Abstract PS4-04-30: Discovery of NKT5097: a first-in-class, highly potent and selective, orally bioavailable CDK2/4 dual degrader for cancer therapy

Abstract CDK4 is the pivotal driver of HR+HER2- breast cancer and CDK4/6 inhibitors in combination with endocrine therapy have revolutionized the treatment landscape. However, several challenges remain for the approved CDK4/6 inhibitors, including severe hematotoxicity associated with CDK6 inhibition and eventual resistance, often mediated by CDK2/cyclin E pathway activation. Therefore, simultaneously and selectively targeting CDK4 and CDK2 represents a promising therapeutic strategy. The high homology between CDK1 and CDK2, as well as between CDK4 and CDK6, poses a significant challenge for the discovery of selective CDK2/4 dual inhibitors. To overcome these limitations, we employed the targeted protein degradation approach and have discovered NKT5097, a first-in-class, selective, and orally bioavailable CDK2/4 dual degrader. Herein, we disclose the evaluation of NKT5097 activity across a panel of human cancer cell lines to assess its ability to induce CDK2 and CDK4 protein degradation. Its selectivity over other CDKs, especially CDK1 andCDK6, was confirmed through a series of cellular and biochemical assays. Additionally, anti-tumor efficacy and potential off-target effects of NKT5097 were assessed and benchmarked against CDK2 or CDK4 specific inhibitors currently in clinical development. NKT5097 degrades CDK2 and CDK4 rapidly and effectively (DC50: 0.6-15 nM), leading to potent inhibition of Rb phosphorylation and proliferation in CDK2- or CDK4-dependent cancer cells and has up to 50-fold greater potency than PF-07104091 (tagtociclib, a CDK2i) or PF-07220060 (atirmociclib, a CDK4i). In addition, NKT5097 demonstrates strong selectivity for CDK2/4 degradation over CDK1/6/7/9 in various cellular assays. Indeed, NKT5097 treatment predominantly arrests CDK2- and/or CDK4-dependent cells at G1 phase of the cell cycle and has minimal impact on G2 distribution, suggesting a lack of CDK1 inhibition. NKT5097 also demonstrates a 68-fold increase in selectivity for CDK2 over CDK1 in comparison to PF-07104091, and a 33-fold increase in selectivity for CDK4 over CDK6 compared to PF-07220060 in functional cellular assays. The selectivity of NKT5097 for CDK2/4 is further confirmed in a Kinome screen as well as by global proteomic profiling, in which CDK2 and CDK4 are the top hits among the >8,000 proteins quantified. Oral administration of NKT5097 dose-dependently degrades CDK2 and CDK4 and shows robust anti-tumor activities across multiple tumor xenograft models including HR+HER2- breast cancer and cyclin E1-high cancer models. Additionally, combination of NKT5097 with fulvestrant leads to deeper degradation of CDK2 and CDK4 in vitro, resulting in better tumor growth inhibition in HR+ breast cancer models. These findings establish NKT5097 as a potent, selective and orally bioavailable dual degrader of CDK2 and CDK4. NKT5097 offers distinct advantages over the combined use of CDK2 and CDK4 inhibitors, including more comprehensive pathway inhibition and a lower risk of overlapping toxicity, owing to its high potency against CDK2/4 and strong selectivity over CDK1/6. Therefore, as the first-in-class CDK2/4 dual degrader, NKT5097 presents a unique opportunity to serve as a backbone therapy for HR+HER2- breast cancer and other cancers with CDK2 and/or CDK4 dysregulation. NKT5097 is currently being investigated in a phase I clinical study. Citation Format: K. Liu, J. Geng, Z. Yu, Y. Yeh, H. Wei, W. Sun, W. Li, J. Lu, J. Deng, C. Yang, L. Geng, X. Luo, Y. Liang, Z. Liu, Z. Gao, Y. Lou. Discovery of NKT5097: a first-in-class, highly potent and selective, orally bioavailable CDK2/4 dual degrader for cancer therapy [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS4-04-30.