Identification of a novel potent, selective and cell permeable inhibitor of protein kinase CK2 from the NIH/NCI Diversity Set Library

Abstract

The anti-apoptotic protein kinase CK2 increasingly becomes an attractive target in cancer research with great therapeutic potential. Here, we have performed an in vitro screening of the Diversity Set III of the DTP program from the NCI/NIH, comprising 1600 compounds. We have identified 1,3-Dichloro-6-[(E)-((4-methoxyphenyl)imino)methyl] dibenzo(b,d) furan-2,7-diol (referred to as D11) to be a potent and selective inhibitor of protein kinase CK2. The D11 compound was tested against 354 eukaryotic protein kinases. By setting the threshold for inhibition to <2% remaining kinase activity, only DYRK1B, IRAK1 and PIM3 were inhibited to an extent as the tetrameric CK2 holoenzyme and its catalytic subunits α and α'. The IC50 values for the CK2α and CK2α' were on average 1-2 nM in comparison to the DYRK1B, IRAK1 and PIM3 kinases, which ranged from 18 to 49 nM. Cell permeability and efficacy of D11 were tested with cells in culture. In MIA PaCa-2 cells (human pancreatic carcinoma cell line), the phosphorylation of the CK2 biomarker CDC37 at S13 was almost completely inhibited in the presence of D11. This was observed both under normoxia and hypoxia. In the case of the human non-small cell lung carcinoma cell line, H1299, increasing amounts of D11 led to an inhibition of S380/T382/383 phosphorylation in PTEN, another biomarker for CK2 activity.

Specific inhibition of CK2α from an anchor outside the active site

“…3c–e and S7†). These results are in contrast to the reported selectivity profiles of the most “selective” ATP competitive CK2α inhibitors; CX4945, 22,30 CX5279, 30 D11, 31 TF 32 and compound 7h by Dowling et al 21 (Fig. S1a†).…”

“…21 CX5279, an analogue of CX4945, inhibits 4 other kinases by 70% or greater at 0.5 μM (102 kinases). 30 D11 inhibits 61 other kinases by 70% or greater at 10 μM (354 kinases) 31 and TF inhibits 7 other kinases by 70% or greater at 10 μM (61 kinases). 32 HIPK2, HIPK3 and PIM1 are noteworthy as they are significantly inhibited by four (HIPK2-3) or 3 (PIM1) of these inhibitors, 21,30–32 but show only 0% ± 4, and 3% ± 4 and –5% ± 5 inhibition, respectively, by CAM4066 at 2 μM.…”

The small-molecule kinase inhibitor D11 counteracts 17-AAG-mediated up-regulation of HSP70 in brain cancer cells

“…The expression of HSP90 was unchanged, however, we observed induction of HSP70 expression in a time and concentration-dependent manner. We, then, analyzed effects of CK2 inhibition on the endogenously expressed chaperone proteins employing the recently identified small-molecule inhibitor D11 [21,25]. Cell treatment with increasing concentrations of D11 resulted in increased cytotoxicity (S1B Fig) and, concomitantly, inhibition of CK2 activity as demonstrated by decreased phosphorylation of NF-κB/p65 at S529 a known CK2 target site (Fig 1B, [26]), however, it did not result in a significant change in the levels of expression of HSP90 and HSP70.…”

Identification and Biological Evaluation of CK2 Allosteric Fragments through Structure-Based Virtual Screening

“…The conventional strategy for CK2 inhibition focused on the discovery of orthosteric molecules that bind into the conserved ATP-binding site [4][5][6]. However, most of the known ATP-competitive inhibitors have been impeded to be the drug candidates due to the off-target and low selectivity [7][8][9][10]. Recently, the allosteric inhibitors targeting the sites out of the catalytic pocket are becoming an alternative strategy to develop the efficient and safe therapeutic agents [11,12].…”