Discovery of pyrazole-based analogs as CDK2 inhibitors with apoptotic-inducing activity: design, synthesis and molecular dynamics study

Abstract

The discovery of novel CDK2 inhibitors is crucial for developing targeted anticancer therapies. Thus, in this study, we aimed to design, synthesize, and evaluate a series of novel pyrazole derivatives (2a–g, 7a–d, 8a and b, 9, and 10) for their potential as CDK2/cyclin A2 enzyme inhibitors. The newly synthesized compounds were screened in vitro at 50 μM for CDK2 inhibition, followed by IC₅₀ profiling of the most promising candidates. Compounds 4, 7a, 7d, and 9 exhibited the strongest inhibition, with IC₅₀ values of 3.82, 2.0, 1.47, and 0.96 μM, respectively. To assess their anti-proliferative effects, all target compounds were further screened against a panel of 60 National Cancer Institute (NCI) cell lines representing various carcinoma types. Among them, compound 4 demonstrated exceptional anti-proliferative activity with a mean growth inhibition (GI) of 96.47% across the panel, while compound 9 showed a mean GI of 65.90%. Additionally, compounds 2b and 7c exhibited notable inhibition against MCF7 breast cancer cells, with GI rates of 86.1% and 79.41%, respectively. Compound 4 was selected for further five-dose concentration evaluations, displaying a full-panel GI₅₀ value of 3.81 μM, with a subpanel range of 2.36–9.17 μM. Western blot analysis of compounds 4 and 9 in HCT-116 cell lines confirmed their inhibitory effects on CDK2. Furthermore, compound 4 induced significant cell cycle arrest at the G1 phase and promoted apoptosis. In silico molecular docking studies revealed that compounds 4, 7a, 7d, and 9 adopt a similar binding mode as AT7519 (I) within the CDK2 binding site. Molecular dynamics simulations further validated the stability of these compounds within the catalytic domain of CDK2. ADME/TOPKAT analyses indicated their favorable pharmacokinetic profiles, which were confirmed by their low toxicity in normal cell lines. Based on these findings, it was concluded that the synthesized pyrazole derivatives, particularly compound 4, show potent CDK2 inhibition and significant anticancer activity, with promising drug-like properties and minimal toxicity. This positions them as strong candidates for further development as CDK2-targeting anticancer agents.