Cytochrome P450: Significance, reaction mechanisms and active site analogues

Heterogeneous C-H Functionalization in Water via Porous Covalent Organic Framework Nanofilms: A Case of Catalytic Sphere Transmutation

Heterogeneous catalysis in water has not been explored beyond certain advantages such as recyclability and recovery of the catalysts from the reaction medium. Moreover, poor yield, extremely low selectivity, and active catalytic site deactivation further underrate the heterogeneous catalysis in water. Considering these facts, we have designed and synthesized solution-dispersible porous covalent organic framework (COF) nanospheres. We have used their distinctive morphology and dispersibility to functionalize unactivated C-H bonds of alkanes heterogeneously with high catalytic yield (42-99%) and enhanced regio- and stereoselectivity (3°:2° = 105:1 for adamantane). Further, the fabrication of catalyst-immobilized COF nanofilms via covalent self-assembly of catalytic COF nanospheres for the first time has become the key toward converting the catalytically inactive homogeneous catalysts into active and effective heterogeneous catalysts operating in water. This unique covalent self-assembly occurs through the protrusion of the fibers at the interface of two nanospheres, transmuting the catalytic spheres into films without any leaching of catalyst molecules. The catalyst-immobilized porous COF nanofilms' chemical functionality and hydrophobic environment stabilize the high-valent transient active oxoiron(V) intermediate in water and restricts the active catalytic site's deactivation. These COF nanofilms functionalize the unactivated C-H bonds in water with a high catalytic yield (45-99%) and with a high degree of selectivity (cis:trans = 155:1; 3°:2° = 257:1, for cis-1,2-dimethylcyclohexane). To establish this approach's "practical implementation", we conducted the catalysis inflow (TON = 424 ± 5) using catalyst-immobilized COF nanofilms fabricated on a macroporous polymeric support.

Structural and energetic analysis to provide insight residues of CYP2C9, 2C11 and 2E1 involved in valproic acid dehydrogenation selectivity

Docking and molecular dynamics (MD) simulation have been two computational techniques used to gain insight about the substrate orientation within protein active sites, allowing to identify potential residues involved in the binding and catalytic mechanisms. In this study, both methods were combined to predict the regioselectivity in the binding mode of valproic acid (VPA) on three cytochrome P-450 (CYP) isoforms CYP2C9, CYP2C11, and CYP2E1, which are involved in the biotransformation of VPA yielding reactive hepatotoxic intermediate 2-n-propyl-4-pentenoic acid (4nVPA). There are experimental data about hydrogen atom abstraction of the C4-position of VPA to yield 4nVPA, however, there are not structural evidence about the binding mode of VPA and 4nVPA on CYPs. Therefore, the complexes between these CYP isoforms and VPA or 4nVPA were studied to explore their differences in binding and energetic stabilization. Docking results showed that VPA and 4nVPA are coupled into CYPs binding site in a similar conformation, but it does not explain the VPA hydrogen atom abstraction. On the other hand, MD simulations showed a set of energetic states that reorient VPA at the first ns, then making it susceptible to a dehydrogenation reaction. For 4nVPA, multiple binding modes were observed in which the different states could favor either undergo other reaction mechanism or ligand expulsion from the binding site. Otherwise, the energetic and entropic contribution point out a similar behavior for the three CYP complexes, showing as expected a more energetically favorable binding free energy for the complexes between CYPs and VPA than with 4nVPA.

Hydrogen-abstraction reactivity patterns from A to Y: the valence bond way

"Give us insight, not numbers" was Coulson's admonition to theoretical chemists. This Review shows that the valence bond (VB)-model provides insights and some good numbers for one of the fundamental reactions in nature, the hydrogen-atom transfer (HAT). The VB model is applied to over 50 reactions from the simplest H + H(2) process, to P450 hydroxylations and H-transfers among closed-shell molecules; for each system the barriers are estimated from raw data. The model creates a bridge to the Marcus equation and shows that H-atom abstraction by a closed-shell molecule requires a higher barrier owing to the additional promotion energy needed to prepare the abstractor for H-abstraction. Under certain conditions, a closed-shell abstractor can bypass this penalty through a proton-coupled electron transfer (PCET) mechanism. The VB model links the HAT and PCET mechanisms conceptually and shows the consequences that this linking has for H-abstraction reactivity.

