Heme-thiolate ferryl of aromatic peroxygenase is basic and reactive

Axial Ligation Impedes Proton-Coupled Electron-Transfer Reactivity of a Synthetic Compound-I Analogue

The nature of the axial ligand in high-valent iron-oxo heme enzyme intermediates and related synthetic catalysts is a critical structural element for controlling proton-coupled electron-transfer (PCET) reactivity of these species. Herein, we describe the generation and characterization of three new 6-coordinate, iron(IV)-oxo porphyrinoid-π-cation-radical complexes and report their PCET reactivity together with a previously published 5-coordinate analogue, FeIV(O)(TBP8Cz+•) (TBP8Cz = octakis(p-tert-butylphenyl)corrolazinato3-) (2) (Cho, K. A high-valent iron-oxo corrolazine activates C-H bonds via hydrogen-atom transfer. J. Am. Chem. Soc. 2012, 134, 7392-7399). The new complexes FeIV(O)(TBP8Cz+•)(L) (L = 1-methyl imidazole (1-MeIm) (4a), 4-dimethylaminopyridine (DMAP) (4b), cyanide (CN-)(4c)) can be generated from either oxidation of the ferric precursors or by addition of L to the Compound-I (Cpd-I) analogue at low temperatures. These complexes were characterized by UV-vis, electron paramagnetic resonance (EPR), and Mössbauer spectroscopies, and cryospray ionization mass spectrometry (CSI-MS). Kinetic studies using 4-OMe-TEMPOH as a test substrate indicate that coordination of a sixth axial ligand dramatically lowers the PCET reactivity of the Cpd-I analogue (rates up to 7000 times slower). Extensive density functional theory (DFT) calculations together with the experimental data show that the trend in reactivity with the axial ligands does not correlate with the thermodynamic driving force for these reactions or the calculated strengths of the O-H bonds being formed in the FeIV(O-H) products, pointing to non-Bell-Evans-Polanyi behavior. However, the PCET reactivity does follow a trend with the bracketed reduction potential of Cpd-I analogues and calculated electron affinities. The combined data suggest a concerted mechanism (a concerted proton electron transfer (CPET)) and an asynchronous movement of the electron/proton pair in the transition state.

Functional Model of Compound II of Cytochrome P450: Spectroscopic Characterization and Reactivity Studies of a FeIV-OH Complex

Herein, we show that the reaction of a mononuclear FeIII(OH) complex (1) with N-tosyliminobenzyliodinane (PhINTs) resulted in the formation of a FeIV(OH) species (3). The obtained complex 3 was characterized by an array of spectroscopic techniques and represented a rare example of a synthetic FeIV(OH) complex. The reaction of 1 with the one-electron oxidizing agent was reported to form a ligand-oxidized FeIII(OH) complex (2). 3 revealed a one-electron reduction potential of -0.22 V vs Fc+/Fc at -15 °C, which was 150 mV anodically shifted than 2 (Ered = -0.37 V vs Fc+/Fc at -15 °C), inferring 3 to be more oxidizing than 2. 3 reacted spontaneously with (4-OMe-C6H4)3C• to form (4-OMe-C6H4)3C(OH) through rebound of the OH group and displayed significantly faster reactivity than 2. Further, activation of the hydrocarbon C-H and the phenolic O-H bond by 2 and 3 was compared and showed that 3 is a stronger oxidant than 2. A detailed kinetic study established the occurrence of a concerted proton-electron transfer/hydrogen atom transfer reaction of 3. Studying one-electron reduction of 2 and 3 using decamethylferrocene (Fc*) revealed a higher ket of 3 than 2. The study established that the primary coordination sphere around Fe and the redox state of the metal center is very crucial in controlling the reactivity of high-valent Fe-OH complexes. Further, a FeIII(OMe) complex (4) was synthesized and thoroughly characterized, including X-ray structure determination. The reaction of 4 with PhINTs resulted in the formation of a FeIV(OMe) species (5), revealing the presence of two FeIV species with isomer shifts of -0.11 mm/s and = 0.17 mm/s in the Mössbauer spectrum and showed FeIV/FeIII potential at -0.36 V vs Fc+/Fc couple in acetonitrile at -15 °C. The reactivity studies of 5 were investigated and compared with the FeIV(OH) complex (3).

Robust Light Driven Enzymatic Oxyfunctionalization via Immobilization of Unspecific Peroxygenase

Unspecific peroxygenases have attracted interest in synthetic chemistry, especially for the oxidative activation of C-H bonds, as they only require hydrogen peroxide (H2 O2 ) instead of a cofactor. Due to their instability in even small amounts of H2 O2 , different strategies like enzyme immobilization or in situ H2 O2 production have been developed to improve the stability of these enzymes. While most strategies have been studied separately, a combination of photocatalysis with immobilized enzymes was only recently reported. To show the advantages and limiting factors of immobilized enzyme in a photobiocatalytic reaction, a comparison is made between free and immobilized enzymes. Adjustment of critical parameters such as (i) enzyme and substrate concentration, (ii) illumination wavelength and (iii) light intensity results in significantly increased enzyme stabilities of the immobilized variant. Moreover, under optimized conditions a turnover number of 334,500 was reached.

