Unexpected CK2-antagonistic functionality of bisubstrate inhibitors targeting protein kinase CK2

Protein kinase CK2, a heterotetrameric holoenzyme composed of two catalytic chains (CK2 alpha) attached to a homodimer of regulatory subunits (CK2 beta), is a target for drug development for cancer therapy. Here, we describe the tetraiodobenzimidazole derivative ARC-3140, a bisubstrate inhibitor addressing the ATP site and the substrate-binding site of CK2 with extraordinary affinity (K-i = 84 pM). In a crystal structure of ARC-3140 in complex with CK2 alpha, three copies of the inhibitor are visible, one of them at the CK2 beta interface of CK2 alpha. Subsequent interaction studies based on microscale thermophoresis and fluorescence anisotropy changes revealed a significant impact of ARC-3140 and of its tetrabromo equivalent ARC-1502 on the CK2 alpha/CK2 beta interaction. A structural inspection revealed that ARC-3140, unlike CK2 beta antagonists described so far, interferes with both sub-interfaces of the bipartite CK2 alpha/CK2 beta interaction. Thus, ARC-3140 is a lead for the further development of highly effective compounds perturbating the quaternary structure of the CK2 alpha(2)beta(2) holoenzyme.