YARMOLUK RESEARCH LAB

Our lab is focused on the development of the protein kinase inhibitors. Our kinase targets are: CK2, ASK1, FGFR1, JNK3, ROCK I, LCK, DAPK1.

Initially, we perform receptor-based virtual screening of in-house drug-like collection (about 500,000 compounds). On the base of analysis of ligand-receptor interactions, our qualified scientists select promising compounds for in vitro tests. Results of the tests together with SAR analysis allowed us to indicate a number of promising chemical cores. Using these data, we synthesize and test their derivatives.

Disclosed results

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

This class of inhibitors 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 (K_i 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 describing the key features of 3-carboxy-4(1H)-quinolones responsible for tight binding to CK2 active site has been developed.

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

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

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.

Development of human Protein Kinase CK2 inhibitors

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.

Here we present the 4,5,6,7-tetrahalogeno-1H-isoindole-1,3(2H)-diones (TID) as a novel potent class of CK2 inhibitors. 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. Binding modes for the most active inhibitors are proposed.

Protein kinase	TID43	TID46	TID48	TID58
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

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.

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.