Heme-copper and Heme O2-derived synthetic (bioinorganic) chemistry toward an understanding of cytochrome c oxidase dioxygen chemistry

Cytochrome c oxidase (CcO), also widely known as mitochondrial electron-transport-chain complex IV, is a multi-subunit transmembrane protein responsible for catalyzing the last step of the electron transport chain, dioxygen reduction to water, which is essential to the establishment and maintenance of the membrane proton gradient that drives ATP synthesis. Although many intermediates in the CcO catalytic cycle have been spectroscopically and/or computationally authenticated, the specifics regarding the IP intermediate, hypothesized to be a heme-Cu (hydro)peroxo species whose O-O bond homolysis is supported by a hydrogen-bonding network of water molecules, are largely obscured by the fast kinetics of the A (FeIII-O2•-/CuI/Tyr) → PM (FeIV=O/CuII-OH/Tyr•) step. In this review, we have focused on the recent advancements in the design, development, and characterization of synthetic heme-peroxo‑copper model complexes, which can circumvent the abovementioned limitation, for the investigation of the formation of IP and its O-O cleavage chemistry. Novel findings regarding (a) proton and electron transfer (PT/ET) processes, together with their contributions to exogenous phenol induced O-O cleavage, (b) the stereo-electronic tunability of the secondary coordination sphere (especially hydrogen-bonding) on the geometric and spin state alteration of the heme-peroxo‑copper unit, and (c) a plausible mechanism for the Tyr-His cofactor biogenesis, are discussed in great detail. Additionally, since the ferric-superoxide and the ferryl-oxo (Compound II) species are critically involved in the CcO catalytic cycle, this review also highlights a few fundamental aspects of these heme-only (i.e., without copper) species, including the structural and reactivity influences of electron-donating trans-axial ligands and Lewis acid-promoted H-bonding.

Factors controlling the reactivity of synthetic compound-I Analogs

A high-valent iron(IV)-oxo porphyrin radical cation (FeIV(O)(porph+•) serves as a key, reactive intermediate for a range of heme enzymes, including cytochrome P450 (CYP), horseradish peroxidase (HRP), and catalase (CAT). Synthetic analogs of this intermediate, known as Compound-I (Cpd-I) in the heme enzyme literature, have been generated with different tetrapyrrolic, macrocyclic ligands, including porphyrin derivatives, and the closely related ring-contracted macrocycles, corroles and corrolazines. These synthetic analogs have been useful for assigning and understanding structural and spectroscopic features and examining the reactivity of Cpd-I-like species in controlled and well-defined environments. This review focuses on summarizing recent developments in the synthesis and reactivity of high-valent iron-oxo porphyrinoid complexes in two main classes of reactions, proton-coupled electron transfer (PCET) and oxygen atom transfer (OAT). The relationship between the structure of the complexes and their reactivity is emphasized, including the influence of axial ligation and peripheral macrocyclic substitution, as well as the effects of solvent and secondary coordination spheres on the reactivity of the Cpd-I analogs. In bringing together the latest findings on Cpd-I analogs, this review intends to broaden our current understanding of the factors that control the stability and reactivity of Cpd-I species. This new knowledge should, in turn, point toward new synthetic strategies for constructing catalysts that rely on Cpd-I-like reactive intermediates.

Dimer-assisted mechanism of (un)saturated fatty acid decarboxylation for alkene production

The enzymatic decarboxylation of fatty acids (FAs) represents an advance toward the development of biological routes to produce drop-in hydrocarbons. The current mechanism for the P450-catalyzed decarboxylation has been largely established from the bacterial cytochrome P450 OleTJE. Herein, we describe OleTPRN, a poly-unsaturated alkene-producing decarboxylase that outrivals the functional properties of the model enzyme and exploits a distinct molecular mechanism for substrate binding and chemoselectivity. In addition to the high conversion rates into alkenes from a broad range of saturated FAs without dependence on high salt concentrations, OleTPRN can also efficiently produce alkenes from unsaturated (oleic and linoleic) acids, the most abundant FAs found in nature. OleTPRN performs carbon-carbon cleavage by a catalytic itinerary that involves hydrogen-atom transfer by the heme-ferryl intermediate Compound I and features a hydrophobic cradle at the distal region of the substrate-binding pocket, not found in OleTJE, which is proposed to play a role in the productive binding of long-chain FAs and favors the rapid release of products from the metabolism of short-chain FAs. Moreover, it is shown that the dimeric configuration of OleTPRN is involved in the stabilization of the A-A' helical motif, a second-coordination sphere of the substrate, which contributes to the proper accommodation of the aliphatic tail in the distal and medial active-site pocket. These findings provide an alternative molecular mechanism for alkene production by P450 peroxygenases, creating new opportunities for biological production of renewable hydrocarbons.

Comparing the Catalytic and Structural Characteristics of a 'Short' Unspecific Peroxygenase (UPO) Expressed in Pichia pastoris and Escherichia coli

Unspecific peroxygenases (UPOs) have emerged as valuable tools for the oxygenation of non-activated carbon atoms, as they exhibit high turnovers, good stability and depend only on hydrogen peroxide as the external oxidant for activity. However, the isolation of UPOs from their natural fungal sources remains a barrier to wider application. We have cloned the gene encoding an 'artificial' peroxygenase (artUPO), close in sequence to the 'short' UPO from Marasmius rotula (MroUPO), and expressed it in both the yeast Pichia pastoris and E. coli to compare the catalytic and structural characteristics of the enzymes produced in each system. Catalytic efficiency for the UPO substrate 5-nitro-1,3-benzodioxole (NBD) was largely the same for both enzymes, and the structures also revealed few differences apart from the expected glycosylation of the yeast enzyme. However, the glycosylated enzyme displayed greater stability, as determined by nano differential scanning fluorimetry (nano-DSF) measurements. Interestingly, while artUPO hydroxylated ethylbenzene derivatives to give the (R)-alcohols, also given by a variant of the 'long' UPO from Agrocybe aegerita (AaeUPO), it gave the opposite (S)-series of sulfoxide products from a range of sulfide substrates, broadening the scope for application of the enzymes. The structures of artUPO reveal substantial differences to that of AaeUPO, and provide a platform for investigating the distinctive activity of this and related'short' UPOs.

