Mechanisms of interaction between persistent organic pollutants (POPs) and CYP2B6: An in silico approach

Essential oil components interacting with insect odorant-binding proteins: a molecular modelling approach

Essential oils (EOs) are natural products currently used to control arthropods, and their interaction with insect odorant-binding proteins (OBPs) is fundamental for the discovery of new repellents. This in silico study aimed to predict the potential of EO components to interact with odorant proteins. A total of 684 EO components from PubChem were docked against 23 odorant binding proteins from Protein Data Bank using AutoDock Vina. The ligands and proteins were optimized using Gaussian 09 and Sybyl-X 2.0, respectively. The nature of the protein-ligand interactions was characterized using LigandScout 4.0, and visualization of the binding mode in selected complexes was carried out by Pymol. Additionally, complexes with the best binding energy in molecular docking were subjected to 500 ns molecular dynamics simulations using Gromacs. The best binding affinity values were obtained for the 1DQE-ferutidine (-11 kcal/mol) and 2WCH-kaurene (-11.2 kcal/mol) complexes. Both are natural ligands that dock onto those proteins at the same binding site as DEET, a well-known insect repellent. This study identifies kaurene and ferutidine as possible candidates for natural insect repellents, offering a potential alternative to synthetic chemicals like DEET.

Congener-specific uptake and accumulation of bisphenols in edible plants: Binding to prediction of bioaccumulation by attention mechanism multi-layer perceptron machine learning model

Plant accumulation of phenolic contaminants from agricultural soils can cause human health risks via the food chain. However, experimental and predictive information for plant uptake and accumulation of bisphenol congeners is lacking. In this study, the uptake, translocation, and accumulation of five bisphenols (BPs) in carrot and lettuce plants were investigated through hydroponic culture (duration of 168 h) and soil culture (duration of 42 days) systems. The results suggested a higher bioconcentration factor (BCF) of bisphenol AF (BPAF) in plants than that of the other four BPs. A positive correlation was found between the log BCF and the log Kow of BPs (R2carrot = 0.987, R2lettuce = 0.801, P < 0.05), while the log (translocation factor) exhibited a negative correlation with the log Kow (R2carrot = 0.957, R2lettuce = 0.960, P < 0.05). The results of molecular docking revealed that the lower binding energy of BPAF with glycosyltransferase, glutathione S-transferase, and cytochrome P450 (-4.34, -4.05, and -3.52 kcal/mol) would be responsible for its higher accumulation in plants. Based on the experimental data, an attention mechanism multi-layer perceptron (AM-MLP) model was developed to predict the BCF of eight untested BPs by machine learning, suggesting the relatively high BCF of bisphenol BP, bisphenol PH, and bisphenol TMC (BCFcarrot = 1.37, 1.50, 1.03; BCFlettuce = 1.02, 0.98, 0.67). The prediction of BCF for ever-increasing varieties of BPs by machine learning would reduce repetitive experimental tests and save resources, providing scientific guidance for the production and application of BPs from the perspective of priority pollutants.

Multidisciplinary Insights into the Structure-Function Relationship of the CYP2B6 Active Site

Cytochrome P450 2B6 (CYP2B6) is a highly polymorphic human enzyme involved in the metabolism of many clinically relevant drugs, environmental toxins, and endogenous molecules with disparate structures. Over the last 20-plus years, in silico and in vitro studies of CYP2B6 using various ligands have provided foundational information regarding the substrate specificity and structure-function relationship of this enzyme. Approaches such as homology modeling, X-ray crystallography, molecular docking, and kinetic activity assays coupled with CYP2B6 mutagenesis have done much to characterize this originally neglected monooxygenase. However, a complete understanding of the structural details that make new chemical entities substrates of CYP2B6 is still lacking. Surprisingly little in vitro data has been obtained about the structure-function relationship of amino acids identified to be in the CYP2B6 active site. Since much attention has already been devoted to elucidating the function of CYP2B6 allelic variants, here we review the salient findings of in silico and in vitro studies of the CYP2B6 structure-function relationship with a deliberate focus on the active site. In addition to summarizing these complementary approaches to studying structure-function relationships, we note gaps/challenges in existing data such as the need for more CYP2B6 crystal structures, molecular docking results with various ligands, and data coupling CYP2B6 active site mutagenesis with kinetic parameter measurement under standard expression conditions. Harnessing in silico and in vitro techniques in tandem to understand the CYP2B6 structure-function relationship will likely offer further insights into CYP2B6-mediated metabolism. SIGNIFICANCE STATEMENT: The apparent importance of cytochrome P450 2B6 (CYP2B6) in the metabolism of various xenobiotics and endogenous molecules has grown since its discovery with many in silico and in vitro studies offering a partial description of its structure-function relationship. Determining the structure-function relationship of CYP2B6 is difficult but may be aided by thorough biochemical investigations of the CYP2B6 active site that provide a more complete pharmacological understanding of this important enzyme.

Impact of mixtures of persistent organic pollutants on breast cancer aggressiveness

INTRODUCTION

Breast cancer (BC) is frequent with a poor prognosis in case of metastasis. The role of the environment has been poorly evaluated in its progression. We searched to assess whether a mixture of pollutants could be responsible of BC aggressiveness.

