Molecular modeling has become an essential tool in predicting and simulating endocrine disrupting effects of chemicals. A key prerequisite for successful application of molecular modeling lies in the correctness of 3D structure for biomacromolecules to be simulated. To date, there are several databases that can provide the experimentally−determined 3D structures. However, commonly, there are many challenges or disadvantageous factors, e.g., (a) lots of 3D structures for a given biomacromolecular target in the protein database; (b) the quality variability for those structures; (c) belonging to different species; (d) mutant amino acid residue in key positions, and so on. Once an inappropriate 3D structure of a target biomacromolecule was selected in molecular modeling, the accuracy and scientific nature of the modeling results could be inevitably affected. In this article, based on literature survey and an analysis of the 3D structure characterization of biomacromolecular targets belonging to the endocrine system in protein databases, six principles were proposed to guide the selection of the appropriate 3D structure of biomacromolecules. The principles include considering the species diversity, the mechanism of action, whether there are mutant amino acid residues, whether the number of protein chains is correct, the degree of structural similarity between the ligand in 3D structure and the target compounds, and other factors, e.g., the experimental pH conditions of the structure determined process and resolution.
■ INTRODUCTIONEndocrine hormones are chemical messengers secreted by endocrine glands, which play an indispensable role during the whole lifetime of an organism. For example, thyroid hormones (THs) regulate growth, differentiation, metamorphosis, and thermogenesis of vertebrates. 1 A key prerequisite for endocrine hormones exerting their biological effects in humans and wildlife is that the organism maintains normal homeostasis of hormones. However, the results from epidemiological and field investigations, as well as in vivo studies, documented that many man-made chemicals, named endocrine disrupting chemicals (EDCs), could influence the homeostasis of hormones, disturb the function of the endocrine system, and consequently cause adverse health effects. 2−4 According to the identified toxicity pathways, EDCs may disrupt the endocrine hormone signaling by (a) impacting the hypothalamic-pituitary-gonad/thyroid/ adrenal axis function and regulation, (b) inhibiting the hormone synthesis, (c) disrupting the hormone transport binding proteins, (d) activating/inhibiting the hormone receptor, and (e) impacting the hormone metabolism. 1,5 This indicated that whether the endocrine hormones exert their biological effects or EDCs cause endocrine-related diseases and endocrine dysfunction, the mechanisms of endocrine disruptor action can be generalized as the interactions between small molecules and biomacromolecular targets (e.g., hormone receptor, hormone transport binding proteins, synthetase and metab...