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October, 2013 UPDATE:

Screening Compounds

Fragment library


Development of human Protein Kinase CK2 inhibitors

 

  • Experimental section

 

The project was started from the Otava CK2 focused library. Initially, the receptor-based virtual screening of OTAVA drug-like collection (50000 compounds) was performed by Development of human Protein Kinase CK2 inhibitorsdocking engine with accounting of ligand flexibility and v-d-w/electrostatic interactions. On the base of analysis of ligand-receptor interactions, 1000 compounds were selected for in vitro tests towards human CK2. Results of the tests together with SAR analysis allowed us to indicate several promising chemical cores. Using these data, we concluded to synthesize and test an additional 314 derivatives of the promising cores.

  • Disclosed results

 

As a result we obtained new and potent classes of human CK2 ATP-competitive inhibitors with in vitro activity in submicromolar range. These classes of inhibitors are not reported in the literature as inhibitors of CK2. Two of the  classes were protected by patents.

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

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



Table 1
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.2.
Binding mode of 3-Carboxy-4-(1H)-Quinolones 7 (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. Evaluation of 3-carboxy-4(1H)-quinolones as inhibitors of human protein kinase CK2. J Med Chem. 2006 Nov 2; 49(22) : 6443-50.

Pat. UА68984 А, C07D215/00, 2004-08-16. Application of 4-substituted 3-carboxyquinolines as protein kinase CK2 inhibitors. Sapelkin V.M., Lukashov S.S., Golub A.G., Bdzhola V. G., Yakovenko O.Ya., Yarmoluk S.M., Dubinina G.G.


- 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 (Fig. 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 2). Binding modes for the most active inhibitors are proposed (Fig. 4).

tid_table.gif

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



Table 2
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 OY, Prykhod'ko AO, Lukashov SS, Bdzhola VG, Yarmoluk SM. Evaluation of 4,5,6,7-tetrahalogeno-1H-isoindole-1,3(2H)-diones as inhibitors of human protein kinase CK2. Biochim Biophys Acta. 2008 Jan; 1784(1) : 143-9.

Pat. UA69165 А, С07D215/00, 2004-08-16. Application of 4,5,6,7-tetrahalogeno-1,3-isoindolinediones as protein kinase CK2 inhibitors. Golub A.G., Yakovenko O.Ya., Yarmoluk S.M., Dubinina G.G., Bdzhola V. G., Prykhod'ko A.O.

 

- 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 inhibitor in the active site of the CK2 catalytic subunit. Hydrogen bonds are shown by the dotted lines

 

Reference: Golub A.G., Bdzhola V.G., Briukhovetska N.V., Balanda A.O., Kukharenko O.P., Kotey I.M., Ostrynska O.V., Yarmoluk S.M. 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. – 2011 Mar; 46(3): 870-6.