Mechanism and structure–reactivity relationships for aromatic hydroxylation by cytochrome P450

Dynamic metal coordination controls chemoselectivity in radical halogenases

The activation of inert C( sp 3 )-H bonds by non-heme Fe enzymes plays a key role in metabolism, epigenetics, and signaling, while providing a powerful biocatalytic platform for the chemical synthesis of molecules with increased sp 3 complexity. In this context, Fe II /α-ketoglutarate-dependent radical halogenases represent a broadly interesting system, as they are uniquely capable of carrying out transfer of a diverse array of bound anions following C-H activation. Here, we provide the first experimental evidence that bifurcation of H-atom abstraction and radical rebound is driven both by the ability of a dynamic metal coordination sphere to reorganize as well as by a second-sphere hydrogen-bond network where only two residues (Asn224 and Ile151) are necessary and sufficient. The identification of this minimal motif provides a paradigm for understanding the evolution of catalytic plasticity in these enzymes and yields new insight into the design principles by which to expand their reaction scope.

Mechanism of 7H-Dibenzo[c,g]carbazole metabolism in cytochrome P450 1A1: Insights from computational studies

7H-Dibenzo[c,g]carbazole (DBC) is a prevalent environmental contaminant that induces tumorigenesis in several experimental animals. Recently, it has been utilized to develop high-performance solar cells and organic phosphorescent materials. It is imperative to strengthen investigations of DBC metabolism to understand its potential risks to human health. In this study, human CYP1A1 was employed as the metabolic enzyme to investigate the metabolic mechanism of DBC by molecular docking, molecular dynamics (MD) simulation, and quantum mechanical (QM) calculation. The results indicate that DBC binds to CYP1A1 in two modes (mode 1 and mode 2) mainly through nonpolar solvation energies (ΔGnonpolar). The formation of the two binding modes is attributed to the anchoring effect of the hydrogen bond formed by DBC with Asp320 (mode 1) or Ser116 (mode 2). Mode 1 is a "reactive" conformation, while mode 2 is not considered a "reactive" conformation. C5 is identified as the dominant site, and the pyrrole nitrogen cannot participate in the metabolism. DBC is metabolized mainly by a distinct electrophilic addition-rearrangement mechanism, with an energy barrier of 21.74 kcal/mol. The results provide meaningful insights into the biometabolic process of DBC and contribute to understanding its environmental effects and health risks.

A comparative genomic study of a hydrocarbon-degrading marine bacterial consortium

Ocean oil pollution has a large impact on the environment and the health of living organisms. Bioremediation cleaning strategies are promising eco-friendly alternatives for tackling this problem. Previously, we designed and reported a hydrocarbon (HC) degrading microbial consortium of four marine strains belonging to the species Alloalcanivorax xenomutans, Halopseudomonas aestusnigri, Paenarthrobacter sp., and Pseudomonas aeruginosa. However, the knowledge about the metabolic potential of this bacterial consortium for HC bioremediation is not yet well understood. Here, we analyzed the complete genomes of these marine bacterial strains accompanied by a phylogenetic reconstruction along with 138 bacterial strains. Synteny between complete genomes of the same species or genus, revealed high conservation among strains of the same species, covering over 91% of their genomic sequences. Functional predictions highlighted a high abundance of genes related to HC degradation, which may result in functional redundancy within the consortium; however, unique and complete gene clusters linked to aromatic degradation were found in the four genomes, suggesting substrate specialization. Pangenome gain and loss analysis of genes involved in HC degradation provided insights into the evolutionary history of these capabilities, shedding light on the acquisition and loss of relevant genes related to alkane and aromatic degradation. Our work, including comparative genomic analyses, identification of secondary metabolites, and prediction of HC-degrading genes, enhances our understanding of the functional diversity and ecological roles of these marine bacteria in crude oil-contaminated marine environments and contributes to the applied knowledge of bioremediation.

Enantioselective bioaccumulation, biotransformation and spatial distribution of chiral fungicide difenoconazole in earthworms (Eisenia fetida)

The enantioselective environmental behavior of difenoconazole, a widely utilized triazole fungicide commonly detected in agricultural soils, has yet to be comprehensively explored within the earthworm-soil system. To address this research gap, we investigated the bioaccumulation and elimination kinetics, degradation pathways, biotransformation mechanisms, spatial distribution, and toxicity of chiral difenoconazole. The four stereoisomers of difenoconazole were baseline separated and analyzed using SFC-MS/MS. Pronounced enantioselectivity was observed during the uptake phase, with earthworms exhibiting a preference for (2R,4R)-difenoconazole and (2R,4S)-difenoconazole. A total of five transformation products (TPs) were detected and identified using UHPLC-QTOF/MS in the earthworm-soil system. Four of the TPs were detected in both earthworm and soil, and one TP was produced only in eaerthwroms. Hydrolysis and hydroxylation were the primary transformation pathways of difenoconazole in both earthworms and soil. Furthermore, a chiral TP, 3-chloro, 4-hydroxy difenoconazole, was generated with significant enantioselectivity, and molecular docking results indicate the greater catalytic bioactivity of (2R,4R)- and (2R,4S)-difenoconazole, leading to the preferential formation of their corresponding hydroxylated TPs. Furthermore, Mass Spectrometry Imaging (MSI) was applied for the first time to explore the spatial distribution of difenoconazole and the TPs in earthworms, and the "secretory zone" was found to be the dominant region to uptake and biodegrade difenoconazole. ECOSAR predictions highlighted the potentially hazardous impact of most difenoconazole TPs on aquatic ecosystems. These findings are important for understanding the environmental fate of difenoconazole, evaluating environmental risks, and offering valuable insights for guiding scientific bioremediation efforts.

