In this research the methods of virtual screening and in vitro inhibitory activity testing were used to search for biologically active compounds against CK2.
Thus, the new inhibitors were found among 1,3-thiazole-5-carboxylic acid, dihydrobenzo[4,5]imidazo[1,2-a]pyrimidine-4-one, 2-pyridone, purine-2,6-dione, pyrido[2,3-d]pyrimidine derivatives. Discovered compounds inhibited CK2 with IC50 values from 0.4 to 20 µM.
Careful binding modes analysis of discovered dihydrobenzo[4,5]imidazo[1,2-a]pyrimidine-4-ones, 2-pyridones, purine-2,6-diones, pyrido[2,3-d]pyrimidines shown two common features. The first, all of them formed hydrogen bond with hinge region of CK2 (Glu114 or Vall116 amino acid residues). The second, core heterocycle of studied compounds located in the adenine-binding region of CK2 ATP-binding site and involved in hydrophobic interactions with amino acid residues Val66, Met163, Val53 and Ile174.
One of the studied inhibitors among 1,3-thiazole-5-carboxylic acid derivative has shown another inhibitor-kinase interactions. Two of three the most active 1,3-thiazole-5-carboxylic acid derivatives formed hydrogen bond with hinge region of CK2 (IC50 of these compounds were 0.8 and 0.4 µM) but compound 2-(3,4-dichlorophenyl)-4-methyl-1,3-thiazole-5-carboxylic didn’t formed hydrogen bond with hinge region and inhibited CK2 with IC50 3.5 µM. This thesis proves that the presence of a hydrogen bond with the hinge is not a mandatory for CK2 inhibition.
Also new highly effective protein kinase CK2 inhibitors were identified among 5-hetarylamino-3-aryl-1h-indazole and aurone derivatives by careful SAR analysis of known CK2 inhibitors. IC50 of the most active compound among 5-hetarylamino-3-aryl-1h-indazoles N-[3-(3,4-dichlorophenyl)-1H-indazol-5-yl]quinazolin-4-amine is 0.002 μM. Indazole heterocycle is involved in the hydrophobic interactions with amino acid residues Val66, Ile95, Phe113, Val116, Met163 and Ile174 in the adenine-binding region. The indazole heterocycle formed a hydrogen bond with Val116 amino acid residues of the CK2 hinge region. R1 substituents oriented to the exit of ATP-binding pocket and formed hydrophobic interaction with Leu45 and Met163. R2 substituents oriented into the hydrophobic pocket I and formed hydrophobic interactions with Phe113, Val53, Lys68 and Ile174. Additionally, R2 formed hydrogen bonds with Lys68 and/or Asp175. According to developed binding mode, SAR-study, and analysis of physicochemical properties the structures of novel high scored 5-amino-3-arylindazole derivatives were designed.
The novel protein kinase CK2 inhibitors were identified among aurones. 21 of them inhibit CK2 with IC50 < 1 µM. The binding mode of aurone derivatives were developed. According to the developed binding mode the rings A and C are located in the adenine-binding region, and carbonyl group at position C-3 of the ring C forms a hydrogen bond with Val116 in the hinge region. The ring B is placed deeper in the ATP-binding pocket and forms stacking-like interaction with Phe113. IC50 values of the most active compounds BFO2 and BFO5 are 0.0035 μM. To enhance the effectiveness and bioavailability of aurones, the property-based optimization was performed. For these reasons, 86 new aurone derivatives were synthesized. As a result of the optimization, 7 nanomolar CK2 inhibitors were developed. IC50 of the most active compound BFO13 is 0.0036 μM and LipE - 4,94.
In general, there were discovered new protein kinase CK2 inhibitors which belongs to 7 chemical classes. 50 of them were identified with IC50 value less than 1 μM and belongs to three chemical classes: 5-heteroylamino-1H-indazoles (compound 5.23 IC50 = 0.002 μM), benzylidenebenzofuran-3 (2H) -ones (compound 6.98 IC50 = 0.0036 μM) and 4-methyl-1 derivatives , 3-thiazole-5-carboxylic acid (compound 4.21 IC50 = 0.4 μM).
