Biology subjects

Mirabi, B.

Publications and source records attributed to Mirabi, B..

3 recordsLinked to original sources

bioRxiv2025

Development of a dual chemical probe for the USP16 and HDAC6 zinc-finger ubiquitin-binding domain

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. Because the precise function of USP16-UBD and its interactions remains unclear, a small molecule antagonist targeting the 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 USP1-UBD, as well as the interaction between ISG15 and HDAC6 UBD, at a concentration of 1 M. The corresponding enantiomer SGC-UBD1031N (16), does not interfere with these interactions, even at concentrations as high as 30 M, and thus serves as a negative control. Table of Contents graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/684218v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@50def6org.highwire.dtl.DTLVardef@15dedc4org.highwire.dtl.DTLVardef@1a50169org.highwire.dtl.DTLVardef@1ffbb4b_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Small molecule screen identifies non-catalytic USP3 chemical handle

Zinc-finger ubiquitin binding domains (ZnF-UBDs) are non-catalytic domains mostly found in deubiquitylases (DUBs). They represent an underexplored opportunity for the development of deubiquitylase-targeting chimeras (DUBTACs) to pharmacologically induce the deubiquitination of target proteins. We have previously shown that ZnF-UBDs are ligandable domains. Here, a focused small molecule library screen against a panel of eleven ZnF-UBDs led to the identification of 59, a ligand engaging the ZnF-UBD of USP3 with a KD of 14 {micro}M. The compound binds the expected C-terminal ubiquitin binding pocket of USP3 as shown by hydrogen-deuterium exchange mass spectrometry experiments and does not inhibit the cleavage of K48-linked di-ubiquitin by USP3. As such this compound could serve as a chemical starting point to develop bifunctional DUBTACs recruiting USP3 for targeted deubiquitination. Table of contents graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/530657v3_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@d4e702org.highwire.dtl.DTLVardef@18a506dorg.highwire.dtl.DTLVardef@1a64ef4org.highwire.dtl.DTLVardef@1898461_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2023

Discovery and characterization of a chemical probe targeting the zinc-finger ubiquitin-binding domain of HDAC6

Histone deacetylase 6 (HDAC6) inhibition is an attractive strategy for treating numerous cancers, and HDAC6 catalytic inhibitors are currently in clinical trials. The HDAC6 zinc-finger ubiquitin-binding domain (UBD) binds free C-terminal diglycine motifs of unanchored ubiquitin polymer chains and protein aggregates, playing an important role in autophagy and aggresome assembly. However, targeting this domain with small molecule antagonists remains an underdeveloped avenue of HDAC6-focused drug discovery. We report SGC-UBD253 (25), a chemical probe potently targeting HDAC6-UBD in vitro with selectivity over nine other UBDs, except for weak USP16 binding. In cells, 25 is an effective antagonist of HDAC6-UBD at 1 {micro}M, with marked proteome-wide selectivity. We identified SGC-UBD253N (32), a methylated derivative of 25 which is 300-fold less active, serving as a negative control. Together, 25 and 32 could enable further exploration of the biological function of the HDAC6 UBD and investigation of the therapeutic potential of targeting this domain.

pharmacology and toxicology↗