Triple-negative breast cancer (TNBC) is a highly aggressive and metastasizing cancer that has the worst prognosis out of all breast cancer subtypes. The epithelial–mesenchymal transition (EMT) and cancer stem cells (CSCs) have been proposed as important mechanisms underlying TNBC metastasis. CDK9 is highly expressed in breast cancer, including TNBC, where it promotes EMT and induces cancer cell stemness. In this study, we have identified a tetrahydroisoquinoline derivative (compound 1) as a potent and selective CDK9-cyclin T1 inhibitor via virtual screening. Interestingly, by targeting the ATP binding site, compound 1 not only inhibited CDK9 activity but also disrupted the CDK9-cyclin T1 protein–protein interaction (PPI). Mechanistically, compound 1 reversed EMT and reduced the ratio of CSCs by blocking the CDK9-cyclin T1 interaction, leading to reduced TNBC cell proliferation and migration. To date, compound 1 is the first reported tetrahydroisoquinoline-based CDK9-cyclin T1 ATP-competitive inhibitor that also interferes with the interaction between CDK9 and cyclin T1. Compound 1 may serve as a promising scaffold for developing more selective and potent anti-TNBC agents. Our work also provides insight into the role of the CDK9-cyclin T1 PPI on EMT and CSCs and highlights the feasibility and significance of targeting CDK9 for the treatment of TNBC.

三阴性乳腺癌 (TNBC) 是一种高度侵袭性和转移性癌症，在所有乳腺癌亚型中预后最差。上皮间质转化 (EMT) 和癌症干细胞 (CSC) 已被认为是 TNBC 转移的重要机制。CDK9 在包括 TNBC 在内的乳腺癌中高度表达，可促进 EMT 并诱导癌细胞干性。在这项研究中，我们通过虚拟筛选确定了一种四氢异喹啉衍生物（化合物1）作为有效和选择性的 CDK9-cyclin T1 抑制剂。有趣的是，通过靶向 ATP 结合位点，化合物1不仅抑制了 CDK9 活性，而且破坏了 CDK9-细胞周期蛋白 T1 蛋白-蛋白相互作用 (PPI)。从机理上讲，化合物1通过阻断 CDK9-cyclin T1 相互作用逆转 EMT 并降低 CSC 的比例，导致 TNBC 细胞增殖和迁移减少。迄今为止，化合物1是第一个报道的基于四氢异喹啉的 CDK9-cyclin T1 ATP 竞争性抑制剂，它也干扰 CDK9 和 cyclin T1 之间的相互作用。化合物1可作为一种有前途的支架，用于开发更具选择性和有效的抗 TNBC 药物。我们的工作还提供了对 CDK9-cyclin T1 PPI 在 EMT 和 CSCs 上的作用的深入了解，并强调了靶向 CDK9 治疗 TNBC 的可行性和意义。