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

Environmental contamination by bisphenols: From plastic production to modulation of the intestinal morphophysiology in experimental models

Bisphenols are frequently found in a range of plastic products and have been associated with the development of diseases such as diabetes mellitus type 2 and obesity. These compounds are known as endocrine disruptors and have led to restrictions on their use due to their presence in the environment and their association with non-communicable chronic diseases. The gastrointestinal tract, being the primary site of food and water absorption, is particularly vulnerable to the effects of bisphenols. For this reason, a review of studies showing associations between bisphenols exposure and adverse effects in the gut microbiota, morphology tissue, gut permeability, and on the enteric nervous system was carried out. We have included perinatal studies and in different adult experimental models. The effects of bisphenol exposure on the gut microbiota are complex and varied. Bisphenol exposure generally leads to a decrease in microbial diversity and may impact the integrity of the intestinal barrier, resulting in elevated levels of inflammation, changes in morphological and metabolic characteristics of the gut, modifications in tight junction expression, and changes in goblet cell expression. In addition, bisphenol exposure in the perinatal phase can lead to important intestinal changes, including increased colonic inflammation and decreased colonic paracellular permeability.

Computational Modeling of the Enzymatic Achmatowicz Rearrangement by Heme-Dependent Chloroperoxidase: Reaction Mechanism, Enantiopreference, Regioselectivity, and Substrate Specificity

The chloroperoxidase from Caldariomyces fumago (CfCPO) catalyzes the oxidative ring expansion of α-heterofunctionalized furans via the Achmatowicz rearrangement, providing an elegant tool to convert furan rings into complex-prefunctionalized scaffolds. However, the mechanism of this transformation remains unclear. Herein, the CfCPO-catalyzed reaction of rac-1-(2-furyl)ethanol (1a) is studied by quantum chemical calculations and molecular dynamics simulations. The calculations reveal that the conversion follows the general mechanism of the Achmatowicz reaction. Notably, the binding of 1a to the enzyme's active site influences the Compound I (Cpd I) formation, and the (R)-1a enantiomer binding results in a lower barrier compared to (S)-1a, explaining the observed (R)-enantiopreference toward a racemic substrate. Additionally, due to the weaker steric hindrance between the porphyrin ring and substrate, the nucleophilic attack of Cpd I on the furan core of 1a is preferred at the less-substituted C4=C5 bond, providing a rationale for the experimentally observed regioselectivity. Finally, the bottleneck residues in the substrate delivery channel and also the active site surroundings are proposed to be responsible for the substrate specificity of CfCPO. This study lays a theoretical foundation for the rational design of new CPOs that catalyze the Achmatowicz rearrangement with a broader substrate spectrum or specific stereopreference.

Theoretical Investigation of Cytochrome P450 Enzyme-Mediated Biotransformation Mechanism of BHPF: Unveiling the Metabolic Safety Aspects of an Alternative to BPA

Fluorene-9-bisphenol (BHPF), emerging as an alternative to bisphenol A (BPA), is extensively utilized in industry and consumer goods. BHPF exhibits antiestrogenic effects and potential reproductive toxicity. Similar to BPA, BHPF can closely access the active site of the cytochrome P450 (CYP450) enzyme, interact with the Fe=O moiety, and potentially initiate metabolic reactions. Using density functional theory (DFT) calculations, we explored the mechanisms underlying BHPF activation using a CYP450 compound I (Cpd I) model, identifying several plausible products. Compared with the higher energy barriers associated with phenyl ring addition reactions, the formation of a phenoxyl-type radical through phenolic hydrogen atom abstraction, followed by OH rebound or radical coupling, represents an energetically favorable pathway. The OH rebound process yields three primary products: 9-(3,4-dihydroxyphenyl)-9-(4-hydroxyphenyl)fluorene (PRD1), semiquinone radical anion (PRD2), and 9-(4-hydroxyphenyl)fluorene carbocation (PRD3), constituting the major outcomes of the BHPF metabolic reaction. Importantly, a lipophilic ether metabolite, BHPF-O-BHPF (PRD4), formed through the coupling of phenoxyl radicals, reflects a widespread metabolic pathway observed in phenolic molecules. Despite constituting a minor proportion, the toxicity of this product necessitates increased attention. These findings contribute significantly to an enhanced understanding of the potential hazards associated with BHPF and other unknown chemical entities.

