An in silico to in vivo approach identifies retinoid-X receptor activating tert-butylphenols used in food contact materials
Abstract The potential for food contact chemicals to disrupt genetic programs in development and metabolism raises concerns. Nuclear receptors (NRs) control many of these programs, and the retinoid-X receptor (RXR) is a DNA-binding partner for one-third of the NRs. RXR disruption could generate adve...
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Nature Portfolio
2025-07-01
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| Online Access: | https://doi.org/10.1038/s41598-025-09244-z |
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| author | Brenda J. Mengeling Azhagiya Singam Ettayapuram Ramaprasad Martyn T. Smith Dania Turkieh Nicole C. Kleinstreuer Kamel Mansouri Kathleen A. Durkin Michele A. La Merrill J. David Furlow |
| author_facet | Brenda J. Mengeling Azhagiya Singam Ettayapuram Ramaprasad Martyn T. Smith Dania Turkieh Nicole C. Kleinstreuer Kamel Mansouri Kathleen A. Durkin Michele A. La Merrill J. David Furlow |
| author_sort | Brenda J. Mengeling |
| collection | DOAJ |
| description | Abstract The potential for food contact chemicals to disrupt genetic programs in development and metabolism raises concerns. Nuclear receptors (NRs) control many of these programs, and the retinoid-X receptor (RXR) is a DNA-binding partner for one-third of the NRs. RXR disruption could generate adverse outcomes in several NR pathways. We used machine learning and other in silico methods to identify RXR-interacting candidates from a list of over 57,000 chemicals. Butylphenols comprised the largest, high-probability, structural group (58 compounds); several are food contact chemicals with widespread commercial use. In vitro ToxCast data suggested that bulky, aliphatic substitution at C4 of 2,6-di-tert-butylphenol facilitated RXR activation. We tested six butylphenols with increasing bulk at C4 in vivo for their ability to disrupt thyroid hormone receptor (TR) signaling, using an integrated luciferase reporter driven by TR-RXR binding and quantifiable morphological changes in a Xenopus laevis precocious metamorphosis assay. Three tert-butylphenols potentiated TH action at nanomolar concentrations. Molecular modeling showed the three positives formed more frequent, stable interactions with RXRα, and bulkiness at C4 increased steric complementarity with the RXR ligand-binding pocket. Our findings establish a paradigm for machine learning coupled with a convenient, in vivo validation approach to identify chemicals interacting with RXR-NR-controlled genetic pathways. |
| format | Article |
| id | doaj-art-a4a52cac9c8b4c39b1137e8567d88994 |
| institution | DOAJ |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-a4a52cac9c8b4c39b1137e8567d889942025-08-20T03:05:26ZengNature PortfolioScientific Reports2045-23222025-07-0115111410.1038/s41598-025-09244-zAn in silico to in vivo approach identifies retinoid-X receptor activating tert-butylphenols used in food contact materialsBrenda J. Mengeling0Azhagiya Singam Ettayapuram Ramaprasad1Martyn T. Smith2Dania Turkieh3Nicole C. Kleinstreuer4Kamel Mansouri5Kathleen A. Durkin6Michele A. La Merrill7J. David Furlow8Department of Neurobiology, Physiology, and Behavior, College of Biological Sciences, University of CaliforniaMolecular Graphics and Computation Facility, College of Chemistry, University of CaliforniaDivision of Environmental Health Sciences, School of Public Health, University of CaliforniaDepartment of Neurobiology, Physiology, and Behavior, College of Biological Sciences, University of CaliforniaNational Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health SciencesNational Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health SciencesMolecular Graphics and Computation Facility, College of Chemistry, University of CaliforniaDepartment of Environmental Toxicology, College of Agricultural and Environmental Studies, University of CaliforniaDepartment of Neurobiology, Physiology, and Behavior, College of Biological Sciences, University of CaliforniaAbstract The potential for food contact chemicals to disrupt genetic programs in development and metabolism raises concerns. Nuclear receptors (NRs) control many of these programs, and the retinoid-X receptor (RXR) is a DNA-binding partner for one-third of the NRs. RXR disruption could generate adverse outcomes in several NR pathways. We used machine learning and other in silico methods to identify RXR-interacting candidates from a list of over 57,000 chemicals. Butylphenols comprised the largest, high-probability, structural group (58 compounds); several are food contact chemicals with widespread commercial use. In vitro ToxCast data suggested that bulky, aliphatic substitution at C4 of 2,6-di-tert-butylphenol facilitated RXR activation. We tested six butylphenols with increasing bulk at C4 in vivo for their ability to disrupt thyroid hormone receptor (TR) signaling, using an integrated luciferase reporter driven by TR-RXR binding and quantifiable morphological changes in a Xenopus laevis precocious metamorphosis assay. Three tert-butylphenols potentiated TH action at nanomolar concentrations. Molecular modeling showed the three positives formed more frequent, stable interactions with RXRα, and bulkiness at C4 increased steric complementarity with the RXR ligand-binding pocket. Our findings establish a paradigm for machine learning coupled with a convenient, in vivo validation approach to identify chemicals interacting with RXR-NR-controlled genetic pathways.https://doi.org/10.1038/s41598-025-09244-zRetinoid-X receptorMolecular dockingEnvironmental exposureFood contact chemicalsMachine learningArtificial intelligence |
| spellingShingle | Brenda J. Mengeling Azhagiya Singam Ettayapuram Ramaprasad Martyn T. Smith Dania Turkieh Nicole C. Kleinstreuer Kamel Mansouri Kathleen A. Durkin Michele A. La Merrill J. David Furlow An in silico to in vivo approach identifies retinoid-X receptor activating tert-butylphenols used in food contact materials Scientific Reports Retinoid-X receptor Molecular docking Environmental exposure Food contact chemicals Machine learning Artificial intelligence |
| title | An in silico to in vivo approach identifies retinoid-X receptor activating tert-butylphenols used in food contact materials |
| title_full | An in silico to in vivo approach identifies retinoid-X receptor activating tert-butylphenols used in food contact materials |
| title_fullStr | An in silico to in vivo approach identifies retinoid-X receptor activating tert-butylphenols used in food contact materials |
| title_full_unstemmed | An in silico to in vivo approach identifies retinoid-X receptor activating tert-butylphenols used in food contact materials |
| title_short | An in silico to in vivo approach identifies retinoid-X receptor activating tert-butylphenols used in food contact materials |
| title_sort | in silico to in vivo approach identifies retinoid x receptor activating tert butylphenols used in food contact materials |
| topic | Retinoid-X receptor Molecular docking Environmental exposure Food contact chemicals Machine learning Artificial intelligence |
| url | https://doi.org/10.1038/s41598-025-09244-z |
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