Bridging the functional gap between reactivity and inhibition in dehaloperoxidase B from Amphitrite ornata: Mechanistic and structural studies with 2,4- and 2,6-dihalophenols

The multifunctional catalytic globin dehaloperoxidase (DHP) from the marine worm Amphitrite ornata was shown to catalyze the H₂O₂-dependent oxidation of 2,4- and 2,6-dihalophenols (DXP; X = F, Cl, Br). Product identification by LC-MS revealed multiple monomeric products with varying degrees of oxidation and/or dehalogenation, as well as oligomers with n up to 6. Mechanistic and ¹⁸O-labeling studies demonstrated sequential dihalophenol oxidation via peroxidase and peroxygenase activities. Binding studies established that 2,4-DXP (X = Cl, Br) have the highest affinities of any known DHP substrate. X-ray crystallography identified different binding positions for 2,4- and 2,6-DXP substrates in the hydrophobic distal pocket of DHP. Correlation between the number of halogens and the substrate binding orientation revealed a halogen-dependent binding motif for mono- (4-halophenol), di- (2,4- and 2,6-dihalophenol) and trihalophenols (2,4,6-trihalopenol). Taken together, the findings here on dihalophenol reactivity with DHP advance our understanding of how these compounds bridge the inhibitory and oxidative functions of their mono- and trihalophenol counterparts, respectively, and provide further insight into the protein structure-function paradigm relevant to multifunctional catalytic globins in comparison to their monofunctional analogs.

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.

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

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

Peroxide-Mediated Oxygenation of Organic Compounds by Fungal Peroxygenases

Unspecific peroxygenases (UPOs), whose sequences can be found in the genomes of thousands of filamentous fungi, many yeasts and certain fungus-like protists, are fascinating biocatalysts that transfer peroxide-borne oxygen (from H2O2 or R-OOH) with high efficiency to a wide range of organic substrates, including less or unactivated carbons and heteroatoms. A twice-proline-flanked cysteine (PCP motif) typically ligates the heme that forms the heart of the active site of UPOs and enables various types of relevant oxygenation reactions (hydroxylation, epoxidation, subsequent dealkylations, deacylation, or aromatization) together with less specific one-electron oxidations (e.g., phenoxy radical formation). In consequence, the substrate portfolio of a UPO enzyme always combines prototypical monooxygenase and peroxidase activities. Here, we briefly review nearly 20 years of peroxygenase research, considering basic mechanistic, molecular, phylogenetic, and biotechnological aspects.

Hemoprotein Catalyzed Oxygenations: P450s, UPOs, and Progress toward Scalable Reactions

The selective oxygenation of nonactivated carbon atoms is an ongoing synthetic challenge, and biocatalysts, particularly hemoprotein oxygenases, continue to be investigated for their potential, given both their sustainable chemistry credentials and also their superior selectivity. However, issues of stability, activity, and complex reaction requirements often render these biocatalytic oxygenations problematic with respect to scalable industrial processes. A continuing focus on Cytochromes P450 (P450s), which require a reduced nicotinamide cofactor and redox protein partners for electron transport, has now led to better catalysts and processes with a greater understanding of process requirements and limitations for both in vitro and whole-cell systems. However, the discovery and development of unspecific peroxygenases (UPOs) has also recently provided valuable complementary technology to P450-catalyzed reactions. UPOs need only hydrogen peroxide to effect oxygenations but are hampered by their sensitivity to peroxide and also by limited selectivity. In this Perspective, we survey recent developments in the engineering of proteins, cells, and processes for oxygenations by these two groups of hemoproteins and evaluate their potential and relative merits for scalable reactions.

A Noncanonical Tryptophan Analogue Reveals an Active Site Hydrogen Bond Controlling Ferryl Reactivity in a Heme Peroxidase

Nature employs high-energy metal-oxo intermediates embedded within enzyme active sites to perform challenging oxidative transformations with remarkable selectivity. Understanding how different local metal-oxo coordination environments control intermediate reactivity and catalytic function is a long-standing objective. However, conducting structure-activity relationships directly in active sites has proven challenging due to the limited range of amino acid substitutions achievable within the constraints of the genetic code. Here, we use an expanded genetic code to examine the impact of hydrogen bonding interactions on ferryl heme structure and reactivity, by replacing the N-H group of the active site Trp51 of cytochrome c peroxidase by an S atom. Removal of a single hydrogen bond stabilizes the porphyrin π-cation radical state of CcP W191F compound I. In contrast, this modification leads to more basic and reactive neutral ferryl heme states, as found in CcP W191F compound II and the wild-type ferryl heme-Trp191 radical pair of compound I. This increased reactivity manifests in a >60-fold activity increase toward phenolic substrates but remarkably has negligible effects on oxidation of the biological redox partner cytc. Our data highlight how Trp51 tunes the lifetimes of key ferryl intermediates and works in synergy with the redox active Trp191 and a well-defined substrate binding site to regulate catalytic function. More broadly, this work shows how noncanonical substitutions can advance our understanding of active site features governing metal-oxo structure and reactivity.

