New Aryl Hydrocarbon Receptor Homology Model Targeted To Improve Docking Reliability (original) (raw)
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Biology, 2014
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that regulates the expression of a diverse group of genes. Exogenous AHR ligands include the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), which is a potent agonist, and the synthetic AHR antagonist N-2-(1H-indol-3yl)ethyl)-9-isopropyl-2- (5-methylpyridin-3-yl)-9H-purin-6-amine (GNF351). As no experimentally determined structure of the ligand binding domain exists, homology models have been utilized for virtual ligand screening (VLS) to search for novel ligands. Here, we have developed an "agonist-optimized" homology model of the human AHR ligand binding domain, and this model aided in the discovery of two human AHR agonists by VLS. In addition, we performed molecular dynamics simulations of an agonist TCDD-bound and antagonist GNF351-bound version of this model in order to gain insights into the mechanics of the AHR ligand-binding pocket. These simulations identified residues 307-329 as a flexible segment of the AHR ligand pocket that adopts discrete conformations upon agonist or antagonist binding. This flexible segment of the AHR may act as a structural switch that determines the agonist or antagonist activity of a given AHR ligand.
Biochemical and biophysical research communications, 2011
Molecular structure of the ligand binding domain of hAhR has been modelled by homology modelling techniques and used for docking simulations with dioxin and nine more xenobiotics and endogenous ligands. The study evidences that different sites may bind these ligands, whereas only one binding site has been previously indicated by past studies on the mouse homologous receptor. The differences in the sequence of mouse and human AhR ligand binding domain may explain this observation, being most of them in the additional sites observed. Preferences of the evaluated ligands for the different sites are reported and discussed in view of their functional role.
Journal of Medicinal Chemistry, 2009
The Aryl Hydrocarbon Receptor (AhR) is a ligand-activated transcription factor; the AhR Per-AhR/Arnt-Sim (PAS) domain binds ligands. We developed homology models of the AhR PAS domain to characterize previously observed intra-and inter-species differences in ligand binding using Molecular Docking. In silico structure-based virtual ligand screening using our model resulted in the identification of pinocembrin and 5-hydroxy-7-methoxyflavone, which promoted nuclear translocation and transcriptional activation of AhR and AhR-dependent induction of endogenous target genes.
Identification of the Ah-Receptor Structural Determinants for Ligand Preferences
Toxicological Sciences, 2012
The aryl hydrocarbon receptor (AHR) is a transcription factor that responds to diverse ligands and plays a critical role in toxicology, immune function, and cardiovascular physiology. The structural basis of the AHR for ligand promiscuity and preferences is critical for understanding AHR function. Based on the structure of a closely related protein HIF2α, we modeled the AHR ligand binding domain (LBD) bound to 2,3,7,8-tet rachlorodibenzo-p-dioxin (TCDD) and benzo(a)pyrene (BaP) and identified residues that control ligand preferences by shape and H-bond potential. Mutations to these residues, particularly Q377 and G298, resulted in robust and opposite changes in the potency of TCDD and BaP and up to a 20-fold change in the ratio of TCDD/BaP efficacy. The model also revealed a flexible "belt" structure; molecular dynamic (MD) simulation suggested that the "belt" and several other structural elements in the AHR-LBD are more flexible than HIF2α and likely contribute to ligand promiscuity. Molecular docking of TCDD congeners to a model of human AHR-LBD ranks their binding affinity similar to experimental ranking of their toxicity. Our study reveals key structural basis for prediction of toxicity and understanding the AHR signaling through diverse ligands.
