding P450s and their roles in pharmacology and toxicology. Another aspect is the discovery of drugs that inhibit P450 to treat diseases.

Metalloid-Cluster Ligands Enabling Stable and Active FeN4 -Ten Motifs for the Oxygen Reduction Reaction

In nature, the oxygen reduction reaction (ORR) is catalyzed by cytochrome P450 (CYP) enzymes containing heme iron centers with an axial thiolate ligand (FeN₄ -S), which are among the most finely developed catalysts by natural selection. However, the exceptional ORR activity and selectivity of CYP enzymes originate from their non-rigid and self-adaptive coordination network with molecular ligands, which sacrifices the stability of the active motifs under electrochemical reaction conditions. Here, a design strategy to circumvent this dilemma by incorporating Fe-N₄ motifs into carbon matrices instead of the protein scaffold and replacing the axial molecular thiolate ligand with a stable tellurium cluster (Te_n ) is demonstrated. Theoretical calculations indicate a moderate interaction between Fe 3d and Te 5p orbitals once n > 2, allowing the FeTe bond to dynamically change its strength to adaptively facilitate the intermediate steps during the ORR process, which renders FeN₄ -Te_n active sites with superior ORR activity. This adaptive behavior mimics the conformational dynamics of an enzyme during the reaction, but retains the stability nature as a heterogeneous catalyst. The experiments validate that the as-designed catalyst with a characterized FeN₄ -Te_n structure outperforms the commercial Pt/C catalyst both on activity and stability.

Oriented External Electric Fields Regurating the Reaction Mechanism of CH4 Oxidation Catalyzed by Fe(IV)-Oxo-Corrolazine: Insight from Density Functional Calculations

Methane is the simplest alkane and can be used as an alternative energy source for oil and coal, but the greenhouse effect caused by its leakage into the air is not negligible, and its conversion into liquid methanol not only facilitates transportation, but also contributes to carbon neutrality. In order to find an efficient method for converting methane to methanol, CH4 oxidation catalyzed by Fe(IV)-Oxo-corrolazine (Fe(IV)-Oxo-Cz) and its reaction mechanism regulation by oriented external electric fields (OEEFs) are systematically studied by density functional calculations. The calculations show that Fe(IV)-Oxo-Cz can abstract one H atom from CH4 to form the intermediate with OH group connecting on the corrolazine ring, with the energy barrier of 25.44 kcal mol-1. And then the product methanol is formed through the following rebound reaction. Moreover, the energy barrier can be reduced to 20.72 kcal mol-1 through a two-state reaction pathway. Furthermore, the effect of OEEFs on the reaction is investigated. We found that OEEFs can effectively regulate the reaction by adjusting the stability of the reactant and the transition state through the interaction of electric field-molecular dipole moment. When the electric field is negative, the energy barrier of the reaction decreases with the increase of electric intensity. Moreover, the OEEF aligned along the intrinsic Fe‒O reaction axis can effectively regulate the ability of forming the OH on the corrolazine ring by adjusting the charges of O and H atoms. When the electric field intensity is -0.010 a.u., the OH can be directly rebounded to the CH3· before it is connecting on the corrolazine ring, thus forming the product directly from the transition state without passing through the intermediate with only an energy barrier of 17.34 kcal mol-1, which greatly improves the selectivity of the reaction.

In Silico simulation of Cytochrome P450-Mediated metabolism of aromatic amines: A case study of N-Hydroxylation

