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Rational discovery of molecular glue degraders via scalable chemical profiling

A Publisher Correction to this article was published on 15 January 2021

This article has been updated

Abstract

Targeted protein degradation is a new therapeutic modality based on drugs that destabilize proteins by inducing their proximity to E3 ubiquitin ligases. Of particular interest are molecular glues that can degrade otherwise unligandable proteins by orchestrating direct interactions between target and ligase. However, their discovery has so far been serendipitous, thus hampering broad translational efforts. Here, we describe a scalable strategy toward glue degrader discovery that is based on chemical screening in hyponeddylated cells coupled to a multi-omics target deconvolution campaign. This approach led us to identify compounds that induce ubiquitination and degradation of cyclin K by prompting an interaction of CDK12–cyclin K with a CRL4B ligase complex. Notably, this interaction is independent of a dedicated substrate receptor, thus functionally segregating this mechanism from all described degraders. Collectively, our data outline a versatile and broadly applicable strategy to identify degraders with nonobvious mechanisms and thus empower future drug discovery efforts.

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Fig. 1: Screening in hyponeddylated cells identifies new molecular glue degrader rewiring the CRL4DCAF15 ligase.
Fig. 2: dCeMM2/3/4 are new and structurally different cyclin K degraders.
Fig. 3: Induced cyclin K degradation is mediated via a CRL4B ligase complex in a SR-independent manner.
Fig. 4: dCeMM2/3/4 induce proximity between CUL4B–DDB1 and CDK12/13–cyclin K.

Data availability

The authors declare that the data supporting the findings of this study are available within the paper and its supplementary information files. Sequencing of sgRNA cassettes from all the CRISPR–Cas9 screens described in this study (Figs. 1h and 3a and Extended Data Figs. 5a and 6b–e) and hybrid-capture experiments (Fig. 3h and Extended Data Figs. 7h and 8d) have been deposited in the NCBI Sequence Read Archive under the accession code PRJNA599346. The analyzed data are provided in Supplementary Tables 2 and 5, respectively. Expression proteomics data (Figs. 1g and 2a and Extended Data Figs. 2a and 4d,e) are provided in Supplementary Table 3. Searches were performed with full tryptic digestion against the human SwissProt database v.2017.06 06 (https://www.uniprot.org/statistics/Swiss-Prot%202017_06). Structure of DDB1 in complex with SV5V peptide (Fig. 3i) corresponds to PDB 2HYE. RNA-seq data (Fig. 2e,f and Extended Data Fig. 4a–c) have been deposited in the GEO under the accession code GSE142405. The analyzed data are provided in Supplementary Table 4. Source data are provided with this paper.

Code availability

A detailed description of the bioinformatics analysis used for CRISPR screens, hybrid capture and RNA-seq is available in the Methods. RNA-seq analysis code available at https://github.com/himrichova/MGs_RNAseq_analysis. Source data are provided with this paper.

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Acknowledgements

CeMM and the Winter laboratory are supported by the Austrian Academy of Sciences. This work has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 851478). This work was further enabled by funding from the Austrian Science Fund (FWF, project nos. P32125-B and P30271-B28). C.M.-R. is supported by an individual Marie Skłodowska-Curie postdoctoral fellowship (grant agreement no. 796010). Z.K. was supported by a European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie grant agreement number 765445. G.P. was supported by the Human Frontier Science Program (HFSP Long-Term Fellowship LT000210/2014) and the European Molecular Biology Organization (EMBO Advanced Fellowship ALTF 761-849 2016). We further acknowledge funding awarded from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program grant agreement no. 666068 and from the Novartis Research Foundation to N.H.T. Sequencing was performed at the Biomedical Sequencing facility and proteomics at the Proteomics facility at CeMM. We thank B. Ebert and M. Slabicki for sharing and discussing results ahead of publication.

Author information

Authors and Affiliations

Authors

Contributions

C.M.-R. planned and performed most of the experiments, analyzed data and made figures. S.B. provided technical help in many experiments and prepared RNA-seq and hybrid-capture sequencing libraries. M.B. analyzed CRISPR screens and hybrid-capture experiments and made figures. Z.K. developed and conducted TR–FRET assays and performed purification and labeling of recombinant proteins. M.S. synthesized tethered analogs of dCeMM3. H.I. analyzed RNA-seq data. I.H.K. performed recombinant kinase assays. E.H and K.R. provided technical help in acquired resistance and experiments with dCeMM3-PAP. A.K. provided technical help in the chemical screen. G.P. performed purification and labeling of recombinant proteins. M.F. cloned the CRL sgRNA library. C.B. provided input on bioinformatic analysis. A.C.M. supervised proteomics experiments. J.Z. supported sgRNA design for the CRL library and supervised the cloning strategy. M.G. supervised recombinant kinase assays. N.H.T. gave critical input to the manuscript and supervised TR–FRET experiments. S.K. supervised and helped to design chemical profiling screen. G.E.W. wrote the manuscript, planned and supervised the presented research and has overall project responsibility.

