Identification of Thyroid Hormone Disruptors among HO-PBDEs: In Vitro Investigations and Coregulator Involved Simulations

High-efficiency effect-directed analysis (EDA) advancing toxicant identification in aquatic environments: Latest progress and application status

Facing the great threats to ecosystems and human health posed by the continuous release of chemicals into aquatic environments, effect-directed analysis (EDA) has emerged as a powerful tool for identifying causative toxicants. However, traditional EDA shows problems of low-coverage, labor-intensive and low-efficiency. Currently, a number of high-efficiency techniques have been integrated into EDA to improve toxicant identification. In this review, the latest progress and current limitations of high-efficiency EDA, comprising high-coverage effect evaluation, high-resolution fractionation, high-coverage chemical analysis, high-automation causative peak extraction and high-efficiency structure elucidation, are summarized. Specifically, high-resolution fractionation, high-automation data processing algorithms and in silico structure elucidation techniques have been well developed to enhance EDA. While high-coverage effect evaluation and chemical analysis should be further emphasized, especially omics tools and data-independent mass acquisition. For the application status in aquatic environments, high-efficiency EDA is widely applied in surface water and wastewater. Estrogenic, androgenic and aryl hydrocarbon receptor-mediated activities are the most concerning, with causative toxicants showing the typical structural features of steroids and benzenoids. A better understanding of the latest progress and application status of EDA would be beneficial to further advance in the field and greatly support aquatic environment monitoring.

Thyroid Hormone Receptor Agonistic and Antagonistic Activity of Newly Synthesized Dihydroxylated Polybrominated Diphenyl Ethers: An In Vitro and In Silico Coactivator Recruitment Study

Dihydroxylated polybrominated diphenyl ethers (DiOH-PBDEs) could be the metabolites of PBDEs of some organisms or the natural products of certain marine bacteria and algae. OH-PBDEs may demonstrate binding affinity to thyroid hormone receptors (TRs) and can disrupt the functioning of the systems modulated by TRs. However, the thyroid hormone disruption mechanism of diOH-PBDEs remains elusive due to the absence of diOH-PBDEs standards. This investigation explores the potential disruptive effects of OH/diOH-PBDEs on thyroid hormones via competitive binding and coactivator recruitment with TRα and TRβ. At levels of 5000 nM and 25,000 nM, 6-OH-BDE-47 demonstrated significant recruitment of steroid receptor coactivator (SRC), whereas none of the diOH-PBDEs exhibited SRC recruitment within the range of 0.32-25,000 nM. AutoDock CrankPep (ADCP) simulations suggest that the conformation of SRC and TR-ligand complexes, particularly their interaction with Helix 12, rather than binding affinity, plays a pivotal role in ligand agonistic activity. 6,6'-diOH-BDE-47 displayed antagonistic activity towards both TRα and TRβ, while the antagonism of 3,5-diOH-BDE-100 for TRα and TRβ was concentration-dependent. 3,5-diOH-BDE-17 and 3,5-diOH-BDE-51 exhibited no discernible agonistic or antagonistic activities. Molecular docking analysis revealed that the binding energy of 3,3',5-triiodo-L-thyronine (T3) surpassed that of OH/diOH-PBDEs. 3,5-diOH-BDE-100 exhibited the highest binding energy, whereas 6,6'-diOH-BDE-47 displayed the lowest. These findings suggest that the structural determinants influencing the agonistic and antagonistic activities of halogen phenols may be more intricate than previously proposed, involving factors beyond high-brominated PBDEs or hydroxyl group and bromine substitutions. It is likely that the agonistic or antagonistic propensities of OH/diOH-PBDEs are instigated by protein conformational changes rather than considerations of binding energy.

Update of the risk assessment of polybrominated diphenyl ethers (PBDEs) in food

The European Commission asked EFSA to update its 2011 risk assessment on polybrominated diphenyl ethers (PBDEs) in food, focusing on 10 congeners: BDE-28, -47, -49, -99, -100, -138, -153, -154, -183 and ‑209. The CONTAM Panel concluded that the neurodevelopmental effects on behaviour and reproductive/developmental effects are the critical effects in rodent studies. For four congeners (BDE-47, -99, -153, -209) the Panel derived Reference Points, i.e. benchmark doses and corresponding lower 95% confidence limits (BMDLs), for endpoint-specific benchmark responses. Since repeated exposure to PBDEs results in accumulation of these chemicals in the body, the Panel estimated the body burden at the BMDL in rodents, and the chronic intake that would lead to the same body burden in humans. For the remaining six congeners no studies were available to identify Reference Points. The Panel concluded that there is scientific basis for inclusion of all 10 congeners in a common assessment group and performed a combined risk assessment. The Panel concluded that the combined margin of exposure (MOET) approach was the most appropriate risk metric and applied a tiered approach to the risk characterisation. Over 84,000 analytical results for the 10 congeners in food were used to estimate the exposure across dietary surveys and age groups of the European population. The most important contributors to the chronic dietary Lower Bound exposure to PBDEs were meat and meat products and fish and seafood. Taking into account the uncertainties affecting the assessment, the Panel concluded that it is likely that current dietary exposure to PBDEs in the European population raises a health concern.

