Design and synthesis of dual-target CDK9-EZH2 inhibitors using a pharmacophore fusion strategy.

Cyclin-dependent kinase 9 (CDK9), a key member of the CDK family, plays a crucial role in transcriptional regulation. As its expression is dysregulated in various cancers, CDK9 is regarded as a promising therapeutic target. However, the clinical efficacy of traditional CDK9 inhibitors is limited by potential on-target toxicity, and degradation-based strategies face similar challenges. In recent years, dual-target inhibitors against CDK9 have gradually become a research focus. Our group previously reported a CDK9/EZH2 dual inhibitor, D16, though its activity still required further improvement. Furthermore, to validate the general applicability of this design strategy, we designed a series of new CDK9/EZH2 dual-target inhibitors by conjugating a self-designed CDK9-targeting fragment with a selective EZH2 inhibitor. Among them, compound A9 demonstrated excellent inhibitory activity, with IC50 values of 19.3 nM in U2932 cells and 9.1 nM in KARPAS-422 cells. Compared to single-target inhibitors, its dual inhibitory action significantly increased the apoptosis rate and induced substantial DNA damage in DLBCL cells.