Mechanism of Selective Aromatic Hydroxylation in the Metabolic Transformation of Paclitaxel Catalyzed by Human CYP3A4

Paclitaxel (PTX) is heralded as one of the most successful natural-product drugs for the treatment of refractory cancers. In humans, the hepatic metabolic transformation of PTX is primarily mediated by two cytochrome P450 enzymes (P450s): CYP3A4 and CYP2C8. The impact of P450 metabolism on the anticancer effectiveness of PTX is significant. However, the precise mechanism underlying selective P450-catalyzed reactions in PTX metabolism remains elusive. To address this knowledge gap, we conducted molecular docking and molecular dynamics simulations using multiple crystal structures of CYP3A4, which originally contained other ligands. These methods enabled us to determine the most plausible binding structure of PTX within the enzyme. By further employing hybrid quantum mechanics and molecular mechanics calculations, we successfully identified two primary pathways for the reaction between compound I (Cpd I) of CYP3A4 and PTX. One of these pathways involves the formation of an epoxide, while the other proceeds through a ketone intermediate.

New insight into biodegradation mechanism of phenylurea herbicides by cytochrome P450 enzymes: Successive N-demethylation mechanism

Phenylurea herbicides (PUHs) present one of the most important herbicides, which have cause serious effects on ecological environment and humans. Nowadays enzyme strategy shows great advantages in degradation of PUHs. Here density functional theory (DFT), quantitative structure - activity relationship (QSAR) and quantum mechanics/molecular mechanics (QM/MM) approaches are used to investigate the degradation mechanism of PUHs catalyzed by P450 enzymes. Two successive N-demethylation pathways are identified and two hydrogen abstraction (H-abstraction) reaction pathways are identified as the rate-determining step through high-throughput DFT calculations. The Boltzmann-weighted average energy barrier of the second H-abstraction pathway (19.95 kcal/mol) is higher than that of the first H-abstraction pathway (16.80 kcal/mol). Two QSAR models are established to predict the energy barriers of the two H-abstraction pathways based on the quantum chemical descriptors and mordred molecular descriptors. The determination coefficient (R2) values of QSAR models are > 0.9, which reveal that the established QSAR models have great predictive capability. QM/MM calculations indicate that human P450 enzymes are more efficient in degradation of PUHs than crop and weed P450 enzymes. Correlations between energy barriers and key structural/charge parameters are revealed and key parameters that have influence on degradation efficiency of PUHs are identified. This study provides lateral insights into the biodegradation strategy and removal method of PUHs and valuable information for designing or engineering of highly efficient degradation enzymes and genetically modified crops.

Theoretical study of the formation of metal-oxo species of the first transition series with the ligand 14-TMC: driving factors of the "Oxo Wall"

Terminal metal-oxo species of the early transition metal series are well known, whereas those for the late transition series are rare, and this is related to the "Oxo Wall". Here, we have undertaken a theoretical study on the formation of metal-oxo species from the metal hydroperoxo species of the 3d series (Cr, Mn, Fe, Co, Ni, and Cu) with the ligand 14-TMC (1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane) via O⋯O bond cleavage. DFT calculations reveal that the barrier for O⋯O bond cleavage is higher with the late transition metals (Co, Ni, and Cu) than the early transition metals (Cr, Mn, and Fe), and the formed late metal-oxo species are also thermodynamically less stable. The higher barrier may be due to electronic repulsion because of the pairing of d electrons. In the late transition metal series, the electron goes into an antibonding orbital, which decreases the bond order and hence decreases the possibility of metal-oxo formation. Computed structural parameters and spin densities suggest that valence tautomerism occurs in the late transition metal-oxo species which remain as a metal-oxyl. Our findings support the concept of the "Oxo Wall".

The Oxidation of Oxygen and Sulfur-Containing Heterocycles by Cytochrome P450 Enzymes

The cytochrome P450 (CYP) superfamily of monooxygenase enzymes play important roles in the metabolism of molecules which contain heterocyclic, aromatic functional groups. Here we study how oxygen- and sulfur-containing heterocyclic groups interact with and are oxidized using the bacterial enzyme CYP199A4. This enzyme oxidized both 4-(thiophen-2-yl)benzoic acid and 4-(thiophen-3-yl)benzoic acid almost exclusively via sulfoxidation. The thiophene oxides produced were activated towards Diels-Alder dimerization after sulfoxidation, forming dimeric metabolites. Despite X-ray crystal structures demonstrating that the aromatic carbon atoms of the thiophene ring were located closer to the heme than the sulfur, sulfoxidation was still favoured with 4-(thiophen-3-yl)benzoic acid. These results highlight a preference of this cytochrome P450 enzyme for sulfoxidation over aromatic hydroxylation. Calculations predict a strong preference for homodimerization of the enantiomers of the thiophene oxides and the formation of a single major product, in broad agreement with the experimental data. 4-(Furan-2-yl)benzoic acid was oxidized to 4-(4'-hydroxybutanoyl)benzoic acid using a whole-cell system. This reaction proceeded via a γ-keto-α,β-unsaturated aldehyde species which could be trapped in vitro using semicarbazide to generate a pyridazine species. The combination of the enzyme structures, the biochemical data and theoretical calculations provides detailed insight into the formation of the metabolites formed from these heterocyclic compounds.

Late-Stage Aryl C-H Bond Cyclopropenylation with Cyclopropenium Cations

Herein, we disclose the first regio-, site- and chemoselective late-stage (hetero)aryl C-H bond cyclopropenylation with cyclopropenium cations (CPCs). The process is fast, operationally simple and shows an excellent functional group tolerance in densely-functionalized drug molecules, natural products, agrochemicals and fluorescent dyes. Moreover, we discovered that the installation of the cyclopropene ring in drug molecules could not only be used to shield against metabolic instability but also as a synthetic tool to reach medicinally-relevant sp3 -rich scaffolds exploiting the highly-strained nature of the cyclopropene ring with known transformations.

