Structure-Based Discovery of HS34: A Highly Selective and Orally Bioavailable CDK9 Inhibitor for Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) is a highly aggressive subtype that lacks effective targeted therapies and exhibits strong dependence on CDK9-driven transcription. Here, we report a structure-based drug design strategy exploiting CDK9-specific conformations to discover a novel series of potent inhibitors. This approach yielded <b>HS34</b>, a coumarin-based CDK9 inhibitor with low-nanomolar potency and exceptional selectivity. In cellular assays, <b>HS34</b> displayed potent antiproliferative activity against TNBC cells, outperforming the reference inhibitor KB-0742. Mechanistically, <b>HS34</b> suppresses RNAP II Ser2 phosphorylation, leading to the downregulation of short-lived survival and oncogenic proteins such as Mcl-1 and c-Myc, and consequently inducing apoptosis and blocking EMT-associated invasion. Furthermore, <b>HS34</b> exhibits favorable DMPK properties, including high oral bioavailability and metabolic stability, which align with the significant antitumor efficacy observed in an orally treated xenograft model. Collectively, these findings establish <b>HS34</b> as a selective CDK9 inhibitor and demonstrate that exploiting target-specific conformational features offers an effective strategy for kinase selectivity.