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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We thank D. Buckley, E. Wang, J. Paulk, and members of the Gray and Bradner laboratories for helpful discussions. This work was supported by the US National Institutes of Health (CA179483-03 to N.K. and N.S.G., and T32GM007753 to Z.Z.), the Koch Institute and Dana-Farber/Harvard Cancer Center Bridge Grant (N.K., N.S.G., R.A.Y., C.M.O.),
N.S.G. is a Scientific Founder and member of the Scientific Advisory Board of C4 Therapeutics, Syros Pharmaceuticals and Petra Pharmaceuticals and is the inventor on intellectual property licensed to these entities. J.E.B. is a Scientific Founder of Syros Pharmaceuticals, SHAPE Pharmaceuticals, Acetylon Pharmaceuticals, Tensha Therapeutics (now Roche) and C4 Therapeutics and is the inventor on intellectual property licensed to these entities. J.E.B. is now an executive and shareholder in Novartis AG. R.A.Y. is a Scientific Founder of Syros Pharmaceuticals and Marauder Therapeutics.
Supplementary Results, Supplementary Tables 1–2, Supplementary Figures 1–9 (PDF 2413 kb)
Chemical Synthesis of THAL-SNS-032, NVP-2, THAL-NVP-2-02-099, THAL-NVP-2- 3 03-069, HAL-NVP-2-03-099, THAL-NVP-2-03-084, THAL-NVP-2-03-105. (PDF 668 kb)
Lysate Kinativ of SNS-032, THAL-SNS-032, and NVP-2 (XLSX 39 kb)
Proteomics of THAL-SNS-032 treatment (XLSX 328 kb)
Selectivity of NVP-2 by Ambit profiling (XLSX 23 kb)
Live cell Kinativ of SNS-032 and THAL-SNS-032 (XLSX 25 kb)
Live cell Kinativ of NVP-2 (XLSX 29 kb)
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Olson, C., Jiang, B., Erb, M. et al. Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation. Nat Chem Biol 14, 163–170 (2018). https://doi.org/10.1038/nchembio.2538
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