Molecular Pharmacology, 2004
The aryl hydrocarbon receptor (AhR) functions as a ligand-activated transcription factor that is responsible for the regulation of several response genes, of which the best characterized is the CYP1A1 gene. The present study was undertaken to elucidate the mechanism of activation of the AhR by omeprazole (OME), 2-mercapto-5-methoxybenzimidazole (MMB), and primaquine (PRQ), compounds that have previously been reported to induce CYP1A1 expression but that are not typical AhR ligands. All compounds caused a significant increase in luciferase activity in rat H4IIE and human HepG2 hepatoma cells transfected with a Gal4-AhR construct and the corresponding Gal4-Luc reporter gene. Furthermore, MMB and PRQ, but not OME, were capable of transforming cytosolic AhR to a DNA-binding form and displacing AhR-bound [ 3 H]TCDD in rat hepatic cytosol in vitro. By performing site-directed mutagenesis of residues in the ligand-binding domain of the Gal4-AhR, a construct containing a Y320F substitution was found to be resistant to activation by OME, MMB, and PRQ, but not by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Comparable affinities of [ 3 H]TCDD-binding to the wild-type and the Y320F mutant Gal4-proteins, expressed in human embryonic kidney 293 cells, were obtained in the ligand-binding assay. In contrast, the competition of receptor-bound [ 3 H]TCDD by PRQ was absent from Gal4-Y320F but not from Gal4-AhR cell extracts. The results of this study confirm that MMB and PRQ are low-affinity ligands for the AhR and suggest that high-and low-affinity ligands interact with different residues of the AhR ligand-binding pocket. In addition, the data presented here indicate that Tyr 320 plays an important role in AhR activation. The aryl hydrocarbon receptor (AhR) is a member of the growing family of basic helix-loop-helix Per-Arnt-Sim (PAS) transcription factors whose members play key roles in development, adaptation to hypoxia, control of circadian rhythmicity, and metabolism of xenobiotic compounds (Gu et al., 2000). Mechanistically, the AhR functions as a ligand-activated transcription factor that is responsible for the transcriptional activation of several AhR-responsive genes (see reviews by Hankinson, 1995; Whitlock, 1999). A variety of environmental pollutants (e.g., polycyclic aromatic hydrocarbons and halogenated aromatic hydrocarbons) are high-affinity ligands for the AhR. These ligands, including the prototype AhR ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), are characterized by being planar, aromatic, and hydrophobic molecules, fitting into a ligand-binding pocket with a maximal dimension of 14 ϫ 12 ϫ 5 Å. In addition, electronic and thermodynamic properties of the ligand have been shown to be critical for favorable interactions between the ligand and the receptor (Gillner et al., 1993; Kafafi et al., 1993; Waller and McKinney, 1995). Recent identification and characterization of novel AhR ligands or AhR activators (reviewed by Denison and Nagy, 2003), which have physicochemical and structural properties that deviate significantly from these typical AhR ligands, challenge the currently defined ligand-binding model. The structural diversity of these atypical AhR ligands/activators is clearly evident by comparison of the molecular structures of,
Molecular Immunology
Activation-induced deaminase (AID) is expressed in activated B lymphocytes and initiates somatic hypermutation and class switch recombination. To determine if different stimuli affect the expression and function of AID, we monitored AID activity in murine B cells stimulated ex vivo with various ligands. AID was rapidly expressed at both the RNA and protein levels following stimulation with LPS, LPS plus IL-4, and anti-CD40 plus IL-4, but was delayed after stimulation with anti-IgM plus IL-4. By day 4, AID was expressed in all groups; however, cells stimulated with anti-IgM plus IL-4 did not undergo switch recombination. These cells expressed normal levels of γ1 germline transcripts, implying that the γ1 switch region was accessible. Furthermore, switching was suppressed by the addition of anti-IgM to cells stimulated with LPS plus IL-4 or anti-CD40 plus IL-4, even though AID was expressed. The lack of class switch recombination could be reversed by inhibition of phosphatidylinositol 3-kinase (PI3K). This suggests that activation through the B cell receptor induces PI3K, which interferes with the function of AID.
2008
The aryl hydrocarbon receptor (AHR) is a ligand-activated member of the bHLH-PAS family of transcription factors. Members of this family include HIF1a, EPAS, and SIM, which are involved in hypoxia and nervous system development. Another member of this family, aryl hydrocarbon nuclear translocator (ARNT), is the dimerization partner for the AHR. The AHR is often classified as a sensor of a wide range of xenobiotics, leading to induction of xenobiotic metabolism through enhanced expression of phase I/II enzymes. The environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a prototypic ligand for the AHR and is often used to study the effects of prolonged AHR activation. Rodent exposure to TCDD results in a plethora of toxic effects, including wasting syndrome, tumor promotion, developmental defects, and liver toxicity (reviewed in Vanden Heuvel and
A model for recognition of polychlorinated dibenzo- p -dioxins by the aryl hydrocarbon receptor
European Journal of Biochemistry, 2002
Ligand binding by the aryl hydrocarbon receptor (AhR), a member of the bHLH-PAS family of transcriptional regulatory proteins, has been mapped to a region within the second ÔPASÕ domain, a conserved sequence motif ®rst discovered in the Per-ARNT-Sim family of proteins. In addition to the bacterial photoactive yellow protein (PYP), which had been proposed as a structural prototype for the three dimensional fold of PAS domains, two crystal structures of the PAS domain have recently been determined: the human potassium channel HERG and the heme binding domain of the bacterial O 2 sensing FixL protein. The three structures reveal a highly conserved structural framework in evolutionary rather distant PAS domains, provide a more general view of how these domains can recognize their ligands and suggest a structure±function relationship that we exploited to build a three-dimensional model of the ligand binding domain (LBD) of the mouse aryl hydrocarbon receptor (mAhR). The model allowed us to putatively identify the residues responsible for the recognition of polychlorinated dibenzop-dioxins (PCDDs) by AhR receptors and to formulate an hypothesis on the signal transduction mechanism.
The NIH mandate An open access landmark
College Research Libraries News, 2008
An open access landmark D ecember 26, 2007, was a historic date for the international movement supporting public access to taxpayerfunded research. With the Consolidated Appropriations Act of 2007 (H.R. 2764) being signed into law, the National Institutes of Health (NIH) became the first U.S. federal agency required to make the results of its funded research freely ac cessible online to the public.