Regioselective oxidation of heterocyclic aromatic hydrocarbons catalyzed by cytochrome P450: A case study of carbazole

Recently there are increasing interests in accurately evaluating the health effects of heterocyclic PAHs. However, the activation mechanism and possible metabolites of heterocyclic PAHs catalyzed by human CYP1A1 is still elusive to a great extent. Here, leveraged to high level QM/MM calculations, the corresponding activation pathways of a representative heterocyclic PAHs, carbazole, were systematically explored. The first stage is electrophilic addition or hydrogen abstraction from N-H group. Electrophilic addition was evidenced to be more feasible and regioselectivity at C3 and C4 sites were identified. Correlations between energy barriers and key structural/electrostatic parameters reveal that O-Cα distance and Fe-O-Cα angle are the main origin for the catalytic regioselectivity. Electrophilic addition was determined as the rate-determining step and the subsequent possible reactions include epoxidation, NIH shift (the hydrogen migration from the site of hydroxylation to the adjacent carbon) and proton shuttle. The corresponding products are epoxides, ketones and hydroxylated carbazoles, respectively. The main metabolites (hydroxylated carbazoles) are estimated to be more toxic than carbazole. The regioselectivity of carbazole activated by CYP1A1 is different from the environmental processes (gas and aqueous phase). Collectively, these results will inform the in-depth understanding the metabolic processes of heterocyclic PAHs and aid the accurate evaluation of their health effects.

Biotransformation of Bisphenol by Human Cytochrome P450 2C9 Enzymes: A Density Functional Theory Study

Bisphenol A (BPA, 2,2-bis-(4-hydroxyphenyl)propane) is used as a precursor in the synthesis of polycarbonate and epoxy plastics; however, its availability in the environment is causing toxicity as an endocrine-disrupting chemical. Metabolism of BPA and their analogues (substitutes) is generally performed by liver cytochrome P450 enzymes and often leads to a mixture of products, and some of those are toxic. To understand the product distributions of P450 activation of BPA, we have performed a computational study into the mechanisms and reactivities using large model structures of a human P450 isozyme (P450 2C9) with BPA bound. Density functional theory (DFT) calculations on mechanisms of BPA activation by a P450 compound I model were investigated, leading to a number of possible products. The substrate-binding pocket is tight, and as a consequence, aliphatic hydroxylation is not feasible as the methyl substituents of BPA cannot reach compound I well due to constraints of the substrate-binding pocket. Instead, we find low-energy pathways that are initiated with phenol hydrogen atom abstraction followed by OH rebound to the phenolic ortho- or para-position. The barriers of para-rebound are well lower in energy than those for ortho-rebound, and consequently, our P450 2C9 model predicts dominant hydroxycumyl alcohol products. The reactions proceed through two-state reactivity on competing doublet and quartet spin state surfaces. The calculations show fast and efficient substrate activation on a doublet spin state surface with a rate-determining electrophilic addition step, while the quartet spin state surface has multiple high-energy barriers that can also lead to various side products including C⁴-aromatic hydroxylation. This work shows that product formation is more feasible on the low spin state, while the physicochemical properties of the substrate govern barrier heights of the rate-determining step of the reaction. Finally, the importance of the second-coordination sphere is highlighted that determines the product distributions and guides the bifurcation pathways.

Reliably assessing the electronic structure of cytochrome P450 on today's classical computers and tomorrow's quantum computers

Chemical simulation is one of the most promising applications for future quantum computers. It is thought that quantum computers may enable accurate simulation for complex molecules that are otherwise impossible to simulate classically; that is, it displays quantum advantage. To better understand quantum advantage in chemical simulation, we explore what quantum and classical resources are required to simulate a series of pharmaceutically relevant molecules. Using classical methods, we show that reliable classical simulation of these molecules requires significant resources and therefore is a promising candidate for quantum simulation. We estimate the quantum resources, both in overall simulation time and the size. The insights from this study pave the way for future quantum simulation of complex molecules.

An accurate assessment of how quantum computers can be used for chemical simulation, especially their potential computational advantages, provides important context on how to deploy these future devices. To perform this assessment reliably, quantum resource estimates must be coupled with classical computations attempting to answer relevant chemical questions and to define the classical algorithms simulation frontier. Herein, we explore the quantum computation and classical computation resources required to assess the electronic structure of cytochrome P450 enzymes (CYPs) and thus define a classical–quantum advantage boundary. This is accomplished by analyzing the convergence of density matrix renormalization group plus n-electron valence state perturbation theory (DMRG+NEVPT2) and coupled-cluster singles doubles with noniterative triples [CCSD(T)] calculations for spin gaps in models of the CYP catalytic cycle that indicate multireference character. The quantum resources required to perform phase estimation using qubitized quantum walks are calculated for the same systems. Compilation into the surface code provides runtime estimates to compare directly to DMRG runtimes and to evaluate potential quantum advantage. Both classical and quantum resource estimates suggest that simulation of CYP models at scales large enough to balance dynamic and multiconfigurational electron correlation has the potential to be a quantum advantage problem and emphasizes the important interplay between classical computations and quantum algorithms development for chemical simulation.

