Identification of chemical inhibitors of protein-kinase CK2 subunit interaction

Abstract

Protein kinase CK2 is a multi-subunit complex whose dynamic assembly appears as a crucial point of regulation. The ability to interfere with specific protein-protein interactions has already provided powerful means of influencing the functions of selected proteins within the cell. CK2beta-derived cyclopeptides that target a well-defined hydrophobic pocket on CK2alpha have been previously characterized as potent inhibitors of CK2 subunit assembly [9]. As a first step toward the rational design of low molecular weight CK2 antagonists, we have in the present study screened a collection of podophyllotoxine indolo-analogues to identify chemical inhibitors of the CK2 subunit interaction. We report the identification of a podophyllotoxine indolo-analogue as a chemical ligand that binds to the CK2alpha/CK2beta interface inducing selective disruption of the CK2alpha/CK2beta assembly and concomitant inhibition of CK2alpha activity.

Structure of the Toxoplasma gondii ROP18 Kinase Domain Reveals a Second Ligand Binding Pocket Required for Acute Virulence

“…This pocket coincides with the site of interaction with the non-catalytic CK2␤ subunit, and a biochemical screen for inhibitors of CK2 subunit association have identified a podophyllotoxine indolo analog (W16) that binds at the CK2 subunit interface and allosterically inhibits the catalytic activity of CK2␣ (65). Binding of CK2␤ alters the substrate preference and the subcellular localization of CK2␣ (66,67), and it has been proposed that CK2 function may be regulated by small molecule metabolites in vivo or small molecule inhibitors that inhibit CK2 subunit association (63)(64)(65). Drawing on these parallels with CK2␣, an additional potential role for the basic pocket in ROP18 may be as a site of interaction with protein interaction partners or substrates, which can be regulated by small molecule metabolite binding.…”

“…Interestingly, crystal structures of CK2␣ have revealed a hydrophobic pocket on the N-terminal lobe, capable of binding glycerol and the small molecule ATP-competitive inhibitor 5,6-dichloro-1-␤-D-ribofuranosylbenzimidazole (63,64). This pocket coincides with the site of interaction with the non-catalytic CK2␤ subunit, and a biochemical screen for inhibitors of CK2 subunit association have identified a podophyllotoxine indolo analog (W16) that binds at the CK2 subunit interface and allosterically inhibits the catalytic activity of CK2␣ (65). Binding of CK2␤ alters the substrate preference and the subcellular localization of CK2␣ (66,67), and it has been proposed that CK2 function may be regulated by small molecule metabolites in vivo or small molecule inhibitors that inhibit CK2 subunit association (63)(64)(65).…”

How druggable is protein kinase CK2?

“…Based on the structure-activity properties of cyclopeptides interacting with this interface, 196 a library of podophyllotoxine indoloanalogues has been created and tested as selective inhibitors of CK2 subunits assembly. 197 Podophyllotoxin is an aryltetralin lignan lactone with antimitotic activity inhibiting protein-protein interaction of tubulin into microtubules. W16 ((3aS,4S,10S,10aR)-10-((S)-4-Benzyl-2-oxo-oxazolidine-3-carbonyl)-4-(3,4,5-trimethoxy-phenyl)-4,9,10,10a-tetrahydro3aH-2-oxa-9-aza-cyclopenta[b]fluorene-1,3-dione, Table II) resulted to be the most active molecule with an IC 50 value of about 20 mM.…”

Protein Kinase CK2 in Health and Disease

“…66,2009 Review Article itive effect of DRB [30] and which is absent if the cavity is impaired and blocked by CK2b. It is possible that some recently described non-ATP-competitive inhibitors that were originally discovered as substances to disturb the CK2a/CK2b interaction [77] are also bound to the remote cavity because CK2b removes their inhibitory effect and obviously displaces them from their binding site. Apart from synthetic small molecules natural metabolites can occupy the remote cavity.…”

“…In the corresponding crystal structure [42] the remote cavity is filled with glycerol, but glycerol itself is no inhibitor of CK2a so that this occupation is certainly not sufficient to promote the inactive conformation. However, other small molecules -like the non-ATP-competitive inhibitors mentioned above [77] -may be more effective (Fig. 6).…”