DDB1 engagement defines the selectivity of S656 analogs for cyclin K degradation over CDK inhibition

EMBO Rep. 2025 Jun;26(11):2836-2854. doi: 10.1038/s44319-025-00448-y. Epub 2025 Apr 28.

Abstract

In efforts to identify additional therapeutic targets for Acute Myeloid Leukemia (AML), we performed a high-throughput screen that includes 56 primary specimens tested with 10,000 structurally diverse small molecules. One specific hit, called S656 acts as a molecular glue degrader (MGD), that mediates the CRL4-dependent proteolysis of cyclin K. Structurally, S656 features a moiety that binds to the ATP binding site of cyclin-dependent kinases (CDKs), allowing the recruitment of the CDK12-cyclin K complex, along with a binding site for DDB1 bridging the CRL4 complex. Structure activity relationship studies reveal that minimal modifications to the dimethylaniline moiety of S656 improve its cyclin K MGD function over CDK inhibition by promoting DDB1 engagement. This includes full occupation of the DDB1 pocket, preferably with hydrophobic terminal groups, and cation-π interaction with Arg928. Additionally, we demonstrate that despite structural diversity, cyclin K degraders exhibit similar functional activity in AML which is distinct from direct CDK12 inhibition.

Keywords: Acute Myeloid Leukemia; CDK12; Cyclin K; DDB1; Molecular Glue Degrader.

MeSH terms

  • Binding Sites
  • Cell Line, Tumor
  • Cyclin-Dependent Kinases* / antagonists & inhibitors
  • Cyclin-Dependent Kinases* / metabolism
  • Cyclins* / chemistry
  • Cyclins* / metabolism
  • DNA-Binding Proteins* / chemistry
  • DNA-Binding Proteins* / metabolism
  • High-Throughput Screening Assays
  • Humans
  • Leukemia, Myeloid, Acute / drug therapy
  • Leukemia, Myeloid, Acute / metabolism
  • Protein Binding
  • Protein Kinase Inhibitors / chemistry
  • Protein Kinase Inhibitors / pharmacology
  • Proteolysis / drug effects
  • Structure-Activity Relationship

Substances

  • Cyclin-Dependent Kinases
  • DDB1 protein, human
  • Cyclins
  • DNA-Binding Proteins
  • CCNK protein, human
  • CDK12 protein, human
  • Protein Kinase Inhibitors