Endocrine-disrupting metabolic activation of 2-nitrofluorene catalyzed by human cytochrome P450 1A1: A QM/MM approach

Nitropolycyclic aromatic hydrocarbons (NPAHs) present one of the most important airborne pollutants. Recent studies have shown that one of the most abundant NPAHs, 2-Nitrofluorene (NF), was supposed to be converted to endocrine-disrupting metabolites by cytochrome P450 1A1 (CYP1A1) in human cells. However, the mechanism is still largely unexplored. Here the metabolic activation and transformation mechanism of NF catalyzed by CYP1A1 were systematically studied with the aid of Molecular Dynamics, Density Functional Theory and Quantum Mechanics/Molecular Mechanics techniques. We evidence that CYP1A1 can activate NF through two elementary processes: (i) electrophilic addition (12.4 kcal·mol-1) or hydrogen abstraction (38.2 kcal·mol-1) and (ii) epoxidation (5.9 and 8.7 kcal·mol-1) or NIH shift (12.5 and 14.9 kcal·mol-1) or proton shuttle (12.1 kcal·mol-1). Electrophilic addition was found to be the rate-determining step while epoxidation rather than NIH shift or proton shuttle is the more feasible pathway after electrophilic addition. Metabolites 6,7-epoxide-2-nitrofluorene and 7,8-epoxide-2-nitrofluorene were identified as the major epoxidation products. Epoxides are unstable and easy to react with hydrated hydrogen ions and hydroxyls to produce endocrine disrupter 7-hydroxy-2-nitrofluorene. Toxic analysis shows that some of the metabolites are more toxic to model aquatic organisms (e.g. Green algea) than NF. Binding affinity analysis to human sex hormone binding globulin reveals that NF metabolites all have endocrine-disrupting potential. This study provides a comprehensive understanding on the biotransformation process of NF and may aid future studies on various NPAHs activation catalyzed by human P450 enzyme.

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

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

Effect of the ring size of TMC ligands in controlling C-H bond activation by metal-superoxo species

Metal-superoxo species play a very important role in many metal-mediated catalytic transformation reactions. Their catalytic reactivity is affected by many factors such as the nature of metal ions and ring size of ligands. Herein, for the first time, we report DFT calculations on the electronic structures of a series of metal-superoxo species (M = V, Cr, Mn, Fe, and Co) with two ring size ligands, i.e., 13-TMC/14-TMC, and a detailed mechanistic study on the C-H bond activation of cyclohexa-1,4-diene followed by the effect of the ring size of ligands. Our DFT results showed that the electron density at the distal oxygen plays an important role in C-H bond activation. By computing the energetics of C-H bond activation and mapping the potential energy surface, it was found that the initial hydrogen abstraction is the rate-determining step with both TMC rings and all the studied metal-superoxo species. The significant electron density at the cyclohex-1,4-diene carbon indicates that the reaction proceeds via the proton-coupled electron transfer mechanism. By mapping the potential energy surfaces, we found that the 13-TMC ligated superoxo with the anti-isomer are more reactive than the 14-TMC superoxo species except for the iron-superoxo species where the 14-TMC ligated superoxo species is more reactive i.e. smaller ring size TMC is more reactive towards C-H bond activation. This is also supported by the structural correlation, i.e., the greater contraction in the smaller ring results in the metal being pushed out of plane along the z-axis, which reduces the steric hindrance. Thus, the ring size can help in designing catalysts with better efficiency for catalytic reactions.

Computational Study of the Peroxygenase Mechanism Catalyzed by Hemoglobin Dehaloperoxidase Involved in the Degradation of Chlorophenols

The biochemical evidence showed that hemoglobin dehaloperoxidase (DHP B) from Amphitrite Ornata is a multifunctional hemoprotein that catalyzes both dehalogenation and hydroxylation of halophenols via the peroxidase and peroxygenase mechanism, respectively, which sets the basis for the degradation of halophenols. In the peroxygenase mechanism, the reaction was previously suggested to be triggered either by the hydrogen atom abstraction by the Fe═O center or by the proton abstraction by His55. To illuminate the peroxygenase mechanism of DHP B at the atomistic level, on the basis of the high-resolution crystal structure, computational models were constructed, and a series of quantum mechanical/molecular mechanical calculations have been performed. According to the calculation results, the pathway (Path a) initiated by the H-abstraction by the Fe═O center is feasible. In another pathway (Path b), His55 can abstract the proton from the hydroxyl group of the substrate (4-Cl-o-cresol) to initiate the reaction; however, its feasibility depends on the prior electron transfer from the substrate to the porphyrin group. The rate-limiting step of Path a is the OH-rebound, which corresponds to an energy barrier of 14.7 kcal/mol at the quartet state. His55 acts as an acid-base catalyst and directly involves in the catalysis. Our mutant study indicates that His55 can be replaced by other titratable residues. These findings may provide useful information for further understanding of the catalytic reaction of DHP B and for the design of enzymes in the degradation of pollutants, in particular, halophenols.

Origin of Site Selectivity in Toluene Hydroxylation by Cytochrome P450 Enzymes

Computational studies are utilized to reveal factors that determine the site selectivity in toluene hydroxylation by cytochrome P450 enzymes (CYPs). The DFT-computed inherent barriers suggest that the priority of product formation is in the order of benzyl alcohol > ortho- ≈ para- > meta-cresol. However, the specific size and shape of the cavities at the active sites of different CYPs dramatically affect the binding orientation of toluene, and thus, the site selectivity can be reordered.

Tyrosyl Radical-Mediated Sequential Oxidative Decarboxylation of Coproporphyrinogen III through PCET: Theoretical Insights into the Mechanism of Coproheme Decarboxylase ChdC

