A structure-based designed small molecule depletes hRpn13Pru and a select group of KEN box proteins
Abstract Proteasome subunit hRpn13 is partially proteolyzed in certain cancer cell types to generate hRpn13Pru by degradation of its UCHL5/Uch37-binding DEUBAD domain and retention of an intact proteasome- and ubiquitin-binding Pru domain. By using structure-guided virtual screening, we identify an...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2024-03-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-46644-7 |
| _version_ | 1797247183199666176 |
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| author | Xiuxiu Lu Monika Chandravanshi Venkata R. Sabbasani Snehal Gaikwad V. Keith Hughitt Nana Gyabaah-Kessie Bradley T. Scroggins Sudipto Das Wazo Myint Michelle E. Clapp Charles D. Schwieters Marzena A. Dyba Derek L. Bolhuis Janusz W. Koscielniak Thorkell Andresson Michael J. Emanuele Nicholas G. Brown Hiroshi Matsuo Raj Chari Deborah E. Citrin Beverly A. Mock Rolf E. Swenson Kylie J. Walters |
| author_facet | Xiuxiu Lu Monika Chandravanshi Venkata R. Sabbasani Snehal Gaikwad V. Keith Hughitt Nana Gyabaah-Kessie Bradley T. Scroggins Sudipto Das Wazo Myint Michelle E. Clapp Charles D. Schwieters Marzena A. Dyba Derek L. Bolhuis Janusz W. Koscielniak Thorkell Andresson Michael J. Emanuele Nicholas G. Brown Hiroshi Matsuo Raj Chari Deborah E. Citrin Beverly A. Mock Rolf E. Swenson Kylie J. Walters |
| author_sort | Xiuxiu Lu |
| collection | DOAJ |
| description | Abstract Proteasome subunit hRpn13 is partially proteolyzed in certain cancer cell types to generate hRpn13Pru by degradation of its UCHL5/Uch37-binding DEUBAD domain and retention of an intact proteasome- and ubiquitin-binding Pru domain. By using structure-guided virtual screening, we identify an hRpn13 binder (XL44) and solve its structure ligated to hRpn13 Pru by integrated X-ray crystallography and NMR to reveal its targeting mechanism. Surprisingly, hRpn13Pru is depleted in myeloma cells following treatment with XL44. TMT-MS experiments reveal a select group of off-targets, including PCNA clamp-associated factor PCLAF and ribonucleoside-diphosphate reductase subunit M2 (RRM2), that are similarly depleted by XL44 treatment. XL44 induces hRpn13-dependent apoptosis and also restricts cell viability by a PCLAF-dependent mechanism. A KEN box, but not ubiquitination, is required for XL44-induced depletion of PCLAF. Here, we show that XL44 induces ubiquitin-dependent loss of hRpn13Pru and ubiquitin-independent loss of select KEN box containing proteins. |
| first_indexed | 2024-04-24T19:54:38Z |
| format | Article |
| id | doaj.art-287afc8f95ca4e0dbcecccb50eebdb48 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-24T19:54:38Z |
| publishDate | 2024-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-287afc8f95ca4e0dbcecccb50eebdb482024-03-24T12:25:43ZengNature PortfolioNature Communications2041-17232024-03-0115111810.1038/s41467-024-46644-7A structure-based designed small molecule depletes hRpn13Pru and a select group of KEN box proteinsXiuxiu Lu0Monika Chandravanshi1Venkata R. Sabbasani2Snehal Gaikwad3V. Keith Hughitt4Nana Gyabaah-Kessie5Bradley T. Scroggins6Sudipto Das7Wazo Myint8Michelle E. Clapp9Charles D. Schwieters10Marzena A. Dyba11Derek L. Bolhuis12Janusz W. Koscielniak13Thorkell Andresson14Michael J. Emanuele15Nicholas G. Brown16Hiroshi Matsuo17Raj Chari18Deborah E. Citrin19Beverly A. Mock20Rolf E. Swenson21Kylie J. Walters22Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthProtein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthChemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of HealthLaboratory of Cancer Biology and Genetics, National Cancer InstituteLaboratory of Cancer Biology and Genetics, National Cancer InstituteLaboratory of Cancer Biology and Genetics, National Cancer InstituteRadiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthProtein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc.Cancer Innovation Laboratory, Frederick National Laboratory for Cancer ResearchGenome Modification Core, Frederick National Laboratory for Cancer ResearchComputational Biomolecular Magnetic Resonance Core, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBiophysics Resource, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthDepartment of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel HillBasic Science Program, Leidos Biomedical Research Inc., NMR Facility for Biological Research, Center for Structural Biology, National Cancer Institute, National Institutes of HealthProtein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc.Department of Pharmacology and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel HillDepartment of Pharmacology and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel HillCancer Innovation Laboratory, Frederick National Laboratory for Cancer ResearchGenome Modification Core, Frederick National Laboratory for Cancer ResearchRadiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthLaboratory of Cancer Biology and Genetics, National Cancer InstituteChemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of HealthProtein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthAbstract Proteasome subunit hRpn13 is partially proteolyzed in certain cancer cell types to generate hRpn13Pru by degradation of its UCHL5/Uch37-binding DEUBAD domain and retention of an intact proteasome- and ubiquitin-binding Pru domain. By using structure-guided virtual screening, we identify an hRpn13 binder (XL44) and solve its structure ligated to hRpn13 Pru by integrated X-ray crystallography and NMR to reveal its targeting mechanism. Surprisingly, hRpn13Pru is depleted in myeloma cells following treatment with XL44. TMT-MS experiments reveal a select group of off-targets, including PCNA clamp-associated factor PCLAF and ribonucleoside-diphosphate reductase subunit M2 (RRM2), that are similarly depleted by XL44 treatment. XL44 induces hRpn13-dependent apoptosis and also restricts cell viability by a PCLAF-dependent mechanism. A KEN box, but not ubiquitination, is required for XL44-induced depletion of PCLAF. Here, we show that XL44 induces ubiquitin-dependent loss of hRpn13Pru and ubiquitin-independent loss of select KEN box containing proteins.https://doi.org/10.1038/s41467-024-46644-7 |
| spellingShingle | Xiuxiu Lu Monika Chandravanshi Venkata R. Sabbasani Snehal Gaikwad V. Keith Hughitt Nana Gyabaah-Kessie Bradley T. Scroggins Sudipto Das Wazo Myint Michelle E. Clapp Charles D. Schwieters Marzena A. Dyba Derek L. Bolhuis Janusz W. Koscielniak Thorkell Andresson Michael J. Emanuele Nicholas G. Brown Hiroshi Matsuo Raj Chari Deborah E. Citrin Beverly A. Mock Rolf E. Swenson Kylie J. Walters A structure-based designed small molecule depletes hRpn13Pru and a select group of KEN box proteins Nature Communications |
| title | A structure-based designed small molecule depletes hRpn13Pru and a select group of KEN box proteins |
| title_full | A structure-based designed small molecule depletes hRpn13Pru and a select group of KEN box proteins |
| title_fullStr | A structure-based designed small molecule depletes hRpn13Pru and a select group of KEN box proteins |
| title_full_unstemmed | A structure-based designed small molecule depletes hRpn13Pru and a select group of KEN box proteins |
| title_short | A structure-based designed small molecule depletes hRpn13Pru and a select group of KEN box proteins |
| title_sort | structure based designed small molecule depletes hrpn13pru and a select group of ken box proteins |
| url | https://doi.org/10.1038/s41467-024-46644-7 |
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