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Development of human Protein Kinase CK2 inhibitors
Development of human Protein Kinase CK2 inhibitors
Protein kinase CK2 (‘casein kinase 2’) is an extremely pleiotropic and constitutively active Ser/Thr kinase that phosphorylates more than 400 physiological substrates (their number is growing continuously). Naturally, these features make this kinase appear at extremely diverse points of cell signalling pathways and be involved in processes leading to the development of various disorders. There is a growing body of evidence that CK2 displays elevated activity and expression in various types of tumors, promotes development of viral infections and involved in transduction of inflammatory signals.
 
To date Otava Ltd has developed 5 classes of potent inhibitors CK2 (reported below). All inhibitors were identified by receptor-based virtual screening of in-house cillection of about 150,000 organic compounds, their binding mode with ATP-binding site was analyzed and structure-activity relationships were determined. Based on obtained results the strategy of structural optimization for some of the chemical classes has been proposed and inhibitors with activity of 100 times higher than their precursors were developed.
 
Now Otava’s compounds collection grew up to about 250,000 small organic molecules. The search for new CK2 inhibitors among this collection and collections of our collaborators using receptor-based virtual screening and 3D-pharmacophore-based virtual screening is in progress.
 

4`-hydroxyflavones:

These novel synthetic flavone inhibitors (4`-hydroxyflavones) were identified with receptor-based virtual screening of combinatorial library of 150,000 organic compounds. Following in vitro tests revealed that 19 flavones out of 49 selected display ability to inhibit activity of CK2 (IC50 < 30 µM). After several cycles of their chemical optimization 31 new inhibitors with activity 0.004 µM – 8 µM have been obtained. The most active compound FNH79 (Fig. 1) have IC50 nearly 100 times higher than IC50 of fisetin, the most active natural flavone known to inhibit CK2. Initial selectivity tests of this compound using four serine/threonine (ASK1, JNK3, Aurora A, ROCK1) and three tyrosine protein kinases (FGFR1, Met, Tie2) as targets revealed negligible inhibitory activity towards these enzymes.
Development of human Protein Kinase CK2 inhibitors
Fig. 1. Binding mode of flavone FNH79 obtained with molecular docking. Intermolecular hydrogen bonds are indicated with dotted lines.
 
 
Table 1. Kinase residual activity of FNH79, determined in the presence of 10 µM of inhibitor is expressed as a percentage of the control without inhibitor. Final concentration of ATP in the experiment was 100 µM.
 
 

Protein Kinase

FNH79

CK2
JNK3
ROCK1I
Tie2
Aurora A
Met
FGFR1
ASK1

0.8
103
89
85
55
87
74
126

 

References:

  • Golub AG, Bdzhola VG, Ostrynska OV, Kyshenia IV, Sapelkin VM, Prykhod’ko AO, Kukharenko OP, Yarmoluk SM (2013) Discovery and characterization of synthetic 4’-hydroxyflavones – New CK2 inhibitors from flavone family. Bioorg Med Chem 21:6681-6689.
 

4´-carboxyflavonols:

Flavonol derivatives as new CK2 inhibitors were identified with virtual screening of 150,000 small organic compounds. In the course of selection, preference has been given to the compounds having carboxyl group. In vitro screening has shown that five carboxyl-containing flavones from 13 tested inhibit CK2 activity (IC50 is < 10 µM). Studying structure–activity relationships of these novel CK2 inhibitors, we analyzed the docking complexes for the 13 tested compounds and developed a binding model of the flavone derivatives in CK2 ATP-binding site. Based on these studies, extra 13 derivatives of 3-hydroxy-4´-carboxyflavone were synthesized and tested in vitro toward CK2. All tested compounds displayed submicromolar IC50 values, and two most active flavonol derivatives have Ki values 13 nM and 2.5 nM. Binding modes of these compounds were studied with docking and molecular dynamics simulation.
 
 
Development of human Protein Kinase CK2 inhibitors
 
Fig. 3. Binding mode of FLC21. The complex has been obtained with molecular dynamics simulation. Intermolecular hydrogen bonds are shown as dotted lines.
 
 
 
Reference:
  • Golub AG, Bdzhola VG, Kyshenia YV, Sapelkin VM, Prykhod'ko AO, Kukharenko OP, Ostrynska OV, Yarmoluk SM (2011) Structure-based discovery of novel flavonol inhibitors of human protein kinase CK2. Mol Cell Biochem 356(1-2):107-115.
 

Thienopyrimidines

A novel series of substituted (thieno[2,3-d]pyrimidin-4-ylthio)carboxylic acids has been synthesized and tested in vitro towards human protein kinase CK2. It was revealed that the most active compound inhibiting CK2 is 3-{[5-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]thio}propanoic acid (IC50=0.1 µM). Structure-activity relationships of 28 tested thienopyrimidine derivatives have been studied and binding mode of this chemical class has been predicted. Evaluation of the inhibitors on seven protein kinases revealed considerable selectivity towards CK2.
CK2 inhibitor

 

Fig. 5. The binding mode of thienopyrimidine inhibitor in the active site of the CK2 catalytic subunit. Hydrogen bonds are shown by the dotted lines.