Computational Risk Assessment of Persistence, Bioaccumulation, and Toxicity of Novel Flame-Retardant Chemicals

Novel brominated flame retardants (NBFRs) have emerged as chemicals of environmental concern, as they have been widely used as an alternative to polybrominated diphenyl ethers (PBDEs). Considering the similar structural features of NBFRs and PBDEs necessitates a comprehensive investigation to understand the physicochemical relationships of these compounds and their ability to alter biological functions. In this study, we investigated the persistent nature of NBFRs in terms of thyroid-disrupting potential by understanding the structure-stability aspects using density functional theory (DFT)-based reactivity parameters and interactions via molecular docking and molecular dynamics (MD) simulations. The results indicate that the DFT-based stability descriptor (chemical hardness) is associated with the persistent nature of NBFRs. The computed molecular interaction profile revealed prominent interactions between thyroid receptor-β (TR-β) and NBFRs. Stable trajectory and interactions with TR-β were obtained with ATE, p-TBX, PBT, PBEB, and TBBPA-DBPE during 100 ns of MD simulation. The results of these studies have suggested that the presence of a higher number of halogenated atoms increases the stability vis-à-vis the persistence and endocrine disruption potential of NBFRs.

Thyroid hormone activities of neutral and anionic hydroxylated polybrominated diphenyl ethers to thyroid receptor β: A molecular dynamics study

Hydroxylated polybrominated diphenyl ethers (OH-PBDEs) have been identified as the strong endocrine disrupting chemicals to humans, which show structural similarity with endogenous thyroid hormones (THs) and thus disrupt the functioning of THs through competitive binding with TH receptors (TRs). Although previous studies have reported the hormone activities of some OH-PBDEs on TH receptor β (TRβ), the interaction mechanism remains unclear. Furthermore, hydroxyl dissociation of OH-PBDEs may alter their TR disrupting activities, which has not yet been investigated in depth. In this work, we selected 18 OH-PBDEs with neutral and anionic forms and performed molecular dynamics (MD) simulations to estimate their binding interactions with the ligand binding domain (LBD) of TRβ. The results demonstrate that most of OH-PBDEs have stronger binding affinities to TRβ-LBD than their anionic counterparts, and the hydroxyl dissociation of ligands differentiate the major driving force for their binding. More Br atoms in OH-PBDEs can result in stronger binding potential with TRβ-LBD. Moreover, 5 hydrophobic residues, including Met313, Leu330, Ile276, Leu346, and Phe272, are identified to have important contributions to bind OH-PBDEs. These results clarify the binding mechanism of OH(O^-)-PBDEs to TRβ-LBD at the molecular level, which can provide a solid theoretical basis for accurate assessment of TH disrupting effects of these chemicals.

Endocrine disruptors and endometriosis

Endometriosis is a hormone-dependent inflammatory gynecological disease of reproductive-age women. It is clinically and pathologically characterized by the presence of functional endometrium as heterogeneous lesions outside the uterine cavity. The two major symptoms are chronic pelvic pain and infertility, which profoundly affect women's reproductive health and quality of life. This significant individual and public health concerns underscore the importance of understanding the pathogenesis of endometriosis. The environmental endocrine-disrupting chemicals (EDCs) are exogenous agents that interfere with the synthesis, secretion, transport, signaling, or metabolism of hormones responsible for homeostasis, reproduction, and developmental processes. Endometriosis has been potentially linked to exposure to EDCs. In this review, based on the robust literature search, we have selected four endocrine disruptors (i) polychlorinated biphenyls (PCB)s (ii) dioxins (TCDD) (iii) bisphenol A (BPA) and its analogs and (iv) phthalates to elucidate their critical role in the etiopathogenesis of endometriosis. The epidemiological and experimental data discussed in this review indicate that these four EDCs activate multiple intracellular signaling pathways associated with proinflammation, estrogen, progesterone, prostaglandins, cell survival, apoptosis, migration, invasion, and growth of endometriosis. The available information strongly indicates that environmental exposure to EDCs such as PCBs, dioxins, BPA, and phthalates individually or collectively contribute to the pathophysiology of endometriosis. Further understanding of the molecular mechanisms of how these EDCs establish endometriosis and therapeutic strategies to mitigate the effects of these EDCs in the pathogenesis of endometriosis are timely needed. Moreover, understanding the interactive roles of these EDCs in the pathogenesis of endometriosis will help regulate the exposure to these EDCs in reproductive age women.

Identification of Glucocorticoid Receptor Antagonistic Activities and Responsible Compounds in House Dust: Bioaccessibility Should Not Be Ignored

More and more contaminants in dust have been found to be glucocorticoid receptor (GR) disrupting chemicals. However, little is known about the related potency and responsible toxicants, especially for the main bioaccessible ones in dust. An effect-directed analysis (EDA)-based workflow was developed, including solvent-based exhaustive extraction/tenax-assisted bioaccessible extraction (TBE), high-throughput bioassays, suspect and non-target analysis, as well as in silico candidate selection, for a more realistic identification of responsible contaminants in dust. None of the 39 dust samples from 23 cities in China exhibited GR agonistic activity, while GR antagonistic potencies were detected in 34.8% of samples, being significantly different from the high detection frequency of GR agonistic activities in other environmental media. The GR antagonistic potencies of the dust samples were all reduced after bioaccessible extraction. The mean bioaccessibility of GR antagonistic potency compared with the related exhaustive extracts was 36.8%, and the lowest value was 9%. By using in silico candidate selection, greater than 99% candidate chemical structures which were found by a non-target screening strategy were removed. Di-n-butyl phthalate (DnBP), diisobutyl phthalate (DiBP), and nicotine (NIC) were responsible for the activities of the exhaustive extracts of dust, contributing up to 91% potencies. DiBP and DnBP were also responsible for the bioaccessible activities, contributing up to 79% potencies. However, the contribution from NIC decreased significantly and can be ignored because of its low bioaccessibility. This study suggests that the improved workflow combining extraction, reporter gene bioassays, suspect and non-target analysis, as well as in silico candidate selection is useful for EDA analysis in dust samples. In addition, exhaustive extraction may overestimate the risk of contaminants, while bioaccessibility evaluation based on bioaccessible extraction is essential in both effect evaluation and toxicant identification.

