Unveiling the hidden interactome of CRBN molecular glues
Abstract Induced proximity by molecular glues refers to strategies that leverage the recruitment of proteins to facilitate their modification, regulation or degradation. As prospective design of molecular glues remains challenging, unbiased discovery methods are necessary to discover new chemical ta...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-62099-w |
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| author | Kheewoong Baek Rebecca J. Metivier Shourya S. Roy Burman Jonathan W. Bushman Hojong Yoon Ryan J. Lumpkin Julia K. Ryan Dinah M. Abeja Megha Lakshminarayan Hong Yue Samuel Ojeda Yuan Xiong Jianwei Che Alyssa L. Verano Anna M. Schmoker Nathanael S. Gray Katherine A. Donovan Eric S. Fischer |
| author_facet | Kheewoong Baek Rebecca J. Metivier Shourya S. Roy Burman Jonathan W. Bushman Hojong Yoon Ryan J. Lumpkin Julia K. Ryan Dinah M. Abeja Megha Lakshminarayan Hong Yue Samuel Ojeda Yuan Xiong Jianwei Che Alyssa L. Verano Anna M. Schmoker Nathanael S. Gray Katherine A. Donovan Eric S. Fischer |
| author_sort | Kheewoong Baek |
| collection | DOAJ |
| description | Abstract Induced proximity by molecular glues refers to strategies that leverage the recruitment of proteins to facilitate their modification, regulation or degradation. As prospective design of molecular glues remains challenging, unbiased discovery methods are necessary to discover new chemical targets. Here we establish a high throughput affinity proteomics workflow leveraging E3 ligase activity-impaired CRBN-DDB1ΔB in cell lysates for the unbiased identification of molecular glue targets. By mapping the interaction landscape of CRBN-binding molecular glues, we unveil 298 protein targets and demonstrate the utility of enrichment methods for identifying targets overlooked by established methods. We use a computational workflow to estimate target confidence and perform biochemical and structural validation of uncharacterized neo-substrates. We further identify a lead compound for the previously untargeted non-zinc finger PPIL4 through a biochemical screen. Our study provides a comprehensive inventory of targets chemically recruited to CRBN and delivers a robust and scalable workflow for identifying drug-induced protein interactions in cell lysates. |
| format | Article |
| id | doaj-art-fa33bdb0c5e24848b1d1deaf0ca6b4bf |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-fa33bdb0c5e24848b1d1deaf0ca6b4bf2025-08-20T04:02:54ZengNature PortfolioNature Communications2041-17232025-07-0116111810.1038/s41467-025-62099-wUnveiling the hidden interactome of CRBN molecular gluesKheewoong Baek0Rebecca J. Metivier1Shourya S. Roy Burman2Jonathan W. Bushman3Hojong Yoon4Ryan J. Lumpkin5Julia K. Ryan6Dinah M. Abeja7Megha Lakshminarayan8Hong Yue9Samuel Ojeda10Yuan Xiong11Jianwei Che12Alyssa L. Verano13Anna M. Schmoker14Nathanael S. Gray15Katherine A. Donovan16Eric S. Fischer17Department of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Medical Oncology, Dana-Farber Cancer InstituteDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford Medical School, Stanford UniversityDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonDepartment of Cancer Biology, Dana-Farber Cancer Institute, BostonAbstract Induced proximity by molecular glues refers to strategies that leverage the recruitment of proteins to facilitate their modification, regulation or degradation. As prospective design of molecular glues remains challenging, unbiased discovery methods are necessary to discover new chemical targets. Here we establish a high throughput affinity proteomics workflow leveraging E3 ligase activity-impaired CRBN-DDB1ΔB in cell lysates for the unbiased identification of molecular glue targets. By mapping the interaction landscape of CRBN-binding molecular glues, we unveil 298 protein targets and demonstrate the utility of enrichment methods for identifying targets overlooked by established methods. We use a computational workflow to estimate target confidence and perform biochemical and structural validation of uncharacterized neo-substrates. We further identify a lead compound for the previously untargeted non-zinc finger PPIL4 through a biochemical screen. Our study provides a comprehensive inventory of targets chemically recruited to CRBN and delivers a robust and scalable workflow for identifying drug-induced protein interactions in cell lysates.https://doi.org/10.1038/s41467-025-62099-w |
| spellingShingle | Kheewoong Baek Rebecca J. Metivier Shourya S. Roy Burman Jonathan W. Bushman Hojong Yoon Ryan J. Lumpkin Julia K. Ryan Dinah M. Abeja Megha Lakshminarayan Hong Yue Samuel Ojeda Yuan Xiong Jianwei Che Alyssa L. Verano Anna M. Schmoker Nathanael S. Gray Katherine A. Donovan Eric S. Fischer Unveiling the hidden interactome of CRBN molecular glues Nature Communications |
| title | Unveiling the hidden interactome of CRBN molecular glues |
| title_full | Unveiling the hidden interactome of CRBN molecular glues |
| title_fullStr | Unveiling the hidden interactome of CRBN molecular glues |
| title_full_unstemmed | Unveiling the hidden interactome of CRBN molecular glues |
| title_short | Unveiling the hidden interactome of CRBN molecular glues |
| title_sort | unveiling the hidden interactome of crbn molecular glues |
| url | https://doi.org/10.1038/s41467-025-62099-w |
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