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HCT116 cells were obtained from the Broad Institute Genetic Perturbation Platform. KP4 cells were purchased from JCRB Cell Bank (Japan). Expi293F cells were purchased from Thermo Scientific. All cell lines were confirmed to be mycoplasma free. Transient transfections were carried using TransIT-LT1 reagent (Mirus Bio). HEK293T, HCT116 and KP4 cells were maintained in DMEM medium (Gibco) containing 10% (v/v) fetal bovine serum (FBS) (Gibco). PC9 and MM.1S cells were maintained in RPMI medium (Gibco) containing 10% FBS (Gibco). Expi293F cells were maintained in Expi293 Expression Medium (Thermo Scientific). Multiplexed quantitative proteomic analysis in Yamato cells Yamato BAF47-NL cells were plated in 10cm dishes at a density of 2x10 6 cells / mL and allowed to grow for 48 hours or until 75% confluency was reached. These cells were treated with BRD1732 at 1 or 5 μM, MG132 at 5 μM, or DMSO for 24 hours at a final DMSO concentration of 1% v/v. Cells were harvested, washed with ice-cold PBS, and lysed in 200μL of RIPA (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.5% sodium deoxycholate, 1mM DTT, and cOmplete Protease Inhibitors (Roche)). Protein concentrations were measured using the DC Protein Assay (Bio-Rad)."],"repository":["Pride"],"labhead":["Steve Gygi"],"instrument_platform":[""],"submission_type":["COMPLETE"],"labhead_affiliation":["Harvard Medical School"],"publication":["40841494 Li W, Garcia-Rivera EM, Mitchell DC, Chick JM, Maetani M, Bhadoria R, Knapp JM, Misu R, Matthews GM, Shirasaki R, de Matos Simoes R, Viswanathan V, Pulice JL, Rees MG, Roth JA, Gygi SP, Mitsiades CS, Kadoch C, Schreiber SL, Ostrem JML. Highly specific intracellular ubiquitination of a small molecule. Nat Chem Biol. 2026 22(4):663-671 10.1038/s41589-025-02011-1"],"submitter_affiliation":["Harvard Medical School"],"labhead_mail":["steven_gygi@hms.harvard.edu"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"disease":["Colon Cancer"],"submitter_keywords":["Degradation","Ubiquitin","Proteomics"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD053243"],"quantification_method":[""],"modification":[""],"data_protocol":["Data were acquired and analyzed as previously described (Chick 2016 Nature). Adjusted p-value was calculated by student’s t-test followed by Benjamini-Hochberg procedure. Proteomic data sets were processed to remove proteins with expression changes by RNA-Seq (Log 2 FC>1 and -Log 10 (p adj )>2). Resulting data sets for 5 µM BRD1732 and5 µM MG132 were compared to identify proteins with Log 2 FC>1.5 and -Log 10 (p adj )>2. Plots weregenerated with GraphPad Prism."],"omics_type":["Proteomics"],"species":["Homo Sapiens (human)"],"submitter_mail":["chick.joel@gmail.com"],"submitter_country":["United States"],"doi":["10.6019/PXD053243"],"pubmed_abstract":["Ubiquitin is a small, highly conserved protein that acts as a posttranslational modification in eukaryotes. Ubiquitination of proteins frequently serves as a degradation signal, marking them for disposal by the proteasome. Here we report a novel small molecule from a diversity-oriented synthesis library, BRD1732, that is directly ubiquitinated in cells, resulting in dramatic accumulation of inactive ubiquitin monomers and polyubiquitin chains, which causes broad inhibition of the ubiquitin-proteasome system. Ubiquitination of BRD1732 and its associated cytotoxicity are stereospecific and dependent on two homologous E3 ubiquitin ligases, RNF19A and RNF19B, and their shared E2 conjugating enzyme, UBE2L3. Our finding opens the possibility for indirect ubiquitination of a target through a ubiquitinated bifunctional small molecule and more broadly raises the potential for posttranslational modification in trans."],"pubmed_title":["Highly specific intracellular ubiquitination of a small molecule."],"pubmed_authors":["Li Weicheng W, Garcia-Rivera Enrique M EM, Mitchell Dylan C DC, Chick Joel M JM, Maetani Micah M, Bhadoria Rohit R, Knapp John M JM, Misu Ryosuke R, Matthews Geoffrey M GM, Shirasaki Ryosuke R, de Matos Simoes Ricardo R, Viswanathan Vasanthi V, Pulice John L JL, Rees Matthew G MG, Roth Jennifer A JA, Gygi Steven P SP, Mitsiades Constantine S CS, Kadoch Cigall C, Schreiber Stuart L SL, Ostrem Jonathan M L JML"],"additional_accession":[]},"is_claimable":false,"name":"Highly-specific intracellular ubiquitination of a small molecule","description":"Ubiquitin is a small, highly conserved protein that acts as a post-translational modification in eukaryotes. Ubiquitination of proteins frequently serves as a degradation signal, marking them for disposal by the proteasomal. Here, we report a novel small molecule from a diversity- oriented synthesis library, BRD1732, that is directly ubiquitinated in cells, resulting in dramatic accumulation of unproductive ubiquitin monomer and polyubiquitin chains and broad inhibition of the ubiquitin-proteasome system. Ubiquitination of BRD1732 and its associated cytotoxicity are stereospecific and dependent upon two homologous E3 ubiquitin ligases, RNF19A and RNF19B. Our finding opens a possibility for indirect ubiquitination of a target through a ubiquitinated bifunctional small molecule, and more broadly raises the potential for post- translational modification in 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