Organophosphate esters cause thyroid dysfunction via multiple signaling pathways in zebrafish brain

Organophosphate esters (OPEs) are widespread in various environmental media, and can disrupt thyroid endocrine signaling pathways. Mechanisms by which OPEs disrupt thyroid hormone (TH) signal transduction are not fully understood. Here, we present in vivo-in vitro-in silico evidence establishing OPEs as environmental THs competitively entering the brain to inhibit growth of zebrafish via multiple signaling pathways. OPEs can bind to transthyretin (TTR) and thyroxine-binding globulin, thereby affecting the transport of TH in the blood, and to the brain by TTR through the blood-brain barrier. When GH3 cells were exposed to OPEs, cell proliferation was significantly inhibited given that OPEs are competitive inhibitors of TH. Cresyl diphenyl phosphate was shown to be an effective antagonist of TH. Chronic exposure to OPEs significantly inhibited the growth of zebrafish by interfering with thyroperoxidase and thyroglobulin to inhibit TH synthesis. Based on comparisons of modulations of gene expression with the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, signaling pathways related to thyroid endocrine functions, such as receptor-ligand binding and regulation of hormone levels, were identified as being affected by exposure to OPEs. Effects were also associated with the biosynthesis and metabolism of lipids, and neuroactive ligand-receptor interactions. These findings provide a comprehensive understanding of the mechanisms by which OPEs disrupt thyroid pathways in zebrafish.

Bisphenol A Analogs Induce Cellular Dysfunction in Human Trophoblast Cells in a Thyroid Hormone Receptor-Dependent Manner: In Silico and In Vitro Analyses

Bisphenol A (BPA) and its analogs are frequently detected in human daily necessities and environmental media. Placental thyroid hormone plays an important role in fetal development. Herein, we followed the adverse outcome pathway (AOP) to explore the toxic mechanisms of BPA and its analogs toward placental thyroid hormone receptor (TR). First, the TOX21 database was used, and the interactions between BPA analogs and the ligand-binding domains (LBDs) of two subtypes of TR (TRα and TRβ) were subjected to in silico screening using molecular docking (MD) and molecular dynamics simulation (MDS). Fluorescence spectra and circular dichroism (CD) showed that BPA and its analogs interfere with TRs as a molecular initiation event (MIE), including static fluorescence quenching and secondary structural content changes in TR-LBDs. Key events (KEs) of the AOP, including the toxicity induced in placental chorionic trophoblast cells (HTR-8/SVneo) by an inverted U-shaped dose effect and changes in ROS levels, were tested in vitro. BPA, BPB, and BPAF significantly changed the expression level of TRβ, and only BPAF significantly downregulated the expression level of TRα. In conclusion, our study contributes to the health risk assessment of BPA and its analogs regarding placental adverse outcomes (AOs).

Thyroid endocrine disruption and hepatotoxicity induced by bisphenol AF: Integrated zebrafish embryotoxicity test and deep learning

Bisphenol AF (BPAF) is an emerging contaminant prevalent in the environment as one of main substitutes of bisphenol A (BPA). It was found that BPAF exhibited estrogenic effects in zebrafish larvae in our previous study, while little is known about its effects on the thyroid and liver. A 7 d zebrafish embryotoxicity test was conducted to study the potential thyroid disruption and hepatotoxicity of BPAF. BPAF decreased levels of thyroid hormones and deiodinases but increased expressions of transthyretin at 12.5 and 125 μg/L after 7 d exposure, indicating that both the metabolism and transport of thyroid hormones were perturbed. The thyroid hormone receptor (TR) levels decreased significantly upon exposure to ≥12.5 μg/L BPAF, implying that BPAF acts as a TR antagonist, which coincided well with the prediction from the Direct Message Passing Neural Network. The liver impairment (mainly cell necrosis of hepatocytes) and apoptosis were triggered by 125 μg/L and ≥12.5 μg/L BPAF respectively, accompanied by the increased activities of caspase 3 and caspase 9. Thus BPAF might not be a safe alternative to BPA given the thyroid and liver toxicity. DMPNN appears useful to screen for thyroid disrupting activity from molecular structures.

Enantioselective Metabolic Mechanism and Metabolism Pathway of Pydiflumetofen in Rat Liver Microsomes: In Vitro and In Silico Study

Pydiflumetofen (PYD) has been used worldwide. However, the enantioselective fate of PYD within mammals is not clear. Thus, the enantioselective metabolism and its potential mechanisms of PYD were explored via in vitro and in silico. Consistent results were observed between metabolism and enzyme kinetics experiments, with S-PYD metabolizing faster than R-PYD in rat liver microsomes. Moreover, CYP3A1 and carboxylesterase 1 were found to be major enzymes participating in the metabolism of PYD. Based on the computational results, S-PYD bound with CYP3A1 and carboxylesterase 1 more tightly with lower binding free energy than R-PYD, explaining the mechanism of enantioselective metabolism. Nine phase I metabolites of PYD were identified, and metabolic pathways of PYD were speculated. This study is the first to clarify the metabolism of PYD in mammals, and further research to evaluate the toxicological implications of these metabolites will help in assessing the risk of PYD.

Review of in silico studies dedicated to the nuclear receptor family: Therapeutic prospects and toxicological concerns

Being in the center of both therapeutic and toxicological concerns, NRs are widely studied for drug discovery application but also to unravel the potential toxicity of environmental compounds such as pesticides, cosmetics or additives. High throughput screening campaigns (HTS) are largely used to detect compounds able to interact with this protein family for both therapeutic and toxicological purposes. These methods lead to a large amount of data requiring the use of computational approaches for a robust and correct analysis and interpretation. The output data can be used to build predictive models to forecast the behavior of new chemicals based on their in vitro activities. This atrticle is a review of the studies published in the last decade and dedicated to NR ligands in silico prediction for both therapeutic and toxicological purposes. Over 100 articles concerning 14 NR subfamilies were carefully read and analyzed in order to retrieve the most commonly used computational methods to develop predictive models, to retrieve the databases deployed in the model building process and to pinpoint some of the limitations they faced.