Tutorial Review on the Set-Up and Running of Quantum Mechanical Cluster Models for Enzymatic Reaction Mechanisms

Enzymes turnover substrates into products with amazing efficiency and selectivity and as such have great potential for use in biotechnology and pharmaceutical applications. However, details of their catalytic cycles and the origins surrounding the regio- and chemoselectivity of enzymatic reaction processes remain unknown, which makes the engineering of enzymes and their use in biotechnology challenging. Computational modelling can assist experimental work in the field and establish the factors that influence the reaction rates and the product distributions. A popular approach in modelling is the use of quantum mechanical cluster models of enzymes that take the first- and second coordination sphere of the enzyme active site into consideration. These QM cluster models are widely applied but often the results obtained are dependent on model choice and model selection. Herein, we show that QM cluster models can give highly accurate results that reproduce experimental product distributions and free energies of activation within several kcal mol-1, regarded that large cluster models with >300 atoms are used that include key hydrogen bonding interactions and charged residues. In this tutorial review, we give general guidelines on the set-up and applications of the QM cluster method and discuss its accuracy and reproducibility. Finally, several representative QM cluster model examples on metal-containing enzymes are presented, which highlight the strength of the approach.

Elucidation and active ingredient identification of aqueous extract of Ficus exasperata Vahl leaf against bisphenol A-induced toxicity through in vivo and in silico assessments

Bisphenol A (BPA), an endocrine-disrupting chemical, poses significant health problems due to its induction of oxidative stress, inflammation, etc. Whereas Ficus exasperata Vahl leaf (FEVL) was reported for its ethnopharmacological properties against several ailments owing to its antioxidant, anti-inflammatory properties, etc. Here, we aim to elucidate and identify the bioactive compounds of aqueous extract of FEVL (AEFEVL) against BPA-induced toxicity using in vivo and in silico assessments. To determine the BPA toxicity mechanism and safe doses of AEFEVL, graded doses of BPA (0-400 μM) and AEFEVL (0-2.0 mg/10 g diets) were separately fed to flies to evaluate survival rates and specific biochemical markers. The mitigating effect of AEFEVL (0.5 and 1.0 mg/10 g diet) against BPA (100 and 200 μM)-induced toxicity in the flies after 7-day exposure was also carried out. Additionally, molecular docking analysis of BPA and BPA-o-quinone (BPAQ) against selected antioxidant targets, and HPLC-MS-revealed AEFEVL compounds against Keap-1 and IKKβ targets, followed by ADMET analysis, was conducted. Emergence rate, climbing ability, acetylcholinesterase, monoamine oxidase-B, and glutathione-S-transferase activities, and levels of total thiols, non-protein thiols, nitric oxide, protein carbonyl, malondialdehyde, and cell viability were evaluated. BPA-induced altered biochemical and behavioral parameters were significantly mitigated by AEFEVL in the flies (p < 0.05). BPAQ followed by BPA exhibited higher inhibitory activity, and epigallocatechin (EGC) showed the highest inhibitory activity among the AEFEVL compounds with desirable ADMET properties. Conclusively, our findings revealed that EGC might be responsible for the mitigative effect displayed by AEFEVL in BPA-induced toxicity in D. melanogaster.

Graphical abstract

Mechanism of the Oxidative Ring-Closure Reaction during Gliotoxin Biosynthesis by Cytochrome P450 GliF

During gliotoxin biosynthesis in fungi, the cytochrome P450 GliF enzyme catalyzes an unusual C-N ring-closure step while also an aromatic ring is hydroxylated in the same reaction cycle, which may have relevance to drug synthesis reactions in biotechnology. However, as the details of the reaction mechanism are still controversial, no applications have been developed yet. To resolve the mechanism of gliotoxin biosynthesis and gain insight into the steps leading to ring-closure, we ran a combination of molecular dynamics and density functional theory calculations on the structure and reactivity of P450 GliF and tested a range of possible reaction mechanisms, pathways and models. The calculations show that, rather than hydrogen atom transfer from the substrate to Compound I, an initial proton transfer transition state is followed by a fast electron transfer en route to the radical intermediate, and hence a non-synchronous hydrogen atom abstraction takes place. The radical intermediate then reacts by OH rebound to the aromatic ring to form a biradical in the substrate that, through ring-closure between the radical centers, gives gliotoxin products. Interestingly, the structure and energetics of the reaction mechanisms appear little affected by the addition of polar groups to the model and hence we predict that the reaction can be catalyzed by other P450 isozymes that also bind the same substrate. Alternative pathways, such as a pathway starting with an electrophilic attack on the arene to form an epoxide, are high in energy and are ruled out.