Effects of Heme Electronic Structure and Local Heme Environment on Catalytic Activity of a Peroxidase-Mimicking Heme-DNAzyme

The catalytic cycle of a peroxidase-mimicking heme-DNAzyme involves an iron(IV)oxo porphyrin π-cation radical intermediate known as compound I formed through heterolytic O-O bond cleavage of an Fe³⁺-bound hydroperoxo ligand (Fe-OOH) in compound 0, like that of a heme enzyme such as horseradish peroxidase (HRP). Peroxidase assaying of complexes composed of chemically modified hemes possessing various electron densities of the heme iron atom (ρ_Fe) and parallel-stranded tetrameric G-quadruplex DNAs of oligonucleotides d(TTAGGG), d(TTAGGGT), and d(TTAGGGA) was performed to elucidate the effects of the heme electronic structure and local heme environment on the catalytic activity of the heme-DNAzyme. The study revealed that the DNAzyme activity is enhanced through an increase in the ρ_Fe and general base catalysis of the adenine base adjacent to the heme, which are reminiscent of the "push" and "pull" mechanisms in the catalytic cycle of HRP, respectively, and that the activity of the heme-DNAzyme can be independently controlled through the heme electronic structure and local heme environment. These findings allow a deeper understanding of the structure-function relationship of the peroxidase-mimicking heme-DNAzyme.

Molecular Dynamics Simulations of a Cytochrome P450 from Tepidiphilus thermophilus (P450-TT) Reveal How Its Substrate-Binding Channel Opens

Cytochrome P450s (P450) are important enzymes in biology with useful biochemical reactions in, for instance, drug and xenobiotics metabolisms, biotechnology, and health. Recently, the crystal structure of a new member of the CYP116B family has been resolved. This enzyme is a cytochrome P450 (CYP116B46) from Tepidiphilus thermophilus (P450-TT) and has potential for the oxy-functionalization of organic molecules such as fatty acids, terpenes, steroids, and statins. However, it was thought that the opening to its hitherto identified substrate channel was too small to allow organic molecules to enter. To investigate this, we performed molecular dynamics simulations on the enzyme. The results suggest that the crystal structure is not relaxed, possibly due to crystal packing effects, and that its tunnel structure is constrained. In addition, the simulations revealed two key amino acid residues at the mouth of the channel; a glutamyl and an arginyl. The glutamyl’s side chain tightens and relaxes the opening to the channel in conjunction with the arginyl’s, though the latter’s side chain is less dramatically changed after the initial relaxation of its conformations. Additionally, it was observed that the effect of increased temperature did not considerably affect the dynamics of the enzyme fold, including the relative solvent accessibility of the amino acid residues that make up the substrate channel wall even as compared to the changes that occurred at room temperature. Interestingly, the substrate channel became distinguishable as a prominent tunnel that is likely to accommodate small- to medium-sized organic molecules for bioconversions. That is, P450-TT has the ability to pass appropriate organic substrates to its active site through its elaborate substrate channel, and notably, is able to control or gate any molecules at the opening to this channel.

Molecular Rationale for Partitioning between C-H and C-F Bond Activation in Heme-Dependent Tyrosine Hydroxylase

The heme-dependent l-tyrosine hydroxylases (TyrHs) in natural product biosynthesis constitute a new enzyme family in contrast to the nonheme iron enzymes for DOPA production. A representative TyrH exhibits dual reactivity of C-H and C-F bond cleavage when challenged with 3-fluoro-l-tyrosine (3-F-Tyr) as a substrate. However, little is known about how the enzyme mediates two distinct reactions. Herein, a new TyrH from the thermophilic bacterium Streptomyces sclerotialus (SsTyrH) was functionally and structurally characterized. A de novo crystal structure of the enzyme-substrate complex at 1.89-Å resolution provides the first comprehensive structural study of this hydroxylase. The binding conformation of l-tyrosine indicates that C-H bond hydroxylation is initiated by electron transfer. Mutagenesis studies confirmed that an active site histidine, His88, participates in catalysis. We also obtained a 1.68-Å resolution crystal structure in complex with the monofluorinated substrate, 3-F-Tyr, which shows one binding conformation but two orientations of the fluorine atom with a ratio of 7:3, revealing that the primary factor of product distribution is the substrate orientation. During in crystallo reaction, a ferric-hydroperoxo intermediate (compound 0, Fe³⁺-OOH) was observed with 3-F-Tyr as a substrate based on characteristic spectroscopic features. We determined the crystal structure of this compound 0-type intermediate and refined it to 1.58-Å resolution. Collectively, this study provided the first molecular details of the heme-dependent TyrH and determined the primary factor that dictates the partitioning between the dual reactivities of C-H and C-F bond activation.

Ascorbate Peroxidase Compound II Is an Iron(IV) Oxo Species

The protonation state of the iron(IV) oxo (or ferryl) form of ascorbate peroxidase compound II (APX-II) is a subject of debate. It has been reported that this intermediate is best described as an iron(IV) hydroxide species. Neutron diffraction data obtained from putative APX-II crystals indicate a protonated oxygenic ligand at 1.88 Å from the heme iron. This finding, if correct, would be unprecedented. A basic iron(IV) oxo species has yet to be spectroscopically observed in a histidine-ligated heme enzyme. The importance of ferryl basicity lies in its connection to our fundamental understanding of C-H bond activation. Basic ferryl species have been proposed to facilitate the oxidation of inert C-H bonds, reactions that are unknown for histidine-ligated hemes enzymes. To provide further insight into the protonation status of APX-II, we examined the intermediate using a combination of Mössbauer and X-ray absorption spectroscopies. Our data indicate that APX-II is an iron(IV) oxo species with an Fe-O bond distance of 1.68 Å, a K-edge pre-edge absorption of 18 units, and Mössbauer parameters of ΔEq = 1.65 mm/s and δ = 0.03 mm/s.

