Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms
Open accessAbstract
Molecular modeling has given important contributions to elucidation of the main stages in the AhR signal transduction pathway. Despite the lack of experimentally determined structures of the AhR functional domains, information derived from homologous systems has been exploited for modeling their structure and interactions. Homology models of the AhR PASB domain have provided information on the binding cavity and contributed to elucidate species-specific differences in ligand binding. Molecular Docking simulations of the ligand binding process have given insights into differences in binding of diverse agonists, antagonists, and selective AhR modulators, and their application to virtual screening of large databases of compounds have allowed identification of novel AhR ligands. Recently available structural information on protein-protein and protein-DNA complexes of other bHLH-PAS systems has opened the way for modeling the AhR:ARNT dimer structure and investigating the mechanisms of AhR transformation and DNA binding. Future research directions should include simulation of the protein dynamics to obtain a more reliable description of intermolecular interactions involved in signal transmission.
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Structural models developed by homology modeling allowed characterization of the binding cavity and prediction of specific residues that play a critical role in ligand binding.
“Such studies have been hampered for many years by the lack of an experimentally determined three-dimensional structure of the AhR LBD, however, structural models developed by Homology Modeling allowed characterization of the binding cavity and prediction of specific residues that play a critical role in ligand binding [as reviewed in19].”
From Modeling the binding of diverse ligands within the Ah receptor ligand binding domain (2019) · cites this paper as [19]
Employment of PAS-B structures of HIF-2α in complex with ligands as templates greatly improved the quality of the modeled binding site, and inclusion of receptor flexibility in docking enabled better description of the binding event.
“Not only did the employment of PAS-B structures of the homologous HIF-2α protein in complex with ligands as templates for modeling greatly improve the quality of the modeled binding site, but the inclusion of a certain degree of receptor flexibility in docking calculations enabled us and other investigators to better describe the binding event19,24–26.”
From Modeling the binding of diverse ligands within the Ah receptor ligand binding domain (2019) · cites this paper as [19]
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Modeling the binding of diverse ligands within the Ah receptor ligand binding domain
Giani Tagliabue, S., Faber, S. C., Motta, S., Denison, M. S., & Bonati, L. (2019) · Scientific Reports · doi:10.1038/s41598-019-47138-z · Cited by 106 · see citing works
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Self-citationIn vitro toxicity and in silico docking analysis of two novel selective AH-receptor modulators
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- Authors
- Bonati, L., Corrada, D., Giani Tagliabue, S., & Motta, S.
- Affiliations
- University of Milano-Bicocca (IT)
- Corresponding author
- Bonati, Laura
- Venue
- Current Opinion in Toxicology
- Publisher
- Elsevier BV
- Published
- 2017-02
- Volume
- 2
- Pages
- 42-49
- ISSN
- 2468-2020 (ISSN-L)
- PMC
- PMC5421400
- OpenAlex
- W2585100782
- Cited by
- 27
- References
- 85
- Citations by year
- 2024: 1 · 2023: 3 · 2022: 4 · 2021: 3 · 2020: 4 · 2019: 6 · 2018: 5 · 2017: 1
- FWCI
- 0.44
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Current Opinion in Toxicology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- BOA (University of Milano-Bicocca) (submittedVersion)
- Funders
- National Institute of Environmental Health Sciences (R01ES07685)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Environmental Science › Health, Toxicology and Mutagenesis › Toxic Organic Pollutants Impact
- Keywords
- aryl hydrocarbon receptor, homology modeling, ligand binding, virtual screening, bHLH-PAS proteins, protein-DNA complex, protein-protein interaction, DNA binding, protein dynamics, molecular docking
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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