2-Phenylquinazolinones as dual-activity tankyrase-kinase inhibitors

Abstract

Tankyrases (TNKSs) are enzymes specialized in catalyzing poly-ADP-ribosylation of target proteins. Several studies have validated TNKSs as anti-cancer drug targets due to their regulatory role in Wnt/β-catenin pathway. Recently a lot of effort has been put into developing more potent and selective TNKS inhibitors and optimizing them towards anti-cancer agents. We noticed that some 2-phenylquinazolinones (2-PQs) reported as CDK9 inhibitors were similar to previously published TNKS inhibitors. In this study, we profiled this series of 2-PQs against TNKS and selected kinases that are involved in the Wnt/β-catenin pathway. We found that they were much more potent TNKS inhibitors than they were CDK9/kinase inhibitors. We evaluated the compound selectivity to tankyrases over the ARTD enzyme family and solved co-crystal structures of the compounds with TNKS2. Comparative structure-based studies of the catalytic domain of TNKS2 with selected CDK9 inhibitors and docking studies of the inhibitors with two kinases (CDK9 and Akt) revealed important structural features, which could explain the selectivity of the compounds towards either tankyrases or kinases. We also discovered a compound, which was able to inhibit tankyrases, CDK9 and Akt kinases with equal µM potency.

Figure 1

Examples of nicotinamide site binding tankyrase inhibitors.

Figure 2

Crystal structures showing the binding mode of (a) 2 (PDB code 4BUY), (b) (+)-8 and (c) 9 to TNKS2 catalytic domain. Black dashed lines represent hydrogen bonds and red spheres represent water molecules. Sigma A weighted 2Fo – Fc electron density map around the ligands is contoured at 1.5 σ.

Figure 3

Crystal structures showing the binding mode of (a) 10 (PDB code 4BU3), (b) 13, (c) 14, and (d) 15 to TNKS2 catalytic domain. The C-ring contains either the amino, hydroxyl or methoxy group in ortho- or meta-position. The compounds which have a meta-substitution are found in double conformations in the crystal structures. Black dashed lines represent hydrogen bonds and red spheres represent water molecules. Sigma A weighted 2Fo – Fc electron density map around the ligands is contoured at 1.5 σ.

Figure 4

Schematic representation of 20 binding to the catalytic domain of TNKS2 as seen in the crystal structure. 20 showed higher potency against TNKS2 in comparison to ortho- and meta-substituted compounds. Black dashed lines represent hydrogen bonds and red spheres represent water molecules. Sigma A weighted 2Fo – Fc electron density map around the ligand is contoured at 1.5 σ.

Figure 5

Crystal structure showing the binding mode of (a) 29, (b) 30, (c) 31, (d) 32, (e) 33, (f) 34 to TNKS2 catalytic domain. Black dashed lines represent hydrogen bonds and red spheres represent water molecules. Sigma A weighted 2Fo – Fc electron density map around the ligands is contoured at 1.5 σ. Ile1075 was left out for clarity.

Figure 6

Crystal structure showing 41. Black dashed lines represent hydrogen bonds and red spheres represent water molecules. Sigma A weighted 2Fo – Fc electron density map around the ligand is contoured at 1.5 σ.

Figure 7

Structural representation showing the binding site of the inhibitors. (a) 42 and (b) 41 were docked into the active site of CDK9 (PDB code 3TNH). (c) Superposed structures of CDK9 (PDB code 3TNH, blue) and Akt (PDB code 4EKK, magenta)^, including compound 42. (d) Crystal structure of CK2 complexed with apigenin (PDB code 4DGM, green). Black dashed lines represent hydrogen bonds and red spheres represent water molecules.