Biodegradation of Herbicides by a Plant Nonheme Iron Dioxygenase: Mechanism and Selectivity of Substrate Analogues

Aryloxyalkanoate dioxygenases are unique herbicide biodegrading nonheme iron enzymes found in plants and hence, from environmental and agricultural point of view they are important and valuable. However, they often are substrate specific and little is known on the details of the mechanism and the substrate scope. To this end, we created enzyme models and calculate the mechanism for 2,4-dichlorophenoxyacetic acid biodegradation and 2-methyl substituted analogues by density functional theory. The work shows that the substrate binding is tight and positions the aliphatic group close to the metal center to enable a chemoselective reaction mechanism to form the C²-hydroxy products, whereas the aromatic hydroxylation barriers are well higher in energy. Subsequently, we investigated the metabolism of R- and S-methyl substituted inhibitors and show that these do not react as efficiently as 2,4-dichlorophenoxyacetic acid substrate due to stereochemical clashes in the active site and particularly for the R-isomer give high rebound barriers.     

Differences and Comparisons of the Properties and Reactivities of Iron(III)–hydroperoxo Complexes with Saturated Coordination Sphere

Heme and nonheme monoxygenases and dioxygenases catalyze important oxygen atom transfer reactions to substrates in the body. It is now well established that the cytochrome P450 enzymes react through the formation of a high‐valent iron(IV)–oxo heme cation radical. Its precursor in the catalytic cycle, the iron(III)–hydroperoxo complex, was tested for catalytic activity and found to be a sluggish oxidant of hydroxylation, epoxidation and sulfoxidation reactions. In a recent twist of events, evidence has emerged of several nonheme iron(III)–hydroperoxo complexes that appear to react with substrates via oxygen atom transfer processes. Although it was not clear from these studies whether the iron(III)–hydroperoxo reacted directly with substrates or that an initial O?O bond cleavage preceded the reaction. Clearly, the catalytic activity of heme and nonheme iron(III)–hydroperoxo complexes is substantially different, but the origins of this are still poorly understood and warrant a detailed analysis. In this work, an extensive computational analysis of aromatic hydroxylation by biomimetic nonheme and heme iron systems is presented, starting from an iron(III)–hydroperoxo complex with pentadentate ligand system (L₅²). Direct C?O bond formation by an iron(III)–hydroperoxo complex is investigated, as well as the initial heterolytic and homolytic bond cleavage of the hydroperoxo group. The calculations show that [(L₅²)Fe^III(OOH)]²⁺ should be able to initiate an aromatic hydroxylation process, although a low‐energy homolytic cleavage pathway is only slightly higher in energy. A detailed valence bond and thermochemical analysis rationalizes the differences in chemical reactivity of heme and nonheme iron(III)–hydroperoxo and show that the main reason for this particular nonheme complex to be reactive comes from the fact that they homolytically split the O?O bond, whereas a heterolytic O?O bond breaking in heme iron(III)–hydroperoxo is found.     

Highly Reactive Nonheme Iron(III) Iodosylarene Complexes in Alkane Hydroxylation and Sulfoxidation Reactions

High‐spin iron(III) iodosylarene complexes bearing an N‐methylated cyclam ligand are synthesized and characterized using various spectroscopic methods. The nonheme high‐spin iron(III) iodosylarene intermediates are highly reactive oxidants capable of activating strong C? H bonds of alkanes; the reactivity of the iron(III) iodosylarene intermediates is much greater than that of the corresponding iron(IV) oxo complex. The electrophilic character of the iron(III) iodosylarene complexes is demonstrated in sulfoxidation reactions.     

Demonstration of the Heterolytic OO Bond Cleavage of Putative Nonheme Iron(II)OOH(R) Complexes for Fenton and Enzymatic Reactions

One‐electron reduction of mononuclear nonheme iron(III) hydroperoxo (Fe^III? OOH) and iron(III) alkylperoxo (Fe^III? OOR) complexes by ferrocene (Fc) derivatives resulted in the formation of the corresponding iron(IV) oxo complexes. The conversion rates were dependent on the concentration and oxidation potentials of the electron donors, thus indicating that the reduction of the iron(III) (hydro/alkyl)peroxo complexes to their one‐electron reduced iron(II) (hydro/alkyl)peroxo species is the rate‐determining step, followed by the heterolytic O? O bond cleavage of the putative iron(II) (hydro/alkyl)peroxo species to give the iron(IV) oxo complexes. Product analysis supported the heterolytic O? O bond‐cleavage mechanism. The present results provide the first example showing the one‐electron reduction of iron(III) (hydro/alkyl)peroxo complexes and the heterolytic O? O bond cleavage of iron(II) (hydro/alkyl)peroxo species to form iron(IV) oxo intermediates which occur in nonheme iron enzymatic and Fenton reactions.     