Structures of Endocrine-Disrupting Chemicals Correlate with the Activation of 12 Classic Nuclear Receptors

Endocrine-disrupting chemicals (EDCs) can inadvertently interact with 12 classic nuclear receptors (NRs) that disrupt the endocrine system and cause adverse effects. There is no widely accepted understanding about what structural features make thousands of EDCs able to activate different NRs as well as how these structural features exert their functions and induce different outcomes at the cellular level. This paper applies the hierarchical characteristic fragment methodology and high-throughput screening molecular docking to comprehensively explore the structural and functional features of EDCs for the 12 NRs based on more than 7000 chemicals from curated datasets. EDCs share three levels of key fragments. The primary and secondary fragments are associated with the binding of EDCs to four groups of receptors: steroidal nuclear receptors (SNRs, including androgen, estrogen, glucocorticoid, mineralocorticoid, and progesterone), retinoic acid receptors, thyroid hormone receptors, and vitamin D receptors. The tertiary fragments determine the activity type by interacting with two key locations in the ligand-binding domains of NRs (N-H5-H3-C and N-H7-H11-C for SNRs and N-H5-H5'-H2'-H3-C and N-H6'-H11-C for non-SNRs). The resulting compiled structural fragments of EDCs together with elucidated compound NR binding modes provide a framework for understanding the interactions between EDCs and NRs, facilitating faster and more accurate screening of EDCs for multiple NRs in the future.

Machine Learning: New Ideas and Tools in Environmental Science and Engineering

The rapid increase in both the quantity and complexity of data that are being generated daily in the field of environmental science and engineering (ESE) demands accompanied advancement in data analytics. Advanced data analysis approaches, such as machine learning (ML), have become indispensable tools for revealing hidden patterns or deducing correlations for which conventional analytical methods face limitations or challenges. However, ML concepts and practices have not been widely utilized by researchers in ESE. This feature explores the potential of ML to revolutionize data analysis and modeling in the ESE field, and covers the essential knowledge needed for such applications. First, we use five examples to illustrate how ML addresses complex ESE problems. We then summarize four major types of applications of ML in ESE: making predictions; extracting feature importance; detecting anomalies; and discovering new materials or chemicals. Next, we introduce the essential knowledge required and current shortcomings in ML applications in ESE, with a focus on three important but often overlooked components when applying ML: correct model development, proper model interpretation, and sound applicability analysis. Finally, we discuss challenges and future opportunities in the application of ML tools in ESE to highlight the potential of ML in this field.

Toxicity and accumulation of 6-OH-BDE-47 and newly synthesized 6,6'-diOH-BDE-47 in early life-stages of Zebrafish (Danio rerio)

Dihydroxylated polybrominated diphenyl ethers (diOH-PBDEs) appear to be natural products or metabolites of PBDEs in some marine organisms, yet its toxicity is still largely unknown. With a newly lab-synthesized diOH-PBDE, 6,6'-dihydroxy-2,2',4'4'-tetrabromodiphenyl ether (6,6'-diOH-BDE-47) in hand, the present study has provided the first data set to compare 6-hydroxy-2,2',4'4'- tetrabromodiphenyl ether (6-OH-BDE-47) and 6,6'-diOH-BDE-47 for their acute toxicity and accumulation, and thyroid hormone levels in treated zebrafish larvae. By real time-PCR technique, transcripts of hypothalamic-pituitary-thyroid axis associated genes were also investigated in developing larvae at 96 h post fertilization (96 hpf). Apparently, 6,6'-diOH-BDE-47 was less toxic than that of 6-OH-BDE-47: 1) the 96-h LC₅₀ (96-h median lethal concentration) of 6-OH-BDE-47 and 6,6'-diOH-BDE-47 were 235 nM and 516 nM, respectively; 2) although severe developmental delays and morphological deformities were observed in zebrafish larvae in high exposure doses, at the exposure concentration of 1-50 nM, the accumulated 6-OH-BDE-47 and 6,6'-diOH-BDE-47 is ranged between 226-2279 nmol/g and 123-539 nmol/g in treated larvae; and 3) for 6-OH-BDE-47, its bioconcentration factor (BCF) were 1.83- to 4.30-fold more than that of 6,6'-diOH-BDE-47, suggesting that the lower internal exposure concentration of 6,6'-diOH-BDE-47 may lead to lower toxicity. The increased thyroid hormone levels were recorded for 1 nM of 6-OH-BDE-47 and 20 nM of 6,6'-diOH-BDE-47, and the exposures both significantly increased thyroid gland-specific transcription of thyroglobulin gene, indicating an adverse effect associated with the HPT axis. Therefore, 6,6'-diOH-BDE-47, with lower toxicity compared to that of 6-OH-BDE-47, still possesses hazards and environmental risk.

