What factors influence the rate constant of substrate epoxidation by compound I of cytochrome P450 and analogous iron(IV)-oxo oxidants?

The cytochromes P450 are a versatile range of mono-oxygenase enzymes that catalyze a variety of different chemical reactions, of which the key reactions include aliphatic hydroxylation and C=C double bond epoxidation. To establish the fundamental factors that govern substrate epoxidation by these enzymes we have done a systematic density functional theory study on substrate epoxidation by the active species of P450 enzymes, namely the iron(IV)-oxo porphyrin cation radical oxidant or Compound I. We show here, for the first time, that the rate constant of substrate epoxidation, and hence the activation energy, correlates with the ionization potential of the substrate as well as with intrinsic electronic properties of the active oxidant such as the polarizability volume. To explain these findings we present an electron-transfer model for the reaction mechanism that explains the factors that determine the barrier heights and developed a valence bond (VB) curve crossing mechanism to rationalize the observed trends. In addition, we have found a correlation for substrate epoxidation reactions catalyzed by a range of heme and nonheme iron(IV)-oxo oxidants with the strength of the O-H bond in the iron-hydroxo complex, i.e. BDE(OH), which is supported by the VB model. Finally, the fundamental factors that determine the regioselectivity change between substrate hydroxylation and epoxidation are discussed. It is shown that the regioselectivity of aliphatic hydroxylation versus double bond epoxidation is not influenced by the choice of the oxidant but is purely substrate dependent.

[1]  Sam P. de Visser,et al.  Trends in substrate hydroxylation reactions by heme and nonheme iron(IV)-oxo oxidants give correlations between intrinsic properties of the oxidant with barrier height , 2010 .

[2]  D. P. Goldberg,et al.  Hydrogen atom abstraction by a high-valent manganese(V)-oxo corrolazine. , 2006, Inorganic chemistry.

[3]  S. D. de Visser,et al.  Electronic properties of pentacoordinated heme complexes in cytochrome P450 enzymes: search for an Fe(I) oxidation state. , 2009, Physical chemistry chemical physics : PCCP.

[4]  F. Guengerich Cytochrome P450 oxidations in the generation of reactive electrophiles: epoxidation and related reactions. , 2003, Archives of biochemistry and biophysics.

[5]  F. Arnold,et al.  Colorimetric High-Throughput Assay for Alkene Epoxidation Catalyzed by Cytochrome P450 BM-3 Variant 139-3 , 2004, Journal of biomolecular screening.

[6]  B. Hoffman,et al.  Rapid freeze-quench ENDOR study of chloroperoxidase compound I: the site of the radical. , 2006, Journal of the American Chemical Society.

[7]  K. Hodgson,et al.  Reactive intermediates in oxygenation reactions with mononuclear nonheme iron catalysts. , 2009, Angewandte Chemie.

[8]  L. Que,et al.  Dioxygen activation at mononuclear nonheme iron active sites: enzymes, models, and intermediates. , 2004, Chemical reviews.

[9]  J Berendzen,et al.  The catalytic pathway of cytochrome p450cam at atomic resolution. , 2000, Science.

[10]  J. I. Brauman,et al.  Mechanistic studies of olefin epoxidation by a manganese porphyrin and hypochlorite: an alternative explanation of saturation kinetics , 1990 .

[11]  A. Becke Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[12]  S. P. Visser Elucidating enzyme mechanism and intrinsic chemical properties of short-lived intermediates in the catalytic cycles of cysteine dioxygenase and taurine/α-ketoglutarate dioxygenase , 2009 .

[13]  J. Dawson,et al.  Heme-Containing Oxygenases. , 1996, Chemical reviews.

[14]  S. D. de Visser,et al.  How does the axial ligand of cytochrome P450 biomimetics influence the regioselectivity of aliphatic versus aromatic hydroxylation? , 2009, Chemistry.

[15]  Sason Shaik,et al.  Active species of horseradish peroxidase (HRP) and cytochrome P450: two electronic chameleons. , 2003, Journal of the American Chemical Society.

[16]  T. Kodadek,et al.  Epoxidation of olefins by cytochrome P-450 model compounds: kinetics and stereochemistry of oxygen atom transfer and origin of shape selectivity , 1985 .

[17]  R. van Eldik,et al.  Spectroscopic and mechanistic studies on oxidation reactions catalyzed by the functional Model SR complex for cytochrome P450: influence of oxidant, substrate, and solvent. , 2009, Chemistry.

