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Nat Chem Biol. 2018 Feb;14(2):163-170. doi: 10.1038/nchembio.2538. Epub 2017 Dec 18.

Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation.

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Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.
Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.
Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA.
ActivX Biosciences, La Jolla, California, USA.
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Novartis Institutes for Biomedical Sciences (NIBR), Cambridge, Massachusetts, USA.
Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.


Cyclin-dependent kinase 9 (CDK9), an important regulator of transcriptional elongation, is a promising target for cancer therapy, particularly for cancers driven by transcriptional dysregulation. We characterized NVP-2, a selective ATP-competitive CDK9 inhibitor, and THAL-SNS-032, a selective CDK9 degrader consisting of a CDK-binding SNS-032 ligand linked to a thalidomide derivative that binds the E3 ubiquitin ligase Cereblon (CRBN). To our surprise, THAL-SNS-032 induced rapid degradation of CDK9 without affecting the levels of other SNS-032 targets. Moreover, the transcriptional changes elicited by THAL-SNS-032 were more like those caused by NVP-2 than those induced by SNS-032. Notably, compound washout did not significantly reduce levels of THAL-SNS-032-induced apoptosis, suggesting that CDK9 degradation had prolonged cytotoxic effects compared with CDK9 inhibition. Thus, our findings suggest that thalidomide conjugation represents a promising strategy for converting multi-targeted inhibitors into selective degraders and reveal that kinase degradation can induce distinct pharmacological effects compared with inhibition.

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