A Chemoproteomic Approach to Query the Degradable Kinome Using a Multi-kinase Degrader
Open accessAbstract
Heterobifunctional molecules that recruit E3 ubiquitin ligases, such as cereblon, for targeted protein degradation represent an emerging pharmacological strategy. A major unanswered question is how generally applicable this strategy is to all protein targets. In this study, we designed a multi-kinase degrader by conjugating a highly promiscuous kinase inhibitor with a cereblon-binding ligand, and used quantitative proteomics to discover 28 kinases, including BTK, PTK2, PTK2B, FLT3, AURKA, AURKB, TEC, ULK1, ITK, and nine members of the CDK family, as degradable. This set of kinases is only a fraction of the intracellular targets bound by the degrader, demonstrating that successful degradation requires more than target engagement. The results guided us to develop selective degraders for FLT3 and BTK, with potentials to improve disease treatment. Together, this study demonstrates an efficient approach to triage a gene family of interest to identify readily degradable targets for further studies and pre-clinical developments.
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Several mechanisms contribute to increased selectivity of PROTACs, including steric incapability of some targets to form a productive ternary complex, or lack of a suitably positioned lysine residue for ubiquitination.
“Several mechanisms have been shown to contribute to this increase in selectivity. This includes steric incapability of some targets to form a productive ternary complex, or lack of a suitably positioned lysine residue for ubiquitination.62−69”
From Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence (2023) · cites this paper as [66]
BTK is one of the most degraded kinases in a promiscuous kinase degrader proteomic analysis, indicating it is a tractable target for degradation.
“Notably, BTK scored as one of the most degraded kinases, indicating that it is a tractable target.”
From Bruton tyrosine kinase degradation as a therapeutic strategy for cancer (2019) · cites this paper as [14]
DD-03-033 lacks a carbonyl on the glutarimide ring of the thalidomide moiety, a modification that significantly reduces its affinity for CRBN.
“As a negative control, we synthesized DD-03-033 (Figure 1A), an analog of DD-03-007 that lacks a carbonyl on the glutarimide ring of the thalidomide moiety, a modification that significantly reduces its affinity for CRBN.14”
From Bruton tyrosine kinase degradation as a therapeutic strategy for cancer (2019) · cites this paper as [14]
By converting a multitargeted kinase inhibitor into a degrader, the authors previously profiled the degradable kinome and identified BTK as a tractable target.
“Previously, by converting a multitargeted kinase inhibitor into a degrader, we profiled the degradable kinome and identified BTK as a tractable target.14”
From Bruton tyrosine kinase degradation as a therapeutic strategy for cancer (2019) · cites this paper as [14]
PROTAC selectivity does not necessarily mimic that of its target-binding warhead, but rather depends sensitively on the linker.
“It has further been shown that PROTAC selectivity does not necessarily mimic that of its target-binding warhead, but rather depends sensitively on the linker 20, 23, 24, 33”
From Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta (2021) · cites this paper as [23]
A significant subset of proteins are recalcitrant to targeted protein degradation using current approaches.
“but a significant subset of proteins are recalcitrant to targeted protein degradation using current approaches4,5.”
From Small-molecule-induced polymerization triggers degradation of BCL6 (2020) · cites this paper as [4]
The ability of these PROTACs to degrade mutant forms of BTK was not evaluated.
“However, the ability of these PROTACs to degrade mutant forms of BTK was not evaluated [115].”
From Proteolysis targeting chimeras (PROTACs) are emerging therapeutics for hematologic malignancies (2020) · cites this paper as [115]
DD-04-015 efficiently and selectively degrades BTK and produces similar antiproliferative activity as RN486 in BTK-dependent TMD8 DLBCL cells.
“The RN486-based degrader, named DD-04-015, efficiently and selectively degraded BTK and produced a similar antiproliferative activity as RN486 in BTK-dependent TMD8 DLBCL cells.”
From Proteolysis targeting chimeras (PROTACs) are emerging therapeutics for hematologic malignancies (2020) · cites this paper as [115]
TL12-186 degrades multiple kinases including BTK.
“Gray’s group reported the degradation of multiple kinases including BTK by a multi-kinase degrader, TL12-186.”
From Proteolysis targeting chimeras (PROTACs) are emerging therapeutics for hematologic malignancies (2020) · cites this paper as [115]
A CRBN-recruiting PROTAC based on a promiscuous kinase inhibitor failed to significantly degrade FLT-3, likely due to poor cell permeability.
“In an early study, using a CRBN-recruiting PROTAC based on a promiscuous kinase inhibitor to target multiple kinases failed to significantly degrade FLT-3, likely due to its poor cell permeability [115].”