[18]  S. Shaik,et al.  A valence bond modeling of trends in hydrogen abstraction barriers and transition states of hydroxylation reactions catalyzed by cytochrome P450 enzymes. , 2008, Journal of the American Chemical Society.

[19]  James M. Mayer,et al.  HYDROGEN ATOM ABSTRACTION BY METAL-OXO COMPLEXES : UNDERSTANDING THE ANALOGY WITH ORGANIC RADICAL REACTIONS , 1998 .

[20]  Sason Shaik,et al.  Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes. , 2005, Chemical reviews.

[21]  Zeev Gross,et al.  A Pronounced Axial Ligand Effect on the Reactivity of Oxoiron(IV) Porphyrin Cation Radicals , 1994 .

[22]  Takehiro Ohta,et al.  Axial ligand substituted nonheme FeIV=O complexes: observation of near-UV LMCT bands and Fe=O Raman vibrations. , 2005, Journal of the American Chemical Society.

[23]  J. Martin Bollinger,et al.  Direct spectroscopic detection of a C-H-cleaving high-spin Fe(IV) complex in a prolyl-4-hydroxylase , 2006, Proceedings of the National Academy of Sciences.

[24]  A. Bell,et al.  Influence of solvent composition on the kinetics of cyclooctene epoxidation by hydrogen peroxide catalyzed by iron(III) [tetrakis(pentafluorophenyl)] porphyrin chloride [(F20TPP)FeCl]. , 2006, Inorganic chemistry.

[25]  Sason Shaik,et al.  How does product isotope effect prove the operation of a two-state "rebound" mechanism in C-H hydroxylation by cytochrome P450? , 2003, Journal of the American Chemical Society.

[26]  W. Nam,et al.  A Thiolate-Ligated Nonheme Oxoiron(IV) Complex Relevant to Cytochrome P450 , 2005, Science.

[27]  C. Helvig,et al.  CYP15A1, the cytochrome P450 that catalyzes epoxidation of methyl farnesoate to juvenile hormone III in cockroach corpora allata , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[28]  M. Hendrich,et al.  Chloroperoxidase compound I: Electron paramagnetic resonance and Mössbauer studies. , 1984, Biochemistry.

[29]  S. P. Visser On the relationship between internal energy and both the polarizability volume and the diamagnetic susceptibility , 1999 .

[30]  J. Groves,et al.  Catalytic asymmetric epoxidations with chiral iron porphyrins , 1983 .

[31]  J. I. Brauman,et al.  Kinetics of (Porphyrin)manganese(III)‐Catalyzed Olefin Epoxidation with a Soluble Iodosylbenzene Derivative , 2006 .

[32]  T. Egawa,et al.  Evidence for compound I formation in the reaction of cytochrome P450cam with m-chloroperbenzoic acid. , 1994, Biochemical and biophysical research communications.

[33]  S. Shaik,et al.  Axial ligand tuning of a nonheme iron(IV)–oxo unit for hydrogen atom abstraction , 2007, Proceedings of the National Academy of Sciences.

[34]  Zeev Gross,et al.  Direct Resonance Raman Evidence for a Trans Influence on the Ferryl Fragment in Models of Compound I Intermediates of Heme Enzymes , 1996 .

[35]  S. Shaik,et al.  Hydrogen Bonding Modulates the Selectivity of Enzymatic Oxidation by P450: Chameleon Oxidant Behavior by Compound I , 2002 .

[36]  Z. Gross The effect of axial ligands on the reactivity and stability of the oxoferryl moiety in model complexes of Compound I of heme-dependent enzymes , 1996, JBIC Journal of Biological Inorganic Chemistry.

[37]  S. P. Visser The axial ligand effect of oxo-iron porphyrin catalysts. How does chloride compare to thiolate? , 2006, JBIC Journal of Biological Inorganic Chemistry.

[38]  W. Nam,et al.  High-valent iron(IV)-oxo complexes of heme and non-heme ligands in oxygenation reactions. , 2007, Accounts of chemical research.

[39]  M. Lim,et al.  Evidence for the Participation of Two Distinct Reactive Intermediates in Iron(III) Porphyrin Complex-Catalyzed Epoxidation Reactions , 2000 .

[40]  M. Crestoni,et al.  Oxygen-atom transfer by a naked manganese(V)-oxo-porphyrin complex reveals axial ligand effect. , 2009, Chemistry.