Machine learning-aided engineering of a cytochrome P450 for optimal bioconversion of lignin fragments

Using machine learning, molecular dynamics simulations, and density functional theory calculations we gain insight into the selectivity patterns of substrate activation by the cytochromes P450. In nature, the reactions catalyzed by the P450s lead to the biodegradation of xenobiotics, but recent work has shown that fungi utilize P450s for the activation of lignin fragments, such as monomer and dimer units. These fragments often are the building blocks of valuable materials, including drug molecules and fragrances, hence a highly selective biocatalyst that can produce these compounds in good yield with high selectivity would be an important step in biotechnology. In this work a detailed computational study is reported on two reaction channels of two P450 isozymes, namely the O-deethylation of guaethol by CYP255A and the O-demethylation versus aromatic hydroxylation of p-anisic acid by CYP199A4. The studies show that the second-coordination sphere plays a major role in substrate binding and positioning, heme access, and in the selectivity patterns. Moreover, the local environment affects the kinetics of the reaction through lowering or raising barrier heights. Furthermore, we predict a site-selective mutation for highly specific reaction channels for CYP199A4.

Computational study on the endocrine-disrupting metabolic activation of Benzophenone-3 catalyzed by cytochrome P450 1A1: A QM/MM approach

Predicting the metabolic activation mechanism and potential hazardous metabolites of environmental endocrine-disruptors is a challenging and significant task in risk assessment. Here the metabolic activation mechanism of benzophenone-3 catalyzed by P450 1A1 was investigated by using Molecular Dynamics, Quantum Mechanics/Molecular Mechanics and Density Functional Theory approaches. Two elementary reactions involved in the metabolic activation of BP-3 with P450 1A1: electrophilic addition and hydrogen abstraction reactions were both discussed. Further conversion reactions of epoxidation products, ketone products and the formaldehyde formation reaction were investigated in the non-enzymatic environment based on previous experimental reports. Binding affinities analysis of benzophenone-3 and its metabolites to sex hormone binding globulin indirectly demonstrates that they all exhibit endocrine-disrupting property. Toxic analysis shows that the eco-toxicity and bioaccumulation values of the benzophenone-3 metabolites are much lower than those of benzophenone-3. However, the metabolites are found to have skin-sensitization effects. The present study provides a deep insight into the biotransformation process of benzophenone-3 catalyzed by P450 1A1 and alerts us to pay attention to the adverse effects of benzophenone-3 and its metabolites in human livers.

CO2 Reduction by an Iron(I) Porphyrinate System: Effect of Hydrogen Bonding on the Second Coordination Sphere

Transforming CO2 into valuable materials is an important reaction in catalysis, especially because CO2 concentrations in the atmosphere have been growing steadily due to extensive fossil fuel usage. From an environmental perspective, reduction of CO2 to valuable materials should be catalyzed by an environmentally benign catalyst and avoid the use of heavy transition-metal ions. In this work, we present a computational study into a novel iron(I) porphyrin catalyst for CO2 reduction, namely, with a tetraphenylporphyrin ligand and analogues. In particular, we investigated iron(I) tetraphenylporphyrin with one of the meso-phenyl groups substituted with o-urea, p-urea, or o-2-amide groups. These substituents can provide hydrogen-bonding interactions in the second coordination sphere with bound ligands and assist with proton relay. Furthermore, our studies investigated bicarbonate and phenol as stabilizers and proton donors in the reaction mechanism. Potential energy landscapes for double protonation of iron(I) porphyrinate with bound CO2 are reported. The work shows that the bicarbonate bridges the urea/amide groups to the CO2 and iron center and provides a tight bonding pattern with strong hydrogen-bonding interactions that facilitates easy proton delivery and reduction of CO2. Specifically, bicarbonate provides a low-energy proton shuttle mechanism to form CO and water efficiently. Furthermore, the o-urea group locks bicarbonate and CO2 in a tight orientation and helps with ideal proton transfer, while there is more mobility and lesser stability with an o-amide group in that position instead. Our calculations show that the o-urea group leads to reduction in proton-transfer barriers, in line with experimental observation. We then applied electric-field-effect calculations to estimate the environmental effects on the two proton-transfer steps in the reaction. These calculations describe the perturbations that enhance the driving forces for the proton-transfer steps and have been used to make predictions about how the catalysts can be further engineered for more enhanced CO2 reduction processes.