Coupling and uncoupling mechanisms in the methoxythreonine mutant of cytochrome P450cam: a quantum mechanical/molecular mechanical study

The Thr252 residue plays a vital role in the catalytic cycle of cytochrome P450cam during the formation of the active species (Compound I) from its precursor (Compound 0). We investigate the effect of replacing Thr252 by methoxythreonine (MeO-Thr) on this protonation reaction (coupling) and on the competing formation of the ferric resting state and H₂O₂ (uncoupling) by combined quantum mechanical/molecular mechanical (QM/MM) methods. For each reaction, two possible mechanisms are studied, and for each of these the residues Asp251 and Glu366 are considered as proton sources. The computed QM/MM barriers indicate that uncoupling is unfavorable in the case of the Thr252MeO-Thr mutant, whereas there are two energetically feasible proton transfer pathways for coupling. The corresponding rate-limiting barriers for the formation of Compound I are higher in the mutant than in the wild-type enzyme. These findings are consistent with the experimental observations that the Thr252MeO-Thr mutant forms the alcohol product exclusively (via Compound I), but at lower reaction rates compared with the wild-type enzyme.

Multistate reactivity in styrene epoxidation by compound I of cytochrome p450: mechanisms of products and side products formation

Density functional theoretical calculations are used to elucidate the epoxidation mechanism of styrene with a cytochrome P450 model Compound I, and the formation of side products. The reaction features multistate reactivity (MSR) with different spin states (doublet and quartet) and different electromeric situations having carbon radicals and cations, as well as iron(III) and iron(IV) oxidation states. The mechanisms involve state-specific product formation, as follows: a) The low-spin pathways lead to epoxide formation in effectively concerted mechanisms. b) The high-spin pathways have finite barriers for ring-closure and may have a sufficiently long lifetime to undergo rearrangement and lead to side products. c) The high-spin radical intermediate, (4)2(rad)-IV, has a ring closure barrier as small as the C--C rotation barrier. This intermediate will therefore lose stereochemistry and lead to a mixture of cis and trans epoxides. The barriers for the production of aldehyde and suicidal complexes are too high for this intermediate. d) The high-spin radical intermediate, (4)2(rad)-III, has a substantial ring closure barrier and may survive long enough time to lead to suicidal, phenacetaldehyde and 2-hydroxostyrene side products. e) The phenacetaldehyde and 2-hydroxostyrene products both originate from crossover from the (4)2(rad)-III radical intermediate to the cationic state, (4)2(cat,z(2) ). The process involves an N-protonated porphyrin intermediate that re-shuttles the proton back to the substrate to form either phenacetaldehyde or 2-hydroxostyrene products. This resembles the internally mediated NIH-shift observed during benzene hydroxylation.

Reactivity of a new class of P450 enzyme models

P450 enzyme models carrying a SO3(-) ligand coordinating to iron have been synthesized and characterized. These complexes show characteristics very similar to those of iron-heme cofactors of P450 enzymes. Their reactivity towards different reactions catalyzed by P450 enzymes such as epoxidation of double bonds, hydroxylation of non-activated C-H bonds, N-dealkylation of amines, and cleavage of diols (C-C-bond cleavage) has been investigated.

A thiolate ligand on a cytochrome P-450 mimic permits the use of simple environmentally benign oxidants for biomimetic steroid hydroxylation in water

Manganese porphyrin systems carrying cyclodextrin binding groups can regioselectively and stereoselectively hydroxylate bound steroid substrates, using iodosobenzene as oxidant, but hydrogen peroxide and other simple oxidants such as sodium hypochlorite are not effective in water. Thiol ligands were then added to the catalyst, both covalently attached and hydrophobically bound, and with these ligands hydrogen peroxide was now an effective oxidant.

Investigation on the regioselectivities of intramolecular oxidation of unactivated C-H bonds by dioxiranes generated in situ

We found that dioxiranes generated in situ from ketones 1-6 and Oxone underwent intramolecular oxidation of unactivated C-H bonds at delta sites of ketones to yield tetrahydropyrans. From the trans/cis ratio of oxidation products 1a and 2a as well as the retention of the configuration at the delta site of ketone 5, we proposed that the oxidation reaction proceeds through a concerted pathway under a spiro transition state. The intramolecular oxidation of ketone 6 showed the preference for a tertiary delta C-H bond over a secondary one. This intramolecular oxidation method can be extended to the oxidation of the tertiary gamma' C-H bond of ketones 9 and 10. For ketone 11 with two delta C-H bonds and one gamma' C-H bond linked respectively by a sp(3) hydrocarbon tether and a sp(2) ester tether, the oxidation took place exclusively at the delta C-H bonds. Finally, by introducing proper tethers, regioselective hydroxylation of steroid ketones 12-14 have been achieved at the C-17, C-16, C-3, and C-5 positions.

