Cited by 295Protein Degradation and InhibitorsHistone Deacetylase Inhibitors ResearchAdvanced Breast Cancer Therapies

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Development of dual and selective degraders of cyclin-dependent kinases 4 and 6

Open access

Abstract

Cyclin‐dependent kinases 4 and 6 (CDK4/6) are key regulators of the cell cycle, and there are FDA‐approved CDK4/6 inhibitors for treating patients with metastatic breast cancer. However, due to conservation of their ATP‐binding sites, development of selective agents has remained elusive. Here, we report imide‐based degrader molecules capable of degrading both CDK4/6, or selectively degrading either CDK4 or CDK6. We were also able to tune the activity of these molecules against Ikaros (IKZF1) and Aiolos (IKZF3), which are well‐established targets of imide‐based degraders. We found that in mantle cell lymphoma cell lines, combined IKZF1/3 degradation with dual CDK4/6 degradation produced enhanced anti‐proliferative effects compared to CDK4/6 inhibition, CDK4/6 degradation, or IKZF1/3 degradation. In summary, we report here the first compounds capable of inducing selective degradation of CDK4 and CDK6 as tools to pharmacologically dissect their distinct biological functions.

Overview

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Written from the paper’s full text.

TL;DR

The paper reports imide-based bifunctional degraders that recruit CRBN to induce dual CDK4/6 degradation or selective degradation of either CDK4 or CDK6, while also tuning IKZF1/3 degradation. In mantle cell lymphoma cell lines, combined CDK4/6 and IKZF1/3 degradation showed enhanced anti-proliferative effects compared with CDK4/6 inhibition, CDK4/6 degradation alone, or IKZF1/3 degradation.

Key findings

  • Palbociclib-, ribociclib-, and abemaciclib-based degraders were generated; most maintained biochemical IC50 values of 1–50 nM, and each inhibitor could be converted into active CDK4/6 degraders in Jurkat cells after 4 h treatment with 1 µM.
  • Selective degraders were identified: BSJ-01–187 selectively degraded CDK4, YKL-06–102 selectively degraded CDK6, and BSJ-02–162 degraded both CDK4 and CDK6. Analogs BSJ-03–204, BSJ-04–132, and BSJ-03–123 retained dual CDK4/6, selective CDK4, or selective CDK6 degradation, respectively, without degrading IKZF1/3.
  • Degradation was CRBN-dependent: in CRISPR/Cas9-generated Crbn−/− Jurkat cells, CDK4/6 and/or IKZF1/3 protein levels were unaffected, and 100 nM BSJ-02–162 induced G1 arrest in wildtype but not Crbn−/− Jurkat cells after 24 h, whereas 100 nM palbociclib induced G1 arrest in both.
  • In MCL cells, 1 µM BSJ-02–162 for 1 day degraded CDK4/6 and IKZF1/3, while BSJ-03–204 degraded only CDK4/6; both reduced phosphorylated Rb and induced G1 arrest. BSJ-02–162 showed increased anti-proliferative effects versus BSJ-03–204 in many MCL cell lines. In Molt4 proteomics at 250 nM for 5 h, BSJ-04–132 reduced CDK4 by ~1.9-fold, below the 2-fold threshold, but more than CDK6, IKZF1, and IKZF3.

Methods

  • Degraders were designed by attaching PEG or alkyl linkers to the piperazine 4-nitrogen of palbociclib, ribociclib, or abemaciclib, terminating at the 4- or 5-position of thalidomide as the CRBN-recruiting moiety.
  • Cellular assays used Jurkat cells (wildtype and Crbn−/−), Molt4 cells, Granta-519 cells, and a panel of MCL cell lines; readouts included enzymatic CDK4/6 kinase inhibition, immunoblotting, propidium iodide cell-cycle analysis, multiplexed mass spectrometry-based proteomics, and anti-proliferative assays.
  • Main analyses compared degrader-induced protein loss, CRBN dependence, cell-cycle effects, and proteome-wide selectivity, with a minimum 2-fold change threshold used for proteomic scatterplot depiction.

Limitations

  • Stated: structural analysis of kinase-degrader-CRBN ternary complexes will be required to reveal the basis for the observed CDK4 versus CDK6 selectivity.
  • Evident: all reported efficacy and degradation data are from cell lines; no in vivo animal or clinical data are reported.
  • Evident: the proteomics analysis used a minimum 2-fold change threshold, and CDK4 reduction by BSJ-04–132 (~1.9-fold) did not meet this threshold, so its selective CDK4 degradation was inferred from Table S2 rather than the scatterplot.

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Integrity signals

Registry

Crossref · 10.1002/anie.201901336

Cites

24 of 24 references verified0 citation errors · 0 not checkable

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  • The paper relies on this without support.

    The ATP-binding pockets of CDK4 and CDK6 are highly conserved/homologous, and current CDK4/6 inhibitors are approximately equipotent for both proteins, making selective inhibition difficult.

    “However, due to conservation of their ATP-binding sites, development of selective agents has remained elusive.”
    “As current CDK4/6 inhibitors target their highly conserved ATP-binding pockets and are approximately equipotent inhibitors of both proteins, we hypothesized that achieving selectivity would require exploiting selectivity determinants outside of the ATP-binding pocket.”
    “The highly homologous ATP-binding pockets of CDK4 and CDK6 has hindered the development of selective CDK4 or CDK6 probes.”
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Metadata

Authors
Jiang, B., Wang, E. S., Donovan, K. A., Liang, Y., Fischer, E. S., Zhang, T., & Gray, N. S.
Affiliations
Dana-Farber Cancer Institute (US)
Corresponding author
  • Zhang, Tinghu
  • Gray, Nathanael S.
Venue
Angewandte Chemie International Edition
Publisher
Wiley
Published
2019-03-29
Volume
58
Issue
19
Pages
6321-6326
ISSN
  • 1433-7851 (ISSN-L)
  • 1521-3773
OpenAlex
W2917565897
Cited by
272
References
24
Citations by year
2026: 19 · 2025: 46 · 2024: 39 · 2023: 26 · 2022: 38 · 2021: 47 · 2020: 43 · 2019: 14
FWCI
12.49
Type
journal article
Language
en
Open access
Locations
  • Angewandte Chemie International Edition (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • Damon Runyon Cancer Research Foundation (DRG-2270-16, DRR-50-18)
  • National Institutes of Health (R01CA218278)
  • 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 › Histone Deacetylase Inhibitors Research
  • Health Sciences › Medicine › Oncology › Advanced Breast Cancer Therapies
Keywords
CDK4, CDK6, selective degradation, mantle cell lymphoma, metastatic breast cancer, cell cycle regulation, antiproliferative activity
MeSH terms
Humans, Imides, Piperazines, Pyridines, Cell Line, Tumor, Protein Kinase Inhibitors, Cell Proliferation, Cyclin-Dependent Kinase 4, Cyclin-Dependent Kinase 6, Ikaros Transcription Factor, Cell Cycle Checkpoints

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