Structure-Guided Design and In-Cell Target Profiling of a Cell-Active Target Engagement Probe for PARP Inhibitors

Inhibition of the
poly­(ADP-ribose) polymerase (PARP) family of
enzymes has become an attractive therapeutic strategy in oncology
and beyond; however, chemical tools to profile PARP engagement in
live cells are lacking. Herein, we report the design and application
of PARPYnD, the first photoaffinity probe (AfBP) for
PARP enzymes based on triple PARP1/2/6 inhibitor AZ9482, which induces multipolar spindle (MPS) formation in breast cancer
cells. PARPYnD is a robust tool for profiling PARP1/2
and is used to profile clinical PARP inhibitor olaparib, identifying
several novel off-target proteins. Surprisingly, while PARPYnD can enrich recombinant PARP6 spiked into cellular lysates and inhibits
PARP6 in cell-free assays, it does not label PARP6 in intact cells.
These data highlight an intriguing biomolecular disparity between
recombinant and endogenous PARP6. PARPYnD provides a
new approach to expand our knowledge of the targets of this class
of compounds and the mechanisms of action of PARP inhibitors in cancer.