Homology models of mouse and rat estrogen receptor-α ligand-binding domain created by in silico mutagenesis of a human template: Molecular docking with 17β-estradiol, diethylstilbestrol, and paraben analogs

Abstract

Crystal structures exist for human, but not rodent, estrogen receptor-α ligand-binding domain (ERα-LBD). Consequently, rodent studies involving binding of compounds to ERα-LBD are limited in their molecular-level interpretation and extrapolation to humans. Because the sequences of rodent and human ERα-LBDs are > 95% identical, we expected their 3D structures and ligand binding to be highly similar. To test this hypothesis, we used the human ERα-LBD structure (PDB 3UUD) as a template to produce rat and mouse homology models. Employing the rodent models and human structure, we generated docking poses of 23 Group A ligands (17ß-estradiol, diethylstilbestrol, and 21 paraben analogs) in AutoDock Vina for interspecies comparisons. Ligand RMSDs (Å) (median, 95% CI) were 0.49 (0.21–1.82) (human-mouse) and 1.19 (0.22–1.82) (human-rat), well below the 2.0–2.5 Å range for equivalent docking poses. Numbers of interspecies ligand-receptor residue contacts were highly similar, with Sorensen Sc (%) = 96.8 (90.0–100) (human-mouse) and 97.7 (89.5–100) (human-rat). Likewise, numbers of interspecies ligand-receptor residue contacts were highly correlated: Pearson r = 0.913 (human-mouse) and 0.925 (human-rat). Numbers of interspecies ligand-receptor atom contacts were even more tightly correlated: r = 0.979 (human-mouse) and 0.986 (human-rat). Pyramid plots of numbers of ligand-receptor atom contacts by residue exhibited high interspecies symmetry and had Spearman rs = 0.977 (human-mouse) and 0.966 (human-rat). Group B ligands included 15 ring-substituted parabens recently shown experimentally to exhibit decreased binding to human ERα and to exert increased antimicrobial activity. Ligand efficiencies calculated from docking ligands into human ERα-LBD were well correlated with those derived from published experimental data (Pearson partial rp = 0.894 and 0.918; Groups A and B, respectively). Overall, the results indicate that our constructed rodent ERα-LBDs interact with ligands in like manner to the human receptor, thus providing a high level of confidence in extrapolations of rodent to human ligand-receptor interactions.

A comprehensive analysis of racial disparities in chemical biomarker concentrations in United States women, 1999-2014

“…Differences in concentrations of methyl and propyl paraben biomarkers were among the highest observed in this study, particularly for the youngest non-Hispanic Black women. These chemicals have been used as preservatives in personal care products, pharmaceuticals, and food additives, and have been found to promote cell growth through multiple mechanisms, including estrogenicity (Gonzalez et al 2018, 2019; Okubo et al 2001) and epidermal growth factor receptor signaling (Pan et al 2016). Particularly relevant to our findings of the greatest methyl and ethyl paraben disparities in the youngest non-Hispanic Black women was the finding that early life paraben exposures can alter developing mammary gland morphology and induce gene expression that resembles an early cancer-like state (Gopalakrishnan et al 2017).…”

Endocrine Disruptors Induced Distinct Expression of Thyroid and Estrogen Receptors in Rat versus Mouse Primary Cerebellar Cell Cultures

“…There are numerous affected signaling pathways after ED exposure in the animals. ERs and TRs are considered conservative receptors-for instance, in the case of ERα, ligand-binding affinity shows a distinct similarity between species [104,105]-however, the cellular composition can differ between rodents. Not only the specific "route of action"-the amounts of innate enzymes or receptors and specific enzyme isoforms-can be different between species, but the overall metabolic activity of the animals or the pace of development can vary between mice and rats as well.…”

Studying the role of estrogen receptor alpha in the developmental toxicity of diethylstilbestrol using alternative testing strategies

“…DES is an analogue of the endogenous female sex hormone 17β-estradiol (E2) and binds to both the estrogen receptor α (ERα) and estrogen receptor β (ERβ) (Bolger et al 1998;Nikov et al 2001). It has been reported that the molecular dimensions of DES are almost identical to those of E2, particularly with regard to the distance between the terminal hydroxyl groups (Gonzalez et al 2019) (Fig. 1).…”

“…DES is an analogue of E2 and binds to both ERα and ERβ with a higher affinity compared to E2 Bolger et al 1998;Nikov et al 2001). It has been reported that the molecular dimensions of DES are almost identical to those of E2 (see figure 3), particularly with regard to the distance between the terminal hydroxyl groups (Gonzalez et al 2019). The length and breadth of both the steroid skeleton and the DES skeleton were shown to fit well into the receptorbinding pocket (Gonzalez et al 2019).…”

“…Molecular docking of E2 and DES into the ligand binding domain of ERα from mouse and rat revealed similar binding orientations and confirmed a role for the hydroxyl moieties in this interaction (Gonzalez et al 2019). The ERα agonist action has generally been associated with stimulation of cell proliferation while ERβ activation has been linked with suppression of cell proliferation and stimulation of apoptosis (Sotoca et al 2008;Thomas and Gustafsson 2011).…”