Biotransformation Mechanism of Pesticides by Cytochrome P450: A DFT Study on Dieldrin

Cytochrome P450 Enzyme-Mediated Enantioselective Biotransformation of Chiral Fungicide Tebuconazole in Earthworm

Tebuconazole is widely used in agricultural practices, leading to elevated residue levels in agricultural soils. However, its biotransformation and the ecotoxicological effects of the corresponding transformation products (TPs) remain insufficiently explored. To fill this research gap, the TPs of tebuconazole in an earthworm-soil system were identified by UHPLC-QTOF/MS combined with UHPLC-QLiT/MS. Six chiral TPs were tentatively identified, with four TPs detected in both earthworms and soil, while two TPs were found exclusively in earthworm. Significant enantioselectivity was observed for tebuconazole and five TPs in earthworms, involving cytochrome P450 enzyme-mediated hydroxylation and dechlorination. In vitro metabolism experiments using earthworm microsomes revealed that CYP1A2, CYP2J2, and CYP2E1 were involved in the hydroxylation pathway of tebuconazole. Molecular docking results confirmed that S-(+)-tebuconazole produced more hydroxylated transformation products than R-(-)-tebuconazole due to its lower binding energy with these enzymes. Predictions from the ECOSAR model indicated that hydroxylation was the most significant transformation pathway for reducing the toxicity of tebuconazole. These findings provide valuable insights into the environmental fate and risk assessment of tebuconazole at the enantiomeric level.

Multiscale calculations reveal new insights into the reaction mechanism between KRASG12C and α, β-unsaturated carbonyl of covalent inhibitors

Utilizing α,β-unsaturated carbonyl group as Michael acceptors to react with thiols represents a successful strategy for developing KRASG12C inhibitors. Despite this, the precise reaction mechanism between KRASG12C and covalent inhibitors remains a subject of debate, primarily due to the absence of an appropriate residue capable of deprotonating the cysteine thiol as a base. To uncover this reaction mechanism, we first discussed the chemical reaction mechanism in solvent conditions via density functional theory (DFT) calculation. Based on this, we then proposed and validated the enzymatic reaction mechanism by employing quantum mechanics/molecular mechanics (QM/MM) calculation. Our QM/MM analysis suggests that, in biological conditions, proton transfer and nucleophilic addition may proceed through a concerted process to form an enolate intermediate, bypassing the need for a base catalyst. This proposed mechanism differs from previous findings. Following the formation of the enolate intermediate, solvent-assisted tautomerization results in the final product. Our calculations indicate that solvent-assisted tautomerization is the rate-limiting step in the catalytic cycle under biological conditions. On the basis of this reaction mechanism, the calculated kinact/ki for two inhibitors is consistent well with the experimental results. Our findings provide new insights into the reaction mechanism between the cysteine of KRASG12C and the covalent inhibitors and may provide valuable information for designing effective covalent inhibitors targeting KRASG12C and other similar targets.

Assessing environmental and human health risks: Insight from the enantioselective metabolism and degradation of fenpropidin

Fenpropidin (FPD), a widely employed chiral fungicide, is frequently detected in diverse environments. In an in vitro rat liver microsomes cultivation (RLMs), the metabolism exhibited the order of R-FPD > S-FPD, with respective half-lives of 10.42 ± 0.11 and 12.06 ± 0.15 min, aligning with kinetic analysis results. CYP3A2 has been demonstrated to be the most significant oxidative enzyme through CYP450 enzyme inhibition experiments. Molecular dynamics simulations unveiled the enantioselective metabolic mechanism, demonstrating that R-FPD forms hydrogen bonds with the CYP3A2 protein, resulting in a higher binding affinity (-6.58 kcal mol-1) than S-FPD. Seven new metabolites were identified by Liquid chromatography time-of-flight high-resolution mass spectrometry, which were mainly generated through oxidation, reduction, hydroxylation, and N-dealkylation reactions. The toxicity of the major metabolites predicted by the TEST procedure was found to be stronger than the predicted toxicity of FPD. Moreover, the enantioselective fate of FPD was studied by examining its degradation in three soils with varying physical and chemical properties under aerobic, anaerobic, and sterile conditions. Enantioselective degradation of FPD occurred in soils without enantiomeric transformation, displaying a preference for R-FPD degradation. R-FPD is a low-risk stereoisomer both in the environment and in mammals. The research presented a systematic and comprehensive method for analyzing the metabolic and degradation system of FPD enantiomers. This approach aids in understanding the behavior of FPD in the environment and provides valuable insights into their potential risks to human health.

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.