Aromatic amines, the widely used raw materials in industry, cause long-term exposure to human bodies. They can be metabolized by cytochrome P450 enzymes to form active electrophilic compounds, which will potentially react with nucleophilic DNA to exert carcinogenesis. The short lifetime and versatility of the oxidant (a high-valent iron (IV)-oxo species, compound I) of P450 enzymes prompts us to use theoretical methods to investigate the metabolism of aromatic amines. In this work, the density functional theory (DFT) has been employed to simulate the hydroxylation metabolism through H-abstraction and to calculate the activation energy of this reaction for 28 aromatic amines. The results indicate that the steric effects, inductive effects and conjugative effects greatly contribute to the metabolism activity of the chemicals. The further correlation reveals that the dissociation energy of -NH₂ (BDE_N-H) can successfully predict the time-consuming calculated activation energy (R² for aromatic and heteroaromatic amines are 0.93 and 0.86, respectively), so BDE_N-H can be taken as a key parameter to characterize the relative stability of aromatic amines in P450 enzymes and further to quickly assess their potential toxicity. The validation results prove such relationship has good statistical performance (q_cv² for aromatic and heteroaromatic amines are 0.95 and 0.90, respectively) and can be used to other aromatic amines in the application domain, greatly reducing computational cost and providing useful support for experimental research.

Rational Design of P450 aMOx for Improving Anti-Markovnikov Selectivity Based on the “Butterfly” Model

Aromatic aldehydes are important industrial raw materials mainly synthesized by anti-Markovnikov (AM) oxidation of corresponding aromatic olefins. The AM product selectivity remains a big challenge. P450 aMOx is the first reported enzyme that could catalyze AM oxidation of aromatic olefins. Here, we reported a rational design strategy based on the “butterfly” model of the active site of P450 aMOx. Constrained molecular dynamic simulations and a binding energy analysis of key residuals combined with an experimental alanine scan were applied. As a result, the mutant A275G showed high AM selectivity of >99%. The results also proved that the “butterfly” model is an effective design strategy for enzymes.

Modeling the Ligand Effect on the Structure of CYP 450 Within the Density Functional Theory

An improved understanding of the P450 structure is relevant to the development of biomimetic catalysts and inhibitors for controlled CH-bond activation, an outstanding challenge of synthetic chemistry. Motivated by the experimental findings of an unusually short Fe-S bond of 2.18 Å for the wild-type (WT) OleT P450 decarboxylase relative to a cysteine pocket mutant form (A369P), a computational model that captures the effect of the thiolate axial ligand on the iron-sulfur distance is presented. With the computational efficiency and streamlined analysis in mind, this model combines a cluster representation of the enzyme─40-110 atoms, depending on the heme and ligand truncation level─with a density functional theory (DFT) description of the electronic structure (ES) and is calibrated against the experimental data. The optimized Fe-S distances show a difference of 0.25 Å between the low and high spin states, in agreement with the crystallographic structures of the OleT WT and mutant forms. We speculate that this difference is attributable to the packing of the ligand; the mutant is bulkier due to an alanine-to-proline replacement, meaning that it is excluded from the energetically favored low-spin minimum because of steric constraints. The presence of pure spin-state pairs and the intersection of the low/high spin states for the enzyme model is indicative of the limitations of single-reference ES methods in such systems and emphasizes the significance of using the proper state when modeling the hydrogen atom transfer (HAT) reaction catalyzed by OleT. At the same time, the correct characterization of both the short and long Fe-S bonds within a small DFT-based model of 42 atoms paves the way for quantum dynamics modeling of the HAT step, which initiates the OleT decarboxylation reaction.

Electronic Structure and Reactivity of Dioxygen-Derived Aliphatic Thiolate-Ligated Fe-Peroxo and Fe(IV) Oxo Compounds