The peroxide-dependent coproheme decarboxylase ChdC from Geobacillus stearothermophilus catalyzes two key steps in the synthesis of heme b, i.e., two sequential oxidative decarboxylations of coproporphyrinogen III (coproheme III) at propionate groups P2 and P4. In the binding site of coproheme III, P2 and P4 are anchored by different residues (Tyr144, Arg217, and Ser222 for P2 and Tyr113, Lys148, and Trp156 for P4); however, strong experimental evidence supports that the generated Tyr144 radical acts as an unique intermediary for hydrogen atom transfer (HAT) from both reactive propionates. So far, the reaction details are still unclear. Herein, we carried out quantum mechanics/molecular mechanics calculations to explore the decarboxylation mechanism of coproheme III. In our calculations, the coproheme Cpd I, Fe(IV) = O coupled to a porphyrin radical cation (por^•+) with four propionate groups, was used as a reactant model. Our calculations reveal that Tyr144 is directly involved in the decarboxylation of propionate group P2. First, the proton-coupled electron transfer (PCET) occurs from Tyr144 to P2, generating a Tyr144 radical, which then abstracts a hydrogen atom from the Cβ of P2. The β-H extraction was calculated to be the rate-limiting step of decarboxylation. It is the porphyrin radical cation (por^•+) that makes the PCET from Tyr144 to P2 to be quite easy to initiate the decarboxylation. Finally, the electron transfers from the Cβ^• through the porphyrin to the iron center, leading to the decarboxylation of P2. Importantly, the decarboxylation of P4 mediated by Lys148 was calculated to be very difficult, which suggests that after the P2 decarboxylation, the generated harderoheme III intermediate should rebind or rotate in the active site so that the propionate P4 occupies the binding site of P2, and Tyr144 again mediates the decarboxylation of P4. Thus, our calculations support the fact that Tyr144 is responsible for the decarboxylation of both P2 and P4.

Insights into the metabolic mechanism of PBDEs catalyzed by cytochrome P450 enzyme 3A4: A QM/MM study

Elucidating the metabolic mechanism and the derivatives of polybrominated diphenyl ethers (PBDEs) is significant to risk assessment. This study delineated the metabolic mechanism of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) catalyzed by P450 enzymes using a combination of molecular dynamic (MD), quantum mechanics/molecular mechanics (QM/MM) and density functional theory (DFT). The calculation results reveal that the electrophilic addition is the main pathway for the biotransformation of BDE-47 catalyzed by P450 enzymes. 6-hydroxy-2,2',4,4'-tetrabromodiphenyl ether (6-OH-BDE-47) is a more kinetically preferable product than 5-hydroxy-2,2',4,4'-tetrabromodiphenyl ether (5-OH-BDE-47). Electrophilic addition reaction can lead to the formation of polybrominated dibenzo-p-dioxins and dibenzofurans (PBDD/Fs). The ecotoxicity assessment indicates that the final products of BDE-47 are still toxic to aquatic organisms, but the solubility increase of the hydroxylated products can accelerate their excretion from the body. We expect that the established metabolic mechanism and the derivatives will be used to predict the biotransformation of other PBDE congeners catalyzed by P450 enzymes in human livers.

Theoretical Investigation on the Elusive Reaction Mechanism of Spirooxindole Formation Mediated by Cytochrome P450s: A Nascent Feasible Charge-Shift C-O Bond Makes a Difference

Spirooxindoles are pivotal biofunctional groups widely distributed in natural products and clinic drugs. However, construction of such subtle chiral skeletons is a long-standing challenge to both organic and bioengineering scientists. The knowledge of enzymatic spirooxindole formation in nature may inspire rational design of new catalysts. To this end, we presented a theoretical investigation on the elusive mechanism of the spiro-ring formation at the 3-position of oxindole mediated by cytochrome P450 enzymes (P450). Our calculated results demonstrated that the electrophilic attack of CpdI, the active species of P450, to the substrate, shows regioselectivity, i.e., the attack at the C9 position forms a tetrahedral intermediate involving an unusual feasible charge-shift C9^δ+-O^δ- bond, while the attack at the C1 position forms an epoxide intermediate. The predominant route is the first route with the charge-shift bonding intermediate due to holding a relatively lower barrier by >5 kcal mol^-1 than the epoxide route, which fits the experimental observations. Such a delocalized charge-shift bond facilitates the formation of a spiro-ring mainly through elongation of the C1-C9 bond to eliminate the aromatization of the tricyclic beta-carboline. Our theoretical results shed profound mechanistic insights for the first time into the elusive spirooxindole formation mediated by P450s.

Computational Studies on the Mechanism and Origin of the Different Regioselectivities of Manganese Porphyrin-Catalyzed C-H Bond Hydroxylation and Amidation of Equilenin Acetate

The manganese porphyrin-catalyzed C-H bond hydroxylation and amidation of equilenin acetate developed by Breslow and his co-worker have been investigated with density functional theory (DFT) calculations. The hydroxylation of C(sp²)-H bond of equilenin acetate leading to the 6-hydroxylated product is more favorable than the hydroxylation of C(sp³)-H bond of equilenin acetate, leading to the 11β-hydroxylation product. The computational results suggest that the C(sp²)-H bond hydroxylation of equilenin acetate undergoes an oxygen-atom-transfer mechanism, which is more favorable than the C(sp³)-H bond hydroxylation undergoing the hydrogen-atom-abstraction/oxygen-rebound (HAA/OR) mechanism by 1.6 kcal/mol. That is why, the 6-hydroxylated product is the major product and the 11β-hydroxylated product is the minor product. In contrast, the 11β-amidated product is the only observed product in manganese porphyrin-catalyzed amidation reaction. The benzylic amidation undergoes a hydrogen-atom-abstraction/nitrogen-rebound (HAA/NR) mechanism, in which hydrogen atom abstraction is followed by nitrogen rebound, leading to the 11β-amidated product. The benzylic C(sp³)-H bond amidation at the C-11 position is more favorable than aromatic amidation at the C-6 position by 4.9 kcal/mol. Therefore, the DFT computational results are consistent with the experiments that manganese porphyrin-catalyzed C-H bond hydroxylation and amidation of equilenin acetate have different regioselectivities.

