Unbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics
Abstract Molecular glue degraders (MGDs) are small molecules that co-opt the ubiquitin-proteasome system to induce degradation of target proteins, including those considered undruggable. Their discovery remains challenging due to the lack of rational design strategies and limited throughput of unbia...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-08-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-62829-0 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849226154309844992 |
|---|---|
| author | Martin Steger Gisele Nishiguchi Qiong Wu Bjoern Schwalb Bachuki Shashikadze Kevin McGowan Marisa Actis Anup Aggarwal Zhe Shi Jeanine Price Anand Mayasundari Lei Yang Anastasia H. Bednarz Sophie Machata Tobias Graef Denis Bartoschek Vadim Demichev Uli Ohmayer Jun Yang Henrik Daub Zoran Rankovic |
| author_facet | Martin Steger Gisele Nishiguchi Qiong Wu Bjoern Schwalb Bachuki Shashikadze Kevin McGowan Marisa Actis Anup Aggarwal Zhe Shi Jeanine Price Anand Mayasundari Lei Yang Anastasia H. Bednarz Sophie Machata Tobias Graef Denis Bartoschek Vadim Demichev Uli Ohmayer Jun Yang Henrik Daub Zoran Rankovic |
| author_sort | Martin Steger |
| collection | DOAJ |
| description | Abstract Molecular glue degraders (MGDs) are small molecules that co-opt the ubiquitin-proteasome system to induce degradation of target proteins, including those considered undruggable. Their discovery remains challenging due to the lack of rational design strategies and limited throughput of unbiased proteome-wide screening approaches. To address this gap, we develop a high-throughput proteomics platform based on label-free, data-independent acquisition mass spectrometry (DIA-MS), enabling integrated proteomics and ubiquitinomics profiling. Screening a diverse set of 100 cereblon (CRBN)-recruiting ligands on this platform leads to identification of a broad array of novel degraders and neosubstrates. Subsequent hit validation and structure-degradation relationship analyses guided by global proteomics reveal highly selective and potent phenyl glutarimide-based degraders targeting previously uncharacterized neosubstrates such as KDM4B, G3BP2 and VCL; none of which contain the classical CRBN β-hairpin degron. These findings underscore the power of unbiased high-throughput proteomics in MGD drug discovery and reveal a substantially expanded CRBN neosubstrate landscape beyond that defined by classical immunomodulatory imid drugs (IMiDs). |
| format | Article |
| id | doaj-art-a6fa43e264d645fbb54f04e431c2d938 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-a6fa43e264d645fbb54f04e431c2d9382025-08-24T11:38:46ZengNature PortfolioNature Communications2041-17232025-08-0116111610.1038/s41467-025-62829-0Unbiased mapping of cereblon neosubstrate landscape by high-throughput proteomicsMartin Steger0Gisele Nishiguchi1Qiong Wu2Bjoern Schwalb3Bachuki Shashikadze4Kevin McGowan5Marisa Actis6Anup Aggarwal7Zhe Shi8Jeanine Price9Anand Mayasundari10Lei Yang11Anastasia H. Bednarz12Sophie Machata13Tobias Graef14Denis Bartoschek15Vadim Demichev16Uli Ohmayer17Jun Yang18Henrik Daub19Zoran Rankovic20NEOsphere Biotechnologies GmbHDepartment of Chemical Biology and Therapeutics, St. Jude Children’s Research HospitalDepartment of Surgery, St. Jude Children’s Research HospitalNEOsphere Biotechnologies GmbHNEOsphere Biotechnologies GmbHDepartment of Chemical Biology and Therapeutics, St. Jude Children’s Research HospitalDepartment of Chemical Biology and Therapeutics, St. Jude Children’s Research HospitalDepartment of Chemical Biology and Therapeutics, St. Jude Children’s Research HospitalDepartment of Chemical Biology and Therapeutics, St. Jude Children’s Research HospitalDepartment of Chemical Biology and Therapeutics, St. Jude Children’s Research HospitalDepartment of Chemical Biology and Therapeutics, St. Jude Children’s Research HospitalDepartment of Chemical Biology and Therapeutics, St. Jude Children’s Research HospitalNEOsphere Biotechnologies GmbHNEOsphere Biotechnologies GmbHNEOsphere Biotechnologies GmbHNEOsphere Biotechnologies GmbHDepartment of Biochemistry, Charité – Universitätsmedizin BerlinNEOsphere Biotechnologies GmbHDepartment of Surgery, St. Jude Children’s Research HospitalNEOsphere Biotechnologies GmbHDepartment of Chemical Biology and Therapeutics, St. Jude Children’s Research HospitalAbstract Molecular glue degraders (MGDs) are small molecules that co-opt the ubiquitin-proteasome system to induce degradation of target proteins, including those considered undruggable. Their discovery remains challenging due to the lack of rational design strategies and limited throughput of unbiased proteome-wide screening approaches. To address this gap, we develop a high-throughput proteomics platform based on label-free, data-independent acquisition mass spectrometry (DIA-MS), enabling integrated proteomics and ubiquitinomics profiling. Screening a diverse set of 100 cereblon (CRBN)-recruiting ligands on this platform leads to identification of a broad array of novel degraders and neosubstrates. Subsequent hit validation and structure-degradation relationship analyses guided by global proteomics reveal highly selective and potent phenyl glutarimide-based degraders targeting previously uncharacterized neosubstrates such as KDM4B, G3BP2 and VCL; none of which contain the classical CRBN β-hairpin degron. These findings underscore the power of unbiased high-throughput proteomics in MGD drug discovery and reveal a substantially expanded CRBN neosubstrate landscape beyond that defined by classical immunomodulatory imid drugs (IMiDs).https://doi.org/10.1038/s41467-025-62829-0 |
| spellingShingle | Martin Steger Gisele Nishiguchi Qiong Wu Bjoern Schwalb Bachuki Shashikadze Kevin McGowan Marisa Actis Anup Aggarwal Zhe Shi Jeanine Price Anand Mayasundari Lei Yang Anastasia H. Bednarz Sophie Machata Tobias Graef Denis Bartoschek Vadim Demichev Uli Ohmayer Jun Yang Henrik Daub Zoran Rankovic Unbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics Nature Communications |
| title | Unbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics |
| title_full | Unbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics |
| title_fullStr | Unbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics |
| title_full_unstemmed | Unbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics |
| title_short | Unbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics |
| title_sort | unbiased mapping of cereblon neosubstrate landscape by high throughput proteomics |
| url | https://doi.org/10.1038/s41467-025-62829-0 |
| work_keys_str_mv | AT martinsteger unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT giselenishiguchi unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT qiongwu unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT bjoernschwalb unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT bachukishashikadze unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT kevinmcgowan unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT marisaactis unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT anupaggarwal unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT zheshi unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT jeanineprice unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT anandmayasundari unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT leiyang unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT anastasiahbednarz unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT sophiemachata unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT tobiasgraef unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT denisbartoschek unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT vadimdemichev unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT uliohmayer unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT junyang unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT henrikdaub unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics AT zoranrankovic unbiasedmappingofcereblonneosubstratelandscapebyhighthroughputproteomics |