VRK1 inhibition leverages paralog synthetic lethality to selectively target VRK2-deficient cancer cells

Vaccinia-related kinases (VRKs) are a family of serine/threonine kinases involved in a variety of cellular processes, including cell signaling, chromatin modification, nuclear envelope dynamics, and cell cycle progression. More than 60% of glioblastomas and nearly all neuroblastomas have low expression of the VRK2 gene resulting in deficient VRK2 activity. VRK1 has been identified as a paralog synthetic lethal target in these VRK2-deficient cancers, with the potential for indication expansion into additional cancer types. Here, we show that inhibition of VRK1 leads to a concomitant loss of Barrier to Autointegration Nuclear Assembly Factor 1 (BANF1 or BAF) phosphorylation leading to aberrant nuclear envelope formation and downstream loss of cellular viability. As a target, VRK1 is both tractable and structurally-enabled, with chemical series capable of achieving >4000-fold biochemical selectivity against its paralog VRK2 and >70-fold viability selectivity in VRK2 isogenic cell line pairs. Compounds show strong correlations between biochemical, cellular target engagement, pharmacodynamic, and functional viability assays. Furthermore, in vivo tolerability studies suggest that VRK1 inhibitors are well-tolerated in immunocompromised mice. Preclinical validation studies support the development of VRK1 inhibitors for the treatment of patients with VRK2-deficient tumors such as glioblastoma and neuroblastoma.