Abstract C114: Discovery of a Novel, Selective Brain-Penetrant CDK2 inhibitor for targeted cancer therapy

Abstract Background Cyclin-dependent kinase 2 (CDK2) regulates DNA synthesis G1/S phase transition, and G2 progression. Aberrant activation of CDK2 is implicated.in many cancers, leading to uncontrolled cell proliferation. The selective inhibition of cyclin/CDK complexes controlling cell cycle progression has been established as the standard of care using selective CDK4 and CDK 6 (CDK4/6) inhibitors for metastatic hormone receptor-positive/human epidermal growth factor receptor 2-negative (mHR+/HER2-) breast cancer. Acquired resistance ultimately occurs in almost all cases, despite the effectiveness of CDK4/6 inhibitors for HR+/HER2- subtypes. Cyclin E is significantly overexpressed in palbociclib-resistant cells and pleural effusion samples of HR-positive breast cancer patients. Selective inhibition of CDK2 offers a novel therapeutic approach in cancer, including targeting CCNE1-amplified tumors and resistance to CDK4/6 inhibitors in ER+ breast cancer. Herein, we report the discovery and characterization of a novel, selective CDK2 inhibitor with potent in vitro and in vivo activity. Methods ZE94-0605 was developed using a structure-guided, AI-enabled design strategy, computational modeling, virtual screening, and medicinal chemistry optimization from Expert Systems. The compound’s potency was evaluated against CDK1, 2, 4, 6, 9 and GSK3ß in biochemical assays, and its cytotoxicity assessed in CDK2 amplified cell lines. Pharmacokinetic (PK) properties were characterized in rodents and dogs. Antitumor efficacy was assessed in U87MG intracranial and OVCAR3 xenograft models. Results ZE94-0605 demonstrated sub-nanomolar inhibition of CDK2 (0.38 nM) with selectivity over CDK1 (12.45 nM), CDK4 (6.1 nM), CDK 6 (18.8 nM) and CDK9 (1720 nM). Cell-based assays showed potent cytotoxicity in breast, ovarian, and glioblastoma cells with aberrant CDK2 signaling (50-950 nM). Mechanism of action studies in U87 and T47D cell lines demonstrated inhibition of phosphorylated retinoblastoma protein, a marker of CDK2 activity. ZE94-0605 demonstrated strong oral bioavailability with excellent blood-brain barrier permeability, making it particularly advantageous for treating both primary tumors as well as brain metastases or tumors such as glioblastoma. In vivo, ZE94-0605 induced tumor inhibition in a U87MG intracranial and OVCAR3 xenograft model. Conclusion ZE94-0605 is a promising, AI-designed, selective CDK2 inhibitor with broad activity across models of breast, ovarian, and brain cancers exhibiting CCNE1 amplification or aberrant CDK2 signaling. Its favorable PK profile, preclinical efficacy, and robust brain penetration support further clinical development. Citation Format: Boris Rogovoy, Dmitrii Shkil, Ruben Karapetian, Alexey Ryakhovskiy, Elena Bulanova, Sergey Shevyakov, Nikolay Savchuk, Iain Dukes, Amy Burd. Discovery of a Novel, Selective Brain-Penetrant CDK2 inhibitor for targeted cancer therapy [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2025 Oct 22-26; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2025;24(10 Suppl):Abstract nr C114.