Quantitative differentiation of toxicity contributions and predicted global risk of fipronil and its transformation products to aquatic invertebrates

Biotransformation often alters chemical toxicity, yet its impacts on risk assessment are hardly quantified due to the challenges in acquiring internal exposure-based thresholds for chemicals that are readily metabolizable. Here, we integrated toxic unit and toxicokinetics to quantitatively assess toxicity contributions and potential risk of both parent compound and transformation products (TPs) to aquatic organisms, using fipronil (FIP) as a representative toxicant. In aquatic invertebrates Chironomus dilutus and Hyalella azteca, approximately 90 % of FIP was transformed to fipronil sulfone (SUL). FIP and SUL exhibited similar intrinsic toxicity to these organisms, which was contrary to conventional perception that SUL was more toxic than FIP. However, biotransformation was still important in risk assessment because the TP had 10-fold slower depuration rate than FIP. The amphipod H. azteca was found to be as sensitive to FIPs as the insect C. dilutus, which was previously considered ten times more sensitive based on external thresholds. This discrepancy has led to overlooking the toxicity of FIP to H. azteca in regional risk assessments. Lastly, we predicted the lethal risk of FIPs in global surface water. When using external thresholds for prediction, FIPs in 3.4 % of the water samples were lethally toxic to H. azteca, and the percentage of water samples at risk increased to 14 % when internal thresholds were used and SUF dominated the risk. This study presents an improved method for quantifying aquatic risk of readily metabolized toxicants. Our findings underscore the urgency of considering TPs in water quality assessments, especially for sensitive species that are at risk in the environment.

DeepP450: Predicting Human P450 Activities of Small Molecules by Integrating Pretrained Protein Language Model and Molecular Representation

Cytochrome P450 enzymes (CYPs) play a crucial role in Phase I drug metabolism in the human body, and CYP activity toward compounds can significantly affect druggability, making early prediction of CYP activity and substrate identification essential for therapeutic development. Here, we established a deep learning model for assessing potential CYP substrates, DeepP450, by fine-tuning protein and molecule pretrained models through feature integration with cross-attention and self-attention layers. This model exhibited high prediction accuracy (0.92) on the test set, with area under the receiver operating characteristic curve (AUROC) values ranging from 0.89 to 0.98 in substrate/nonsubstrate predictions across the nine major human CYPs, surpassing current benchmarks for CYP activity prediction. Notably, DeepP450 uses only one model to predict substrates/nonsubstrates for any of the nine CYPs and exhibits certain generalizability on novel compounds and different categories of human CYPs, which could greatly facilitate early stage drug design by avoiding CYP-reactive compounds.

New insight into molecular mechanism of P450-Catalyzed metabolism of emerging contaminants and its consequence for human health: A case study of preservative methylparaben

Hydroxylated metabolites in the living body are considered as a potential biomarker of exposure to emerging contaminations (ECs) and breast cancer, but their formation mechanism has not received enough attention. Besides, the adverse impacts of metabolites during the metabolic transformation of ECs largely remain unknown. In this study, we employed a density functional calculation combing with in-vitro incubation of human liver microsomes to explore the bio-transformation of preservative methylparaben (MPB) in human bodies. Our results showed that hydroxylated metabolites of MPB (OH-MPB) were observed experimentally, while a formation mechanism was revealed at the molecular level. That is, hydroxylated metabolite was exclusively formed via the hydrogen abstraction from the phenolic hydroxyl group of MPB followed by the OH-rebound pathway, rather than the direct hydroxylation on the benzene ring. The increasing of hydroxyl groups on ECs could improve the metabolisms. This was confirmed in the metabolism of ECs without hydroxyl group and with multiple-hydroxyl groups, respectively. Furthermore, toxicity assessments show that compared to parent MPB, the hydroxylated metabolites have increased negative impacts on the gastrointestinal system and liver. A semiquinone product exhibits potential damage in the cardiovascular system and epoxides are toxic to the blood and gastrointestinal system. The findings deepen our insight into the biotransformation of parabens in human health, especially by providing health warnings about the potential impacts caused by semiquinone and epoxides.