METHODS

Patients undergoing surgery for their BC were prospectively included in the METAPOP cohort. Forty-two POPs were extracted, among them 17 dioxins (PCDD/F), 16 polychlorobiphenyls (PCB), 8 polybromodiphenylethers (PBDE) and 2,2',4,4',5,5'-hexabromobiphenyl (PBB153) were measured in the adipose tissue surrounding the tumor. BC aggressiveness was defined using tumor size and metastasis (distant or lymph nodes). Two complementary models were used to evaluate the impact of the mixture of pollutants: the BKMR (Bayesian Kernel machine regression) and WQS (weighted quantile sum regression) models. The WQS estimates the weight (positive or negative) of a certain chemical based on its quantile and the BKMR model applies a kernel-based approach to estimate posterior inclusion probabilities. The sub-group of patients with a body mass index (BMI) > 22 kg/ m² was also analyzed.

RESULTS

Ninety-one patients were included. Of these, 38 patients presented a metastasis, and the mean tumor size was 25.4 mm. The mean BMI was 24.5 kg/m² (+/- 4.1). No statistical association was found in the general population. However, in patients with a BMI > 22 kg/ m², our mixture was positively associated with tumor size (OR: 9.73 95 %CI: 1.30-18.15) and metastasis (OR = 3.98 95 %CI = 1.09-17.53) using the WQS model. Moreover, using the BKMR model on chemical families, dioxin like chemicals and PCDD were associated with a higher risk of metastasis.

DISCUSSION

These novel findings identified a mixture associated with breast cancer aggressiveness in patients with a BMI > 22 kg/ m².

Bioaccumulation of organochlorine pesticides in Antarctic krill (Euphausia superba): Profile, influencing factors, and mechanisms

Accumulation of organochlorine pesticides (OCPs) in Antarctic krill (Euphausia superba), a keystone species in the Southern Ocean, is potentially harmful to the Antarctic ecosystem and human health. In the current study, we collected E. superba specimens (including muscle and carapace tissues) from Bransfield Strait in northern Antarctic Peninsula and South Georgia to analyze the profile, influencing factors and mechanisms of OCPs bioaccumulation in them. Results indicated that the biological traits (δ¹³C, δ¹⁵N and lipid contents) of krill were significantly affected by habitat. There may exist growth dilution of OCPs in Antarctic krill and no fresh OCPs input in Antarctica, except for endosulfan I. Based on lipid-normalized concentrations, no significant differences were observed between the two regions at most sampling sites. However, OCP levels showed tissue and sex dependence. Boosted regression trees (BRTs) and partial least squares structural equation models (PLS-SEMs) were built to better investigate the main factors affecting the bioaccumulation of OCPs. Lipid content, negatively correlated with OCP levels, was the main factor. In vitro silicon modeling indicated that CYP3A4 metabolism capacity in krill contributed to the OCP residues except for endosulfan I. The results of this study expand current knowledge of OCPs in Antarctic marine biota, as well as their influencing factors and potential mechanisms.

Insights into mechanisms involved in the uptake, translocation, and metabolism of phthalate esters in Chinese cabbage (Brassica rapa var. chinensis)

In the present study, the uptake and translocation mechanisms of phthalate esters (PAEs) and their primary mono esters metabolites (mPAEs), and the mechanisms of PAEs metabolism in plants were elucidated. The objectives of this study were to: (i) elucidate the fractionation of PAEs and mPAEs in Chinese cabbage (Brassica rapa var. chinensis) by hydroponic experiment, (ii) investigate the PAEs and mPAEs uptake mechanisms in root by inhibitor experiments, (iii) explain the molecular mechanisms of PAE interactions with the plant macromolecules by proteomics analysis and molecular docking, and (iv) reveal the involvement of carboxylesterase in the plant metabolism of PAEs. The results demonstrated that both the apoplastic and symplastic pathways contributed to the uptake of di-n-butyl phthalate (DnBP), di-(2-ethylhexyl) phthalate (DEHP), mono-n-butyl phthalate (MnBP), and mono-(2-ethylhexyl) phthalate (MEHP) by vacuum-infiltration-centrifugation method. The energy-dependent active process was involved for the uptake of DnBP, DEHP, MnBP, and MEHP. The passive uptake pathways of anion mPAEs and neutral PAEs differ. Aquaporins contributed to the uptake of anion MnBP and MEHP, and slow-type anion channel was also responsible for the uptake of anion MEHP. Molecular interactions of PAEs and macromolecules were further characterized by proteomic analysis and molecular docking. PAEs were transferred via non-specific lipid transfer protein by binding hydroponic amino acid residues. The carboxylesterase enzyme was attributed to the metabolism of PAEs to form mPAEs by using crude enzyme extract and commercial pure enzyme. This study provides both experimental and theoretical evidence for uptake, accumulation, and metabolism of PAEs in plants.