Corresponding author

Correspondence to Georg E. Winter.

Ethics declarations

Competing interests

C.M.-R. and G.E.W. are listed as inventors of a patent application for glue discovery in neddylation-deficient cellular systems. C.M.-R., S.K. and G.E.W. are listed as inventors of patent applications covering the chemical space of dCeMM2/3/4. M.B., S.K., G.E.W and CeMM are founders and equity holders of Proxygen.

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Extended data

Extended Data Fig. 1 Additional hypo-neddylated models show resistance to dCeMM1/2/3/4.

a, DMSO-normalized viability in WT KBM7 cells after 3-day MLN4924 treatment. Mean ± SEM; n = 3 independent treatments. b, Genomic characterization of a UBE2M LOF KBM7 clone. c, Growth curves of WT and UBE2Mmut KBM7 cells. Representative of 3 independent experiments. d, Genomic characterization of a UBE2M LOF HCT116 clone. e, Hypo-neddylation of cullin backbones in a UBE2M LOF clone compared to WT HCT116 cells. f, DMSO-normalized viability in WT or LOF UBE2M HCT116 cells after 3-day treatments. Mean ± SEM; n = 3 independent treatments. EC50s dCeMM1/2/3/4 (µM) WT = 6.5;4.8;7.9;0.4 UBE2Mmut = 12.2;11.6;5.7;33.9. g, Growth curves of the KBM7 mutant CRL-focused library treated with DMSO or dCeMM1 in duplicates for 14 days. h, Genomic characterization of a DCAF15 LOF KBM7 clone.

Source data

Extended Data Fig. 2 dCeMM2/3/4 selectively induce acute cyclin K destabilization and milder CDK12/13 destabilization.

a, b, Log2FCs in protein abundance of all detected CDKs (a) and cyclins (b) in drug-treated compared to DMSO-treated KBM7 cells by quantitative expression proteomics. n = 2 independent treatments. c, Cyclin K and CDK12 degradation upon exposure to dCeMM2 (2.5 μM), dCeMM3 (7 μM) and dCeMM4 (3.5 μM) for 20 h in WT and UBE2Mmut KBM7 cells. d, KBM7 cell treated with dCeMM2 (2.5 μM) for 5 h, 20 h or 5 h + PBS-washing followed by collection after additional 15 h. e, Chemical structures of the inactive analogs of dCeMM2/3/4. f, CCNKCyclin K destabilization upon exposure to dCeMM2/2×(2.5 μM), dCeMM3/3×(6 μM) and dCeMM4/4×(3.5 μM) for 3 h in WT KBM7 cells. g, DMSO-normalized viability in WT KBM7 cells after 3-day dCeMM2X/3×/4Xtreatment. Mean ± SEM; n = 3 independent treatments.

Source data

Extended Data Fig. 3 dCeMM2/3/4 induce apoptosis without a phase-specific cell-cycle arrest.

a, Recombinant kinase assays of dCeMM3/3×/4/4X inhibition on enzymatic activity of CDK12/13/7. Mean ± SD, n = 2 individual treatments. b, Apoptosis induction assessed by flow cytometry after staining with AnnexinV/propidium iodide (PI) in WT KBM7 cells treated with DMSO, dCeMM2 (2.5 µM), dCeMM3 (7 µM) or dCeMM4 (3.5 µM) for the indicated times. Representative of 3 independent experiments. Gating: AnnexinV/propidium iodide: FSC/SSC; singlets; AnnexinV/PI + . c, Time-resolved cell cycle analysis by PI in WT KBM7 cells treated with DMSO, dCeMM2 (2.5 µM), dCeMM3 (7 µM) or dCeMM4 (3.5 µM) for the indicated times. Gating: FSC/SSC; singlets; PI+.

