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Updated: Jun 2, 2026

Identification of Novel CK2 Kinase Substrates Using a Versatile Biochemical Approach
Published on: February 21, 2019
ATP site-directed inhibitors of protein kinase CK2: an update
S Sarno1, E Papinutto, C Franchin
1Department of Biological Chemistry and CNR Institute of Neurosciences, University of Padova, Italy.
Abstract:
CK2 denotes a pleiotropic, constitutively active protein kinase whose abnormally high level in many cancer cells is held as an example of "non oncogene addiction". A wide spectrum of cell permeable, fairly specific ATP site-directed CK2 inhibitors are currently available which are proving useful to dissect its biological functions and which share the property of inducing apoptosis of cancer cells with no comparable effect on their "normal" counterparts. One of these, CX-4945, has recently entered clinical trials for the treatment of advanced solid tumors, Castelman's disease and multiple myeloma. The solution of a wide range of 3D structures of inhibitors bound to the catalytic subunits of CK2 reveals that their efficacy substantially relies on hydrophobic interactions within a cavity which is smaller than in other protein kinases. Accordingly the potency of tetra-halogenated benzimidazoles increases upon replacement of chlorine by bromine and, even more, by iodine, and decreases if two unique bulky side chains on CK2 (Val66 and Ile174) are mutated to alanines. Many CK2 inhibitors have been tested on a panel of more than 60 kinases providing Promiscuity Scores useful to evaluate their selectivity, the lowest value (9.47), denoting highest selectivity, being displayed by quinalizarin. The observation that CK2 inhibitors with medium/high promiscuity scores share the ability to inhibit a group of protein kinases as effectively as CK2 discloses the possibility of using their scaffolds for the rational development of selective inhibitors of these kinases, with special reference to PIMs, DYRKs, HIPK2, PKD and ERK8.
Insights
Specific CK2 inhibitors induce cancer cell apoptosis and show promise in clinical trials. Their efficacy depends on hydrophobic interactions, and new drug development can leverage their scaffolds for targeting other kinases.
Area of Science:
- Biochemistry and Molecular Biology
- Cancer Therapeutics
- Drug Discovery
Background:
- Casein kinase 2 (CK2) is a constitutively active protein kinase overexpressed in many cancers, representing a 'non oncogene addiction' target.
- Specific ATP-site directed CK2 inhibitors induce apoptosis in cancer cells selectively, with one candidate, CX-4945, entering clinical trials.
Purpose of the Study:
- To analyze the structural basis of CK2 inhibitor efficacy and selectivity.
- To explore the potential of CK2 inhibitor scaffolds for developing inhibitors of other protein kinases.
Main Methods:
- Analysis of 3D structures of CK2 inhibitors bound to CK2 catalytic subunits.
- Structure-activity relationship studies involving halogen substitutions and specific amino acid mutations (Val66, Ile174) in CK2.
- Kinase selectivity profiling using a panel of over 60 kinases and calculating Promiscuity Scores.
Main Results:
- CK2 inhibitor efficacy is linked to hydrophobic interactions within a constrained binding cavity.
- Potency of tetra-halogenated benzimidazoles increases with halogen size (Cl < Br < I) and decreases with mutations of Val66 and Ile174.
- Quinalizarin exhibits the highest selectivity (Promiscuity Score 9.47); medium/high promiscuity inhibitors can target multiple kinases.
Conclusions:
- The structural features of CK2 inhibitors dictate their potency and selectivity.
- CK2 inhibitor scaffolds can be rationally adapted for developing selective inhibitors against kinases like PIMs, DYRKs, HIPK2, PKD, and ERK8.
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