PT  - JOURNAL ARTICLE
AU  - Michael R. Lazear
AU  - Jarrett R. Remsberg
AU  - Martin G. Jaeger
AU  - Katherine Rothamel
AU  - Hsuan-lin Her
AU  - Kristen E. DeMeester
AU  - Evert Njomen
AU  - Simon J. Hogg
AU  - Jahan Rahman
AU  - Landon R. Whitby
AU  - Sang Joon Won
AU  - Michael A. Schafroth
AU  - Daisuke Ogasawara
AU  - Minoru Yokoyama
AU  - Garrett L. Lindsey
AU  - Haoxin Li
AU  - Jason Germain
AU  - Sabrina Barbas
AU  - Joan Vaughan
AU  - Thomas W. Hanigan
AU  - Vincent F. Vartabedian
AU  - Christopher J. Reinhardt
AU  - Melissa M. Dix
AU  - Seong Joo Koo
AU  - Inha Heo
AU  - John R. Teijaro
AU  - Gabriel M. Simon
AU  - Brahma Ghosh
AU  - Omar Abdel-Wahab
AU  - Kay Ahn
AU  - Alan Saghatelian
AU  - Bruno Melillo
AU  - Stuart L. Schreiber
AU  - Gene W. Yeo
AU  - Benjamin F. Cravatt
TI  - Proteomic discovery of chemical probes that perturb protein complexes in human cells
AID  - 10.1101/2022.12.12.520090
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.12.12.520090
4099  - http://biorxiv.org/content/early/2022/12/13/2022.12.12.520090.short
4100  - http://biorxiv.org/content/early/2022/12/13/2022.12.12.520090.full
AB  - 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.Competing Interest StatementG.M Simon V.F. Vartabedian and L.R. Whitby are employees of Vividion Therapeutics. B.F. Cravatt is a founder and advisor to Vividion Therapeutics. G.W.Y. is a co-founder and advisor for Locanabio and Eclipse BioInnovations. G.W.Y. is a visiting professor at the National University of Singapore. G.W.Y. interests have been reviewed and approved by the University of California San Diego in accordance with its conflict-of-interest policies.