Structure-Based Virtual Screening Discovers Potent PLK1 Inhibitors with Anticancer Activity

Polo-like kinase 1 (PLK1), a key regulatory protein in cell cycle progression, is a promising target for cancer therapy. In this study, we efficiently identified potential PLK1 inhibitors through a rigorously validated computational–experimental pipeline that included antitumor kinase scaffold prioritization, structure-based docking, molecular dynamics (MD) simulations, and in vitro biochemical and cellular assays. Among the candidates, BDE30671203 and PB4767006058 demonstrated strong binding affinities to PLK1, with calculated binding free energies (Δ GB ) of −55.328 ± 0.447 kcal/mol and −55.898 ± 2.035 kcal/mol, respectively. Both compounds exhibited significant antiproliferative effects across seven cancer cell lines, with IC 50 values below 10 μM. Notably, BDE30671203 exhibited potent enzymatic inhibition of PLK1 (IC 50 = 2.163 ± 0.401 nM). It also effectively induced G2/M phase arrest (88.45%) and apoptosis (17.77%) in HepG2 cells, concomitant with downregulation of key cell cycle regulators ( CDC20, CDK1, etc.) and the antiapoptotic gene Bcl-2 . Importantly, follow-up kinase selectivity profiling revealed that BDE30671203 is a highly selective PLK1 inhibitor, showing over 450-fold and 1200-fold selectivity against the closely related AURKA and AURKB kinases, respectively. Therefore, this study not only provides promising chemical starting points for PLK1-targeted drug discovery, but more significantly validates a robust screening strategy for kinase inhibitor discovery.