Development of a Dual Chemical Probe for the USP16 and HDAC6 Zinc-Finger Ubiquitin-Binding Domain

  • J Med Chem. 2026 Mar 12;69(5):5703-5711. doi: 10.1021/acs.jmedchem.5c02976.
Madhushika Silva  1 ,  Mandeep Mann  1 ,  Bijan Mirabi  2 ,  Magdalena M Szewczyk  1 ,  Joachim Loup  2 ,  Aurelien Dupeux  2 ,  Renu Chandrasekaran  1 ,  Jonathan Bajohr  2 ,  Cheryl Arrowsmith  1  3 ,  Matthieu Schapira  1  4 ,  Mark Lautens  2 ,  Dalia Barsyte-Lovejoy  1  4 ,  Rachel J Harding  1 ,  Vijayaratnam Santhakumar  1
Affiliations
  • 1. Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
  • 2. Davenport Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.
  • 3. Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
  • 4. Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
PMID: 41718545 DOI: 10.1021/acs.jmedchem.5c02976
Abstract

Ubiquitin-specific peptidase 16 (USP16) is a Deubiquitinase that specifically cleaves ubiquitin from histone H2A and modulates gene expression, cell cycle regulation, and various Other cellular processes. The USP16 zinc-finger ubiquitin-binding domain (UBD) binds the free C-terminal end of both ubiquitin and ISG15, two major signaling proteins that mediate many biological pathways, but the precise function of USP16-UBD remains unclear. A small-molecule antagonist targeting USP16-UBD could enable cellular studies to elucidate its biological role. Here we report SGC-UBD1031 (15), a chemical probe targeting USP16-UBD with similar in vitro binding profiles to HDAC6-UBD and selectivity over nine Other UBDs. In cellular assays, 15 disrupts the interaction between the C-terminus of ISG15 and USP16-UBD, as well as the interaction between ISG15 and HDAC6-UBD, at a concentration of 1 μM. The corresponding enantiomer SGC-UBD1031N (16) does not interfere with these interactions and thus serves as a negative control.

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