Discovery of a New Scaffold RSK2 Inhibitor With Virtual and Phenotypical Screening

Ribosomal S6 kinase (RSK2) is regarded as an important target for the treatment of breast and ovarian cancers. However, most reported RSK2 inhibitors suffer from insufficient selectivity and unfavorable pharmacokinetic properties due to their similar chemical scaffolds. Therefore, the discovery of novel RSK2 inhibitors with high potency, selectivity, and desirable drug‐like properties remains highly desirable. In this work, we established a virtual screening workflow combining pharmacophore modeling, molecular docking, and molecular dynamics simulations. By screening the Chemdiv database (1.6 million compounds), 39 potential RSK2 inhibitors were obtained. Further phenotypic screening identified compound M39 as a promising cell‐active RSK2 inhibitor. Surface plasmon resonance assays verified that M39 binds to RSK2 with a Kd value of 156 nM. M39 inhibits the catalytic activity of RSK2 by suppressing YB1 phosphorylation and shows stronger anti‐tumor activity than the control LJH685 in breast and ovarian cancer cells. In summary, M39 features a unique chemical scaffold and serves as a promising lead compound for further optimization, as well as a useful chemical tool for exploring the biological functions of RSK2.