Enhancing Tris(pyrazolyl)borate-Based Models of Cysteine/Cysteamine Dioxygenases through Steric Effects: Increased Reactivities,Full Product Characterization and Hints to Initial Superoxide Formation

The design of biomimetic model complexes for the cysteine dioxygenase (CDO) and cysteamine dioxygenase (ADO) is reported, where the 3-His coordination of the iron ion is simulated by three pyrazole donors of a trispyrazolyl borate ligand (Tp) and protected cysteine and cysteamine represent substrate ligands. It is found that the replacement of phenyl groups—attached at the 3-positions of the pyrazole units in a previous model—by mesityl residues has massive consequences, as the latter arrange to a more spacious reaction pocket. Thus, the reaction with O₂ proceeds much faster and afterwards the first structural characterization of an iron(II) η²-O,O-sulfinate product became possible. If one of the three Tp-mesityl groups is placed in the 5-position, an even larger reaction pocket results, which leads to yet faster rates and accumulation of a reaction intermediate at low temperatures, as shown by UV/Vis and Mössbauer spectroscopy. After comparison with the results of investigations on the cobalt analogues this intermediate is tentatively assigned to an iron(III) superoxide species.     

细胞色素P450酶催化的烷烃选择性羟化

碳氢键选择氧化是合成化学领域的重要课题,其中烷烃选择性羟化反应更是面临着化学选择性、区域选择性和立体选择性等多重挑战.细胞色素P450酶广泛分布于动植物和微生物体内,是公认的多功能生物氧化催化剂. P450酶对惰性C—H键的选择性氧化具有独特优势,在催化烷烃选择性羟化反应方面拥有巨大潜力.本综述简述了P450单加氧酶及其催化烷烃选择性羟化的反应机理,梳理了来自CYP153家族、CYP52家族和其他家族的天然P450酶催化各类烷烃底物的氧化反应和选择性,讨论了理性设计和定向进化策略在开发烷烃羟化P450突变酶过程中的经典案例,介绍了底物工程、诱饵分子、双功能小分子协同催化等几种化学活化P450酶的策略及其在烷烃羟化上的应用,探讨了P450酶在烷烃选择性羟化方面所面临的挑战和解决途径,并展望了其应用前景.     

Structural and Dynamic Basis of Human Cytochrome P450 7B1: A Survey of Substrate Selectivity and Major Active Site Access Channels

Cytochrome P450 (CYP) 7B1 is a steroid cytochrome P450 7α‐hydroxylase that has been linked directly with bile salt synthesis and hereditary spastic paraplegia type 5 (SPG5). The enzyme provides the primary metabolic route for neurosteroids dehydroepiandrosterone (DHEA), cholesterol derivatives 25‐hydroxycholesterol (25‐HOChol), and other steroids such as 5α‐androstane‐3β,17β‐diol (anediol), and 5α‐androstene‐3β,17β‐diol (enediol). A series of investigations including homology modeling, molecular dynamics (MD), and automatic docking, combined with the results of previous experimental site‐directed mutagenesis studies and access channels analysis, have identified the structural features relevant to the substrate selectivity of CYP7B1. The results clearly identify the dominant access channels and critical residues responsible for ligand binding. Both binding free energy analysis and total interaction energy analysis are consistent with the experimental conclusion that 25‐HOChol is the best substrate. According to 20 ns MD simulations, the Phe cluster residues that lie above the active site, particularly Phe489, are proposed to merge the active site with the adjacent channel to the surface and accommodate substrate binding in a reasonable orientation. The investigation of CYP7B1–substrate binding modes provides detailed insights into the poorly understood structural features of human CYP7B1 at the atomic level, and will be valuable information for drug development and protein engineering.     