Investigating the molecular mechanism of hydroxylated bromdiphenyl ethers to inhibit the thyroid hormone sulfotransferase SULT1A1

Hydroxylated bromodiphenyl ethers (OH-BDEs) have raised great concern due to their potential endocrine disrupting effects on humans. In vitro experiments have indicated OH-BDEs can inhibit the activity of thyroid hormone (TH) sulfotransferases (SULTs); however, the molecular mechanism has not been investigated in depth. In this work, we employed 17 OH-BDEs with five or fewer Br atoms, and performed integrated computational simulations to unravel the possible inhibition mechanism of OH-BDEs on human SULT1A1. The molecular docking results demonstrate that OH-BDEs form hydrogen bonds with residues Lys106 and His108, and the neutral OH-BDEs show comparable binding energies with their anionic counterparts. The further hybrid quantum mechanical/molecular mechanical (QM/MM) calculations unravel a metabolic mechanism of OH-BDEs comprised by proton abstraction and sulfation steps. This mechanism is involved in the SULT1A1 inhibition by some OH-BDEs comprised of three or fewer Br atoms, while other OH-BDEs likely only form ternary complexes to competitively inhibit SULT1A1 activity. Moreover, the effect of the hydroxyl group of OH-BDEs on SULT1A1 inhibition potential follows the order of ortho-OH BDE > meta-OH BDE > para-OH BDE. These results provide an insight into the inhibition mechanism of OH-BDEs to SULT1A1 at the molecular level, which are beneficial in illuminating the molecular initiating events involved in the TH disruption of OH-BDEs.

Tetrabromobisphenol A Perturbs Erythropoiesis and Impairs Blood Circulation in Zebrafish Embryos

Tetrabromobisphenol A (TBBPA), a ubiquitous environmental pollutant, has been implicated in developmental toxicity of aquatic animals. However, the impact of TBBPA on development and the related mechanism have not been fully elucidated. In this study, using a live imaging technique and transgenic labeling of zebrafish embryos, we described the toxic effects of TBBPA on hematopoietic development in zebrafish. We demonstrated that TBBPA induced erythroid precursor expansion in the intermediate cell mass (ICM), which perturbed the onset of blood circulation at 24-26 hours postfertilization (hpf). Consequently, excessive blood cells accumulated in the posterior blood island (PBI) and vascular cells formed defective caudal veins (CVs), preventing blood cell flow to the heart at 32-34 hpf. We found that the one-cell to 50% epiboly stage was the most sensitive period to TBBPA exposure during hematopoietic development. Furthermore, our results demonstrated that PBI malformation induced by TBBPA resulted from effects on erythroid precursor cells, which might involve THR signaling in complex ways. These findings will improve the understanding of TBBPA-induced developmental toxicity in teleost.

Structures of Endocrine-Disrupting Chemicals Determine Binding to and Activation of the Estrogen Receptor α and Androgen Receptor

Endocrine-disrupting chemicals (EDCs) can interact with nuclear receptors, including estrogen receptor α (ERα) and androgen receptor (AR), to affect the normal endocrine system function, causing severe symptoms. Limited studies queried the EDC mechanisms, focusing on limited chemicals or a set of structurally similar compounds. It remained uncertain how hundreds of diverse EDCs could bind to ERα and AR and cause distinct functional consequences. Here, we employed a series of computational methodologies to investigate the structural features of EDCs that bind to and activate ERα and AR based on more than 4000 compounds. We used molecular docking and molecular dynamics simulations to elucidate the functional consequences and validated structure-function correlations experimentally using a time-resolved fluorescence resonance energy-transfer assay. We found that EDCs share three levels of key fragments. Primary (20 for ERα and 18 for AR) and secondary fragments (38 for ERα and 29 for AR) are responsible for the binding to receptors, and tertiary fragments determine the activity type (agonist, antagonist, or mixed). In summary, our study provides a general mechanism for the EDC function. Discovering the three levels of key fragments may drive fast screening and evaluation of potential EDCs from large sets of commercially used synthetic compounds.

Mechanistic in silico modeling of bisphenols to predict estrogen and glucocorticoid disrupting potentials

Endocrine disrupting chemicals (EDCs) can act as agonists, antagonists or mixed agonists/antagonists toward estrogen receptor α (ERα) and glucocorticoid receptor (GR) in a tissue- and cell-specific manner. However, the activation/inhibition mechanism by which structurally different chemicals induce various types of disruption remain ambiguous. This unrevealed theory limited the in silico modeling of EDCs and the prioritization of potential EDCs for experimental testing. As a kind of chemical widely used in manufacture, bisphenols (BPs) have attracted great attentions on their potential endocrine disrupting effects. BPs used in this study exhibited pure agonistic, pure antagonistic or mixed agonistic/antagonistic activities toward ERα and/or GR. According to the mechanistic modeling, the pure agonistic and pure antagonistic activities were attributed to a single type of protein conformation induced by BPs-ERα and/or BPs-GR interactions, whereas the mixed agonistic/antagonistic activities were attributed to multiple conformations that concomitantly exist. After interacting with BPs, the active conformation recruits coactivator to induce agonistic activity and the blocked conformation inhibits coactivator to induce antagonistic activity, whereas the concomitantly-existing multiple conformations (active, blocked and competing conformations) recruit coactivator, recruit corepressor and/or inhibit coactivator to dually induce the agonistic and antagonistic activities. Therefore, the in silico modeling in this study can not only predict ERα and GR disrupting activities but also, especially, identify the potential mechanisms. This mechanistic study breaks the current bottleneck of computational toxicology and can be widely used to prioritize potential estrogen/glucocorticoid disruptor for experimental testing in both pre-clinic and clinic studies.