C-H bond activation by high-valent iron/cobalt-oxo complexes: a quantum chemical modeling approach

High-valent metal-oxo species serve as key intermediates in the activation of inert C-H bonds. Here, we present a comprehensive DFT analysis of the parameters that have been proposed as influencing factors in modeled high-valent metal-oxo mediated C-H activation reactions. Our approach involves utilizing DFT calculations to explore the electronic structures of modeled FeIVO (species 1) and CoIVO ↔ CoIII-O˙ (species 2), scrutinizing their capacity to predict improved catalytic activity. DFT and DLPNO-CCSD(T) calculations predict that the iron-oxo species possesses a triplet as the ground state, while the cobalt-oxo has a doublet as the ground state. Furthermore, we have investigated the mechanistic pathways for the first C-H bond activation, as well as the desaturation of the alkanes. The mechanism was determined to be a two-step process, wherein the first hydrogen atom abstraction (HAA) represents the rate-limiting step, involving the proton-coupled electron transfer (PCET) process. However, we found that the second HAA step is highly exothermic for both species. Our calculations suggest that the iron-oxo species (Fe-O = 1.672 Å) exhibit relatively sluggish behavior compared to the cobalt-oxo species (Co-O = 1.854 Å) in C-H bond activation, attributed to a weak metal-oxygen bond. MO, NBO, and deformation energy analysis reveal the importance of weakening the M-O bond in the cobalt species, thereby reducing the overall barrier to the reaction. This catalyst was found to have a C-H activation barrier relatively smaller than that previously reported in the literature.

Constructing a CdS QDs/silica gel composite with high photosensitivity and prolonged recyclable operability for enhanced visible-light-driven NADH regeneration

Visible-light-driven nicotinamide adenine dinucleotide (NADH) regeneration is one of the most effective measures, and cadmium sulfide (CdS) materials are typically used as low-cost photocatalysts. The CdS photocatalysts, however, still suffer from low regeneration efficiency and poor cycle stability. In this work, the CdS quantum dots (QDs) less than 10 nm embedded onto silica gel (CdS QDs/Silica gel) were constructed for visible-light-driven NADH regeneration by a successive ionic layer adsorption reaction and ball milling method. Results demonstrate that the photosensitivity of the CdS QDs/Silica gel composite was 31 times higher than that of the bulk CdS. Moreover, the conduction band (CB) edge of the CdS QDs/Silica gel composite is -1.34 eV, which is more negative 0.5 eV than that of the bulk CdS. The obtained CdS QDs/Silica gel composites showed the highest NADH regeneration yields of 68.8% under visible-light (LED, 420 nm) illumination and can be reused for over 40 cycles. Finally, the bioactivity of NADH toward enzyme catalysis is further confirmed by the hydrogenation of benzaldehyde to benzyl alcohol catalyzed with an alcohol dehydrogenase as enzyme catalysis.

Insights into Cytochrome P450 Enzyme Catalyzed Defluorination of Aromatic Fluorides

Density functional calculations establish a novel mechanism of aromatic defluorination by P450 Compound I. This is achieved via either an initial epoxide intermediate or through a 1,2-fluorine shift in an electrophilic intermediate, which highlights that the P450s can defluorinate fluoroarenes. However, in the absence of a proton donor a strong Fe-F bond can be obtained as shown from the calculations.

Melatonin Activation by Human Cytochrome P450 Enzymes: A Comparison between Different Isozymes

Cytochrome P450 enzymes in the human body play a pivotal role in both the biosynthesis and the degradation of the hormone melatonin. Melatonin plays a key role in circadian rhythms in the body, but its concentration is also linked to mood fluctuations as well as emotional well-being. In the present study, we present a computational analysis of the binding and activation of melatonin by various P450 isozymes that are known to yield different products and product distributions. In particular, the P450 isozymes 1A1, 1A2, and 1B1 generally react with melatonin to provide dominant aromatic hydroxylation at the C6-position, whereas the P450 2C19 isozyme mostly provides O-demethylation products. To gain insight into the origin of these product distributions of the P450 isozymes, we performed a comprehensive computational study of P450 2C19 isozymes and compared our work with previous studies on alternative isozymes. The work covers molecular mechanics, molecular dynamics and quantum mechanics approaches. Our work highlights major differences in the size and shape of the substrate binding pocket amongst the different P450 isozymes. Consequently, substrate binding and positioning in the active site varies substantially within the P450 isozymes. Thus, in P450 2C19, the substrate is oriented with its methoxy group pointing towards the heme, and therefore reacts favorably through hydrogen atom abstraction, leading to the production of O-demethylation products. On the other hand, the substrate-binding pockets in P450 1A1, 1A2, and 1B1 are tighter, direct the methoxy group away from the heme, and consequently activate an alternative site and lead to aromatic hydroxylation instead.

