The Aryl Hydrocarbon Receptor (AHR) is a ligand-activated transcription factor that regulates the expression of a diverse group of genes. Interestingly, the PAS-B ligand binding domain of AHR binds ligands with a variety of chemical scaffolds, including the potent carcinogenic 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), which to date is the most potent AHR agonist. In the absence of an experimentally-determined structure of this domain, previous AHR homology models in the apo conformation were successfully used for virtual ligand screening (VLS) to predict new AHR ligands that were confirmed with testing in cells. In this study, we sought to refine this technique by optimizing the protein model with the agonist TCDD docked within its binding pocket. The result was an �agonist-optimized� homology model which increased the volume of the binding pocket and had reduced energy strained compared to the previous apo model. We found that the agonist-optimized model was able to discriminate known AHR agonists including TCDD from inactive compounds, indicating that it was an improved version with the potential to identify novel AHR agonists. To search for new agonists, we performed VLS against our agonist-optimized model and identified sixteen candidate compounds. In cells, four of these compounds were able to significantly activate the AHR gene CYP1A1. In addition, we performed molecular dynamics simulations of an agonist-bound, and antagonist-bound version of this improved model in order to gain insight on the mechanics of the AHR PAS-B domain. In the context of these simulations we discovered that a specific portion of the protein comprised a flexible segment with helices that coiled or uncoiled as needed to accommodate the different ligand shapes. Based on these findings, we hypothesize that this segment is a key adaptable component that might disrupt HSP90 binding and highly influences how AHR interacts with either an agonist or an antagonist.

Identification of novel ligands and insight into the structural switch between agonist and antagonist activity from an optimized model of the human aryl hydrocarbon receptor ligand binding domain

247th National Meeting (2014)

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