Discovery of ZLC491 as a Potent, Selective, and Orally Bioavailable CDK12/13 PROTAC Degrader

J Med Chem. 2024 Oct 24;67(20):18247-18264. doi: 10.1021/acs.jmedchem.4c01596. Epub 2024 Oct 10.

Abstract

Selective degradation of cyclin-dependent kinases 12 and 13 (CDK12/13) emerges as a new potential therapeutic approach for triple-negative breast cancer (TNBC) and other human cancers. While several proteolysis-targeting chimera (PROTAC) degraders of CDK12/13 were reported, none are orally bioavailable. Here, we report the discovery of ZLC491 as a potent, selective, and orally bioavailable CDK12/13 PROTAC degrader. The compound effectively degraded CDK12 and CDK13 with DC50 values of 32 and 28 nM, respectively, in TNBC MDA-MB-231 cells. Global proteomic assessment and mechanistic studies revealed that ZLC491 selectively induced CDK12/13 degradation in a cereblon- and proteasome-dependent manner. Furthermore, the molecule efficiently suppressed transcription and expression of long genes, predominantly a subset of genes associated with DNA damage response, and significantly inhibited proliferation of multiple TNBC cell lines. Importantly, ZLC491 achieved an oral bioavailability of 46.8% in rats and demonstrated potent in vivo degradative effects on CDK12/13 in an MDA-MB-231 xenografted mouse model.

MeSH terms

  • Administration, Oral
  • Animals
  • Antineoplastic Agents* / chemistry
  • Antineoplastic Agents* / pharmacokinetics
  • Antineoplastic Agents* / pharmacology
  • Biological Availability*
  • CDC2 Protein Kinase
  • Cell Line, Tumor
  • Cell Proliferation / drug effects
  • Cyclin-Dependent Kinases* / antagonists & inhibitors
  • Cyclin-Dependent Kinases* / metabolism
  • Drug Discovery
  • Female
  • Humans
  • Mice
  • Mice, Nude
  • Proteolysis* / drug effects
  • Rats
  • Rats, Sprague-Dawley
  • Structure-Activity Relationship
  • Triple Negative Breast Neoplasms / drug therapy
  • Triple Negative Breast Neoplasms / pathology
  • Xenograft Model Antitumor Assays

Substances

  • CDK12 protein, human
  • Cyclin-Dependent Kinases
  • Antineoplastic Agents
  • CDK13 protein, human
  • CDC2 Protein Kinase