[41]  E. Solomon,et al.  Synthesis, characterization, and reactivities of manganese(V)-oxo porphyrin complexes. , 2007, Journal of the American Chemical Society.

[42]  M. Crestoni,et al.  Probing the Compound I-like reactivity of a bare high-valent oxo iron porphyrin complex: the oxidation of tertiary amines. , 2008, Journal of the American Chemical Society.

[43]  J. Pople,et al.  Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules , 1972 .

[44]  S. Shaik,et al.  Enhanced reactivities of iron(IV)-oxo porphyrin pi-cation radicals in oxygenation reactions by electron-donating axial ligands. , 2009, Chemistry.

[45]  Mindy I. Davis,et al.  Geometric and electronic structure/function correlations in non-heme iron enzymes. , 2000, Chemical reviews.

[46]  J. Groves,et al.  Hydroxylation by cytochrome P-450 and metalloporphyrin models: evidence for allylic rearrangement , 1984 .

[47]  Sam P. de Visser,et al.  What Factors Influence the Ratio of C¿H Hydroxylation versus C¿C Epoxidation by a Nonheme Cytochrome P450 Biomimetic? , 2006 .

[48]  Sason Shaik,et al.  Valence Bond Diagrams and Chemical Reactivity. , 1999, Angewandte Chemie.

[49]  Sason Shaik,et al.  Quantum mechanical/molecular mechanical investigation of the mechanism of C-H hydroxylation of camphor by cytochrome P450cam: theory supports a two-state rebound mechanism. , 2004, Journal of the American Chemical Society.

[50]  G. van Koten,et al.  Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies. , 2008, Chemical Society reviews.

[51]  Jin‐Pei Cheng,et al.  Substituent effects on the stabilities of phenoxyl radicals and the acidities of phenoxyl radical cations , 1991 .

[52]  J. Groves,et al.  A highly reactive p450 model compound I. , 2009, Journal of the American Chemical Society.

[53]  J. Collins,et al.  THEORETICAL AND EXPERIMENTAL ANALYSIS OF THE ABSOLUTE STEREOCHEMISTRY OF CIS-BETA -METHYLSTYRENE EPOXIDATION BY CYTOCHROME P450CAM , 1991 .

[54]  J. Groves The bioinorganic chemistry of iron in oxygenases and supramolecular assemblies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[55]  Sason Shaik,et al.  Mechanism of oxidation reactions catalyzed by cytochrome p450 enzymes. , 2004, Chemical reviews.

[56]  S. D. de Visser,et al.  Effect of porphyrin ligands on the regioselective dehydrogenation versus epoxidation of olefins by oxoiron(IV) mimics of cytochrome P450. , 2009, The journal of physical chemistry. A.

[57]  A. Munro,et al.  Variations on a (t)heme--novel mechanisms, redox partners and catalytic functions in the cytochrome P450 superfamily. , 2007, Natural product reports.

[58]  S. Shaik,et al.  Radical clock substrates, their C-H hydroxylation mechanism by cytochrome P450, and other reactivity patterns: what does theory reveal about the clocks' behavior? , 2004, Journal of the American Chemical Society.

[59]  M. Palcic,et al.  Spectrum of chloroperoxidase compound I. , 1980, Biochemical and biophysical research communications.

[60]  S. P. Visser Substitution of hydrogen by deuterium changes the regioselectivity of ethylbenzene hydroxylation by an oxo-iron-porphyrin catalyst. , 2006 .

[61]  Mi Hee Lim,et al.  Crystallographic and spectroscopic characterization of a nonheme Fe(IV)-O complex. , 2003, Science.

[62]  Sam P. de Visser,et al.  Propene activation by the oxo-iron active species of taurine/α- ketoglutarate dioxygenase (TauD) enzyme. How does the catalysis compare to heme-enzymes? , 2006 .

[63]  James M Mayer,et al.  Proton-coupled electron transfer: a reaction chemist's view. , 2004, Annual review of physical chemistry.

[64]  Lars Olsen,et al.  Prediction of activation energies for hydrogen abstraction by cytochrome p450. , 2006, Journal of medicinal chemistry.

[65]  L. Que,et al.  Nonheme FeIVO complexes that can oxidize the C-H bonds of cyclohexane at room temperature. , 2004, Journal of the American Chemical Society.

[66]  T. Kodadek,et al.  Mechanism of oxygen atom transfer from high valent iron porphyrins to olefins: implications to the biological epoxidation of olefins by cytochrome P-450 , 1985 .

