In silico exploration of hydroxylated polychlorinated biphenyls as estrogen receptor β ligands by 3D-QSAR, molecular docking and molecular dynamics simulations

Hydroxylated polychlorinated biphenyls (HO-PCBs), as the major metabolites of PCBs, have been reported to act as estrogen receptor β (ERβ) agonists. However, the chemical-biological interactions governing their activities toward ERβ have not been elucidated. Therefore, three dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulations, to the best of our knowledge, for the first time were performed to explore the correlation between the structures and activities. The best 3D-QSAR model presented higher predictive ability (R²_cv=0.543, R²_pred=0.5793/R²_cv=0.543, R²_pred=0.6795) based on comparative molecular field analysis (CoMFA) and comparative similarity indices analysis (CoMSIA), respectively. At the same time, the derived contour maps indicated the important structural features required for improving the activity. Furthermore, molecular docking studies and MD simulations predicted the binding mode and the interactions between the ligand and the receptor. All the results would lead to a better understanding of the specific mechanism of HO-PCBs on estrogen receptor β (ERβ).Communicated by Ramaswamy H. Sarma.

Molecular docking and 3D-QSAR studies on the glucocorticoid receptor antagonistic activity of hydroxylated polychlorinated biphenyls

The glucocorticoid receptor (GR) antagonistic activities of hydroxylated polychlorinated biphenyls (HO-PCBs) were recently characterised. To further explore the interactions between HO-PCBs and the GR, and to elucidate structural characteristics that influence the GR antagonistic activity of HO-PCBs, molecular docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed. Comparative molecular similarity indices analysis (CoMSIA) was performed using both ligand- and receptor-based alignment schemes. Results generated from the receptor-based model were found to be more satisfactory, with q(2) of 0.632 and r(2) of 0.931 compared with those from the ligand-based model. Some internal validation strategies (e.g. cross-validation analysis, bootstrapping analysis and Y-randomisation) and an external validation method were used respectively to further assess the stability and predictive ability of the derived model. Graphical interpretation of the model provided some insights into the structural features that affected the GR antagonistic activity of HO-PCBs. Molecular docking studies revealed that some key residues were critical for ligand-receptor interactions by forming hydrogen bonds (Glu540) and hydrophobic interactions with ligands (Ile539, Val543 and Trp577). Although CoMSIA sometimes depends on the alignment of the molecules, the information provided is beneficial for predicting the GR antagonistic activities of HO-PCB homologues and is helpful for understanding the binding mechanisms of HO-PCBs to GR.

Bioaccumulation of hydroxylated polychlorinated biphenyls and pentachlorophenol in the serum of northern elephant seal pups (Mirounga angustirostris)

Northern elephant seals (NES) (Mirounga angustirostris) from the Año Nuevo State Reserve (CA, USA) were sampled at 1-, 4-, 7- and 10-week post-weaning. Concentrations of hydroxylated polychlorinated biphenyls (HO-PCBs) and their parent PCBs were measured in the serum of each individual. The ΣHO-PCB concentrations in the serum increased significantly between early and late fast (from 282 ± 20 to 529 ± 31 pg/mL). This increase might result from a mobilisation of HO-PCBs transferred from the mother during gestation and/or lactation and stored in the pup's liver. Food deprivation has been shown to exacerbate biotransformation capacities in mammals, birds and fish. The HO-penta-CBs was the predominant homologue group, followed by HO-hexa-CBs and HO-hepta-CBs. No preferential pathway for the metabolism of HO-PCBs (HO-direct insertion or NIH-shift of a chlorine atom) could be evidenced. The concentrations of pentachlorophenol (PCP) in the serum of weaned NES increased from 103 ± 7 pg/mL at early fast to 246 ± 41 pg/mL at late fast, which is within the range of PCP concentrations usually encountered in marine mammals.

Methoxylated PBDEs (MeO-PBDEs), hydroxylated PBDEs (HO-PBDEs) and hydroxylated PCBs (HO-PCBs) in the liver of harbor seals from the northwest Atlantic

Metabolites of PCBs and PBDEs are shown to influence the thyroid hormone homeostasis and therefore, could have an influence on the growth of newborn or young animals. We have investigated the occurrence of hydroxylated PCBs (HO-PCBs), hydroxylated PBDEs (HO-PBDEs), and methoxylated PBDEs (MeO-PBDEs) in the liver (48 pups; 6 adults) and blubber (4 pups; 1 adult) of harbor seals (Phoca vitulina concolor) from the northwest Atlantic. The sum of HO-PCBs in the liver ranged from 90 to 22,450 pg/g wet weight (ww) for pups and from 410 to 5290 pg/g ww for adults. Congener 4-HO-CB 107 was predominant in almost all samples regardless of age or gender, except in one adult male. Sum HO-PCB concentrations were highly correlated with the sum of precursor PCBs in the liver of harbor seals (r(2) = 0.79; p<0.0001). Concentrations of sum HO-PBDEs in the liver ranged from 70 to 1850 pg/g ww for pups and from 90 to 230 pg/g ww for adults. HO-PBDEs were also correlated with PBDEs (r(2) = 0.58; p<0.0001). Sum MeO-PBDE concentrations in the liver ranged from 20 to 1460 pg/g ww in pups and from 10 to 270 pg/g ww in adults. HO-PCBs and HO-PBDEs were not detected in the blubber. Levels of MeO-PBDEs in the blubber ranged from 1500 to 4400 pg/g ww. In all blubber samples, 6-MeO-BDE 47 was the predominant MeO-PBDE congener, followed by 2'-MeO-BDE 68 and 5-MeO-BDE 47, respectively. The presence of HO-metabolites in pup liver suggests that young harbor seals may have some, yet limited, metabolic capacity for PCBs and PBDEs, which can lead to an excessive accumulation of these chemicals in the body. Moreover, the presence of HO-PCB and HO-PBDE metabolites may pose an additional stress for young harbor seals due to their influence on the thyroid hormone system and could have consequences for the entire population.

Molecular docking, molecular dynamics simulation, and structure-based 3D-QSAR studies on the aryl hydrocarbon receptor agonistic activity of hydroxylated polychlorinated biphenyls

The binding interactions between hydroxylated polychlorinated biphenyls (HO-PCBs) and the aryl hydrocarbon receptor (AhR) are suspected of causing toxic effects. To understand the binding mode between HO-PCBs and AhR, and to explore the structural characteristics that influence the AhR agonistic activities of HO-PCBs, the combination of molecular docking, three-dimensional quantitative structure-activity relationship (3D-QSAR), and molecular dynamics (MD) simulations was performed. Using molecular docking, the HO-PCBs were docked into the binding pocket of AhR, which was generated by homology modeling. Comparative molecular similarity index analysis (CoMSIA) models were subsequently developed from three different alignment rules. The optimum 3D-QSAR model showed good predictive ability (q(2)=0.583, R(2)=0.913) and good mechanism interpretability. The statistical reliability of the CoMSIA model was also validated. In addition, molecular docking and MD simulations were applied to explore the binding modes between the ligands and AhR. The results obtained from this study may lead to a better understanding of the interaction mechanism between HO-PCBs and AhR.