Identification of a novel spirocyclic Nek2 inhibitor using high throughput virtual screening

NIMA Related Kinase 2 (Nek2) kinase is an attractive target for the development of therapeutic agents for several types of highly invasive cancers. Despite this, no small molecule inhibitor has advanced to the late clinical stages thus far. In this work, we have identified a novel spirocyclic inhibitor (V8) of Nek2 kinase, utilizing a high-throughput virtual screening (HTVS) approach. Using recombinant Nek2 enzyme assays, we show that V8 can inhibit Nek2 kinase activity (IC₅₀ = 2.4 ± 0.2 µM) by binding to the enzyme's ATP pocket. The inhibition is selective, reversible and is not time dependent. To understand the key chemotype features responsible for Nek2 inhibition, a detailed structure-activity relationships (SAR) was performed. Using molecular models of the energy-minimized structures of Nek2-inhibitory complexes, we identify key hydrogen-bonding interactions, including two from the hinge-binding region, likely responsible for the observed affinity. Finally, using cell-based studies, we show that V8 attenuates (a) pAkt/PI3 Kinase signaling in a dose-dependent manner, and (b) proliferative and migratory phenotypes of highly aggressive human MDA-MB-231 breast and A549 lung cancer cell lines. Thus, V8 is an important novel lead compound for the development of highly potent and selective Nek2 inhibitory agents.