Mother to Fetus Transfer of Hydroxylated Polychlorinated Biphenyl Congeners (OH-PCBs) in the Japanese Macaque (Macaca fuscata): Extrapolation of Exposure Scenarios to Humans

Prenatal hydroxylated polychlorinated biphenyls (OH-PCBs) exposure may disrupt fetal brain development during the critical period of thyroid hormone (TH) action. However, there are limited studies on the OH-PCB transfer to the fetal brain, particularly in primates. In this study, we selected the Japanese macaque (Macaca fuscata) as a model animal for the fetal transfer of OH-PCBs in humans and revealed OH-PCB concentrations and their relationships in maternal and fetal blood, liver, and brain. l-thyroxine (T4)-like OH-PCBs including 4OH-CB187, a major congener in humans, were found in high proportions in the blood, liver, brain, and placenta of pregnant Japanese macaques. OH-PCBs were detected in the fetal brain and liver in the first trimester, indicating their transfer to the brain in the early pregnancy stage. 4OH-CB187 and 4OH-CB202 were the major congeners found in fetal brain, indicating that these T4-like OH-PCBs are transported from maternal blood to the fetal brain via the placenta. These results indicate that further studies are needed on the effects of OH-PCBs on the developing fetal brain.

Human CYP2E1-activated mutagenicity of dioxin-like PCBs 105 and 118-Experimental data consistent with molecular docking results

Polychlorinated biphenyls (PCBs) are persistent organic pollutants with human carcinogenicity. Many lower chlorinated and non-dioxin-like PCBs have been observed to be mutagenic following activation by human CYP2E1, while activation of dioxin-like (DL-) PCBs by this enzyme has never been evidenced. In this study, each DL-PCB was analyzed by molecular docking to human CYP2E1 protein for predicting a substrate interaction. All compounds demonstrated high affinities with the active site of human CYP2E1, binding energy being -8.7 ∼ -9.7 kcal/mol. However, most compounds demonstrated ligand-heme distances as ≥ 6.8 Å, while the values for 2,3,3',4,4'- (PCB 105) and 2,3',4,4',5-pentachlorobiphenyl (PCB 118) were 5.3 and 5.4 Å, respectively (valid for electron transfer). Experimentally, both PCB 105 and 118 induced micronuclei in a V79-derived cell line engineered for expression of human CYP2E1 at low micromolar concentrations, while inactive or weakly positive in V79-Mz control cells; these effects were blocked or reduced by 1-aminobenzotriazole, a suicide CYP inhibitor. However, DL-PCBs 77, 81 and 126 were all negative in both cell lines. In a human hepatoma (C3A) cell line, PCB 105 and 118 induced micronuclei marginally, while with ethanol pretreatment (to stabilize CYP2E1) both compounds induced micronuclei efficiently, and co-exposure to trans-1,2-dichloroethylene (a selective CYP2E1 inhibitor) led to clearly negative results with both compounds. Finally, both PCB 105 and 118 induced PIG-A gene mutations in C3A cells, which was blocked by trans-1,2-dichloroethylene. In summary, in silico and experimental results consistently suggest that DL- PCBs 105 and 118 may be activated by human CYP2E1 for mutagenic activities.

Hepatic Transcriptomic Patterns in the Neonatal Rat After Pentabromodiphenyl Ether Exposure

Human exposure to pentabromodiphenyl ether (PBDE) mixture (DE-71) and its PBDE-47 congener can occur both in utero and during lactation. Here, we tested the hypothesis that PBDE-induced neonatal hepatic transcriptomic alterations in Wistar Han rat pups can inform on potential toxicity and carcinogenicity after longer term PBDE exposures. Wistar Han rat dams were exposed to either DE-71 or PBDE-47 daily from gestation day (GD 6) through postnatal day 4 (PND 4). Total plasma thyroxine (T4) was decreased in PND 4 pups. In liver, transcripts for CYPs and conjugation enzymes, Nrf2, and ABC transporters were upregulated. In general, the hepatic transcriptomic alterations after exposure to DE-71 or PBDE-47 were similar and provided early indicators of oxidative stress and metabolic alterations, key characteristics of toxicity processes. The transcriptional benchmark dose lower confidence limits of the most sensitive biological processes were lower for PBDE-47 than for the PBDE mixture. Neonatal rat liver transcriptomic data provide early indicators on molecular pathway alterations that may lead to toxicity and/or carcinogenicity if the exposures continue for longer durations. These early toxicogenomic indicators may be used to help prioritize chemicals for a more complete toxicity and cancer risk evaluation.

Integrated Framework for Identifying Toxic Transformation Products in Complex Environmental Mixtures

Complex environmental mixtures consist of hundreds to thousands of unknown and unregulated organic compounds that may have toxicological relevance, including transformation products (TPs) of anthropogenic organic pollutants. Non-targeted analysis and suspect screening analysis offer analytical approaches for potentially identifying these toxic transformation products. However, additional tools and strategies are needed in order to reduce the number of chemicals of interest and focus analytical efforts on chemicals that may pose risks to humans and the environment. This brief review highlights recent developments in this field and suggests an integrated framework that incorporates complementary instrumental techniques, computational chemistry, and toxicity analysis, for prioritizing and identifying toxic TPs in the environment.