The molecular mechanism of the antagonistic activity of hydroxylated polybrominated biphenyl (OH-BB80) toward thyroid receptor β

Polybrominated biphenyls (PBBs) were widely used as additive brominated flame retardants. Their hydroxylated products (OH-PBBs) have been detected frequently in various marine mammals, causing an increased health risk. Till now, there lacks information on the potential disruption of OH-PBBs toward thyroid hormone receptor (TR) and the molecular characteristics of their interactions remain largely unknown. We herein in vitro and in silico evaluated the disrupting effect of 3,3',5,5'-tetrabromobiphenyl (BB80) and its metabolite 2,2'-dihydroxy- 3,3',5,5'-tetrabromobiphenyl (OH-BB80) toward human TR. The recombinant human TRβ two-hybrid yeast assay reveals the moderate antagonistic activity of OH-BB80 with IC₂₀ at 2 μmol/L, while BB80 shows no agonistic or antagonistic activity. OH-BB80 binds at the binding cavity of TRβ ligand binding domain (LBD) and forms one hydrogen bond with Phe272. Electrostatic interactions and hydrophobic interactions contribute much to their interactions. The binding of OH-BB80 quenches the intrinsic fluorescence of TRβ LBD at static quenching mode. Our study extends knowledge on the endocrine disrupting effect of OH-PBBs and suggests the full consideration of the biotransformation for further health risk assessment of PBBs and related structurally similar emerging contaminants.

In silico study of molecular mechanisms of action: Estrogenic disruptors among phthalate esters

Phthalate esters (PAEs), as widely used plasticizers, have been concerned for their possible disruption of estrogen functions via binding to and activating the transcription of estrogen receptors (ERs). Nevertheless, the computational interpretation of the mechanism of ERs activities modulated by PAEs at the molecular level is still insufficient, which hinders the reliable screening of the ERs-active PAEs with high speed and high throughput. To bridge the gap, the in silico simulations considering the effects of coactivators were accomplished to explore the molecular mechanism of action for the purpose of predicting the estrogenic potencies of PAEs. The transcriptional activation functions of human ERα (hERα) modulated by PAEs is predicted via the simulations including binding interaction of PAEs and hERα, conformational changes of PAEs-hERα complexes and recruitment of coactivators. Molecular insight into the diverse estrogen mechanism of action among PAEs with regard to hERα agonists and selective estrogen receptor modulators (SERMs) is provided. Agonist-modulated conformational change of hERα leads to the optimal exposure of its Activation Function 2 (AF-2) surface which, in turn, facilitates the recruitment of coactivators, therefore promoting the transcriptional activation functions of hERα. Conversely, binding interaction of hERα with SERMs among PAEs leads to the conformational change with blocked AF-2 surface, thus preventing the recruitment of coactivators and consequently inhibiting the AF-2 activity. The two-hybrid recombinant yeast is experimentally used for verification. The established in silico evaluation methodology exhibits great promise to speed up the prediction of chemicals which work as hERα agonist or SERMs.

Limited Chemical Structural Diversity Found to Modulate Thyroid Hormone Receptor in the Tox21 Chemical Library

BACKGROUND

Thyroid hormone receptors (TRs) are critical endocrine receptors that regulate a multitude of processes in adult and developing organisms, and thyroid hormone disruption is of high concern for neurodevelopmental and reproductive toxicities in particular. To date, only a small number of chemical classes have been identified as possible TR modulators, and the receptors appear highly selective with respect to the ligand structural diversity. Thus, the question of whether TRs are an important screening target for protection of human and wildlife health remains.

OBJECTIVE

Our goal was to evaluate the hypothesis that there is limited structural diversity among environmentally relevant chemicals capable of modulating TR activity via the collaborative interagency Tox21 project.

METHODS

We screened the Tox21 chemical library (8,305 unique structures) in a quantitative high-throughput, cell-based reporter gene assay for TR agonist or antagonist activity. Active compounds were further characterized using additional orthogonal assays, including mammalian one-hybrid assays, coactivator recruitment assays, and a high-throughput, fluorescent imaging, nuclear receptor translocation assay.

RESULTS

Known agonist reference chemicals were readily identified in the TR transactivation assay, but only a single novel, direct agonist was found, the pharmaceutical betamipron. Indirect activation of TR through activation of its heterodimer partner, the retinoid-X-receptor (RXR), was also readily detected by confirmation in an RXR agonist assay. Identifying antagonists with high confidence was a challenge with the presence of significant confounding cytotoxicity and other, non-TR-specific mechanisms common to the transactivation assays. Only three pharmaceuticals-mefenamic acid, diclazuril, and risarestat-were confirmed as antagonists.

DISCUSSION

The results support limited structural diversity for direct ligand effects on TR and imply that other potential target sites in the thyroid hormone axis should be a greater priority for bioactivity screening for thyroid axis disruptors. https://doi.org/10.1289/EHP5314.

Concentrations, spatial distributions, and congener profiles of polychlorinated dibenzo-p-dioxins and dibenzofurans around original plastic solid waste recovery sites in China

The concentrations, profiles, and spatial distributions of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in soil and sediment samples from several typical plastic solid waste (PSW) recovery sites (particularly from areas in which PSW is burned openly) in China were investigated. The results showed that burning PSW directly influenced PCDD/F concentrations immediately around the burning area. All of the samples in which soil contained black burning residue, collected from immediately around burning areas, had PCDD/F concentrations (mean 21708 ng kg^-1) and toxic equivalent (TEQ) concentrations (mean 2140 ng I-TEQ kg^-1 or 1877 ng WHO₂₀₀₆-TEQ kg^-1) more than 100 times higher than the concentrations in samples collected away from burning areas (mean 222 ng kg^-1, 8.75 ng I-TEQ kg^-1, 7.96 ng WHO₂₀₀₆-TEQ kg^-1). Principal component analysis and hierarchical cluster analysis indicated that the PCDD/F concentrations in seven soil samples from near PSW burning areas were influenced by PSW burning but that the PCDD/Fs in these soil samples may have had other or multiple sources. PCDD/F distributions at PSW recovery sites have been investigated in few previous studies. The results presented here indicate that appropriate measures should be taken to decrease the ecological risks posed by PSW recovery and to prevent, control, and remediate PCDD/F and other chemical contamination caused by PSW recovery.

