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

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

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: remsberg@scripps.edu.
  • 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: cravatt@scripps.edu.
PMID: 37084731 DOI: 10.1016/j.molcel.2023.03.026
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.

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