Elucidation of endocrine-disrupting polychlorinated biphenyls binding potency with steroidogenic genes: Integration of in silico methods and ensemble docking approaches

Investigating PCB degradation by indigenous fungal strains isolated from the transformer oil-contaminated site: degradation kinetics, Bayesian network, artificial neural networks, QSAR with DFT, molecular docking, and molecular dynamics simulation

The widespread prevalence of polychlorinated biphenyls (PCBs) in the environment has raised major concerns due to the associated risks to human health, wildlife, and ecological systems. Here, we investigated the degradation kinetics, Bayesian network (BN), quantitative structure-activity relationship-density functional theory (QSAR-DFT), artificial neural network (ANN), molecular docking (MD), and molecular dynamics stimulation (MS) of PCB biodegradation, i.e., PCB-10, PCB-28, PCB-52, PCB-138, PCB-153, and PCB-180 in the soil system using fungi isolated from the transformer oil-contaminated sites. Results revealed that the efficacy of PCB biodegradation best fits the first-order kinetics (R2 ≥ 0.93). The consortium treatment (29.44-74.49%) exhibited more efficient degradation of PCBs than those of Aspergillus tamarii sp. MN69 (27.09-71.25%), Corynespora cassiicola sp. MN69 (23.76-57.37%), and Corynespora cassiicola sp. MN70 (23.09-54.98%). 3'-Methoxy-2, 4, 4'-trichloro-biphenyl as an intermediate derivative was detected in the fungal consortium treatment. The BN analysis predicted that the biodegradation efficiency of PCBs ranged from 11.6 to 72.9%. The ANN approach showed the importance of chemical descriptors in decreasing order, i.e., LUMO > MW > IP > polarity no. > no. of chlorine > Wiener index > Zagreb index > HOMU > Pogliani index > APE in PCB removal. Furthermore, the QSAR-DFT model between the chemical descriptors and rate constant (log K) exhibited a high fit and good robustness of R2 = 99.12% in predicting ability. The MD and MS analyses showed the lowest binding energy through normal mode analysis (NMA), implying stability in the interactions of the docked complexes. These findings provide crucial insights for devising strategies focused on natural attenuation, holding substantial potential for mitigating PCB contamination within the environment.

Human-Based New Approach Methodologies in Developmental Toxicity Testing: A Step Ahead from the State of the Art with a Feto-Placental Organ-on-Chip Platform

Developmental toxicity testing urgently requires the implementation of human-relevant new approach methodologies (NAMs) that better recapitulate the peculiar nature of human physiology during pregnancy, especially the placenta and the maternal/fetal interface, which represent a key stage for human lifelong health. Fit-for-purpose NAMs for the placental-fetal interface are desirable to improve the biological knowledge of environmental exposure at the molecular level and to reduce the high cost, time and ethical impact of animal studies. This article reviews the state of the art on the available in vitro (placental, fetal and amniotic cell-based systems) and in silico NAMs of human relevance for developmental toxicity testing purposes; in addition, we considered available Adverse Outcome Pathways related to developmental toxicity. The OECD TG 414 for the identification and assessment of deleterious effects of prenatal exposure to chemicals on developing organisms will be discussed to delineate the regulatory context and to better debate what is missing and needed in the context of the Developmental Origins of Health and Disease hypothesis to significantly improve this sector. Starting from this analysis, the development of a novel human feto-placental organ-on-chip platform will be introduced as an innovative future alternative tool for developmental toxicity testing, considering possible implementation and validation strategies to overcome the limitation of the current animal studies and NAMs available in regulatory toxicology and in the biomedical field.

Integration of in silico methods to determine endocrine-disrupting tobacco pollutants binding potency with steroidogenic genes: comprehensive QSAR modeling and ensemble docking strategies

