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Modeling of the Aryl Hydrocarbon Receptor (AhR) Ligand Binding Domain and Its Utility in Virtual Ligand Screening to Predict New AhR Ligands

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Cancer Biology Laboratory
§ Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon 97331
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
*To whom correspondence should be addressed. Phone: 001-541-737-1799 E-mail: [email protected]
#Equally contributed to this work.
Cite this: J. Med. Chem. 2009, 52, 18, 5635–5641
Publication Date (Web):August 31, 2009
Copyright © 2009 American Chemical Society

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    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 interspecies 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.

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    Binding energy calculations from molecular docking of natural compounds database into mouse AhR ligand binding domain and activation of AhR transcription by compounds identified by virtual ligand screening to bind the AhR ligand binding pocket (Supplemental Table 1). 6-Hydroxy-7-methoxyflavone is an AhR antagonist (Supplemental Figure 1). Semi-quantitative polymerase chain reaction (Experimental Methods). This material is available free of charge via the Internet at

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