[67]  M. Bagherzadeh,et al.  Origin of the correlation of the rate constant of substrate hydroxylation by nonheme iron(IV)-oxo complexes with the bond-dissociation energy of the C-H bond of the substrate. , 2009, Chemistry.

[68]  Sason Shaik,et al.  What factors affect the regioselectivity of oxidation by cytochrome p450? A DFT study of allylic hydroxylation and double bond epoxidation in a model reaction. , 2002, Journal of the American Chemical Society.

[69]  R. L. Kuczkowski,et al.  HYDROGEN-DEUTERIUM EXCHANGE DURING PROPYLENE EPOXIDATION BY CYTOCHROME P-450 , 1986 .

[70]  F. Guengerich,et al.  Common and uncommon cytochrome P450 reactions related to metabolism and chemical toxicity. , 2001, Chemical research in toxicology.

[71]  H. Fujii,et al.  Catalytic reactivity of a meso-N-substituted corrole and evidence for a high-valent iron-oxo species. , 2009, Journal of the American Chemical Society.

[72]  Sason Shaik,et al.  The "Rebound Controversy": An Overview and Theoretical Modeling of the Rebound Step in C-H Hydroxylation by Cytochrome P450 , 2004 .

[73]  Sam P. de Visser,et al.  Differences in and Comparison of the Catalytic Properties of Heme and Non-Heme Enzymes with a Central Oxo–Iron Group† , 2006 .

[74]  S. Shaik,et al.  Multi-state epoxidation of ethene by cytochrome P450: a quantum chemical study. , 2001, Journal of the American Chemical Society.

[75]  M. J. Ryle,et al.  Direct detection of oxygen intermediates in the non-heme Fe enzyme taurine/alpha-ketoglutarate dioxygenase. , 2004, Journal of the American Chemical Society.

[76]  Qin Wang,et al.  Kinetics and activation parameters for oxidations of styrene by Compounds I from the cytochrome P450(BM-3) (CYP102A1) heme domain and from CYP119. , 2009, Biochemistry.

[77]  S. Shaik,et al.  Multistate reactivity in styrene epoxidation by compound I of cytochrome p450: mechanisms of products and side products formation. , 2005, Chemistry.

[78]  A. Munro,et al.  Structural Biology and Biochemistry of Cytochrome P450 Systems in Mycobacterium tuberculosis , 2008, Drug metabolism reviews.

[79]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[80]  D. Koop,et al.  Regio- and stereoselective epoxidation of arachidonic acid by human cytochromes P450 2C8 and 2C9. , 1994, The Journal of pharmacology and experimental therapeutics.

[81]  Ying-Ji Sun,et al.  Mechanistic insights into the reversible formation of iodosylarene-iron porphyrin complexes in the reactions of oxoiron(IV) porphyrin pi-cation radicals and iodoarenes: equilibrium, epoxidizing intermediate, and oxygen exchange. , 2005, Chemistry.

[82]  V. Manner,et al.  Trends in ground-state entropies for transition metal based hydrogen atom transfer reactions. , 2009, Journal of the American Chemical Society.

[83]  Arani Chanda,et al.  Chemical and Spectroscopic Evidence for an FeV-Oxo Complex , 2007, Science.

[84]  R. Speight,et al.  Enantioselective epoxidation of linolenic acid catalysed by cytochrome P450(BM3) from Bacillus megaterium. , 2005, Organic & biomolecular chemistry.

[85]  John T. Groves,et al.  Preparation and Reactivity of Oxoiron(IV) Porphyrins , 1994 .

[86]  C. Walsh,et al.  Two interconverting Fe(IV) intermediates in aliphatic chlorination by the halogenase CytC3. , 2007, Nature chemical biology.

[87]  S. Shaik,et al.  Two-state reactivity mechanisms of hydroxylation and epoxidation by cytochrome P-450 revealed by theory. , 2002, Current opinion in chemical biology.

[88]  G. Brudvig,et al.  Manganese catalysts with molecular recognition functionality for selective alkene epoxidation. , 2009, Inorganic chemistry.

[89]  L. Que,et al.  Olefin-dependent discrimination between two nonheme HO-FeV=O tautomeric species in catalytic H2O2 epoxidations. , 2009, Chemistry.

[90]  S. P. Visser Is the μ‐Oxo‐μ‐Peroxodiiron Intermediate of a Ribonucleotide Reductase Biomimetic a Possible Oxidant of Epoxidation Reactions? , 2008 .

