A Chemoproteomic Approach to Query the Degradable Kinome Using a Multi-kinase Degrader

Huang, Hai‐Tsang; Dobrovolsky, Dennis; Paulk, Joshiawa; Yang, Guang; Weisberg, Ellen; Doctor, Zainab M.; Buckley, Dennis L.; Cho, Joong-Heui; Ko, Eunhwa; Jang, Jaebong; Shi, Kun; Choi, Hwan Geun; Griffin, James D.; Liu, Ying; Treon, Steven P.; Fischer, Eric S.; Bradner, James E.; Li, Tan; Gray, Nathanael S.

doi:10.1016/j.chembiol.2017.10.005

Cited by 349 publications

(371 citation statements)

References 64 publications

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“…While this is evidently possible, the design of such molecules remains an empirical process in which molecules for new targets frequently fail 27,28 , likely due to insufficient understanding of the fundamental principles that govern these neo-interactions. Our structural understanding is limited to the recruitment of the second bromodomain of BRD4 (BRD4 BD2 ) to the CUL2-RBX1-ElongB/C-VHL (CRL2 VHL ) ubiquitin ligase by the small molecule MZ1 ( 1 ) 5 , a degrader based on a VHL-ligand 21 conjugated to the BRD4 ligand JQ1 ( 2 ) 29 .…”

Section: Introductionmentioning

confidence: 99%

“…In general, degraders have been found to exhibit different efficacy and selectivity profiles depending on the nature of the E3-moiety used, sometimes exhibiting improved selectivity over the parental target-moiety 27,28,30 . While positive cooperativity can explain certain cases – such as MZ1 –, it is unlikely to exist for a broad number of ligase-substrate pairs.…”

Section: Introductionmentioning

confidence: 99%

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Plasticity in binding confers selectivity in ligand-induced protein degradation

et al. 2018

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SUMMARY Heterobifunctional small molecule degraders that induce protein degradation through ligase-mediated ubiquitination have shown considerable promise as a new pharmacological modality. However, we currently lack a detailed understanding of the molecular basis for target recruitment and selectivity, which is critically required to enable rational design of degraders. Here we utilize comprehensive characterization of the ligand dependent CRBN/BRD4 interaction to demonstrate that binding between proteins that have not evolved to interact is plastic. Multiple X-ray crystal structures show that plasticity results in several distinct low energy binding conformations, which are selectively bound by ligands. We demonstrate that computational protein-protein docking can reveal the underlying inter-protein contacts and inform the design of a BRD4 selective degrader that can discriminate between highly homologous BET bromodomains. Our findings that plastic inter-protein contacts confer selectivity for ligand-induced protein dimerization provide a conceptual framework for the development of heterobifunctional ligands.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Plasticity in binding confers selectivity in ligand-induced protein degradation

et al. 2018

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“…Despite these advantages, to date, only a handful of the 600+ human E3 ligases have been found to support ligand-mediated protein degradation [5][6][7][9][10][11] . Importantly, these E3 ligases has been found to show distinct and restricted substrate specificities 12,13 , a parameter that is not yet predictable or easily controlled, underscoring the need to discover additional ligandable E3 ligases with differentiated properties to realize the full scope of targeted protein degradation as a pharmacological strategy.…”