Theoretical Kinetic Isotope Effects in Establishing the Precise Biodegradation Mechanisms of Organic Pollutants

Compound-specific isotope analysis (CSIA) for natural isotope ratios has been recognized as a promising tool to elucidate biodegradation pathways of organic pollutants by microbial enzymes by relating reported kinetic isotope effects (KIEs) to apparent KIEs (AKIEs) derived from bulk isotope fractionations (ε_bulk). However, for many environmental reactions, neither are the reference KIE ranges sufficiently narrow nor are the mechanisms elucidated to the point that rate-determining steps have been identified unequivocally. In this work, besides providing reference KIEs and rationalizing AKIEs, good relationships have been explained by DFT computations for diverse biodegradation pathways with known enzymatic models between the theoretical isotope fractionations (ε_bulk^') from intrinsic KIEs on the rate-determining steps and the observed ε_bulk. (1) To confirm the mechanistic details of previously reported pathway-dependent CSIA, it includes isotope changes in MTBE biodegradation between hydroxylation by CYP450 and S_N2 reaction by cobalamin-dependent methyltransferase, the regioselectivity of toluene biodegradation by CYP450, and the rate-determining step in toluene biodegradation by benzylsuccinate synthase. (2) To yield new fundamental insights into some unclear biodegradation pathways, it consists of the oxidative function of toluene dioxygenase in biodegradation of TCE, the epoxidation mode in biodegradation of TCE by toluene 4-monooxygenase, and the weighted average mechanism in biodegradation of cDCE by CYP450.

Environmental behavior of the chiral fungicide epoxiconazole in earthworm-soil system: Enantioselective enrichment, degradation kinetics, chiral metabolite identification, and biotransformation mechanism

The environmental impact of the chiral fungicide epoxiconazole and its chiral transformation products (TPs) on non-target organisms and the environment has become a significant concern due to its widespread use in agricultural practice. Enantioselectivity studies of parent contaminants cannot adequately assess the complexity of its chiral TPs in the environment. This study aimed to investigate the environmental behavior of epoxiconazole in an earthworm-soil system. 2S,3R-(-)-epoxiconazole was preferentially enriched in earthworms during the accumulation phase (p < 0.05), but no enantioselectivity was observed during the elimination phase. One methoxylated and four hydroxylated chiral TPs were identified in soil, earthworm, and excrement. The epoxy ring hydroxylated TP and methoxylated TP of epoxiconazole were discovered for the first time in the environment. The chemically specific enantioselectivity with enantiomer fraction (EF) > 0.8 was observed for the TPs in different matrices. The CYP450 monooxygenase of earthworm was significant activated. In vitro enzyme metabolism experiments (earthworm microsomes and recombinant CYP450 enzymes CYP2A6, CYP 2C9, and CYP 3A4) were carried out to further explain the biotransformation mechanism of epoxiconazole in earthworm. This study provides new evidence of enantiomeric biotransformation of chiral fungicide epoxiconazole in the earthworm-soil system and could provide valuable insights into their environmental risk assessment.

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.

Regioselective hydroxylation of carbendazim by mammalian cytochrome P450: A combined experimental and computational study

Carbendazim (CBZ), a broad-spectrum pesticide frequently detected in fruits and vegetables, could trigger potential toxic risks to mammals. To facilitate the assessment of health risks, this study aimed to characterize the cytochrome P450 (CYPs)-mediated metabolism profiles of CBZ by a combined experimental and computational study. Our results demonstrated that CYPs-mediated region-selective hydroxylation was a major metabolism pathway for CBZ in liver microsomes from various species including rat, mouse, minipig, dog, rabbit, guinea pig, monkey, cow and human, and the metabolite was biosynthesized and well-characterized as 6-OH-CBZ. CYP1A displayed a predominant role in the region-selective hydroxylation of CBZ that could attenuate its toxicity through converting it into a less toxic metabolite. Meanwhile, five other common pesticides including chlorpyrifos-methyl, prochloraz, chlorfenapyr, chlorpyrifos, and chlorothalonil could significantly inhibit the region-selective hydroxylation of CBZ, and consequently remarkably increased CBZ exposure in vivo. Furthermore, computational study clarified the important contribution of the key amino acid residues Ser122, and Asp313 in CYP1A1, as well as Asp320 in CYP1A2 to the hydroxylation of CBZ through hydrogen bonds. These results would provide some useful information for the metabolic profiles of CBZ by mammalian CYPs, and shed new insights into CYP1A-mediated metabolic detoxification of CBZ and its health risk assessment.

Computational insight into biotransformation of halophenols by cytochrome P450: Mechanism and reactivity for epoxidation

