Proteomic discovery of chemical probes that perturb protein complexes in human cells PMID: 37084731

ADC Targets in Oncology

2026-04-10

Proteomic discovery of chemical probes that perturb protein complexes in human cells

Mol Cell. 2023 May 18;83(10):1725-1742.e12. doi: 10.1016/j.molcel.2023.03.026.

Michael R Lazear ¹ , Jarrett R Remsberg ² , Martin G Jaeger ¹ , Katherine Rothamel ³ , Hsuan-Lin Her ³ , Kristen E DeMeester ¹ , Evert Njomen ¹ , Simon J Hogg ⁴ , Jahan Rahman ⁴ , Landon R Whitby ⁵ , Sang Joon Won ¹ , Michael A Schafroth ¹ , Daisuke Ogasawara ¹ , Minoru Yokoyama ¹ , Garrett L Lindsey ¹ , Haoxin Li ¹ , Jason Germain ¹ , Sabrina Barbas ¹ , Joan Vaughan ⁶ , Thomas W Hanigan ¹ , Vincent F Vartabedian ⁷ , Christopher J Reinhardt ¹ , Melissa M Dix ¹ , Seong Joo Koo ⁸ , Inha Heo ⁸ , John R Teijaro ⁷ , Gabriel M Simon ⁵ , Brahma Ghosh ⁹ , Omar Abdel-Wahab ⁴ , Kay Ahn ¹⁰ , Alan Saghatelian ⁶ , Bruno Melillo ¹¹ , Stuart L Schreiber ¹² , Gene W Yeo ³ , Benjamin F Cravatt ¹³

Affiliations

1. Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA.
2. Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA. Electronic address: [email protected].
3. Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
4. Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA.
5. Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA 92121, USA.
6. Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA.
7. Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA.
8. Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium.
9. Discovery Chemistry, Janssen Research & Development, Spring House, PA 19477, USA.
10. Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Spring House, PA 19477, USA.
11. Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA; Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA.
12. Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
13. Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA. Electronic address: [email protected].

Abstract

Most human proteins lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such "binding-first" assays affect protein function, nonetheless, often remains unclear. Here, we describe a "function-first" proteomic strategy that uses size exclusion chromatography (SEC) to assess the global impact of electrophilic compounds on protein complexes in human cells. Integrating the SEC data with cysteine-directed activity-based protein profiling identifies changes in protein-protein interactions that are caused by site-specific liganding events, including the stereoselective engagement of cysteines in PSME1 and SF3B1 that disrupt the PA28 Proteasome regulatory complex and stabilize a dynamic state of the spliceosome, respectively. Our findings thus show how multidimensional proteomic analysis of focused libraries of electrophilic compounds can expedite the discovery of chemical probes with site-specific functional effects on protein complexes in human cells.

Keywords

activity-based protein profiling; chemical probe; covalent; cysteine; proteasome; protein complexes; proteomics; size-exclusion chromatography; spliceosome.