Spectroscopic and Computational Study of a Nonheme Iron Nitrosyl Center in a Biosynthetic Model of Nitric Oxide Reductase

A major barrier to understanding the mechanism of nitric oxide reductases (NORs) is the lack of a selective probe of NO binding to the nonheme Fe_B center. By replacing the heme in a biosynthetic model of NORs, which structurally and functionally mimics NORs, with isostructural ZnPP, the electronic structure and functional properties of the Fe_B nitrosyl complex was probed. This approach allowed observation of the first S=3/2 nonheme {FeNO}⁷ complex in a protein‐based model system of NOR. Detailed spectroscopic and computational studies show that the electronic state of the {FeNO}⁷ complex is best described as a high spin ferrous iron (S=2) antiferromagnetically coupled to an NO radical (S= 1/2) [Fe²⁺‐NO^.]. The radical nature of the Fe_B‐bound NO would facilitate N? N bond formation by radical coupling with the heme‐bound NO. This finding, therefore, supports the proposed trans mechanism of NO reduction by NORs.     

Beneficial Effect of Acetic Acid on the Formation of FeIII(OOH) Species and on the Catalytic Activity of Bioinspired Nonheme FeII Complexes.

Three new amine/pyridine Fe^II complexes bearing pentadentate ligand with one, two or three electron enriched 4-methoxy-3,5-dimethylpyridine were used as catalysts for the oxidation of small organic molecules by hydrogen peroxide. The distribution of products formed suggests that these ligands are not enough electron donating to promote the O−O heterolytic cleavage of the oxidant in order to generate selective Fe^V(O) species. Using acetic acid in the reaction mixtures results in a significant increase of the efficiency of these catalytic systems. Our investigations show that the use of AcOH leads to the protonation/dissociation of a pyridyl moiety and the formation of (N₄)Fe^II(OAc)(OH) species. These complexes readily react with excess hydrogen peroxide to yield (N₄)Fe^III(OAc)(OOH) intermediates. These latter intermediates are proposed to evolve into (N₄)Fe^IV(OAc)(O), which are more efficient than the usual (N₄)Fe^IV(O) and (N₅)Fe^IV(O).     

Water as an Oxygen Source in the Generation of Mononuclear Nonheme Iron(IV) Oxo Complexes

Give me an “O”! Mononuclear nonheme iron(IV) oxo complexes have been generated using water as an oxygen source and cerium(IV) as an oxidant. The high‐yield oxygenation of organic substrates in this system (see picture, Fe green, O red, N blue, C gray) is catalyzed by iron(II) complexes. The source of oxygen in the iron(IV) oxo complexes and the oxygenated products has been assigned unambiguously by isotopic labeling experiments.

     

Nonheme Iron Mediated Oxidation of Light Alkanes with Oxone: Characterization of Reactive Oxoiron(IV) Ligand Cation Radical Intermediates by Spectroscopic Studies and DFT Calculations

The oxidation of light alkanes that is catalyzed by heme and nonheme iron enzymes is widely proposed to involve highly reactive {Fe^V?O} species or {Fe^IV?O} ligand cation radicals. The identification of these high‐valent iron species and the development of an iron‐catalyzed oxidation of light alkanes under mild conditions are of vital importance. Herein, a combination of tridentate and bidentate ligands was used for the generation of highly reactive nonheme {Fe?O} species. A method that employs [Fe^III(Me₃tacn)(Cl‐acac)Cl]⁺ as a catalyst in the presence of oxone was developed for the oxidation of hydrocarbons, including cyclohexane, propane, and ethane (Me₃tacn=1,4,7‐trimethyl‐1,4,7‐triazacyclononane; Cl‐acac=3‐chloro‐acetylacetonate). The complex [Fe^III(Tp)₂]⁺ and oxone enabled stoichiometric oxidation of propane and ethane. ESI‐MS, EPR and UV/Vis spectroscopy, ¹⁸O labeling experiments, and DFT studies point to [Fe^IV(Me₃tacn)({Cl‐acac}^.+)(O)]²⁺ as the catalytically active species.     

Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes

AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N¹‐methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate‐determining hydrogen‐atom abstraction on competitive σ‐ and π‐pathways on a quintet spin‐state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen‐bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained.     