Interspecies Variation between Fish and Human Transthyretins in Their Binding of Thyroid-Disrupting Chemicals

Thyroid-disrupting chemicals (TDCs) are xenobiotics that can interfere with the endocrine system and cause adverse effects in organisms and their offspring. TDCs affect both the thyroid gland and regulatory enzymes associated with thyroid hormone homeostasis. Transthyretin (TTR) is found in the serum and cerebrospinal fluid of vertebrates, where it transports thyroid hormones. Here, we explored the interspecies variation in TDC binding to human and fish TTR (exemplified by Gilthead seabream ( Sparus aurata)). The in vitro binding experiments showed that TDCs bind with equal or weaker affinity to seabream TTR than to the human TTR, in particular, the polar TDCs (>500-fold lower affinity). Crystal structures of the seabream TTR-TDC complexes revealed that all TDCs bound at the thyroid binding sites. However, amino acid substitution of Ser117 in human TTR to Thr117 in seabream prevented polar TDCs from binding deep in the hormone binding cavity, which explains their low affinity to seabream TTR. Molecular dynamics and in silico alanine scanning simulation also suggested that the protein backbone of seabream TTR is more rigid than the human one and that Thr117 provides fewer electrostatic contributions than Ser117 to ligand binding. This provides an explanation for the weaker affinities of the ligands that rely on electrostatic interactions with Thr117. The lower affinities of TDCs to fish TTR, in particular the polar ones, could potentially lead to milder thyroid-related effects in fish.

Spatial distribution, risk and potential sources of lead in soils in the vicinity of a historic industrial site

Because of measures taken by local and national government agencies to control releases of metals, former industrial sites in China that are contaminated with lead (Pb) in soils have been abandoned. Compared with historic sites themselves, little attention has been paid to contamination with Pb in areas surrounding these sites. In this study, a method by integrating sequential extraction and isotopic fingerprinting was proposed to reveal the key fractions of Pb contaminants in soils, trace their sources and determine the subject of liability for remediation. Topsoils from near a historic site, where lead oxide was produced, were found to be contaminated. Concentrations of Pb in soils were inversely proportional to distances from the industrial site and depth in soils. The predominant form of Pb was the Fe/Mn-oxide-bound fraction (FM3), which accounted for from 53.39% to 82.07% of total concentrations of Pb. Concentrations of Pb in vegetables produced on contaminated soils exceeded those allowed in food for consumption by humans. An assessment of hazards and risks posed by consumption of vegetables grown on these soils indicated relatively high potential for adverse effects on local residents around the closed plant. By use of isotopic finger printing for Pb, the abandoned factory was determined to be the most likely source of Pb in topsoils, especially fraction FM3. To mitigate exposures of people to Pb via consumption of locally produced food, recommended strategies should target legacy sources of Pb to soils in the vicinity of this historic industrial site.

Iodoacetic Acid Disrupting the Thyroid Endocrine System in Vitro and in Vivo

Exposure to drinking water disinfection byproducts (DBPs) is potentially associated with adverse developmental effects. Iodoacetic acid (IAA), an unregulated DBP, has been shown to be cytotoxic, mutagenic, genotoxic, and tumorigenic. However, its endocrine-disrupting effects remain unknown. This study evaluated the IAA-induced disruption of the thyroid endocrine system using in vitro and in vivo assays. Rat pituitary tumor GH3 cells were treated with IAA in the presence and absence of triiodothyronine (T3). IAA exposure significantly reduced T3-activated GH3 cell proliferation, indicating the antagonistic activity of IAA in vitro. Sprague-Dawley rats were also subjected to IAA treatment through oral gavage for 28 consecutive days. IAA exposure significantly down-regulated the mRNA expression levels of the thyrotropin receptor (TSHR), the sodium/iodide symporter (NIS), and type I deiodinase and simultaneously reduced the protein expression levels of TSHR and NIS. IAA exposure decreased T3 levels but increased the weights of hypothalamus and the levels of thyrotropin releasing hormone and thyrotropin. In addition, IAA induced the formation of smaller and more depleted follicles or even vacuolization in the thyroid. These results suggested that IAA potentially disrupts the thyroid endocrine system both in vitro and in vivo.

Thyroid Disruption by Bisphenol S Analogues via Thyroid Hormone Receptor β: in Vitro, in Vivo, and Molecular Dynamics Simulation Study

Bisphenol S (4-hydroxyphenyl sulfone, BPS) is increasingly used as a bisphenol A (BPA) alternative. The global usage of BPS and its analogues (BPSs) resulted in the frequent detection of their residues in multiple environmental media. We investigated their potential endocrine-disrupting effects toward thyroid hormone receptor (TR) β. The molecular interaction of BPSs toward TRβ ligand binding domain (LBD) was probed by fluorescence spectroscopy and molecular dynamics (MD) simulations. BPSs caused the static fluorescence quenching of TRβ LBD. The 100 ns MD simulations revealed that the binding of BPSs caused significant changes in the distance between residue His435 at helix 11(H11) and residue Phe459 at H12 in comparison to no ligand-bound TRβ LBD, indicating relative repositioning of H12. The recombinant two-hybrid yeast assay showed that tetrabromobisphenol S (TBBPS) and tetrabromobisphenol A (TBBPA) have potent antagonistic activity toward TRβ, with an IC₁₀ of 10.1 and 21.1 nM, respectively. BPS and BPA have the antagonistic activity with IC₁₀ of 312 and 884 nM, respectively. BPSs significantly altered the expression level of mRNA of TRβ gene in zebrafish embryos. BPS and TBBPS at environmentally relevant concentrations have antagonistic activity toward TRβ, implying that BPSs are not safe BPA alternatives in many BPA-free products. Future health risk assessments for TR disruption and other adverse effects should focus more on the structure-activity relationship in the design of environmentally benign BPA alternatives.