Strategies to Mitigate the Bioactivation of Aryl Amines

The bioactivation of xenobiotics to yield reactive metabolites can lead to tolerability and toxicity concerns within a drug discovery program. Development of strategies for mitigating the metabolic liability of commonly encountered toxicophores, such as anilines, relies on an understanding of the relative tendency of these functionalities to undergo bioactivation. In this report, we present the first systematic study of the structure-activity relationships of the bioactivation of aryl amine fragments (molecular weight < 250 Da) using a glutathione (GSH) trapping assay in the presence of human liver microsomes and the reduced form of nicotinamide adenine dinucleotide phosphate. This study demonstrates that conversion of anilines to nitrogen-containing heteroarylamines results in a lower abundance of GSH conjugates in the order phenyl > pyrimidine ≈ pyridine > pyridazine. Introduction of electron-withdrawing functionality on the aromatic ring had a less pronounced effect on the extent of GSH conjugation. Examination of more drug-like compounds sourced from in-house drug discovery programs revealed similar trends in bioactivation between matched pairs containing (hetero)aryl amines. This study provides medicinal chemists with insights and qualitative guidance for the minimization of risks related to aryl amine metabolism.

Truncated Itraconazole Analogues Exhibiting Potent Anti-Hedgehog Activity and Improved Drug-like Properties

We conducted a structure-activity relationship study to explore simplified analogues of the itraconazole (ITZ) scaffold for their ability to inhibit the hedgehog (Hh) signaling pathway. These analogues were based on exploring the effects of chemical modifications to the linker and triazolone/side chain region of ITZ. Analogue 11 was identified as the most potent compound in our first generation, with an IC₅₀ value of 81 nM in a murine Hh-dependent basal cell carcinoma. Metabolic identification studies led us to identify truncated piperazine (26) as the major metabolite in human liver microsomes (HLMs) and an improved Hh pathway inhibitor (IC₅₀ = 22 nM). This work verifies that continued truncation of the ITZ scaffold is a practical method to maintain potent anti-Hh activity while also reducing the molecular weight for the ITZ scaffold and achieving improved pharmacokinetic properties.

Carcinogenic Metabolic Activation Process of Naphthalene by the Cytochrome P450 Enzyme 1B1: A Computational Study

The metabolic activation and transformation of naphthalene by the cytochrome P450 enzyme (CYP 1B1) plays an important role in its potential carcinogenicity. The process has been explored by a quantum mechanics/molecular mechanics (QM/MM) computational method. Molecular dynamic simulations were performed to explore the interaction between naphthalene and CYP 1B1. Naphthalene involves α- and β-carbon, the electrophilic addition of which would result in different reaction pathways. Our computational results show that both additions on α- and β-carbon can generate naphthalene 1,2-oxide. The activation barrier for the addition on β-carbon is higher than that for the α-carbon by 2.6 kcal·mol^-1, which is possibly caused by the proximity between β-carbon and the iron-oxo group of Cpd I in the system. We also found that naphthalene 1,2-oxide is unstable and the O-C bond cleavage easily occurs via cellular hydronium ion, hydroxyl radical/anion; then it will convert to the potential ultimate carcinogen 1,2-naphthoquinone. The results demonstrate and inform a detailed process of generating naphthalene 1,2-oxide and new predictions for its conversion.

Computational Insight into the Activation Mechanism of Carcinogenic N'-Nitrosonornicotine (NNN) Catalyzed by Cytochrome P450

Tobacco-specific N'-nitrosonornicotine (NNN), a genotoxic nitrosamine classified as Group 1 carcinogen, is also present in atmospheric particulate matter and has even been detected as a new disinfection byproduct in wastewaters. NNN generally requires metabolic activation by cytochrome P450 enzymes to exert its genotoxicity, but the respective biotransformation pathways have not been described in detail. In this work, we performed density functional theory (DFT) calculations to unravel possible NNN activation pathways including α-hydroxylation, β-hydroxylation, pyridine N-oxidation, and norcotinine formation. The results reveal an initial rate-determining H_α-atom abstraction step for α-hydroxylation, followed by an unexpected kinetic competition between denitrosation and OH rebound, leading to ( iso-)myosmine as a detoxified product and α-hydroxyNNNs as the precursor of carcinogenic diazohydroxides, respectively. Further detoxification routes are given by β-hydroxylation with relative high reaction barrier and N-oxidation with comparable barrier to the toxifying α-hydroxylation. Moreover, we show for the first time how norcotinine can be generated as a minor NNN metabolite that is formed from iso-myosmine through a unique porphyrin-assisted H atom 1,2-transfer mechanism. These results demonstrate that the carcinogenic potential of NNN is subject to a kinetic competition between activating and deactivating metabolic routes, and identify respective biomarkers to inform about the individual risk associated with NNN exposure.

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.

Selectivity of C-H versus C-F Bond Oxygenation by Homo- and Heterometallic Fe4 , Fe3 Mn, and Mn4 Clusters

A series of tetranuclear [LM3 (HFArPz)3 OM'][OTf]2 (M, M'=Fe or Mn) clusters that displays 3-(2-fluorophenyl)pyrazolate (HFArPz) as bridging ligand is reported. With these complexes, manganese was demonstrated to facilitate C(sp2 )-F bond oxygenation via a putative terminal metal-oxo species. Moreover, the presence of both ortho C(sp2 )-H and C(sp2 )-F bonds in proximity of the apical metal center provided an opportunity to investigate the selectivity of intramolecular C(sp2 )-X bond oxygenation (X=H or F) in these isostructural compounds. With iron as the apical metal center, (M'=Fe) C(sp2 )-F bond oxygenation occur almost exclusively, whereas with manganese (M'=Mn), the opposite reactivity is preferred.

