American Chemical Society
ja3c13448_si_003.xlsx (10.16 kB)

Proteomic Ligandability Maps of Spirocycle Acrylamide Stereoprobes Identify Covalent ERCC3 Degraders

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posted on 2024-04-03, 19:33 authored by Zhonglin Liu, Jarrett R. Remsberg, Haoxin Li, Evert Njomen, Kristen E. DeMeester, Yongfeng Tao, Guoqin Xia, Rachel E. Hayward, Minjin Yoo, Tracey Nguyen, Gabriel M. Simon, Stuart L. Schreiber, Bruno Melillo, Benjamin F. Cravatt
Covalent chemistry coupled with activity-based protein profiling (ABPP) offers a versatile way to discover ligands for proteins in native biological systems. Here, we describe a set of stereo- and regiochemically defined spirocycle acrylamides and the analysis of these electrophilic “stereoprobes” in human cancer cells by cysteine-directed ABPP. Despite showing attenuated reactivity compared to structurally related azetidine acrylamide stereoprobes, the spirocycle acrylamides preferentially liganded specific cysteines on diverse protein classes. One compound termed ZL-12A 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 causes collateral loss of RNA polymerases. ZL-12A and triptolide cross-antagonized one another’s protein degradation profiles. Finally, we provide evidence that the antihypertension drug spironolactone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 targeting the same cysteine can produce strikingly different functional outcomes.