Multiple approaches to assess the effects of F-53B, a Chinese PFOS alternative, on thyroid endocrine disruption at environmentally relevant concentrations

A Chinese perfluorooctane sulfonate (PFOS) substitute frequently detected in the environment, 6:2 chlorinated polyfluorinated ether sulfonate (F-53B), has a similar structure to PFOS and it is proposed to cause thyroid dysfunction. To further confirm this hypothesis, the effects of F-53B on the thyroid endocrine system and underlying mechanisms were investigated in vitro and in vivo using rat pituitary GH3 cells and developing zebrafish, respectively. In GH3 cells, F-53B enhanced cell proliferation in a dose-dependent manner, indicative of thyroid receptor agonistic activity. In zebrafish larvae, F-53B exposure induced significant developmental inhibition and increased thyroxine (T₄) but not 3,5,3'-triiodothyronine (T₃) levels accompanied by a decrease in thyroglobulin (TG) protein and transcript levels of most genes involved in the hypothalamic-pituitary-thyroid (HPT) axis. Interestingly, T₄ levels remained significantly increased while TG protein and gene transcription levels were markedly upregulated after depuration. Molecular docking studies revealed that F-53B binds to transthyretin (TTR) by forming hydrogen bonds with Lys123 and Lys115, thereby interfering with thyroid hormone homeostasis. Our collective in vitro, in vivo and in silico studies provide novel evidence that F-53B disrupts the thyroid endocrine system at environmentally relevant concentrations, which cannot be recovered after depuration. Given the persistence of F-53B in the environment, the long-term consequences of thyroid hormone disruption by this chemical warrant further investigation.

Structural aspects of thyroid hormone binding to proteins and competitive interactions with natural and synthetic compounds

Thyroid hormones and their metabolites constitute a vast class of related iodothyronine compounds that contribute to the regulation of metabolic activity and cell differentiation. They are in turn transported, transformed and recognized as signaling molecules through binding to a variety of proteins from a wide range of evolutionary unrelated protein families, which renders these proteins and their iodothyronine binding sites an example for extensive convergent evolution. In this review, we will briefly summarize what is known about iodothyronine binding sites in proteins, the modes of protein/iodothyronine interaction, and the ligand conformations. We will then discuss physiological and synthetic compounds, including popular drugs and food components, that can interfere with iodothyronine binding and recognition by these proteins. The discussion also includes compounds persisting in the environment and acting as endocrine disrupting chemicals.

Extended Virtual Screening Strategies To Link Antiandrogenic Activities and Detected Organic Contaminants in Soils

A tiered screening strategy based on extensive virtual fractionation and elucidation was developed to simplify identification of toxicants in complex environments. In tier1-virtual fractionation, multivariate analysis (MVA) was set up as an alternative of physical fractionation. In tier2-virtual structure elucidation, in-house quantitative structure-retention relationship (QSRR) models and toxicity simulation methods were developed to simplify nontarget identification. The efficiency of the tiered virtual strategy was tentatively verified by soil samples from a chemical park contaminated by antiandrogenic substances. Eight out of 18 sites were detected as antiandrogenic, while none of them exhibited androgenic agonist potencies. Sixty-seven peaks were selected for further identification by MVA, among which over 90% were verified in androgenic fractions in traditional effect-directed analysis (EDA). With 579 tentative structures generated by in silico fragmentation, 74% were elucidated by QSRR and 65% were elucidated by in silico toxicity prediction. All prior peaks were identified at different confidence levels with over 40% of the identified peaks above confidence level 2b, which has been increased over 40% with less than half of the time spent compared to traditional EDA. Such a combination of tiered virtual screening methods provides more efficient and rapid identifications of key toxicants at contaminated sites.

Revealing the importance of linkers in K-series oxime reactivators for tabun-inhibited AChE using quantum chemical, docking and SMD studies

Inhibition of acetylcholinesterase (AChE) with organophosphorus compounds has a detrimental effect on human life. Oxime K203 seems to be one of the promising reactivators for tabun-inhibited AChE than (K027, K127, and K628). These reactivators differ only in the linker units between the two pyridinium rings. The conformational analyses performed with quantum chemical RHF/6-31G* level for K027, K127, K203 and K628 showed that the minimum energy conformers have different orientations of the active and peripheral pyridinium rings for these reactivator molecules. K203 with (-CH₂-CH=CH-CH₂-) linker unit possesses more open conformation compared to the other reactivators. Such orientation of K203 experiences favorable interaction with the surrounding residues of catalytic anionic site (CAS) and peripheral anionic site (PAS) of tabun-inhibited AChE. From the steered molecular dynamics simulations, it has been observed that the oxygen atom of the oxime group of K203 reactivator approaches nearest to the P-atom of the SUN203 (3.75 Å) at lower time scales (less than ~1000 ps) as compared to the other reactivators. K203 experiences less number of hydrophobic interaction with the PAS residues which is suggested to be an important factor for the efficient reactivation process. In addition, K203 crates large number of H-bonding with CAS residues SUN203, Phe295, Tyr337, Phe338 and His447. K203 barely changes its conformation during the SMD simulation process and hence the energy penalty to adopt any other conformation is minimal in this case as compared to the other reactivators. The molecular mechanics and Poisson-Boltzmann surface area binding energies obtained for the interaction of K203 inside the gorge of tabun inhibited AChE is substantially higher (-290.2 kcal/mol) than the corresponding K628 reactivator (-260.4 kcal/mol), which also possess unsaturated aromatic linker unit.