Chemoproteomic Screening of Covalent Ligands Reveals UBA5 As a Novel Pancreatic Cancer Target

Chemical genetic screening of small-molecule
libraries has been a promising strategy for discovering unique and
novel therapeutic compounds. However, identifying the targets of lead
molecules that arise from these screens has remained a major bottleneck
in understanding the mechanism of action of these compounds. Here,
we have coupled the screening of a cysteine-reactive fragment-based
covalent ligand library with an isotopic tandem orthogonal proteolysis-enabled
activity-based protein profiling (isoTOP-ABPP) chemoproteomic platform
to rapidly couple the discovery of lead small molecules that impair
pancreatic cancer pathogenicity with the identification of druggable
hotspots for potential cancer therapy. Through this coupled approach,
we have discovered a covalent ligand DKM 2–93 that impairs
pancreatic cancer cell survival and in vivo tumor
growth through covalently modifying the catalytic cysteine of the
ubiquitin-like modifier activating enzyme 5 (UBA5), thereby inhibiting
its activity as a protein that activates the ubiquitin-like protein
UFM1 to UFMylate proteins. We show that UBA5 is a novel pancreatic
cancer therapeutic target and show DKM 2–93 as a relatively
selective lead inhibitor of UBA5. Our results underscore the utility
of coupling the screening of covalent ligand libraries with isoTOP-ABPP
platforms for mining the proteome for druggable hotspots for cancer
therapy.