A myriad of tobacco-associated chemicals may have possibilities to developmental/reproductive axis and endocrine-disruption impacts. Mostly they breach the biotransformation of cholesterol in mitochondria by interfering with steroidogenic pathway genes, prompting to adverse effects in steroid biosynthesis; however, studies are scanty. The quantitative structure-activity relationship (QSAR) modeling and comparative docking strategies were used to understand structural features of dataset compounds that influence developmental/reproductive toxicity and estrogen and androgen receptor-binding abilities, and to predict binding levels of toxicants with steroidogenic acute regulatory protein (StAR) and cholesterol side-chain cleavage enzyme (CYP11A1) active sites. Developed QSAR models presented good robustness and predictive ability that were determined from the applicability domain and, clustering and classification of chemicals by performing self-organizing maps. Accordingly, the exorbitant amount of polycyclic aromatic hydrocarbons (PAHs) and a limited number of other chemicals including N-nitrosamines and nicotine was represented as potential developmental/reproductive toxicants as well as estrogen and androgen receptor binders. From the docking analysis, hydrogen bonding, nonpolar, atomic π-stacking, and π-cation interactions were found between PAHs (bay and fjord structural pockets) and functional hotspot residues of StAR and CYP11A1, which strengthened the subtle structural changes at domains. These govern barrier effects to cholesterol binding and/or locking cholesterol to complicate its ejection from the Ω1 loop of StAR, and further mitigates steroid biosynthesis through cholesterol by CYP11A1; therefore, they are presumably considered as block-cluster mechanisms. These outcomes are significant to be hopeful to estimate developmental/reproductive toxicity and endocrine-disruption activities of other environmental pollutants, and could be useful for further assessment to discover binding mechanisms of PAHs with other steroidogenesis pathway genes.

An introduction to the sources, fate, occurrence and effects of endocrine disrupting chemicals released into the environment

Many classes of compounds are known or suspected to disrupt the endocrine system of vertebrate and invertebrate organisms. This review of the sources and fate of selected endocrine disrupting chemicals (EDCs) in the environment includes classes of compounds that are "legacy" contaminants, as well as contaminants of emerging concern. EDCs included for discussion are organochlorine compounds, halogenated aromatic hydrocarbons, brominated flame retardants, per- and polyfluoroalkyl substances, alkylphenols, phthalates, bisphenol A and analogues, pharmaceuticals, drugs of abuse and steroid hormones, personal care products, and organotins. An exhaustive survey of the fate of these contaminants in all environmental media (e.g., air, water, soil, biota, foods and beverages) is beyond the scope of this review, so the priority is to highlight the fate of EDCs in environmental media for which there is a clear link between exposure and endocrine effects in humans or in biota from other taxa. Where appropriate, linkages are also made between the fate of EDCs and regulatory limits such as environmental quality guidelines for water and sediments and total daily intake values for humans.

Human CYP enzyme-activated clastogenicity of 2-ethylhexyl diphenyl phosphate (a flame retardant) in mammalian cells

2-Ethylhexyl diphenyl phosphate (EHDPP) is a common flame retardant and environmental pollutant, exposing humans with endocrinal disrupting potentials. Its mutagenicity, especially following metabolism, remains unclear. In this study, molecular docking analysis indicated that EHDPP was a potential substrate for several human CYP enzymes except for CYP1A1. Among V79-derived cell lines genetically engineered for the expression of each CYP, EHDPP (6 h exposure/18 h recovery) did not induce micronuclei in the V79 or V79-derived cells expressing human CYP1A1, however, it was positive in V79-derived cell lines expressing human CYP2E1, 3A4, and 2B6. In a human hepatoma (HepG2) cell line, EHDPP (48 h exposure) moderately induced micronuclei, which was blocked by 1-aminobenzotriazole (ABT, 60 μM, inhibitor of CYPs); pretreating HepG2 cells with bisphenol AF, another organic pollutant as inducer of CYPs (0.1 μM for 16 h), significantly potentiated micronuclei formation by EHDPP, threshold being decreased from 10 to 1.25 μM. This effect was blocked by ABT, drastically reduced by ketoconazole (inhibiting CYP3A expression/activity), and moderately inhibited by trans-1,2-dichloroethylene (selective CYP2E1 inhibitor). Immunofluorescent centromere protein B staining indicated that EHDPP-induced micronuclei in V79-derived cell lines expressing human CYP2E1 and 3A4 were predominantly centromere-negative, and that in HepG2 cells pretreated with bisphenol AF (for inducing multiple CYPs) were purely centromere-negative. In bisphenol AF-pretreated HepG2 cells EHDPP potently induced DNA breaks, as indicated by the comet assay and Western blot analysis of γ-H2AX. In conclusion, our study suggests that EHDPP is potently clastogenic, following activation by several human CYP enzymes, CYP3A4 being a major one.

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.