Source data

Extended Data Fig. 4 dCeMM2/3/4 induce global transcriptional downregulation with phenotypic similarity to CDK12/13 inhibition by THZ531.

ac, DMSO-normalized gene expression by RNAseq after 5 h THZ531 (600 nM), dCeMM2 (2.5 µM), dCeMM3 (7 µM), dCeMM4 (3.5 µM) or dCeMM1 (25 µM) treatments in KBM7 cells. Highlighted dots in the volcano plots (a) indicate genes with |log2FC|> 2 and adj. P-value < 0.05. Violin plots (b) represent the log2FC in gene expression for 27,051 transcripts and statistical significance was determined by two-sided unpaired t-test. Gray boxes represent the 25th–75th percentiles; white dots denote median; whiskers denote minima and maxima (1.5× the interquartile range). Waterfall plots (c) show log2FC in gene expression (drug vs DMSO). d, DMSO-normalized expression proteomics after 12 h dCeMM2/3/4 treatment (2.5 μM, 7 μM, 3.5 μM) in KBM7 cells. e, Protein-protein interaction analysis (STRING) with the top100 differentially expressed proteins. Functional enrichments in the networks are color-coded as indicated.

Source data

Extended Data Fig. 5 CRL-focused CRISPR screens show that dCeMM2/3/4 mechanism of action is mediated via a CRL4B ligase complex in a SR-independent manner.

a, CRL-focused CRISPR screens of dCeMM2/3/4 resistance in KBM7 cells with constitutive (upper panel) or inducible (lower panel) Cas9 expression. Results shown are the median of 2 independent screens per drug. Top: bubble plot displaying median enrichment over DMSO for each gene, bubble size indicates significance. Bottom: enrichment of sgRNAs targeting indicated genes, background indicates distribution of all sgRNAs in the screen. b, Growth curves of the KBM7 mutant CRL-focused libraries (top) treated with DMSO or dCeMM2/3/4 in duplicates. Growth curves of the KBM7 mutant genome-scale library (bottom) treated with DMSO or dCeMM2/3/4 for 15 days. c, Depiction of the relevant hits found in the dCeMM2/3/4 CRISPR screens. Note the absence of a dedicated SR.

Source data

Extended Data Fig. 6 Quality controls of genome-scale and CRL-focused CRISPR screens.

a, Dose-resolved, DMSO-normalized viability after 3-day dCeMM1/2/3/4 treatment in the indicated cell lines. Mean ± SEM. n = 3 independent treatments. b, Rank order plots of sgRNAs (DMSO at the end of the screens vs plasmid library) of the genome-wide Brunello sgRNA library (KBM7-Cas9 cells) and the CRL-focused sgRNA library (KBM7-Cas9 and KBM7-iCas9 cells). Red: essential genes. Green: negative controls. c, Heatmaps of the pair-wise Pearson correlation coefficient calculated on the cpm (counts per million)-normalized reads of the different drugs in the three kind of CRISPR screens performed. d, Volcano plots of the different screens performed. In blue the genes with FDR-corrected q-value < 0.05 that were called as hits (STARS algorithm, based on a null distribution with 10.000 permutations). e, Top20 sgRNA reads per million (%) of both replicates in the screens performed with dCeMM2/3/4 (CRL-focused library). dCeMM2 screens were the most stringent.

Source data

Extended Data Fig. 7 Inactivation of DDB1, UBE2G1 and CUL4B but not CUL4A rescue cytotoxicity induced by dCeMM2/3/4.

a, Genomic characterization of CUL4B and UBE2G1 individual LOF KBM7 clones. b, DDB1 protein levels after 3-day doxycycline (dox) treatment of dox-inducible Cas9 expressing (iCas9) KBM7 cells with sgRNAs against DDB1. c, DMSO-normalized viability in WT and 3-day dox pretreated sgDDB1 iCas9 KBM7 cells after 3-day treatments. Mean ± SEM; n = 3 independent treatments. d, DMSO-normalized viability in WT, UBE2Mmut, UBE2G1mut, CUL4Bmut_1 and CUL4Amut_1 KBM7 cells after 3-day THZ532 treatment. Mean ± SEM; n = 3 independent treatments. e, DMSO-normalized viability in WT and UBE2G1mut KBM7 cells after 3-day dCeMM2/3/4 treatments. Mean ± SEM; n = 3 independent treatments. f, CUL4B and CUL4A protein levels in 2 individual LOF CUL4B or CUL4A KBM7 clones generated with CRISPR/Cas9. g, DMSO-normalized viability in WT cells, and 2 individual LOF CUL4B or CUL4A KBM7 clones after 3-day treatments. Mean ± SEM; n = 3. h, Depiction of CUL4A and CUL4B domain structure. Despite sharing 83% sequence identity dCeMM2/3/4 are selectively dependent on CUL4B. i, CUL4B protein levels after exposure to dCeMM2 (2.5 µM), dCeMM3 (6 µM) dCeMM4 (3.5 µM) and dCeMM1 (10 µM) for 5 h in WT KBM7 cells. j, H2A-K119ub1 levels after exposure to dCeMM2 (2.5 µM), dCeMM3 (6 µM) dCeMM4 (3.5 µM) and dCeMM1 (10 µM) for 5 h in WT KBM7 cells.

