2. Academic Validation
  3. A structure-based designed small molecule depletes hRpn13Pru and a select group of KEN box proteins

A structure-based designed small molecule depletes hRpn13Pru and a select group of KEN box proteins

  • Nat Commun. 2024 Mar 20;15(1):2485. doi: 10.1038/s41467-024-46644-7.
Xiuxiu Lu 1,  Monika Chandravanshi 1,  Venkata R Sabbasani 2,  Snehal Gaikwad 3,  V Keith Hughitt 3,  Nana Gyabaah-Kessie 3,  Bradley T Scroggins 4,  Sudipto Das 5,  Wazo Myint 6,  Michelle E Clapp 7,  Charles D Schwieters 8,  Marzena A Dyba 9,  Derek L Bolhuis 10,  Janusz W Koscielniak 11,  Thorkell Andresson 5,  Michael J Emanuele 12,  Nicholas G Brown 12,  Hiroshi Matsuo 6,  Raj Chari 7,  Deborah E Citrin 4,  Beverly A Mock 3,  Rolf E Swenson 2,  Kylie J Walters 13
Affiliations

Affiliations

  • 1 Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
  • 2 Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
  • 3 Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, USA.
  • 4 Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
  • 5 Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA.
  • 6 Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
  • 7 Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
  • 8 Computational Biomolecular Magnetic Resonance Core, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
  • 9 Biophysics Resource, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
  • 10 Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • 11 Basic Science Program, Leidos Biomedical Research Inc., NMR Facility for Biological Research, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
  • 12 Department of Pharmacology and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • 13 Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA. [email protected].
PMID: 38509117 DOI: 10.1038/s41467-024-46644-7
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.

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Products
  • Cat. No.
    Product Name
    Description
    Target
    Research Area
  • HY-162393
    Apoptosis Inducer