Direct Electrophilic Attack of Compound I on the Indole Ring in the Peroxygenase Mechanism of Dehaloperoxidase DHP B in Degrading Haloindole: Electron Transfer Promotes the Reaction

The H2O2-dependent degradation of haloindole catalyzed by the dehaloperoxidase (DHP) from Amphitrite ornate has been reported to employ the peroxygenase mechanism, and the two oxidized products 5-halo-2-oxindole and 5-halo-3-oxindole have a similar amount. According to a previous experimental study, compound I (Cpd I) was suggested to be responsible for triggering the reaction, and the reaction may undergo three possible intermediates; however, the reaction details are still unclear. To clarify the reaction mechanism of DHP, the computational model was constructed on the basis of the high-resolution crystal structure, and a series of the quantum mechanical/molecular mechanical calculations were performed. Based on our calculation results, it is confirmed that the reaction starts from the direct electrophilic attack of Cpd I on the indole ring of the substrate, and the resulted intermediate contains both a carbocation and an oxygen anion, whereas the common hydrogen abstraction by Cpd I was calculated to correspond to a relatively higher barrier. In addition, a net electron transfer from the substrate to the iron center is observed during the attack of Cpd I on the indole ring; therefore, the carbocation/oxygen anion intermediate can easily undergo an intramolecular hydride transfer to form the product 5-halo-2-oxindole or isomerize to the epoxide intermediate which finally generates another product 5-halo-3-oxindole. It is the zwitterionic characteristic of the intermediate that makes the intermolecular hydride transfer quite easy, and it is the high electron affinity of the iron center that promotes the single-electron oxidation of the reaction intermediate. Our calculations well explain the formation of two oxidized products 5-halo-2-oxindole and 5-halo-3-oxindole.

Vitamin E (α-Tocopherol) Does Not Ameliorate the Toxic Effect of Bisphenol S on the Metabolic Analytes and Pancreas Histoarchitecture of Diabetic Rats

This study investigated whether the coadministration of vitamin E (VitE) diminishes the harmful effects provoked by plasticizer bisphenol S (BPS) in the serum metabolites related to hepatic and renal metabolism, as well as the endocrine pancreatic function in diabetic male Wistar rats. Rats were divided into five groups (n = 5-6); the first group was healthy rats (Ctrl group). The other four groups were diabetic rats induced with 45 mg/kg bw of streptozotocin: Ctrl-D (diabetic control); VitE-D (100 mg/kg bw/d of VitE); BPS-D (100 mg/kg bw/d of BPS); The animals from the VitE + BPS-D group were administered 100 mg/kg bw/d of VitE + 100 mg/kg bw/d of BPS. All compounds were administered orally for 30 days. Body weight, biochemical assays, urinalysis, glucose tolerance test, pancreas histopathology, proximate chemical analysis in feces, and the activity of antioxidants in rat serum were assessed. The coadministration of VitE + BPS produced weight losses, increases in 14 serum analytes, and degeneration in the pancreas. Therefore, the VitE + BPS coadministration did not have a protective effect versus the harmful impact of BPS or the diabetic metabolic state; on the contrary, it partially aggravated the damage produced by the BPS. VitE is likely to have an additive effect on the toxicity of BPS.

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.

Melatonin Activation by Cytochrome P450 Isozymes: How Does CYP1A2 Compare to CYP1A1?

Cytochrome P450 enzymes are versatile enzymes found in most biosystems that catalyze mono-oxygenation reactions as a means of biosynthesis and biodegradation steps. In the liver, they metabolize xenobiotics, but there are a range of isozymes with differences in three-dimensional structure and protein chain. Consequently, the various P450 isozymes react with substrates differently and give varying product distributions. To understand how melatonin is activated by the P450s in the liver, we did a thorough molecular dynamics and quantum mechanics study on cytochrome P450 1A2 activation of melatonin forming 6-hydroxymelatonin and N-acetylserotonin products through aromatic hydroxylation and O-demethylation pathways, respectively. We started from crystal structure coordinates and docked substrate into the model, and obtained ten strong binding conformations with the substrate in the active site. Subsequently, for each of the ten substrate orientations, long (up to 1 μs) molecular dynamics simulations were run. We then analyzed the orientations of the substrate with respect to the heme for all snapshots. Interestingly, the shortest distance does not correspond to the group that is expected to be activated. However, the substrate positioning gives insight into the protein residues it interacts with. Thereafter, quantum chemical cluster models were created and the substrate hydroxylation pathways calculated with density functional theory. These relative barrier heights confirm the experimental product distributions and highlight why certain products are obtained. We make a detailed comparison with previous results on CYP1A1 and identify their reactivity differences with melatonin.