Iron(III) and iron(IV) corroles: synthesis, spectroscopy, structures, and no indications for corrole radicals

A delicate control of reaction conditions allows the isolation of several distinctively different iron complexes of tris(pentafluorophenyl)- and tris(2,6-dichlorophenyl)corrole. As long as coordinating ligands are present, the iron(III) complexes are stable in solution. Otherwise they are aerobically oxidized to either mononuclear chloroiron(IV) or dinuclear (mu-oxo)iron(IV) complexes, in acidic and basic solutions, respectively (the latter holds only for tris(pentafluorophenyl)corrole). When treated with NaNO(2), the mononuclear chloroiron(IV) corroles are efficiently converted into diamagnetic iron nitrosyl complexes. The low- and intermediate-spin iron(III), iron nitrosyl, and chloroiron(IV) corroles were fully characterized by a combination of spectroscopic methods and X-ray crystallography. There was no indication for an open-shell corrole in any of the complexes.

Catalytic oxidations of steroid substrates by artificial cytochrome p-450 enzymes

Catalysts comprising manganese-porphyrins carrying cyclodextrin binding groups are able to perform hydroxylations with substrate selectivity and regio- and stereoselectivity and high catalytic turnovers. The geometries of the catalyst/substrate complexes override intrinsic substrate reactivities, permitting attack on geometrically accessible saturated carbons of steroids in the presence of secondary carbinol groups and carbon-carbon double bonds, as in enzymatic reactions. Selective hydroxylations of steroid carbon 9 positions are of particular practical interest.

The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations

The primary oxidant of cytochrome P450 enzymes, Compound I, is hard to detect experimentally; in the case of cytochrome P450(cam), this intermediate does not accumulate in solution during the catalytic cycle even at temperatures as low as 200 K (ref 4). Theory can play an important role in characterizing such elusive species. We present here combined quantum mechanical/molecular mechanical (QM/MM) calculations of Compound I of cytochrome P450(cam) in the full enzyme environment as well as density functional studies of the isolated QM region. The calculations assign the ground state of the species, quantify the effect of polarization and hydrogen bonding on its properties, and show that the protein environment and its specific hydrogen bonding to the cysteinate ligand are crucial for sustaining the Fe-S bond and for preventing the full oxidation of the sulfur.

Oxidative dealkylation of aromatic amines by "bare" FeO+ in the gas phase

The gas-phase oxidations of aniline, N-methylaniline, and N,N-dimethylaniline by FeO+ cation are examined by using mass spectrometric techniques. Although bare FeO+ is capable of hydroxylating aromatic C—H bonds, the fate of the oxidation of arylamines is determined by docking of the FeO+ unit at nitrogen. The major reactions of the metastable aniline/FeO+ complex are losses of molecular hydrogen, ammonia, and water, all involving at least one N-H proton. N-alkylation results in a complete shift of the course of the reaction. The unimolecular processes observed can be regarded as initial steps of an oxidative dealkylation of the amines mediated by FeO+. More detailed mechanistic insight is obtained by examining the C—H(D) bond activation of N-methyl-N-([D3]-methyl)aniline by bare and ligated FeO+ species. The gas-phase reactions of FeO+ with methylanilines show some similarities to the enzymatic dealkylation of amines by cytochrome P-450. The kinetic isotope effects observed experimentally suggest an electron transfer mechanism for the gas-phase reaction.Key words: mass spectrometry, gas-phase chemistry, iron, dealkylation, N,N-dimethylaniline.

Identification of intermediates in the catalytic cycle of chloroperoxidase

BACKGROUND

Chloroperoxidase (CPO) is the most versatile of the hemethiolate proteins, catalyzing the chlorination of activated C-H bonds and reactions reminiscent of peroxidase, catalase, and cytochrome P450. Despite 30 years of continuous efforts, no intermediates of the enzyme's catalytic cycle have been identified except for compound I. Thus, in the absence of conclusive evidence it is generally believed that the halogenation of substrates proceeds by means of 'free HOCI' in solution.

RESULTS

The pH profile of chloroperoxidase from Caldariomyces fumago revealed a new active-site complex that can be detected only at pH 4.4. According to ultra-violet (UV) spectroscopy, and by comparison with suitable enzyme models, this intermediate is the HOCl adduct of the iron(III) protoporphyrin(IX). Inactivation of chloroperoxidase by diethyl pyrocarbonate, which interrupts the proton shuttle by modification of the distal histidine, led to the formation of the -OCl adduct of the iron complex, which was identified by comparison with a corresponding active site analogue.

CONCLUSIONS

The availability of enzyme models of heme-thiolate proteins allowed the identification by UV spectroscopy of both the -OCl adduct and the HOCl adduct of the iron(III) protoporphyrin(IX) of chloroperoxidase. The existence of these previously elusive intermediates suggests that the chlorination catalyzed by CPO, and its corresponding active site analogue, proceeds by Cl+ transfer from the HOCl adduct to the substrate bound in the distal pocket of the enzyme.