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 <i>in vitro</i> biochemical and cellular assays. Among the candidates, BDE30671203 and PB4767006058 demonstrated strong binding affinities to PLK1, with calculated binding free energies (Δ<i>GB</i>) 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 IC₅₀ values below 10 μM. Notably, BDE30671203 exhibited potent enzymatic inhibition of PLK1 (IC₅₀ = 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 (<i>CDC20</i>, <i>CDK1</i>, etc.) and the antiapoptotic gene <i>Bcl-2</i>. 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.