Computational study on the detoxifying mechanism of DDT metabolized by cytochrome P450 enzymes

An in silico study on human carcinogenicity mechanism of polybrominated biphenyls exposure

Polybrominated biphenyls (PBBs) are associated with an increased risk of thyroid cancer; however, relevant mechanistic studies are lacking. In this study, we investigated the mechanisms underlying PBB-induced human thyroid cancer. Molecular docking and molecular dynamics methods were employed to investigate the metabolism of PBBs by the cytochrome P450 enzyme under aryl hydrocarbon receptor mediation into mono- and di-hydroxylated metabolites. This was taken as the molecular initiation event. Subsequently, considering the interactions of PBBs and their metabolites with the thyroxine-binding globulin protein as key events, an adverse outcome pathway for thyroid cancer caused by PBBs exposure was constructed. Based on 2D quantitative structure activity relationship (2D-QSAR) models, the contribution of amino acid residues and binding energy were analyzed to understand the mechanism underlying human carcinogenicity (adverse effect) of PBBs. Hydrogen bond and van der Waals interactions were identified as key factors influencing the carcinogenic adverse outcome pathway of PBBs. Analysis of non-bonding forces revealed that PBBs and their hydroxylation products were predominantly bound to the thyroxine-binding globulin protein through hydrophobic and hydrogen bond interactions. The key amino acids involved in hydrophobic interactions were alanine 330, arginine 381 and lysine 270, and the key amino acids involved in hydrogen bond interactions were arginine 381 and lysine 270. This study provides valuable insights into the mechanisms underlying human health risk associated with PBBs exposure.

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.

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.

Photochemical transformation of anthracene (ANT) in surface soil: Chlorination and hydroxylation

To reveal the fate of anthracene (ANT) in soil, the photodegradation behavior of ANT was systematically studied using SiO₂ to simulate a soil environment. Under xenon lamp irradiation, more than 90% of ANT loaded on SiO₂ could be removed after 240 min. Moreover, the effects of water content, chloride ions (Cl^-) and humic acid (HA) were examined. It was found that the presence of water and HA can significantly inhibit the photolysis of ANT on SiO₂, while the addition of chloride alone has no obvious effect. However, when water is present, the inhibition effect of chloride became more obvious. According to radical quenching experiments and electron paramagnetic resonance (EPR) spectra, hydroxyl radicals (•OH) and chlorine radicals (Cl•) were formed in the system. Possible reaction pathways were speculated based on products identified by mass spectrometry. ANT was attacked by •OH to form hydroxylated products, which can be further hydroxylated and oxidized with the final formation of ring-opening products. ANT directly excited by light may also react with Cl• to produce chlorinated polycyclic aromatic hydrocarbons (Cl-PAHs). Finally, the experimental results were verified on real soil. This study provides important information for understanding the photochemical transformation mechanism of ANT at the soil/air interface.

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.

Oxidative stress and detoxification mechanisms of earthworms (Eisenia fetida) after exposure to flupyradifurone in a soil-earthworm system

Flupyradifurone (FLU) has great application potential in agricultural production as a new generation of neonicotinoid insecticide after imidacloprid. Nevertheless, the toxic effects of FLU on non-target soil organisms remain unclear, resulting in considerable environmental risks. We evaluated the acute and subchronic toxicities of FLU to earthworms. The results of acute toxicity show that the median lethal concentration (LC₅₀) values (14 d) of FLU were 186.9773 mg kg^-1 for adult earthworms and 157.6502 mg kg^-1 for juveniles, respectively. The subchronic toxicity of FLU that focused on the activities of antioxidant and detoxication enzymes showed the superoxide dismutase (SOD), catalase (CAT), and glutathione-S transferase (GST) activities in earthworms increased while the peroxidase (POD) and acetylcholinesterase (AChE) activities decreased after exposure to FLU. Oxidative damage analyses revealed that the reactive oxygen species (ROS) level and malonaldehyde (MDA) content in earthworms were increased by FLU, resulting in DNA damage. Transcriptomics and RT-qPCR confirmed that FLU influenced the expression of genes related to antioxidant response and detoxification of earthworms. Ultimately detoxification metabolism, environmental information processing, cell processes, and immune system pathways are significantly enriched to respond jointly to FLU. Our study fills the gaps in the toxicity of FLU to earthworms, providing a basis for its risk assessment of soil ecosystems and non-target biological toxicity.

