Cited by 437Protein Degradation and InhibitorsUbiquitin and proteasome pathwaysChemical Synthesis and Analysis

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

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Huang, Hai-Tsang, Dobrovolsky, Dennis, Paulk, Joshiawa, Yang, Guang, Weisberg, Ellen L., Doctor, Zainab M., Buckley, Dennis L., Cho, Joong-Heui +11 more·2018·Cell Chemical Biology

Abstract

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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Crossref · 10.1016/j.chembiol.2017.10.005

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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”
  • 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.”
  • 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”
  • 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”
  • 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”

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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.
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
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
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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