New Aryl Hydrocarbon Receptor Homology Model Targeted To Improve Docking Reliability

Abstract

The aryl hydrocarbon receptor (AhR) is a ligand-dependent, basic helix-loop-helix Per-ARNT-Sim (PAS) containing transcription factor that can bind and be activated by structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). As no experimentally determined structures of the AhR ligand binding domain (LBD) are available and previous homology models were only derived from apo template structures, we developed a new model based on holo X-ray structures of the hypoxia-inducible factor 2α (HIF-2α) PAS B domain, targeted to improve the accuracy of the binding site for molecular docking applications. We experimentally confirmed the ability of two HIF-2α crystallographic ligands to bind to the mAhR with relatively high affinity and demonstrated that they are AhR agonists, thus justifying the use of the holo HIF-2α structures as templates. A specific modeling/docking approach was proposed to predict the binding modes of AhR ligands in the modeled LBD. It was validated by comparison of the calculated and the experimental binding affinities of active THS ligands and TCDD for the mAhR and by functional activity analysis using several mAhR mutants generated on the basis of the modeling results. Finally the ability of the proposed approach to reproduce the different affinities of TCDD for AhRs of different species was confirmed, and a first test of its reliability in virtual screening is carried out by analyzing the correlation between the calculated and experimental binding affinities of a set of 14 PCDDs.

Ligand Promiscuity of Aryl Hydrocarbon Receptor Agonists and Antagonists Revealed by Site-Directed Mutagenesis

“…THS-017 (Fig. 4D) is an atypical AhR ligand that also binds to HIF2␣ and was used to further refine the homology model of the AhR PASB LBD (32,44). YH439 (Fig.…”

“…Consistent with this hypothesis is the identification of AhR antagonists that appear to be ligand selective in that they can preferentially inhibit the ability of some ligands (i.e., TCDD and related HAHs) to bind to and activate the AhR, while other AhR ligands (i.e., PAHs, flavonoids, indirubin) are not affected (31). Although progress in understanding the details of the molecular mechanisms of ligand binding and ligand-dependent AhR activation/transformation has been hampered by the lack of a 3-dimensional structure of the AhR LBD, site-directed mutagenesis studies and structure-function analysis using a homology model of the AhR LBD have produced some insights (32,33).…”

“…However, several specific residues whose mutation resulted in ligand-specific differences in AhR functionality and agonist activity have been identified (1,(34)(35)(36). Interestingly, when these specific residues (H285, F289, F318, and H320) are mapped onto the mouse AhR LBD homology model (32,33), they are located in proximity to each other, suggesting that they may encompass a distinct region of the LBD involved in ligand-specific activation of the AhR. This region is also adjacent to amino acids previously implicated in ligand binding (Ala375) and hsp90 binding (Phe281), indicating possible involvement of ligand-dependent hsp90 displacement in ligand-selective effects (10,37).…”

Measured and predicted affinities of binding and relative potencies to activate the AhR of PAHs and their alkylated analogues

“…This ligand-dependent transcription factor responds to diverse ligands and plays a critical role not only in toxicity, but also in immune function, cardiovascular physiology, and xenobiotic metabolism (Ma, 2001;Motto et al, 2011;Xing et al, 2012). Interaction of chemicals with the AhR can influence expression of a large battery of genes and induce diverse biological or toxic effects in a wide range of species and tissues (Ma, 2001;Motto et al, 2011). Cytochrome P450 (CYP) 1A, a xenobiotic-metabolizing enzyme, is also regulated by AhR activation (Bak et al, 2013).…”

In Silico Identification of an Aryl Hydrocarbon Receptor Antagonist with Biological Activity In Vitro and In Vivo

“…In its stead, researchers have developed structural homology models on the basis of ligandbinding domains of familial proteins (Motto et al, 2011;Xing et al, 2012). Although recent advancements in AHR-LBD models have improved our understanding of the requirements for AHR binding, the abilities of these programs to predict AHR ligands is only beginning to be realized.…”