From Proteolysis targeting chimeras (PROTACs) are emerging therapeutics for hematologic malignancies (2020) · cites this paper as [115]
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Electrophilic PROTACs that degrade nuclear proteins by engaging DCAF16
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Development of targeted protein degradation therapeutics
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Delineating the role of cooperativity in the design of potent PROTACs for BTK
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Self-citationAddressing Kinase-Independent Functions of Fak via PROTAC-Mediated Degradation
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Targeted degradation of aberrant tau in frontotemporal dementia patient-derived neuronal cell models
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Self-citationSmall-molecule-induced polymerization triggers degradation of BCL6
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Self-citationPROTACs: great opportunities for academia and industry (an update from 2020 to 2021)
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Development of dual and selective degraders of cyclin-dependent kinases 4 and 6
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Self-citationHomolog-Selective Degradation as a Strategy to Probe the Function of CDK6 in AML
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Self-citationProteolysis Targeting Chimeras (PROTACs) of Anaplastic Lymphoma Kinase (ALK)
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Targeting BCR-ABL1 in Chronic Myeloid Leukemia by PROTAC-Mediated Targeted Protein Degradation
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PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes
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Proteolysis‐targeting chimeras in drug development: A safety perspective
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Functional TRIM24 degrader via conjugation of ineffectual bromodomain and VHL ligands
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Self-citationEfficient targeted degradation via reversible and irreversible covalent PROTACs
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Chemically Induced Degradation of Anaplastic Lymphoma Kinase (ALK)
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Self-citationPROTAC-Mediated Degradation of Bruton’s Tyrosine Kinase Is Inhibited by Covalent Binding
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PROTACs: A novel strategy for cancer therapy
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Harnessing the Power of Proteolysis for Targeted Protein Inactivation
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Self-citationBruton tyrosine kinase degradation as a therapeutic strategy for cancer
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Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta
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Discovery and resistance mechanism of a selective CDK12 degrader
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Self-citationDT2216—a Bcl-xL-specific degrader is highly active against Bcl-xL-dependent T cell lymphomas
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Cancer therapies based on targeted protein degradation — lessons learned with lenalidomide
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Targeted protein degradation and the enzymology of degraders
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Proteolysis targeting chimeras (PROTACs) are emerging therapeutics for hematologic malignancies
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A Nimbolide-Based Kinase Degrader Preferentially Degrades Oncogenic BCR-ABL
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Snapshots and ensembles of BTK and cIAP1 protein degrader ternary complexes
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Cereblon modulators: Low molecular weight inducers of protein degradation
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From Inhibition to Degradation: Targeting the Antiapoptotic Protein Myeloid Cell Leukemia 1 (MCL1)
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PROTAC degraders as chemical probes for studying target biology and target validation
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Development of PDE6D and CK1α Degraders through Chemical Derivatization of FPFT-2216
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Self-citationTargeting of the FOXM1 Oncoprotein by E3 Ligase-Assisted Degradation
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Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence
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Self-citationIdentification and characterization of cancer vulnerabilities via targeted protein degradation
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Unifying Catalysis Framework to Dissect Proteasomal Degradation Paradigms
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Self-citation
- Authors
- Huang, H.-T., Dobrovolsky, D., Paulk, J., Yang, G., Weisberg, E. L., Doctor, Z. M., Buckley, D. L., Cho, J.-H., Ko, E., Jang, J., Shi, K., Choi, H. G., Griffin, J. D., Li, Y., Treon, S. P., Fischer, E. S., Bradner, J. E., Tan, L., & Gray, N. S.
- Affiliations
- Harvard University (US)
- Dana-Farber Cancer Institute (US)
- Daegu-Gyeongbuk Medical Innovation Foundation (KR)
- Chinese Academy of Sciences (CN)
- Corresponding author
- Tan, Li
- Gray, Nathanael S.
- ORCID
- Venue
- Cell Chemical Biology
- Publisher
- Elsevier BV
- Published
- 2018-01
- Volume
- 25
- Issue
- 1
- Pages
- 88-99.e6
- ISSN
- 2451-9448 (ISSN-L)
- 2451-9456
- PMC
- PMC6427047
- OpenAlex
- W2767426216
- Cited by
- 437
- References
- 66
- Citations by year
- 2026: 28 · 2025: 45 · 2024: 52 · 2023: 46 · 2022: 64 · 2021: 55 · 2020: 65 · 2019: 53 · 2018: 27
- FWCI
- 16.52
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell chemical biology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (R01CA214608)
- Damon Runyon Cancer Research Foundation (DRG-2196-14)
- Roche
- Harvard Medical School
- Dana-Farber Cancer Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Keywords
- cereblon, heterobifunctional molecules, targeted protein degradation, E3 ubiquitin ligase, kinome, Bruton's tyrosine kinase, FLT3, cyclin-dependent kinases, AURKA, Aurora B kinase, target identification, chemoproteomics, quantitative proteomics
- MeSH terms
- Agammaglobulinaemia Tyrosine Kinase, Humans, Proteomics, Protein Kinase Inhibitors, fms-Like Tyrosine Kinase 3, Proteolysis
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