Discovery of Inhibitor of Wnt Production 2 (IWP-2) and Related Compounds As Selective ATP-Competitive Inhibitors of Casein Kinase 1 (CK1) δ/ε

Abstract

Inhibitors of Wnt production (IWPs) are known antagonists of the Wnt pathway, targeting the membrane-bound O-acyltransferase porcupine (Porcn) and thus preventing a crucial Wnt ligand palmitoylation. Since IWPs show structural similarities to benzimidazole-based CK1 inhibitors, we hypothesized that IWPs could also inhibit CK1 isoforms. Molecular modeling revealed a plausible binding mode of IWP-2 in the ATP binding pocket of CK1δ which was confirmed by X-ray analysis. In vitro kinase assays demonstrated IWPs to be ATP-competitive inhibitors of CK1δ. IWPs also strongly inhibited the gatekeeper mutantCK1δ. When profiled in a panel of 320 kinases, IWP-2 specifically inhibited CK1δ. IWP-2 and IWP-4 also inhibited the viability of various cancer cell lines. By a medicinal chemistry approach, we developed improved IWP-derived CK1 inhibitors. Our results suggest that the effects of IWPs are not limited to Porcn, but also might influence CK1δ/ε-related pathways.

Newly Developed CK1-Specific Inhibitors Show Specifically Stronger Effects on CK1 Mutants and Colon Cancer Cell Lines

“…Therefore, the sensitivity of CK1δ hyperactive mutants toward different CK1-specific inhibitors was analyzed and residual kinase activities upon inhibitor treatment are summarized in Table 2. Interestingly, all tested inhibitors (Bischof-5 [14], Richter-2 [17], IWP-2, and IWP-4 [15,22]) showed significantly stronger inhibitory effects on CK1δ R127Q compared to CK1δ WT , leading to a residual activity between 19% and 37%. In addition, kinase activity of CK1δ R168H was also influenced stronger by the benzimidazole-based compounds Bischof-5 and Richter-2.…”

“…Being most sensitive to benzimidazole-based inhibitor compounds and IWPs, mutants CK1δ R115H , CK1δ R127Q , and CK1δ R168H were selected for subsequent analysis. Kinase activity of CK1δ WT and mutants was tested in presence of the CK1-specific inhibitors Bischof-5, Richter-2, IWP-2, and IWP-4, which were used in the IC 50 concentration previously determined for CK1δ WT [14,15,17].…”

“…Inhibitor PF-4800567 showed increased selectivity toward CK1ε compared to CK1δ and induced remarkable anti-proliferative effects in different cell lines [12]. Furthermore, benzimidazole-based CK1 isoform-specific inhibitors like SR-3029, Bischof-5, Richter-2, and IWP-based compounds were demonstrated to inhibit viability and/or proliferation of tumor cell lines of different origin-among them also cell lines derived from colon and rectum tissue [13][14][15][16][17]. Although cure rates of colon and rectal cancer patients are continuously increasing for early and locally advanced stages (UICC I-III) [18], the prognosis is still poor for patients displaying distant metastases in liver or lung.…”

Targeting Protein Kinase CK1δ with Riluzole: Could It Be One of the Possible Missing Bricks to Interpret Its Effect in the Treatment of ALS from a Molecular Point of View?

“…Curiously,t hree ATP-competitivei nhibitors belong to the benzothiazole and benzimidazole families:inp articular,ass hown in Figure2,the compound 9XK (PDB ID:5 OKT) is a2 -aminobenzothiazole, whereas compounds 37J (PDB ID:4 TWC)a nd 386 (PDB ID:4 TW9) are 2-aminobenzimidazoles. [16][17][18] Looking at the ATP-binding site, both benzothiazole and benzimidazole scaffolds are anchored to the hinge region of the protein kinase throughaconserved hydrogen bond network, similar to what wasa lso observed for the ATPb inding mode. Furthermore, the benzothiazole scaffold has been extensivelyi nvestigateda sas tartingp oint for computer-aided designa nd for the subsequents ynthesis of potent CK1d inhibitors, for which structural data are not available.…”

“…Our computational work started with a conventional visual inspection of all co‐crystallized ligands followed by scaffold clustering based on different similarity metrics such as MACCS‐driven Tanimoto and Dice indexes. Curiously, three ATP‐competitive inhibitors belong to the benzothiazole and benzimidazole families: in particular, as shown in Figure , the compound 9XK (PDB ID: https://www.rcsb.org/structure/5OKT) is a 2‐aminobenzothiazole, whereas compounds 37J (PDB ID: https://www.rcsb.org/structure/4TWC) and 386 (PDB ID: https://www.rcsb.org/structure/4TW9) are 2‐aminobenzimidazoles . Looking at the ATP‐binding site, both benzothiazole and benzimidazole scaffolds are anchored to the hinge region of the protein kinase through a conserved hydrogen bond network, similar to what was also observed for the ATP binding mode.…”