Computational explanation for bioactivation mechanism of targeted anticancer agents mediated by cytochrome P450s: A case of Erlotinib

EGFR inhibitors, even with therapeutics superiorities in anticancer, can cause idiosyncratic pulmonary and hepatic toxicities that are associated with the reactive electrophile bioactivated by Cytochrome P450s (P450s). Until now, neither has the electrophilic intermediate been caught experimentally, nor has the subtle mechanism been declared. Herein, the underlying mechanism of bioactivation mediated by P450s was explored by DFT calculations for a case of EGFR inhibitor, Erlotinib. Based on the calculation and analysis, we suggest that with other metabolites, reactive electrophiles of Erlotinib: epoxide and quinine-imine, can be generated by several steps along the oxidative reaction pathway. The generation of epoxide needs two steps: (1) the addition of Erlotinib to Compound I (Cpd I) and (2) the rearrangement of protons. Whereas, quinine-imine needs a further oxidation step (3) via which quinone is generated and ultimately turns into quinine-imine. Although both reactive electrophiles can be produced for either face-on or side-on pose of Erlotinib, the analysis of energy barriers indicates that the side-on path is preferred in solvent environment. In the rate-determining step, e.g. the addition of Erlotinib to the porphyrin, the reaction barrier for side-on conformation is decreased in aqueous and protein environment compared with gas phase, whereas, the barrier for face-on pose is increased in solvent environment. The simulated mechanism is in good agreement with the speculation in previous experiment. The understanding of the subtle mechanism of bioactivation of Erlotinib will provide theoretical support for toxicological mechanism of EGFR inhibitors.

Combined Docking and Quantum Chemical Study on CYP-Mediated Metabolism of Estrogens in Man

Long-term exposure to estrogens seriously increases the incidence of various diseases including breast cancer. Experimental studies indicate that cytochrome P450 (CYP) enzymes catalyze the bioactivation of estrogens to catechols, which can exert their harmful effects via various routes. It has been shown that the 4-hydroxylation pathway of estrogens is the most malign, while 2-hydroxylation is considered a benign pathway. It is also known experimentally that with increasing unsaturation of ring B of estrogens the prevalence of the 4-hydroxylation pathway significantly increases. In this study, we used a combination of structural analysis, docking, and quantum chemical calculations at the B3LYP/6-311+G* level to investigate the factors that influence the regioselectivity of estrogen metabolism in man. We studied the structure of human estrogen metabolizing enzymes (CYP1A1, CYP1A2, CYP1B1, and CYP3A4) in complex with estrone using docking and investigated the susceptibility of estrone, equilin, and equilenin (which only differ in the unsaturation of ring B) to undergo 2- and 4-hydroxylation using several models of CYP enzymes (Compound I, methoxy, and phenoxy radical). We found that even the simplest models could account for the experimental difference between the 2- and 4- hydroxylation pathways and thus might be used for fast screening purposes. We also show that reactivity indices, specifically in this case the radical and nucleophilic condensed Fukui functions, also correctly predict the likeliness of estrogen derivatives to undergo 2- or 4-hydroxylation.

Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I?

1,2-dihydro-1,2-azaborine is a structural and electronic analogue of benzene which is able to occupy benzene-binding pockets in T4 lysozyme and has been proposed as suitable arene-mimicking group for biological and pharmaceutical applications. Its applicability in a biological context requires it to be able to resist modification by xenobiotic-degrading enzymes like the P450 cytochromes. Quantum chemical computations described in this work show that 1,2-dihydro-1,2-azaborine is much more prone to modification by these enzymes than benzene, unless steric crowding of the ring prevents it from reaching the active site, or otherwise only allows reaction at the less reactive C₄-position. This novel heterocyclic compound is therefore expected to be of limited usefulness as an aryl bioisostere.

Evaluation of the Substrate Scope of Benzoic Acid (De)carboxylases According to Chemical and Biochemical Parameters

The enzymatic carboxylation of phenolic compounds has been attracting increasing interest in recent years, owing to its regioselectivity and technical potential as a biocatalytic equivalent for the Kolbe-Schmitt reaction. Mechanistically the reaction was demonstrated to occur through electrophilic aromatic substitution/water elimination with bicarbonate as a cosubstrate. The effects of the substituents on the phenolic ring have not yet been elucidated in detail, but this would give detailed insight into the substrate-activity relationship and would provide predictability for the acceptance of future substrates. In this report we show how the kinetic and (apparent) thermodynamic behavior can be explained through the evaluation of linear free energy relationships based on electronic, steric, and geometric parameters and through the consideration of enzyme-ligand interactions. Moreover, the similarity between the benzoic acid decarboxylases and the amidohydrolases superfamily is investigated, and promiscuous hydrolytic activity of the decarboxylase in the context of the hydrolysis of an activated ester bond has been established.

Mechanism of the P450-Catalyzed Oxidative Cyclization in the Biosynthesis of Griseofulvin

Griseofulvin is an anti-fungal agent which has recently been determined to have potential anti-viral and anti-cancer applications. The role of specific enzymes involved in the biosynthesis of this natural product has previously been determined, but the mechanism by which a p450, GsfF, catalyzes the key oxidative cyclization of griseophenone B remains unknown. Using density functional theory (DFT), we have determined the mechanism of this oxidation that forms the oxa-spiro core of griseofulvin. Computations show GsfF preferentially performs two sequential phenolic O-H abstractions rather than epoxidation to form an arene oxide intermediate. This conclusion is supported by experimental kinetic isotope effects.

Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations

Cytochrome P450 BM3 (CYP102A1) mutant M11 is able to metabolize a wide range of drugs and drug-like compounds. Among these, M11 was recently found to be able to catalyze formation of human metabolites of mefenamic acid and other nonsteroidal anti-inflammatory drugs (NSAIDs). Interestingly, single active-site mutations such as V87I were reported to invert regioselectivity in NSAID hydroxylation. In this work, we combine crystallography and molecular simulation to study the effect of single mutations on binding and regioselective metabolism of mefenamic acid by M11 mutants. The heme domain of the protein mutant M11 was expressed, purified, and crystallized, and its X-ray structure was used as template for modeling. A multistep approach was used that combines molecular docking, molecular dynamics (MD) simulation, and binding free-energy calculations to address protein flexibility. In this way, preferred binding modes that are consistent with oxidation at the experimentally observed sites of metabolism (SOMs) were identified. Whereas docking could not be used to retrospectively predict experimental trends in regioselectivity, we were able to rank binding modes in line with the preferred SOMs of mefenamic acid by M11 and its mutants by including protein flexibility and dynamics in free-energy computation. In addition, we could obtain structural insights into the change in regioselectivity of mefenamic acid hydroxylation due to single active-site mutations. Our findings confirm that use of MD and binding free-energy calculation is useful for studying biocatalysis in those cases in which enzyme binding is a critical event in determining the selective metabolism of a substrate.

Mechanistic study of allopurinol oxidation using aldehyde oxidase, xanthine oxidase and cytochrome P450 enzymes

The oxidation reaction of allopurinol to its active metabolite (oxypurinol) is investigated using the AO and P450 enzymes. To the contrary of AO (and XO), the P450 enzyme can metabolize the allopurinol with a not self-inhibitory mechanism.

Detoxification of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) by cytochrome P450 enzymes: A theoretical investigation

Two types of detoxification routes, N-demethylation to form 4-phenyl-1,2,3,6-tetrahydropyridine (PTP) and aromatic hydroxylation to generate 4-(4'-hydroxyphenyl)-1-methyl-1,2,3,6-tetrahydropyridine (MPTP-OH), for 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mediated by Compound I (Cpd I) of cytochrome P450 are investigated theoretically using hybrid density functional calculations. Quantum chemical results reveal that for the N-demethylation, the initial C-H bond activation is achieved via a hydrogen atom transfer (HAT) mechanism. This is followed by a subsequent O-rebound to yield the carbinolamine intermediate. Due to the nature of pericyclic reaction, the generated carbinolamine decomposes in a non-enzymatic aqueous environment with the assistance of water molecules, forming amine and hydrated formaldehyde. For the aromatic hydroxylation, an initial addition of Cpd I to the substrate occurs mainly through a side-on approach with a subsequent proton shuttle to form the phenol product. A comparison of the energy barriers for both routes indicates that the N-demethylation (7.5/5.7kcal/mol for the quartet/doublet state in solvent) is thermodynamically more favorable than the aromatic hydroxylation process (14.9/14.8kcal/mol for the quartet/doublet state in solvent). This trend is in good agreement with the experimental product distribution, viz., the N-demethylation product PTP is more than the aromatic hydroxylation product MPTP-OH. Taken together, these observations not only enrich our knowledge on the mechanistic details of the N-dealkylation and the aromatic hydroxylation by P450s, but also provide certain insights into the metabolism of other analogous toxins.

Prediction of cytochrome P450 mediated metabolism

Cytochrome P450 enzymes (CYPs) form one of the most important enzyme families involved in the metabolism of xenobiotics. CYPs comprise many isoforms, which catalyze a wide variety of reactions, and potentially, a large number of different metabolites can be formed. However, it is often hard to rationalize what metabolites these enzymes generate. In recent years, many different in silico approaches have been developed to predict binding or regioselective product formation for the different CYP isoforms. These comprise ligand-based methods that are trained on experimental CYP data and structure-based methods that consider how the substrate is oriented in the active site or/and how reactive the part of the substrate that is accessible to the heme group is. We will review key aspects for various approaches that are available to predict binding and site of metabolism (SOM), what outcome can be expected from the predictions, and how they could potentially be improved.

Transformation pathways of MeO-PBDEs catalyzed by active center of P450 enzymes: a DFT investigation employing 6-MeO-BDE-47 as a case

Recent in vivo and in vitro experiments indicated that methoxylated polybrominated diphenyl ethers (MeO-PBDEs) can be biotransformed into hydroxylated PBDEs (HO-PBDEs) that are more toxic than PBDEs and MeO-PBDEs. Nevertheless, the enzymatic transformation mechanism is not clear. We hypothesized that cytochrome P450 enzymes (CYPs) play a key role in the transformation and employed the density functional theory calculations to unveil the mechanism. The transformation of a model compound, 6-MeO-BDE-47, catalyzed by the active center of CYPs (Compound I), was computed. For the first time, our results show that the energy barriers for the addition of Compound I to the C atoms on the phenyl of 6-MeO-BDE-47 are much higher than that for hydroxylation of the methoxyl, indicating that O-demethylation is a dominating metabolic pathway. This is in line with experimental observations performed by others. The pathways for the transformation of 6-MeO-BDE-47 catalyzed by Compound I were clarified. A C-H bond of the methoxyl is activated by Compound I, followed by radical rebound to form carbinol intermediates, then the carbinols decompose to form 6-HO-BDE-47 with the assistance of water molecules. The computational method can be potentially employed to develop models that predict biotransformation of xenobiotics catalyzed by CYPs.

Recent progress on structural bioinformatics research of cytochrome P450 and its impact on drug discovery

Cytochrome P450 is predominantly responsible for human drug metabolism, which is of critical importance for drug discovery and development. Structural bioinformatics focuses on analysis and prediction of three-dimentional structure of biological macromolecules and elucidation of structure-function relationship as well as identification of important binding interactions. Rapid advancement of structural bioinformatics has been made over the last decade. With more information available for CYP structures, the methods of structural bioinformatics may be used in the CYP field. In this review, we demonstrate three previous studies on CYP using the methods of structural bioinformatics, including the investigation of reasons for decrease of enzymatic activity of CYP1A2 caused by a peripheral mutation, the construction of a pharmacophore model specific to active site of CYP1A2 and the prediction of the functional consequences of single residue mutation in CYP. By illustrating these studies we attempt to show the potential role of structural bioinformatics in CYP research and help better understanding the importance of structural bioinformatics in drug designing.