Mapping and Exploiting the Promiscuity of OxyB toward the Biocatalytic Production of Vancomycin Aglycone Variants

Vancomycin is one of the most important clinical antibiotics in the fight against infectious disease. Its biological activity relies on three aromatic cross-links, which create a cup-shaped topology and allow tight binding to nascent peptidoglycan chains. The cytochrome P450 enzymes OxyB, OxyA, and OxyC have been shown to introduce these synthetically challenging aromatic linkages. The ability to utilize the P450 enzymes in a chemo-enzymatic scheme to generate vancomycin derivatives is appealing but requires a thorough understanding of their reactivities and mechanisms. Herein, we systematically explore the scope of OxyB biocatalysis and report installation of diverse diaryl ether and biaryl cross-links with varying macrocycle sizes and compositions, when the enzyme is presented with modified vancomycin precursor peptides. The structures of the resulting products were determined using one-dimensional/two-dimensional nuclear magnetic resonance spectroscopy, high-resolution mass spectrometry (HR-MS), tandem HR-MS, and isotopic labeling, as well as ultraviolet-visible light absorption and fluorescence emission spectroscopies. An exploration of the biological activities of these alternative OxyB products surprisingly revealed antifungal properties. Taking advantage of the promiscuity of OxyB, we chemo-enzymatically generated a vancomycin aglycone variant containing an expanded macrocycle. Mechanistic implications for OxyB and future directions for creating vancomycin analogue libraries are discussed.

M[TPP]Cl (M = Fe or Mn)-Catalyzed Oxidative Amination of Phenols by Primary and Secondary Anilines

Iron- and manganese-catalyzed para-selective oxidative amination of (4-R)phenols by primary and secondary anilines was developed. Depending on the identity of the R group, the products of this efficient reaction are either benzoquinone anils (C–N coupling) that are produced via a sequential oxidative amination/dehydrogenation (R = H), oxidative amination/elimination (R = OMe) steps, or N,O-biaryl compounds (C–C coupling) that are formed when R = alkyl through an oxidative amination/[3,3]-sigmatropic rearrangement (quinamine rearrangement) process.

Rewiring the "Push-Pull" Catalytic Machinery of a Heme Enzyme Using an Expanded Genetic Code

Nature employs a limited number of genetically encoded axial ligands to control diverse heme enzyme activities. Deciphering the functional significance of these ligands requires a quantitative understanding of how their electron-donating capabilities modulate the structures and reactivities of the iconic ferryl intermediates compounds I and II. However, probing these relationships experimentally has proven to be challenging as ligand substitutions accessible via conventional mutagenesis do not allow fine tuning of electron donation and typically abolish catalytic function. Here, we exploit engineered translation components to replace the histidine ligand of cytochrome c peroxidase (CcP) by a less electron-donating N_δ-methyl histidine (Me-His) with little effect on the enzyme structure. The rate of formation (k₁) and the reactivity (k₂) of compound I are unaffected by ligand substitution. In contrast, proton-coupled electron transfer to compound II (k₃) is 10-fold slower in CcP Me-His, providing a direct link between electron donation and compound II reactivity, which can be explained by weaker electron donation from the Me-His ligand (“the push”) affording an electron-deficient ferryl oxygen with reduced proton affinity (“the pull”). The deleterious effects of the Me-His ligand can be fully compensated by introducing a W51F mutation designed to increase “the pull” by removing a hydrogen bond to the ferryl oxygen. Analogous substitutions in ascorbate peroxidase lead to similar activity trends to those observed in CcP, suggesting that a common mechanistic strategy is employed by enzymes using distinct electron transfer pathways. Our study highlights how noncanonical active site substitutions can be used to directly probe and deconstruct highly evolved bioinorganic mechanisms.

Heme-FeIII Superoxide, Peroxide and Hydroperoxide Thermodynamic Relationships: FeIII-O2•- Complex H-Atom Abstraction Reactivity

Establishing redox and thermodynamic relationships between metal-ion-bound O2 and its reduced (and protonated) derivatives is critically important for a full understanding of (bio)chemical processes involving dioxygen processing. Here, a ferric heme peroxide complex, [(F8)FeIII-(O22-)]- (P) (F8 = tetrakis(2,6-difluorophenyl)porphyrinate), and a superoxide complex, [(F8)FeIII-(O2•-)] (S), are shown to be redox interconvertible. Using Cr(η-C6H6)2, an equilibrium state where S and P are present is established in tetrahydrofuran (THF) at -80 °C, allowing determination of the reduction potential of S as -1.17 V vs Fc+/0. P could be protonated with 2,6-lutidinium triflate, yielding the low-spin ferric hydroperoxide species, [(F8)FeIII-(OOH)] (HP). Partial conversion of HP back to P using a derivatized phosphazene base gave a P/HP equilibrium mixture, leading to the determination of pKa = 28.8 for HP (THF, -80 °C). With the measured reduction potential and pKa, the O-H bond dissociation free energy (BDFE) of hydroperoxide species HP was calculated to be 73.5 kcal/mol, employing the thermodynamic square scheme and Bordwell relationship. This calculated O-H BDFE of HP, in fact, lines up with an experimental demonstration of the oxidizing ability of S via hydrogen atom transfer (HAT) from TEMPO-H (2,2,6,6-tetramethylpiperdine-N-hydroxide, BDFE = 66.5 kcal/mol in THF), forming the hydroperoxide species HP and TEMPO radical. Kinetic studies carried out with TEMPO-H(D) reveal second-order behavior, kH = 0.5, kD = 0.08 M-1 s-1 (THF, -80 °C); thus, the hydrogen/deuterium kinetic isotope effect (KIE) = 6, consistent with H-atom abstraction by S being the rate-determining step. This appears to be the first case where experimentally derived thermodynamics lead to a ferric heme hydroperoxide OO-H BDFE determination, that FeIII-OOH species being formed via HAT reactivity of the partner ferric heme superoxide complex.

