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

Bisson, William H.; Koch, Daniel C.; O’Donnell, Edmond F.; Khalil, Sammy M.; Kerkvliet, Nancy I.; Tanguay, Robert L.; Abagyan, Ruben; Kolluri, Siva Kumar

doi:10.1021/jm900199u

Cited by 151Computational Drug Discovery MethodsToxic Organic Pollutants ImpactProtein Interaction Studies and Fluorescence Analysis

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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Bisson, William H., Koch, Daniel C., O’Donnell, Edmond F., Khalil, Sammy M., Kerkvliet, Nancy I., Tanguay, Robert L., Abagyan, Ruben, Kolluri, Siva Kumar·2009·Journal of Medicinal Chemistry

DOI 10.1021/jm900199uPMC PMC3289977

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Abstract

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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Homology models of the AHR ligand-binding domain exist for only a small number of species.
“homology models of the AHR ligand-binding domain (LBD) are available for only a few species.”
From Comparative Analysis of Homology Models of the Ah Receptor Ligand Binding Domain: Verification of Structure–Function Predictions by Site-Directed Mutagenesis of a Nonfunctional Receptor (2013) · cites this paper as [20]
The model-construction passage (section labeled Abstract; page not provided) describes AHR-LBD homology models for mouse, human, rat, and two zebrafish isoforms. That supports the existence of models for a small set of species, but the paper does not establish that models are available for only a few species overall. (LLM, conf=0.78)
Experimental — accuracy not yet measured
The absence of three-dimensional structure information for the AHR LBD has prevented detailed molecular analysis of AHR ligand binding mechanisms.
“While the lack of any three-dimensional structure information on the AHR ligand binding domain (LBD) has prevented detailed molecular analysis of the mechanisms of AHR ligand binding, we and others have used the availability of crystal and nuclear magnetic resonance (NMR) structures of homologous protein domains to develop homology models of the AHR LBD for such analysis (12,17-20).”
From Comparative Analysis of Homology Models of the Ah Receptor Ligand Binding Domain: Verification of Structure–Function Predictions by Site-Directed Mutagenesis of a Nonfunctional Receptor (2013) · cites this paper as [20]
The Experimental Section (Homology Modeling; page unavailable) says the authors used an NMR structure of a homologous domain as a template for AhR-LBD models, supporting the need to model its structure. The paper does not say that the lack of an AhR-LBD structure prevented detailed molecular analysis; its Abstract instead reports structural analyses made using those models. (LLM, conf=0.78)
Experimental — accuracy not yet measured
Experimental confirmation of predicted binding modes for TCDD and other ligands in the AHR LBD is generally lacking.
“While the binding modes of TCDD and other ligands within the AHR LBD of a given species (typically that of mouse or human AHR) have been predicted by these approaches, experimental confirmation of these proposed interactions are generally lacking.”
From Comparative Analysis of Homology Models of the Ah Receptor Ligand Binding Domain: Verification of Structure–Function Predictions by Site-Directed Mutagenesis of a Nonfunctional Receptor (2013) · cites this paper as [20]
The paper’s modeling discussion (page unavailable in our copy) predicts TCDD docking orientations in mouse, human, and zebrafish AhR-LBD models. It also reports cell-based tests of predicted ligands, but these test activity rather than directly confirming their proposed binding modes. The paper does not state the broader claim that experimental confirmation of such interactions is generally lacking. (LLM, conf=0.80)
Experimental — accuracy not yet measured
The authors and others have used crystal and NMR structures of homologous protein domains to build homology models of the AHR LBD.
“While the lack of any three-dimensional structure information on the AHR ligand binding domain (LBD) has prevented detailed molecular analysis of the mechanisms of AHR ligand binding, we and others have used the availability of crystal and nuclear magnetic resonance (NMR) structures of homologous protein domains to develop homology models of the AHR LBD for such analysis (12,17-20).”
From Comparative Analysis of Homology Models of the Ah Receptor Ligand Binding Domain: Verification of Structure–Function Predictions by Site-Directed Mutagenesis of a Nonfunctional Receptor (2013) · cites this paper as [20]
A prior homology modeling study proposed that zfAHR1a cannot bind TCDD because its internal cavity residues differ from zfAHR2, reducing cavity volume and changing pocket polarity.
“A previous homology modeling study suggested that the inability of zfAHR1a to bind TCDD was due to the presence of different internal cavity residues from those in zfAHR2 that decreased the volume and altered the polarity of the binding pocket itself (20).”
From Comparative Analysis of Homology Models of the Ah Receptor Ligand Binding Domain: Verification of Structure–Function Predictions by Site-Directed Mutagenesis of a Nonfunctional Receptor (2013) · cites this paper as [20]

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Authors: Bisson, W. H., Koch, D. C., O’Donnell, E. F., Khalil, S. M., Kerkvliet, N. I., Tanguay, R. L., Abagyan, R., & Kolluri, S. K.
Affiliations: Oregon State University (US)
Scripps Research Institute (US)
Corresponding author: Kolluri, Siva Kumar
ORCID: Bisson, William H.
O’Donnell, Edmond F.
Kerkvliet, Nancy I.
Tanguay, Robert L.
Abagyan, Ruben
Kolluri, Siva Kumar
Venue: Journal of Medicinal Chemistry
Publisher: American Chemical Society (ACS)
Published: 2009-08-31
Volume: 52
Issue: 18
Pages: 5635-5641
ISSN: 0022-2623 (ISSN-L)
1520-4804
DOI: 10.1021/jm900199u
PMC: PMC3289977
OpenAlex: W2170025066
Cited by: 149
References: 29
Citations by year: 2026: 5 · 2025: 4 · 2024: 8 · 2023: 7 · 2022: 13 · 2021: 15 · 2020: 8 · 2019: 11 · 2018: 9 · 2017: 11 · 2016: 8 · 2015: 7 · 2014: 9 · 2013: 7 · 2012: 7
FWCI: 8.38
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Journal of Medicinal Chemistry (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: National Institute of Environmental Health Sciences (R01ES016651, P30ES000210, P42ES016465, T32ES007060)
Topics: Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
Physical Sciences › Environmental Science › Health, Toxicology and Mutagenesis › Toxic Organic Pollutants Impact
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Interaction Studies and Fluorescence Analysis
Keywords: aryl hydrocarbon receptor, PAS domain, homology modeling, virtual ligand screening, structure-based drug design, pinocembrin, flavonoids, nuclear translocation, transcriptional activation, ligand specificity
MeSH terms: Amino Acid Sequence, Animals, Cell Line, Cell Nucleus, Drug Evaluation, Preclinical, Humans, Ligands, Models, Molecular, Molecular Sequence Data, Phylogeny, Protein Conformation, User-Computer Interface, Transcriptional Activation, Protein Structure, Tertiary, Receptors, Aryl Hydrocarbon, Protein Transport, Mice

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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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