Structure-Based Drug Design to Identify Potent, Selective, and Orally Available Cyclin-Dependent Kinase 9 Inhibitors for the Treatment of Castration-Resistant Prostate Cancer.

Castration-resistant prostate cancer (CRPC) progression relies on androgen receptor (AR)-driven oncogenic transcription, a process requiring cyclin-dependent kinase 9 (CDK9) as a critical cofactor. In this work, we identified and targeted a distinct subpocket specific to CDK9, leading to the discovery of a series of selective CDK9 inhibitors through structure-based drug design. Compound 91 emerged as a potent and selective CDK9 inhibitor, demonstrating robust antiproliferative activity against 22Rv1 cells. Mechanistic studies revealed its ability to disrupt Pol II phosphorylation and downregulate short-lived oncoproteins, including AR-V7 and Myc. 91 exhibited favorable pharmacokinetic properties (F = 41%) and significant tumor growth inhibition in CRPC orthotopic models, achieving 66% TGI. This study characterized a distinct subpocket of CDK9 and validated 91 as a promising candidate, paving the way for developing CDK9-targeted therapies to overcome AR dependency in CRPC.