Proteomic Ligandability Maps of Spirocycle Acrylamide Stereoprobes Identify Covalent ERCC3 Degraders

  • J Am Chem Soc. 2024 Apr 17;146(15):10393-10406. doi: 10.1021/jacs.3c13448.
Zhonglin Liu  1 ,  Jarrett R Remsberg  1 ,  Haoxin Li  1 ,  Evert Njomen  1 ,  Kristen E DeMeester  1 ,  Yongfeng Tao  1 ,  Guoqin Xia  1 ,  Rachel E Hayward  1 ,  Minjin Yoo  1 ,  Tracey Nguyen  2 ,  Gabriel M Simon  2 ,  Stuart L Schreiber  3  4 ,  Bruno Melillo  1  3 ,  Benjamin F Cravatt  1  2
Affiliations
  • 1. Department of Chemistry, Scripps Research, La Jolla, California 92037, United States.
  • 2. Vividion Therapeutics, San Diego, California 92121, United States.
  • 3. Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, Massachusetts 02142, United States.
  • 4. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.
PMID: 38569115 DOI: 10.1021/jacs.3c13448
Abstract

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.

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