Design of pyrrolo[2,3-d]pyrimidine-endoperoxide hybrids as first-in-class dual degraders of cyclin D1/3 and CDK4/6 with potent antiproliferative effects

Abstract

The hyperactive Cyclin D-CDK4/6 heterodimer is a key cell cycle regulator in breast cancer, and CDK4/6 inhibitors featuring pyridine/pyrrolo[2,3-d]pyrimidine scaffolds are clinically used treatments. In addition, numerous studies have reported the antitumor activity of endoperoxide compounds. In this study, we designed and synthesized a series of novel endoperoxide-pyridine/pyrrolo[2,3-d]pyrimidine derivatives. ADMET predictions indicate that the C log P values (ranging from 2 to 4) for all target compounds satisfy drug-likeness criteria, implying favorable solubility and membrane permeability. All synthesized compounds exhibited antiproliferative activities that were either superior to or comparable with the positive control drugs, Palbociclib and Ribociclib. Notably, compound E2 demonstrated enhanced antiproliferative effects in MCF-7 and T47D cell lines (IC₅₀ = 2.16 ± 0.28 μM/0.42 ± 0.03 μM) compared to Palbociclib (IC₅₀ = 4.13 ± 0.13 μM/10.66 ± 1.63 μM), without exhibiting significant toxicity in normal breast cells MCF-10A. Kinase inhibition assays demonstrated that E2 exhibits an inhibitory activity against CDK6/Cyclin D3 (IC₅₀ = 6.1 nM), which is more than twice as potent as that of Palbociclib (IC₅₀ = 12.9 nM). Mechanistic studies revealed that, unlike traditional CDK4/6 inhibitors, compound E2 facilitates the targeted degradation of Cyclin D1/3 and CDK4/6 through the Ubiquitin-Proteasome System pathway.