References:

  • Golub AG, Bdzhola VG, Briukhovetska NV, Balanda AO, Kukharenko OP, Kotey IM, Ostrynska OV, Yarmoluk SM (2011) Synthesis and biological evaluation of substituted (thieno[2,3-d]pyrimidin-4-ylthio)carboxylic acids as inhibitors of human protein kinase CK2. Eur J Med Chem 46(3):870-876.
 

4,5,6,7-tetrahalogeno-1H-isoindole-1,3(2H)-diones

Here we present the 4,5,6,7-tetrahalogeno-1H-isoindole-1,3(2H)-diones (TID) as a novel potent class of CK2 inhibitors (Table 3). We identified this class of inhibitors by high-throughput docking of a compound collection in the ATP binding site of human CK2. The most active compounds are 2-(4,5,6,7-tetraiodo-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propanoic acid and 2-(4,5,6,7-tetraiodo-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)acetic acid with IC50 values 0.15 µM and 0.3 µM, respectively. These inhibitors are ATP-competitive and they only minimally inhibit the activities of protein kinases DYRK1a, MSK1, GSK3 and CDK5 (Table 4). Binding modes for the most active inhibitors are proposed (Fig. 4).

tid_table.gif


Table 3. Structures and IC50 values of TID 43, 45, 46, 48, 58, 59.


Table 4. Specificity spectrum of TID 43, 46, 48 and 58. Residual activity, determined in the presence of 10 µM inhibitor, is expressed as a percentage of the control without inhibitor. Final concentration of ATP in the experiment was 100 µM.

 

Protein Kinase TID43 TID 46 TID48 TID 58
CK2
DYRK1a
MSK1
GSK3
CDK5
11
80
64
>50
>50
7
83
70
>50
>50
15
60
78
>50
>50
18
70
76
>50
>50



tid_3d.jpg

Fig. 4. TID46-CK2 complex obtained by molecular docking. (A) General view. (B) Detailed view. Intermolecular hydrogen bonds are shown as dotted lines, their lengths (in Å) are indicated. Key hydrophobic interactions are indicated by arrows.

References:

  • Golub AG, Yakovenko OYa, Prykhod'ko AO, Lukashov SS, Bdzhola VG, Yarmoluk SM (2008) Evaluation of 4,5,6,7-tetrahalogeno-1H-isoindole-1,3(2H)-diones as inhibitors of human protein kinase CK2. Biochimica et Biophysica Acta 1784(1): 143–149.
  • Pat. UA69165 А, С07D215/00, 16.08.2004. Application of 4,5,6,7-tetrahalogeno-1,3-isoindolinediones as protein kinase CK2 inhibitors. Golub AG, Yakovenko OYa, Yarmoluk SM, Dubinina GG, Bdzhola VG, Prykhod’ko AO.
     

 

3-carboxy-4(1H)-quinolones:

This class of inhibitors (Fig. 2) has been selected via receptor-based virtual screening of the Otava compound library. It was revealed that the most active compounds, 5,6,8-trichloro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (7) (IC50 = 0.3 µM) and 4-oxo-1,4-dihydrobenzo[h]quinoline-3-carboxylic acid (9) (IC50 = 1 µM), are ATP competitive (Ki values are 0.06 µM and 0.28 µM, respectively). Evaluation of the inhibitors on seven protein kinases shows considerable selectivity toward CK2 (Table 2). According to theoretical calculations and experimental data, a structural model (Fig. 2) describing the key features of 3-carboxy-4(1H)-quinolones responsible for tight binding to CK2 active site has been developed.

Protein Kinase CK2 inhibitors

Fig. 2. 3-Carboxy-4-(1H)-Quinolones 7 and 9 - inhibitors of human Protein Kinase CK2



Table 2. Specificity spectrum of inhibitors 7 and 9. Residual activity determined in the presence of 10 µM inhibitor is expressed as a percentage of the control without inhibitor. Final concentration of ATP in the experiment was 100 µM.

 

Protein Kinase Inhibitor 7 Inhibitor 9
CK2
JNK3
ROCK-I
p56 LCK
DYRK1a
MSK1
GSK3
CDK5
11
74
85
87
35
71
>50
>50
25
81
78
80
85
89
>50
>50


 
Development of human Protein Kinase CK2 inhibitors

Fig. 3. Binding mode of 3-Carboxy-4-(1H)-Quinolones (А) and 9 (B) predicted using flexible docking and molecular dynamics simulation

 

References:

  • Golub AG, Yakovenko OY, Bdzhola VG, Sapelkin VM, Zien P, Yarmoluk SM (2006) Evaluation of 3-Carboxy-4(1H)-quinolones as Inhibitors of Human Protein Kinase CK2. J Med Chem 49(22):6443-6450.
  • Pat. UА68984 А, C07D215/00, 16.08.2004. Application of 4-substituted 3-carboxyquinolines as protein kinase CK2 inhibitors. Sapelkin VM, Lukashov SS, Golub AG, Bdzhola VG, Yakovenko OYa, Yarmoluk SM, Dubinina GG.