Unraveling the Mechanism of Water Oxidation Catalyzed by Nonheme Iron Complexes

Density functional theory (DFT) is employed to: 1) propose a viable catalytic cycle consistent with our experimental results for the mechanism of chemically driven (Ce^IV) O₂ generation from water, mediated by nonheme iron complexes; and 2) to unravel the role of the ligand on the nonheme iron catalyst in the water oxidation reaction activity. To this end, the key features of the water oxidation catalytic cycle for the highly active complexes [Fe(OTf)₂(Pytacn)] (Pytacn: 1‐(2′‐pyridylmethyl)‐4,7‐dimethyl‐1,4,7‐triazacyclononane; OTf: CF₃SO₃^?) ( 1 ) and [Fe(OTf)₂(mep)] (mep: N,N′‐bis(2‐pyridylmethyl)‐N,N′‐dimethyl ethane‐1,2‐diamine) ( 2 ) as well as for the catalytically inactive [Fe(OTf)₂(tmc)] (tmc: N,N′,N′′,N′′′‐tetramethylcyclam) ( 3 ) and [Fe(NCCH₃)(^MePy₂CH‐tacn)](OTf)₂ (^MePy₂CH‐tacn: N‐(dipyridin‐2‐yl)methyl)‐N′,N′′‐dimethyl‐1,4,7‐triazacyclononane) ( 4 ) were analyzed. The DFT computed catalytic cycle establishes that the resting state under catalytic conditions is a [Fe^IV(O)(OH₂)(LN₄)]²⁺ species (in which LN₄=Pytacn or mep) and the rate‐determining step is the O?O bond‐formation event. This is nicely supported by the remarkable agreement between the experimental (ΔG^≠=17.6±1.6 kcal mol^?1) and theoretical (ΔG^≠=18.9 kcal mol^?1) activation parameters obtained for complex 1 . The O?O bond formation is performed by an iron(V) intermediate [Fe^V(O)(OH)(LN₄)]²⁺ containing a cis‐Fe^V(O)(OH) unit. Under catalytic conditions (Ce^IV, pH 0.8) the high oxidation state Fe^V is only thermodynamically accessible through a proton‐coupled electron‐transfer (PCET) process from the cis‐[Fe^IV(O)(OH₂)(LN₄)]²⁺ resting state. Formation of the [Fe^V(O)(LN₄)]³⁺ species is thermodynamically inaccessible for complexes 3 and 4 . Our results also show that the cis‐labile coordinative sites in iron complexes have a beneficial key role in the O?O bond‐formation process. This is due to the cis‐OH ligand in the cis‐Fe^V(O)(OH) intermediate that can act as internal base, accepting a proton concomitant to the O?O bond‐formation reaction. Interplay between redox potentials to achieve the high oxidation state (Fe^V?O) and the activation energy barrier for the following O?O bond formation appears to be feasible through manipulation of the coordination environment of the iron site. This control may have a crucial role in the future development of water oxidation catalysts based on iron.     

Mononuclear Nonheme Iron(III)‐Iodosylarene and High‐Valent Iron‐Oxo Complexes in Olefin Epoxidation Reactions

High‐spin iron(III)‐iodosylarene complexes are highly reactive in the epoxidation of olefins, in which epoxides are formed as the major products with high stereospecificity and enantioselectivity. The reactivity of the iron(III)‐iodosylarene intermediates is much greater than that of the corresponding iron(IV)‐oxo complex in these reactions. The iron(III)‐iodosylarene species—not high‐valent iron(IV)‐oxo and iron(V)‐oxo species—are also shown to be the active oxidants in catalytic olefin epoxidation reactions. The present results are discussed in light of the long‐standing controversy on the one oxidant versus multiple oxidants hypothesis in oxidation reactions.     

Hydroxylation of sesquiterpenes by enzymes from chicory (Cichorium intybus L.) roots

A microsomal enzyme preparation of chicory roots catalyses the hydroxylation of various sesquiterpene olefins in the presence of NADPH. Most of these hydroxylations take place at an isopropenyl or isopropylidene group. The number of products obtained from any of the substrates is confined to one or, in a few cases, two sesquiterpene alcohols. In addition, the conversion of (+)-valencene into nootkatone through β-nootkatol was observed. The involvement of (+)-germacrene A hydroxylase (a cytochrome P450 enzyme) and other enzymes of sesquiterpene lactone biosynthesis in these reactions is discussed.     

细胞色素p450的结构与催化机理

细胞色素P450酶是广泛存在的含亚铁血红素单加氧酶, 参与甾类激素的合成、脂溶性维生素代谢、多不饱和脂肪酸转换为生物活性分子, 以及致癌作用和药物代谢. 综述了细胞色素p450结构与功能的关系, 特别是细胞色素P450活性位点经历大幅度开/关运动结合底物和释放产物以及电子迁移途径.