Halophenols (XPs) have aroused great interests due to their high toxicity and low biodegradability. Previous experimental studies have shown that XPs can be catalytically transformed into epoxides and haloquinones by cytochrome P450 enzymes (CYPs). However, these metabolites have never been detected directly. Moreover, the effects of the reaction site and the type and number of halogen substituents on the biotransformation reactivity of halophenols still remain unknown. In this work, we performed density functional theory (DFT) calculations to simulate the CYP-mediated biotransformation of 36 XPs with mono-, di-, and tri-halogen (F, Cl, and Br) substitutions to unravel the mechanism and relevant kinetics of XPs epoxidation. The whole epoxidation process consists of initial rate-determining O-addition and subsequent ring-closure steps. The simulation results show that the epoxidation in low-spin (LS) state is kinetically preferred over that in high-spin (HS) state, and the formation of epoxide metabolite is strongly exothermic. For all XPs, the epoxidation reactivity follows the order of ortho/para O-addition > meta O-addition. Moreover, the O-addition with higher energy barriers roughly corresponds to chlorophenols and fluorophenols with more halogen atoms. Compared with dichlorophenols, the additional ortho-Cl substitution on trichlorophenols can slightly increase the energy barriers of meta O-addition. By contrast, the additional inclusion of an ortho-Cl to monochlorophenols enhances the meta O-addition reactivity of dichlorophenols. Overall, the present work clarifies the biotransformation routes of XPs to produce epoxides, and identifies the key factors affecting the epoxidation reactivity, which are beneficial in understanding comprehensively the metabolic fate and toxicity of XPs.

Water biocatalytic effect attenuates cytochrome P450-mediated carcinogenicity of diethylnitrosamine: A computational insight

The mechanism-based mutagenicity and carcinogenicity of diethylnitrosamine (DEN) are believed to act through interactions with cytochrome P450 (P450) enzymes. DFT calculations to explore the conceivable mechanisms underlying the reaction of P450 with DEN with and without water as a biocatalyst were performed. The results shed light on the biocatalytic role of water in lowering the H-abstraction energy barriers because of the electrostatic effect driven by hydrogen bonding. Our DFT analysis revealed how metabolites are formed in the dealkylation (toxification) and denitrosation (detoxification) pathways. Also, our findings uncovered the active position of DEN vulnerable to P450 interactions. Two factors control the toxification and detoxification rates: the stability of denitrosation products and the HS rebound barrier of the α-pathway. Thus, water biocatalytic attenuation of DEN carcinogenicity was attained by stabilizing denitrosation products and slowing the α-HS rebound process. Docking and MD simulations were performed to assess the binding modes of DEN to P450's active site and to inspect the denitrosation and dealkylation processes, respectively.

In Vitro and In Vivo Study on the Toxic Effects of Propiconazole Fungicide in the Pathogenesis of Liver Fibrosis

Propiconazole (PCZ) is a hepatotoxic triazole fungicide. There are insufficient data on how PCZ induces liver fibrosis in humans. This study aimed to investigate the effect of PCZ on liver fibrosis and its underlying mechanisms. HepG2 cells and Sprague-Dawley rats were exposed to PCZ at doses of 0-160 μM (3-72 h) and 0.5-50 mg/kg body weight/day (28 days), respectively. PCZ-treated cells activated intracellular oxidative stress via cytochrome P450 and had higher mRNA levels of interleukin-1β, tumor necrosis factor-α, matrix metalloproteinase (MMP)-2, MMP-9, and transforming growth factor-β (TGF-β) than the control. PCZ treatment in cells induced a morphological transition with E-cadherin decrease and vimentin and Snail increase via the oxidative stress and TGF-β/Smad pathways. PCZ administration in rats induced liver fibrosis through pathological changes, epithelial-mesenchymal transition, and collagen deposition. Thus, our data suggest that exposure of PCZ to humans may be a risk factor for the functional integrity of the liver.

Occurrence and trophic transfer of synthetic musks in the freshwater food web of a large subtropical lake

Synthetic musks (SMs) have drawn worldwide attention, as they are persistent, bioaccumulative, and toxic to many organisms. There is not enough information on the bioaccumulation and trophodynamic behavior of SMs in freshwater food webs to reliably understand the associated ecological risks. In this study, the concentrations of six SM congeners in fifteen aquatic species from Lake Chaohu, China, was investigated. The total concentrations of the six SMs ranged from 0.29 to 59.7 ng/g dry weight (median, 4.41) in fish muscle tissue and in the whole body tissues of small fish species and shrimps. Galaxolide (HHCB) and tonalide (AHTN) were the predominant congeners, accounting for 65.0% and 28.5% of the total SM concentration, respectively. On the whole, the total concentrations of SMs in livers and gills were 0.18-32.8 and 0.84-254 times higher than those in muscle tissues in fish species, respectively. In the food web of Lake Chaohu, cashmeran (DPMI) and HHCB showed a trend towards trophic magnification, and AHTN tended to show trophic dilution, but these trends were not statistically significant. This suggested that the trophic transfer of these chemicals through the food web was strongly influenced by many factors, including tissue-specific distribution within individuals at higher trophic levels. More investigation into the trophic transfer of SMs in aquatic ecosystems and the factors influencing uptake is needed.