Proteomic ligandability maps of spirocycle acrylamide stere-oprobes identify covalent ERCC3 degraders

ABSTRACT: Covalent chemistry coupled with activity-based protein profiling (ABPP) offers a versatile way to discover ligands for pro-teins in native biological systems. Here, we describe a set of stereo- and regio-chemically defined spirocycle acrylamides and the analysis of these electrophilic ‘stereoprobes’ in human cancer cells by cysteine-directed ABPP. Despite showing attenuat-ed reactivity compared to structurally related azetidine acrylamide stereoprobes, the spirocycle acrylamides preferentially liganded specific cysteines on diverse protein classes. One compound ZL-12A stereoselectively promoted the degradation of the TFIIH helicase ERCC3. Interestingly, ZL-12A reacts with the same cysteine (C342) in ERCC3 as the natural product triptolide, which did not lead to ERCC3 degradation, but instead caused collateral loss of RNA polymerases. ZL-12A and triptolide cross-antagonized one another’s protein degradation profiles. Finally, we show that the anti-hypertension drug spi-ronolactone — previously found to promote ERCC3 degradation through an enigmatic mechanism — also reacts with ERCC3_C342. Our findings thus describe monofunctional degraders of ERCC3 and highlight how covalent ligands target-ing the same cysteine can produce strikingly different functional outcomes.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Prostate Adenocarcinoma

SUBMITTER: Zhonglin Liu  

LAB HEAD: Ben Cravatt

PROVIDER: PXD050872 | Pride | 2025-11-06

REPOSITORIES: Pride