Herein, we examine the electronic and geometric structural properties of O₂-derived aliphatic thiolate-ligated Fe-peroxo, Fe-hydroxo, and Fe(IV) oxo compounds. The latter cleaves strong C-H bonds (96 kcal mol^-1) on par with the valine C-H bond cleaved by isopencillin N synthase (IPNS). Stopped-flow kinetics studies indicate that the barrier to O₂ binding to [Fe^II(S^Me2N₄(tren))]⁺ (3) is extremely low (E_a = 36(2) kJ mol^-1), as theoretically predicted for IPNS. Dioxygen binding to 3 is shown to be reversible, and a superoxo intermediate, [Fe^III(S^Me2N₄(tren))(O₂)]⁺ (6), forms in the first 25 ms of the reaction at -40 °C prior to the rate-determining (E_a = 46(2) kJ mol^-1) formation of peroxo-bridged [(S^Me2N₄(tren))Fe(III)]₂(μ-O₂)²⁺ (7). A log(k_obs) vs log([Fe]) plot for the formation of 7 is consistent with the second-order dependence on iron, and H₂O₂ assays are consistent with a 2:1 ratio of Fe/H₂O₂. Peroxo 7 is shown to convert to ferric-hydroxo [Fe^III(S^Me2N(tren))(OH)]⁺ (9, g_⊥ = 2.24, g_∥ = 1.96), the identity of which was determined via its independent synthesis. Rates of the conversion 7 → 9 are shown to be dependent on the X-H bond strength of the H-atom donor, with a k_H/k_D = 4 when CD₃OD is used in place of CH₃OH as a solvent. A crystallographically characterized cis thiolate-ligated high-valent iron oxo, [Fe^IV(O)(S^Me2N₄(tren))]⁺ (11), is shown to form en route to hydroxo 9. Electronic structure calculations were shown to be consistent with 11 being an S = 1 Fe(IV)═O with an unusually high ν_Fe-O stretching frequency at 918 cm^-1 in line with the extremely short Fe-O bond (1.603(7) Å).

Second coordination sphere effects on the mechanistic pathways for dioxygen activation by a ferritin: involvement of a Tyr radical and the identification of a cation binding site

Ferritins are ubiquitous diiron enzymes involved in iron(II) detoxification and oxidative stress responses and can act as metabolic iron stores. The overall reaction mechanisms of ferritin enzymes are still unclear, particularly concerning the role of the conserved, near catalytic center Tyr residue. Thus, we carried out a computational study of a ferritin using a large cluster model of well over 300 atoms including its first- and second-coordination sphere. The calculations reveal important insight into the structure and reactivity of ferritins. Specifically, the active site Tyr residue delivers a proton and electron in the catalytic cycle prior to iron(II) oxidation. In addition, the calculations highlight a likely cation binding site at Asp65, which through long-range electrostatic interactions, influences the electronic configuration and charge distributions of the metal center. The results are consistent with experimental observations but reveal novel detail of early mechanistic steps that lead to an unusual mixed-valent iron(III)-iron(II) center.

Efficient biodegradation of tetrabromobisphenol A by the novel strain Enterobacter sp. T2 with good environmental adaptation: Kinetics, pathways and genomic characteristics

T2, a gram-positive bacterium capable of rapidly degrading tetrabromobisphenol A (TBBPA), and affiliated with the genus Enterobacter, was isolated for the first time from sludge that had been contaminated for several years. The TBBPA degradation data fitted the first-order model well. Under optimal conditions (pH of 7, temperature of 31 °C, TBBPA concentration of 5 mg L^-1, and inoculum size of 5%), 99.4% of the initially added TBBPA was degraded after 48 h. TBBPA degradation fitted the first-order model with the half-life of 3.3 h. These results illustrated that the TBBPA degradation capability of strain T2 was significantly better than that of previously reported bacteria. A total of 17 intermediates were detected, among which five were reported for the first time. Whole-genome sequencing revealed that strain T2 had a chromosome with the total length of 4 854 376 bp and a plasmid with the total length of 21 444 bp. It harbored essential genes responsible for debromination, such as cyp450, gstB, gstA, and HADH, and genes responsible for subsequent complete mineralization, such as bioC, yrrM, Tam, and Ubil. A key protein of haloacid dehalogenases responsible for the biodegradation of TBBPA may also be involved in the regulation of TBBPA degradation in natural environment. In soil bioremediation experiments, strain T2 showed excellent environmental adaptation. It was able to biodegrade TBBPA and its typical intermediate bisphenol A efficiently. Therefore, it could potentially be applied to treat TBBPA-contaminated sites.

