Homology modeling of the estrogen receptor subtype beta (ER-beta) and calculation of ligand binding affinities

Estrogen is a steroid hormone playing critical roles in physiological processes such as sexual differentiation and development, female and male reproductive processes, and bone health. Numerous natural and synthetic environmental compounds have been shown capable of estrogenic effects. This area has been the focus of significant fundamental and applied research due both to the potential detrimental effects of these compounds upon normal physiological processes and to the potential beneficial effects of tissue-selective estrogen agonists/antagonists for the prevention and treatment of numerous diseases. Genomic effects of the active form of estrogen, 17beta-estradiol, are mediated through at least two members of the steroid hormone receptor superfamily, estrogen receptor subtype alpha (ER-alpha) and estrogen receptor subtype beta (ER-beta). At the time of this work, the X-ray crystal structure of the ER-alpha had been elucidated, however, coordinates of the ER-beta were not publicly available. Based upon the significant structural conservation across members of the steroid hormone receptor family, and the high sequence homology between ER-alpha and ER-beta (>60%), we have developed a homology model of the ER-beta structure. Using the crystal structure of ER-alpha and the homology model of ER-beta, we demonstrate a strong correlation between computed values of the binding-energy and published values of the observed relative binding affinity (RBA) for a variety of compounds for both receptors, as well as the ability to identify receptor subtype selective compounds. Furthermore, using the recently available crystal structure of ER-beta for comparison purposes, we show that not only is the predicted homology model structurally accurate, but that it can be used to assess ligand binding affinities.