Enhanced Rates of C-H Bond Cleavage by a Hydrogen-Bonded Synthetic Heme High-Valent Iron(IV) Oxo Complex

Secondary coordination sphere interactions are critical in facilitating the formation, stabilization, and enhanced reactivity of high-valent oxidants required for essential biochemical processes. Herein, we compare the C-H bond oxidizing capabilities of spectroscopically characterized synthetic heme iron(IV) oxo complexes, F8Cmpd-II (F8 = tetrakis(2,6-difluorophenyl)porphyrinate), and a 2,6-lutidinium triflate (LutH+) Lewis acid adduct involving ferryl O-atom hydrogen-bonding, F8Cmpd-II(LutH+). Second-order rate constants utilizing C-H and C-D substrates were obtained by UV-vis spectroscopic monitoring, while products were characterized and quantified by EPR spectroscopy and gas chromatography (GC). With xanthene, F8Cmpd-II(LutH+) reacts 40 times faster (k2 = 14.2 M-1 s-1; -90 °C) than does F8Cmpd-II, giving bixanthene plus xanthone and the heme product [F8FeIIIOH2]+. For substrates with greater C-H bond dissociation energies (BDEs) F8Cmpd-II(LutH+) reacts with the second order rate constants k2(9,10-dihydroanthracene; DHA) = 0.485 M-1 s-1 and k2(fluorene) = 0.102 M-1 s-1 (-90 °C); by contrast, F8Cmpd-II is unreactive toward these substrates. For xanthene vs xanthene-(d2), large, nonclassical deuterium kinetic isotope effects are roughly estimated for both F8Cmpd-II and F8Cmpd-II(LutH+). The deuterated H-bonded analog, F8Cmpd-II(LutD+), was also prepared; for the reaction with DHA, an inverse KIE (compared to F8Cmpd-II(LutH+)) was observed. This work originates/inaugurates experimental investigation of the reactivity of authentic H-bonded heme-based FeIV═O compounds, critically establishing the importance of oxo H-bonding (or protonation) in heme complexes and enzyme active sites.

NMR Reveals That a Highly Reactive Nonheme FeIV =O Complex Retains Its Six-Coordinate Geometry and S=1 State in Solution

The [Fe^IV (O)(Me₃ NTB)]²⁺ (Me₃ NTB=tris[(1-methyl-benzimidazol-2-yl)methyl]amine) complex 1 has been shown by Mössbauer spectroscopy to have an S=1 ground state at 4 K, but is proposed to become an S=2 trigonal-bipyramidal species at higher temperatures based on a DFT model to rationalize its very high C-H bond-cleavage reactivity. In this work, ¹ H NMR spectroscopy was used to determine that 1 does not have C₃ -symmetry in solution and is not an S=2 species. Our results show that 1 is unique among nonheme Fe^IV =O complexes in retaining its S=1 spin state and high reactivity at 193 K, providing evidence that S=1 Fe^IV =O complexes can be as reactive as their S=2 counterparts. This result emphasizes the need to identify factors besides the ground spin state of the Fe^IV =O center to rationalize nonheme oxoiron(IV) reactivity.

Heme and Nonheme High-Valent Iron and Manganese Oxo Cores in Biological and Abiological Oxidation Reactions

Utilization of O₂ as an abundant and environmentally benign oxidant is of great interest in the design of bioinspired synthetic catalytic oxidation systems. Metalloenzymes activate O₂ by employing earth-abundant metals and exhibit diverse reactivities in oxidation reactions, including epoxidation of olefins, functionalization of alkane C-H bonds, arene hydroxylation, and syn-dihydroxylation of arenes. Metal-oxo species are proposed as reactive intermediates in these reactions. A number of biomimetic metal-oxo complexes have been synthesized in recent years by activating O₂ or using artificial oxidants at iron and manganese centers supported on heme or nonheme-type ligand environments. Detailed reactivity studies together with spectroscopy and theory have helped us understand how the reactivities of these metal-oxygen intermediates are controlled by the electronic and steric properties of the metal centers. These studies have provided important insights into biological reactions, which have contributed to the design of biologically inspired oxidation catalysts containing earth-abundant metals like iron and manganese. In this Outlook article, we survey a few examples of these advances with particular emphasis in each case on the interplay of catalyst design and our understanding of metalloenzyme structure and function.

A Mononuclear Nonheme Iron(IV)-Amido Complex Relevant for the Compound II Chemistry of Cytochrome P450

A mononuclear nonheme iron(IV)-amido complex bearing a tetraamido macrocyclic ligand, [(TAML)Fe^IV(NHTs)]^- (1), was synthesized via a hydrogen atom (H atom) abstraction reaction of an iron(V)-imido complex, [(TAML)Fe^V(NTs)]^- (2), and fully characterized using various spectroscopies. We then investigated (1) the p K_a of 1, (2) the reaction of 1 with a carbon-centered radical, and (3) the H atom abstraction reaction of 1. To the best of our knowledge, the present study reports for the first time the synthesis and chemical properties/reactions of a high-valent iron(IV)-amido complex.