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confidence: 99%

Electrophilic PROTACs that degrade nuclear proteins by engaging DCAF16

Zhang

Crowley

Wucherpfennig

et al. 2018

Preprint

101

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Ligand-dependent protein degradation has emerged as a compelling strategy to pharmacologically control the protein content of cells. So far, only a limited number of E3 ligases have been found to support this process. Here, we use a chemical proteomic strategy to discover that DCAF16 -a poorly characterized substrate recognition component of CUL4-DDB1 E3 ubiquitin ligases -promotes nuclear-restricted protein degradation upon modification by cysteine-directed heterobifunctional electrophilic compounds.Conventional small-molecule probes and drugs act by directly perturbing the functions of proteins (e.g., blocking enzyme catalysis or antagonizing receptor signaling). Many proteins, however, possess multiple functional domains, and therefore a compound that binds to only one of these domains may fail to fully inactivate the protein. An alternative emerging strategy uses chemical probes that direct proteins to the proteolytic degradation machinery of the cell, leading to the loss of protein expression 1, 2 . This targeted protein degradation approach leverages two types of small molecules -those that form tripartite complexes with specific E3 ubiquitin ligases and neosubstrate proteins (e.g., the IMiD class of therapeutics 3,4 ) and bifunctional compounds, often referred to as PROTACs (proteolysis targeting chimeras), which couple E3 ligase ligands to substrate ligands via a variably structured linker [5][6][7] . Targeted protein degradation has the potential to act in a catalytic manner 8 that may lower the drug concentrations required to produce a pharmacological effect and operate sub-stoichiometrically to avoid antagonizing the natural functions of the participating E3 ligase. Despite these advantages, to date, only a handful of the 600+ human E3 ligases have been found to support ligand-mediated protein degradation [5][6][7][9][10][11] . Importantly, these E3 ligases has been found to show distinct and restricted substrate specificities 12, 13 , a parameter that is not yet predictable or easily controlled, 3 underscoring the need to discover additional ligandable E3 ligases with differentiated properties to realize the full scope of targeted protein degradation as a pharmacological strategy.We have recently introduced chemical proteomic platforms for globally and sitespecifically mapping the reactivity of electrophilic small molecules in native biological systems [14][15][16] . These experiments have identified a subset of fragment electrophiles, referred to hereafter as 'scouts' 15 , that capture a remarkably broad fraction of the 100s-1000s of covalent small molecule-cysteine interactions discovered so far by chemical proteomics. We surmised herein that these scout fragments, when incorporated into heterotypic bifunctional compounds containing optimized protein ligands, may offer an expedited path to discover E3 ligases capable of supporting targeted protein degradation through covalent reactivity with cysteine residues. With this goal in mind, we fused three scout fragments -KB02, KB03, and KB05 -to the SLF l...

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“…Current Protocols in Chemical Biology validate engagement of a heterobifunctional multi-kinase degrader molecule (Huang et al, 2018), demonstrating the extensive capabilities of this probe technology.…”

Section: Of 19mentioning

confidence: 91%

Activity‐Based Kinome Profiling Using Chemical Proteomics and ATP Acyl Phosphates

Franks

Hsu

2019

CP Chemical Biology

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Human kinases are a large family of proteins (500+) that catalyze ATPdependent phosphorylation of protein and metabolite substrates to regulate diverse facets of cell biology. Dysregulation and mutations of protein kinases are linked to human disease, providing opportunities for developing pharmacological agents as potential therapy. Assessing the selectivity of pharmacological compounds targeting this enzyme class is critical given that off-target activity of kinase inhibitor drugs may result in toxicity. This set of protocols outlines use of ATP acyl phosphate activity-based probes to evaluate the potency and selectivity of kinase inhibitors via fluorescent gel-and mass spectrometry-based detection methods. These competitive chemical proteomic assays can evaluate engagement of >200 native kinase targets directly in complex proteomes. C 2019 by John Wiley & Sons, Inc.Keywords: activity-based protein profiling r chemical proteomics r chemoproteomics r kinase r KiNativ r kinome r mass spectrometry

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A Chemoproteomic Approach to Query the Degradable Kinome Using a Multi-kinase Degrader

Cited by 349 publications

References 64 publications

Plasticity in binding confers selectivity in ligand-induced protein degradation

Plasticity in binding confers selectivity in ligand-induced protein degradation

Electrophilic PROTACs that degrade nuclear proteins by engaging DCAF16

Activity‐Based Kinome Profiling Using Chemical Proteomics and ATP Acyl Phosphates

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