Bioinorganic Chemistry on Electrodes: Methods to Functional Modeling

One of the major goals of bioinorganic chemistry has been to mimic the function of elegant metalloenzymes. Such functional modeling has been difficult to attain in solution, in particular, for reactions that require multiple protons and multiple electrons (nH⁺/ne^-). Using a combination of heterogeneous electrochemistry, electrode and molecule design one may control both electron transfer (ET) and proton transfer (PT) of these nH⁺/ne^- reactions. Such control can allow functional modeling of hydrogenases (H⁺ + e^- → 1/2 H₂), cytochrome c oxidase (O₂ + 4 e^- + 4 H⁺ → 2 H₂O), monooxygenases (RR'CH₂ + O₂ + 2 e^- + 2 H⁺ → RR'CHOH + H₂O) and dioxygenases (S + O₂ → SO₂; S = organic substrate) in aqueous medium and at room temperatures. In addition, these heterogeneous constructs allow probing unnatural bioinspired reactions and estimation of the inner- and outer-sphere reorganization energy of small molecules and proteins.

Catalytic Reductive Carbene Transfer Reactions

Efforts to develop catalytic carbene transfer reactions have largely relied on the use of diazo precursors. However, diazoalkanes are susceptible to undergoing violent exothermic decomposition unless they contain stabilizing substituents. Consequently, most synthetic methods are restricted to diazoacetates or related derivatives. In this Perspective, we describe an alternative approach to carbene transfer catalysis based on the generation of metal carbenoids from gem-dihaloalkanes and gem-dihaloalkenes. These precursors are readily available and stable in unsubstituted form or with a variety of donor and acceptor substituents. Using this approach, it is possible to design cyclopropanation reactions with non-stabilized carbenes, such as methylene, isopropylidene, and vinylidene. Furthermore, due to the distinct mechanistic pathways of these reactions, novel modes of cycloaddition can be carried out, including [4 + 1]-cycloadditions.

Second Sphere Effects on Oxygen Reduction and Peroxide Activation by Mononuclear Iron Porphyrins and Related Systems

Activation and reduction of O₂ and H₂O₂ by synthetic and biosynthetic iron porphyrin models have proved to be a versatile platform for evaluating second-sphere effects deemed important in naturally occurring heme active sites. Advances in synthetic techniques have made it possible to install different functional groups around the porphyrin ligand, recreating artificial analogues of the proximal and distal sites encountered in the heme proteins. Using judicious choices of these substituents, several of the elegant second-sphere effects that are proposed to be important in the reactivity of key heme proteins have been evaluated under controlled environments, adding fundamental insight into the roles played by these weak interactions in nature. This review presents a detailed description of these efforts and how these have not only demystified these second-sphere effects but also how the knowledge obtained resulted in functional mimics of these heme enzymes.

The Cytochrome P450 OxyA from the Kistamicin Biosynthesis Cyclization Cascade is Highly Sensitive to Oxidative Damage

Cytochrome P450 enzymes (P450s) are a superfamily of monooxygenases that utilize a cysteine thiolate–ligated heme moiety to perform a wide range of demanding oxidative transformations. Given the oxidative power of the active intermediate formed within P450s during their active cycle, it is remarkable that these enzymes can avoid auto-oxidation and retain the axial cysteine ligand in the deprotonated—and thus highly acidic—thiolate form. While little is known about the process of heme incorporation during P450 folding, there is an overwhelming preference for one heme orientation within the P450 active site. Indeed, very few structures to date contain an alternate heme orientation, of which two are OxyA homologs from glycopeptide antibiotic (GPA) biosynthesis. Given the apparent preference for the unusual heme orientation shown by OxyA enzymes, we investigated the OxyA homolog from kistamicin biosynthesis (OxyA_kis), which is an atypical GPA. We determined that OxyA_kis is highly sensitive to oxidative damage by peroxide, with both UV and EPR measurements showing rapid bleaching of the heme signal. We determined the structure of OxyA_kis and found a mixed population of heme orientations present in this enzyme. Our analysis further revealed the possible modification of the heme moiety, which was only present in samples where the alternate heme orientation was present in the protein. These results suggest that the typical heme orientation in cytochrome P450s can help prevent potential damage to the heme—and hence deactivation of the enzyme—during P450 catalysis. It also suggests that some P450 enzymes involved in GPA biosynthesis may be especially prone to oxidative damage due to the heme orientation found in their active sites.