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

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

Stepwise O-Atom Transfer in Heme-Based Tryptophan Dioxygenase: Role of Substrate Ammonium in Epoxide Ring Opening

Heme-based tryptophan dioxygenases are established immunosuppressive metalloproteins with significant biomedical interest. Here, we synthesized two mechanistic probes to specifically test if the α-amino group of the substrate directly participates in a critical step of the O atom transfer during catalysis in human tryptophan 2,3-dioxygenase (TDO). Substitution of the nitrogen atom of the substrate to a carbon (probe 1) or oxygen (probe 2) slowed the catalytic step following the first O atom transfer such that transferring the second O atom becomes less likely to occur, although the dioxygenated products were observed with both probes. A monooxygenated product was also produced from probe 2 in a significant quantity. Analysis of this new product by HPLC coupled UV-vis spectroscopy, high-resolution mass spectrometry, 1H NMR, 13C NMR, HSQC, HMBC, and infrared (IR) spectroscopies concluded that this monooxygenated product is a furoindoline compound derived from an unstable epoxyindole intermediate. These results prove that small molecules can manipulate the stepwise O atom transfer reaction of TDO and provide a showcase for a tunable mechanism by synthetic compounds. The product analysis results corroborate the presence of a substrate-based epoxyindole intermediate during catalysis and provide the first substantial experimental evidence for the involvement of the substrate α-amino group in the epoxide ring-opening step during catalysis. This combined synthetic, biochemical, and biophysical study establishes the catalytic role of the α-amino group of the substrate during the O atom transfer reactions and thus represents a substantial advance to the mechanistic comprehension of the heme-based tryptophan dioxygenases.

A Reactive Manganese(IV)-Hydroxide Complex: A Missing Intermediate in Hydrogen Atom Transfer by High-Valent Metal-Oxo Porphyrinoid Compounds

High-valent metal-hydroxide species are invoked as critical intermediates in both catalytic, metal-mediated O₂ activation (e.g., by Fe porphyrin in Cytochrome P450) and O₂ production (e.g., by the Mn cluster in Photosystem II). However, well-characterized mononuclear M^IV(OH) complexes remain a rarity. Herein we describe the synthesis of Mn^IV(OH)(ttppc) (3) (ttppc = tris(2,4,6-triphenylphenyl) corrole), which has been characterized by X-ray diffraction (XRD). The large steric encumbrance of the ttppc ligand allowed for isolation of 3. The complexes Mn^V(O)(ttppc) (4) and Mn^III(H₂O)(ttppc) (1·H₂O) were also synthesized and structurally characterized, providing a series of Mn complexes related only by the transfer of hydrogen atoms. Both 3 and 4 abstract an H atom from the O-H bond of 2,4-di- tert-butylphenol (2,4-DTBP) to give a radical coupling product in good yield (3 = 90(2)%, 4 = 91(5)%). Complex 3 reacts with 2,4-DTBP with a rate constant of k₂ = 2.73(12) × 10⁴ M^-1 s^-1, which is ∼3 orders of magnitude larger than 4 ( k₂ = 17.4(1) M^-1 s^-1). Reaction of 3 with a series of para-substituted 2,6-di- tert-butylphenol derivatives (4-X-2,6-DTBP; X = OMe, Me, tBu, H) gives rate constants in the range k₂ = 510(10)-36(1.4) M^-1 s^-1 and led to Hammett and Marcus plot correlations. Together with kinetic isotope effect measurements, it is concluded that O-H cleavage occurs by a concerted H atom transfer (HAT) mechanism and that the Mn^IV(OH) complex is a much more powerful H atom abstractor than the higher-valent Mn^V(O) complex, or even some Fe^IV(O) complexes.

Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins

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

Immune-modulating enzyme indoleamine 2,3-dioxygenase is effectively inhibited by targeting its apo-form

Indoleamine 2,3-dioxygenase (IDO1) is a heme protein that catalyzes the dioxygenation of tryptophan. Cells expressing this activity are able to profoundly alter their surrounding environment to suppress the immune response. Cancer cells exploit this pathway to avoid immune-mediated destruction. Through a range of kinetic, structural, and cellular assays, we show that two classes of highly selective inhibitors of IDO1 act by competing with heme binding to apo-IDO1. This shows that IDO1 is dynamically bound to its heme cofactor in what is likely a critical step in the regulation of this enzyme. These results have elucidated a previously undiscovered role for the ubiquitous heme cofactor in immune regulation, and it suggests that other heme proteins in biology may be similarly regulated.

For cancer cells to survive and proliferate, they must escape normal immune destruction. One mechanism by which this is accomplished is through immune suppression effected by up-regulation of indoleamine 2,3-dioxygenase (IDO1), a heme enzyme that catalyzes the oxidation of tryptophan to N-formylkynurenine. On deformylation, kynurenine and downstream metabolites suppress T cell function. The importance of this immunosuppressive mechanism has spurred intense interest in the development of clinical IDO1 inhibitors. Herein, we describe the mechanism by which a class of compounds effectively and specifically inhibits IDO1 by targeting its apo-form. We show that the in vitro kinetics of inhibition coincide with an unusually high rate of intrinsic enzyme–heme dissociation, especially in the ferric form. X-ray crystal structures of the inhibitor–enzyme complexes show that heme is displaced from the enzyme and blocked from rebinding by these compounds. The results reveal that apo-IDO1 serves as a unique target for inhibition and that heme lability plays an important role in posttranslational regulation.