Origin of metabolites diversity and selectivity of P450 catalyzed benzo[a]pyrene metabolic activation

Polycyclic Aromatic Hydrocarbon (PAHs) presents one of the most abundant class of environmental pollutants. Recent study shows a lab-synthesized PAHs derivative, helicenium, can selectively kill cancer cells rather than normal cells, calling for the in-depth understanding of the metabolic process. However, the origin of metabolites diversity and selectivity of P450 catalyzed PAHs metabolic activation is still unclear to a great extent. Here we systematically investigated P450 enzymes catalyzed activation mechanism of a representative PAHs, benzo[a]pyrene (BaP), and found the corresponding activation process mainly involves two elementary steps: electrophilic addition and epoxidation. Electrophilic addition step is evidenced to be rate determining step. Two representative binding modes of BaP with P450 were found, which enables the electrophilic addition of Heme (FeO) to almost all the carbons of BaP. This electrophilic addition was proposed to be accelerated by the P450 enzyme environment when compared with the gas phase and water solvent. To dig deeper on the origin of metabolites diversity, we built several linear regression models to explore the structural-energy relationships. The selectivity was eventually attributed to the integrated effects of structural (e.g. O-C distance and O-C-Fe angle) and electrostatic parameters (e.g. charge of C and O) from both BaP and P450.

Biotransformation of sulfamethoxazole by microalgae: Removal efficiency, pathways, and mechanisms

Recently, the biotransformation of sulfamethoxazole (SMX) by microalgae has attracted increasing interest. In particular, cytochrome P450 (CYP450) has been suggested to be the main enzymatic contributor to this biodegradation. However, the molecular evidence of CYP450 enzymes being involved in SMX biodegradation remains relatively unclear, hindering its applicability. Herein, the biodegradation of SMX by Chlorella sorokiniana (C. sorokiniana) was investigated, and comprehensively elucidated the reaction mechanism underlying CYP450-mediated SMX metabolism. C. sorokiniana was able to efficiently remove over 80% of SMX mainly through biodegradation, in which CYP450 enzymes responded substantially to metabolize SMX in cells. Additionally, screening of transformation products (TPs) revealed that N⁴-hydroxylation-SMX (TP270) was the main TP in the SMX biodegradation pathway of microalgae. Molecular dynamics (MD) simulation suggested that the aniline of SMX was the most prone to undergo metabolism, while density functional theory (DFT) indicated that SMX was metabolized by CYP450 enzymes through H-abstraction-OH-rebound reaction. Collectively, this work reveals key details of the hydroxylamine group of SMX, elucidates the SMX biodegradation pathway involving CYP450 in microalgae in detail, and accelerates the development of using microalgae-mediated CYP450 to eliminate antibiotics.

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.

Photochemical transformation of hexachlorobenzene (HCB) in solid-water system: Kinetics, mechanism and toxicity evaluation

As one of the first batch of persistent organic pollutants (POPs) included in Stockholm Convention, hexachlorobenzene (HCB) has attracted great attention because of its wide occurrence and great environmental risks. Considering the easy adsorption of HCB on solids and the complexity of natural particles, we systematically investigated the photodegradation of HCB on the surface of silica gel (SG) in aqueous solution in this work to reveal its fate in natural waters. Under mercury lamp irradiation, more than 90% of HCB loaded on SG could be removed after 240 min. Moreover, the effects of solution pH and water constituents were examined, and results showed that the presence of NO₂^-, NO₃^-, Fe³⁺ and humic acid (HA) significantly inhibited the reaction due to the scavenging of ROS and/or competitive absorption of light. According to radical quenching experiments and electron paramagnetic resonance (EPR) spectra, hydroxyl radicals and singlet oxygen generated on the surface of SG could participate in the transformation of HCB, but •OH played a dominant role. Based on products identified by high performance liquid chromatography-mass spectrometry (HPLC-MS) and gas chromatography-mass spectrometry (GC-MS), two main pathways were proposed for the removal of HCB, including dechlorination and hydroxylation which represent direct and indirect photodegradation, respectively, and the occurrence of these two reactions was further supported by density functional theory (DFT) calculations. From the quantitative analysis of penta-chlorobenzene, it was estimated that dechlorination and hydroxylation contributed to approximately 44.4% and 55.6% of initial HCB degradation, respectively. Furthermore, toxicity predictions by the ecological structure-activity relationship model (ECOSAR) suggested that the toxicity of HCB was decreased in the photodegradation process. This study would provide important information for understanding the photochemical transformation mechanism of HCB at the solid/water interface.

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.

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.