[91]  Gildas Bertho,et al.  First evidence that cytochrome P450 may catalyze both S-oxidation and epoxidation of thiophene derivatives. , 2005, Biochemical and biophysical research communications.

[92]  M. J. Coon,et al.  Epoxidation of olefins by cytochrome P450: evidence from site-specific mutagenesis for hydroperoxo-iron as an electrophilic oxidant. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[93]  Cheal Kim,et al.  Remarkable Anionic Axial Ligand Effects of Iron(III) Porphyrin Complexes on the Catalytic Oxygenations of Hydrocarbons by H2O2 and the Formation of Oxoiron(IV) Porphyrin Intermediates by m‐Chloroperoxybenzoic Acid , 2000 .

[94]  A. Fulco,et al.  Epoxidation of unsaturated fatty acids by a soluble cytochrome P-450-dependent system from Bacillus megaterium. , 1981, The Journal of biological chemistry.

[95]  T. C. Bruice,et al.  Intermediates in the epoxidation of alkenes by cytochrome P-450 models. 5. Epoxidation of alkenes catalyzed by a sterically hindered (meso-tetrakis(2,6-dibromophenyl)porphinato)iron(III) chloride , 1989 .

[96]  Sason Shaik,et al.  What happens to molecules as they react? A valence bond approach to reactivity , 1981 .

[97]  J. Groves,et al.  The mechanism of olefin epoxidation by oxo-iron porphyrins. Direct observation of an intermediate. , 1986, Journal of the American Chemical Society.

[98]  W. R. Wadt,et al.  Ab initio effective core potentials for molecular calculations , 1984 .

[99]  Xian‐Man Zhang,et al.  Bond dissociation energies in DMSO related to the gas phase values , 1991 .

[100]  Michael T. Green,et al.  Resonance Raman spectroscopy of chloroperoxidase compound II provides direct evidence for the existence of an iron(IV)–hydroxide , 2006, Proceedings of the National Academy of Sciences.

[101]  R. van Eldik,et al.  Low-temperature rapid-scan detection of reactive intermediates in epoxidation reactions catalyzed by a new enzyme mimic of cytochrome p450. , 2007, Journal of the American Chemical Society.

[102]  Yong Wang,et al.  P450 enzymes: their structure, reactivity, and selectivity-modeled by QM/MM calculations. , 2010, Chemical reviews.

[103]  T. Kodadek,et al.  Oxygenation of styrene by cytochrome P-450 model systems. A mechanistic study , 1986 .

[104]  S. D. de Visser,et al.  Combined experimental and theoretical study on aromatic hydroxylation by mononuclear nonheme iron(IV)-oxo complexes. , 2007, Inorganic chemistry.

[105]  Z. Gross,et al.  Reaction profile of the last step in cytochrome P-450 catalysis revealed by studies of model complexes , 1997, JBIC Journal of Biological Inorganic Chemistry.

[106]  R. van Eldik,et al.  Factors that affect the nature of the final oxidation products in "peroxo-shunt" reactions of iron-porphyrin complexes. , 2009, Chemistry.

[107]  L. Que,et al.  High-valent nonheme iron. Two distinct iron(IV) species derived from a common iron(II) precursor. , 2005, Journal of the American Chemical Society.

[108]  Carsten Krebs,et al.  EXAFS spectroscopic evidence for an Fe=O unit in the Fe(IV) intermediate observed during oxygen activation by taurine:alpha-ketoglutarate dioxygenase. , 2004, Journal of the American Chemical Society.

[109]  M. M. Fitzgerald,et al.  Resonance Raman spectroscopy of the catalytic intermediates and derivatives of chloroperoxidase from Caldariomyces fumago. , 1994, The Journal of biological chemistry.

[110]  T. Egawa,et al.  Effects of a thiolate axial ligand on the π→π* electronic states of oxoferryl porphyrins: a study of the optical and resonance Raman spectra of compounds I and II of chloroperoxidase , 2000, JBIC Journal of Biological Inorganic Chemistry.

[111]  S. P. Visser Preferential hydroxylation over epoxidation catalysis by a horseradish peroxidase mutant: a cytochrome P450 mimic. , 2007 .

[112]  Tomasz Borowski,et al.  Modeling enzymatic reactions involving transition metals. , 2006, Accounts of chemical research.

[113]  Stephen G. Sligar,et al.  Kinetic Characterization of Compound I Formation in the Thermostable Cytochrome P450 CYP119* , 2002, The Journal of Biological Chemistry.