Extended Data Fig. 8 dCeMM2/3/4-selected populations of MLH1-deficient models identify relevant mutations in CDK12/13 outside of the kinase domain.

a, MLH1 protein levels in individual LOF KBM7 and MV4;11 clones generated with CRISPR/Cas9. b, Genomic characterization of MLH1 individual LOF KBM7 and MV4;11 clones. c, Cyclin K destabilization upon exposure to dCeMM2 (10 µM), dCeMM3 (25 µM) and dCeMM4 (15 µM) for 3 h in WT and DDB1 + /L932P HCT116 cells. d, Schematic depiction of CDK12/13 mutations identified by hybrid capture sequencing in drug-resistant cell pools. Stars: point mutations, arrows: frameshift mutations. e, Cyclin K destabilization upon exposure to dCeMM2 (10 µM), dCeMM3 (25 µM) and dCeMM4 (15 µM) for 3 h in WT and CDK13 + /P1043H HCT116 cells. f, CDK13 levels of WT and CDK13 + /P1043H HCT116 cells used in (e) by flow cytometry. Gating strategy for CDK13 staining: FSC/SSC; singlets; CDK13-488 + . CDK13-488 + is shown.

Extended Data Fig. 9 dCeMM2-induced cyclin K ubiquitination and sensitivity of additional cell lines.

a, Cycloheximide pulse-chase assay in WT and CUL4Bmut KBM7 cells shows similar cyclin K half-life. b, Ubiquitin-K48 pulldown of carfilzomib-pretreated KBM7 cells after 2 h DMSO, dCeMM2 or THZ531 + dCeMM2 (10 µM) treatments. c,. Depiction of the TR-FRET assay. d, TR-FRET signal for CDK12-Alexa488cyclin K (0–5 μM) titrated to terbiumDDB1 in DMSO or 10 μM dCeMM4/4×/2×. “No DDB1” only contains streptavidin-terbium. Data are means ± SD (n = 3). Kapparent (nM): DMSO = n.d., no DDB1 = n.d., dCeMM4 = 651, dCeMM4X = n.d., dCeMM2X = n.d. e, Cyclin K degradation in the specified leukemia lines. f, Dose-resolved DMSO-normalized viability after 3-day dCeMM2/3/4 treatment in the indicated leukemia lines. Mean ± SEM, n = 3 independent treatments. g, Correlation of cyclin K degradation and EC50 in the indicated lines. Linear regression line is shown.

Extended Data Fig. 10 Cyclin K degradation and correlation with sensitivity in T-ALL cell lines.

a, Cyclin K degradation in a panel of T-ALL lines. b, Dose-resolved DMSO-normalized viability after 3-day dCeMM2/3/4 treatment in T-ALL lines lines. Mean ± SEM. n = 3 independent treatments. c, Correlation of cyclin K degradation and EC50 in the indicated lines. Linear regression line is shown. d, Dose-response matrices showing the deviations from Bliss synergy scores. Deviation>0 (= red) is defined as synergy, deviation<0 (=blue) is defined as antagonism.

Supplementary information

Supplementary Information

Supplementary Note (synthetic procedures), Fig. 1 (flow cytometry gating strategy) and Table 1 (HTS Table).

Reporting Summary

Supplementary Table 2

CRISPR–Cas9 resistance screens

Supplementary Table 3

Expression proteomics

Supplementary Table 4

RNA-seq analysis

Supplementary Table 5

Hybrid capture

Supplementary Table 6

Oligo sequences

Supplementary Table 7

Oligo sequences for CRISPR NGS

Source data

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Mayor-Ruiz, C., Bauer, S., Brand, M. et al. Rational discovery of molecular glue degraders via scalable chemical profiling. Nat Chem Biol 16, 1199–1207 (2020). https://doi.org/10.1038/s41589-020-0594-x

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  • DOI: https://doi.org/10.1038/s41589-020-0594-x

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