Comparative In Vitro and In Silico Analysis of the Selectivity of Indirubin as a Human Ah Receptor Agonist
Open accessAbstract
The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that modulates gene expression following its binding and activation by structurally diverse chemicals. Species differences in AhR functionality have been observed, with the mouse AhR (mAhR) and human AhR (hAhR) exhibiting significant differences in ligand binding, coactivator recruitment, gene expression and response. While the AhR agonist indirubin (IR) is a more potent activator of hAhR-dependent gene expression than the prototypical ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), it is a significantly less potent activator of the mAhR. DNA binding analysis confirmed the greater potency/efficacy of IR in stimulating transformation/DNA binding of the hAhR in vitro and domain-swapping experiments demonstrated that the enhanced response to IR was primarily due to the hAhR ligand binding domain (LBD). Site-directed mutagenesis and functional analysis studies revealed that mutation of H326 and A349 in the mAhR LBD to the corresponding residues in the hAhR LBD significantly increased the potency of IR. Since these mutations had no significant effect on ligand binding, these residues likely contribute to an enhanced efficiency of transformation/DNA binding by IR-bound hAhR. Molecular docking to mAhR LBD homology models further elucidated the different roles of the A375V mutation in TCDD and IR binding, as revealed by [3H]TCDD competitive binding results. These results demonstrate the differential binding of structurally diverse ligands within the LBD of a given AhR and confirm that amino acid differences within the LBD of AhRs contribute to significant species differences in ligand response.
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Recent docking studies allowed prediction of the binding modes of several AhR ligands and led to the discovery of novel AhR agonists and SAhRMs.
“On the basis of these novel approaches, recent docking studies not only allowed prediction of the binding modes of several AhR ligands but also led to the discovery of novel AhR agonists and SAhRMs25,27–30.”
From Modeling the binding of diverse ligands within the Ah receptor ligand binding domain (2019) · cites this paper as [27]
The Results (§2.5) and Discussion (§3; page unavailable in our copy) report that molecular docking predicted binding geometries for indirubin and TCDD in mouse and human AhR. They do not report that docking led to the discovery of novel AhR agonists or SAhRMs. (LLM, conf=0.88)
Experimental — accuracy not yet measuredIndirubin demonstrated the strongest binding to AHR among these ligands, consistent with previous reports.
“Nevertheless, Indirubin demonstrated the strongest binding to AHR among these ligands, consistent with previous reports45,46.”
From Structural basis for the ligand-dependent activation of heterodimeric AHR-ARNT complex (2025) · cites this paper as [46]
The Discussion (page not provided) says indirubin may have higher binding affinity for human AhR than TCDD, consistent with competitive-binding results. It does not establish that indirubin binds most strongly among the citing sentence’s unspecified set of ligands, and it presents the comparison as a suggestion rather than a definitive ranking. (LLM, conf=0.86)
Experimental — accuracy not yet measured
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de Tollenaere, M., Zanchetta, C., Durduret, A., Martinez, J., Portet, B., Tiguemounine, J., Scandolera, A., & Reynaud, R. (2025) · Cosmetics · doi:10.3390/cosmetics12060237
In vitro pharmacological profiling of ITE amide bioisosteric aryl hydrocarbon receptor agonist
Dvořák, Z., Grycová, A., Vrzal, R., Soural, M., Zůvalová, I., & Přikryl, J. (2026) · Frontiers in Pharmacology · doi:10.3389/fphar.2026.1931941
- Authors
- Faber, S. C., Soshilov, A. A., Giani Tagliabue, S., Bonati, L., & Denison, M. S.
- Affiliations
- University of California, Davis (US)
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
- University of Milano-Bicocca (IT)
- Corresponding author
- Denison, Michael S.
- Venue
- International Journal of Molecular Sciences
- Publisher
- MDPI AG
- Published
- 2018-09-10
- Volume
- 19
- Issue
- 9
- Pages
- 2692
- ISSN
- 1422-0067 (ISSN-L)
- PMC
- PMC6165432
- OpenAlex
- W2891255649
- Cited by
- 36
- References
- 56
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 6 · 2023: 3 · 2022: 8 · 2021: 5 · 2020: 4 · 2019: 4 · 2018: 1
- FWCI
- 1.73
- Type
- journal article
- Language
- en
- Open access
- gold
- dx.doi.org
- Licence
- Locations
- International Journal of Molecular Sciences (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- BOA (University of Milano-Bicocca) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Institute of Environmental Health Sciences (R01ES007685, P42ES004699, T32ES007059)
- Topics
- Physical Sciences › Environmental Science › Health, Toxicology and Mutagenesis › Toxic Organic Pollutants Impact
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Pharmacology › Pharmacogenetics and Drug Metabolism
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Carcinogens and Genotoxicity Assessment
- Keywords
- indirubin, aryl hydrocarbon receptor, ligand-binding domain, ligand binding affinity, DNA binding, TCDD, molecular docking, homology model, competitive binding
- MeSH terms
- Polychlorinated Dibenzodioxins, Animals, Binding Sites, Computer Simulation, Humans, Indoles, Models, Molecular, Protein Binding, Species Specificity, Mutagenesis, Site-Directed, Protein Structure, Secondary, Receptors, Aryl Hydrocarbon, Mice, Basic Helix-Loop-Helix Transcription Factors, Basic Helix-Loop-Helix Proteins, Molecular Docking Simulation, In Vitro Techniques
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