Spectroscopic studies of the cytochrome P450 reaction mechanisms

The cytochrome P450 monooxygenases (P450s) are thiolate heme proteins that can, often under physiological conditions, catalyze many distinct oxidative transformations on a wide variety of molecules, including relatively simple alkanes or fatty acids, as well as more complex compounds such as steroids and exogenous pollutants. They perform such impressive chemistry utilizing a sophisticated catalytic cycle that involves a series of consecutive chemical transformations of heme prosthetic group. Each of these steps provides a unique spectral signature that reflects changes in oxidation or spin states, deformation of the porphyrin ring or alteration of dioxygen moieties. For a long time, the focus of cytochrome P450 research was to understand the underlying reaction mechanism of each enzymatic step, with the biggest challenge being identification and characterization of the powerful oxidizing intermediates. Spectroscopic methods, such as electronic absorption (UV-Vis), electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electron nuclear double resonance (ENDOR), Mössbauer, X-ray absorption (XAS), and resonance Raman (rR), have been useful tools in providing multifaceted and detailed mechanistic insights into the biophysics and biochemistry of these fascinating enzymes. The combination of spectroscopic techniques with novel approaches, such as cryoreduction and Nanodisc technology, allowed for generation, trapping and characterizing long sought transient intermediates, a task that has been difficult to achieve using other methods. Results obtained from the UV-Vis, rR and EPR spectroscopies are the main focus of this review, while the remaining spectroscopic techniques are briefly summarized. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.

Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution

Extensive research efforts have been dedicated to describing degradation of wood, which is a complex process; hence, microorganisms have evolved different enzymatic and non-enzymatic strategies to utilize this plentiful plant material. This review describes a number of fungal and bacterial organisms which have developed both competitive and mutualistic strategies for the decomposition of wood and to thrive in different ecological niches. Through the analysis of the enzymatic machinery engaged in wood degradation, it was possible to elucidate different strategies of wood decomposition which often depend on ecological niches inhabited by given organism. Moreover, a detailed description of low molecular weight compounds is presented, which gives these organisms not only an advantage in wood degradation processes, but seems rather to be a new evolutionatory alternative to enzymatic combustion. Through analysis of genomics and secretomic data, it was possible to underline the probable importance of certain wood-degrading enzymes produced by different fungal organisms, potentially giving them advantage in their ecological niches. The paper highlights different fungal strategies of wood degradation, which possibly correlates to the number of genes coding for secretory enzymes. Furthermore, investigation of the evolution of wood-degrading organisms has been described.

meso-Tetraphenylporphyrin Iron Chloride Catalyzed Selective Oxidative Cross-Coupling of Phenols

A novel catalytic system for oxidative cross-coupling of readily oxidized phenols with poor nucleophilic phenolic partners based on an iron meso-tetraphenylporphyrin chloride (Fe[TPP]Cl) complex in 1,1,1,3,3,3-hexafluoropropan-2-ol (HFIP) was developed. The unique chemoselectivity of this reaction is attributed to the coupling between a liberated phenoxyl radical with an iron-ligated phenolic coupling partner. The conditions are scalable for preparing a long list of unsymmetrical biphenols assembled from a less reactive phenolic unit substituted with alkyl or halide groups.

The Enigmatic P450 Decarboxylase OleT Is Capable of, but Evolved To Frustrate, Oxygen Rebound Chemistry

OleT is a cytochrome P450 enzyme that catalyzes the removal of carbon dioxide from variable chain length fatty acids to form 1-alkenes. In this work, we examine the binding and metabolic profile of OleT with shorter chain length (n ≤ 12) fatty acids that can form liquid transportation fuels. Transient kinetics and product analyses confirm that OleT capably activates hydrogen peroxide with shorter substrates to form the high-valent intermediate Compound I and largely performs C-C bond scission. However, the enzyme also produces fatty alcohol side products using the high-valent iron oxo chemistry commonly associated with insertion of oxygen into hydrocarbons. When presented with a short chain fatty acid that can initiate the formation of Compound I, OleT oxidizes the diagnostic probe molecules norcarane and methylcyclopropane in a manner that is reminiscent of reactions of many CYP hydroxylases with radical clock substrates. These data are consistent with a decarboxylation mechanism in which Compound I abstracts a substrate hydrogen atom in the initial step. Positioning of the incipient substrate radical is a crucial element in controlling the efficiency of activated OH rebound.

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.

Fast Hydrogen Atom Abstraction by a Hydroxo Iron(III) Porphyrazine

A reactive hydroxoferric porphyrazine complex, [(PyPz)Fe^III(OH) (OH₂)]⁴⁺ (1, PyPz = tetramethyl-2,3-pyridino porphyrazine), has been prepared via one-electron oxidation of the corresponding ferrous species [(PyPz)Fe^II(OH₂)₂]⁴⁺ (2). Electrochemical analysis revealed a pH-dependent and remarkably high Fe^III-OH/Fe^II-OH₂ reduction potential of 680 mV vs Ag/AgCl at pH 5.2. Nernstian behavior from pH 2 to pH 8 indicates a one-proton, one-electron interconversion throughout that range. The O-H bond dissociation energy of the Fe^II-OH₂ complex was estimated to be 84 kcal mol^-1. Accordingly, 1 reacts rapidly with a panel of substrates via C-H hydrogen atom transfer (HAT), reducing 1 to [(PyPz)Fe^II(OH₂)₂]⁴⁺ (2). The second-order rate constant for the reaction of [(PyPz)Fe^III(OH) (OH₂)]⁴⁺ with xanthene was 2.22 × 10³ M^-1 s^-1, 5-6 orders of magnitude faster than other reported Fe^III-OH complexes and faster than many ferryl complexes.