Structural analysis of PIM1 kinase complexes with ATP-competitive inhibitors

Abstract

PIM1 is an oncogenic kinase overexpressed in a number of cancers where it correlates with poor prognosis. Several studies demonstrated that inhibition of PIM1 activity is an attractive strategy in fighting overexpressing cancers, while distinct structural features of ATP binding pocket make PIM1 an inviting target for the design of selective inhibitors. To facilitate development of specific PIM1 inhibitors, in this study we report three crystal structures of ATP-competitive inhibitors at the ATP binding pocket of PIM1. Two of the reported structures (CX-4945 and Ro-3306) explain the off-target effect on PIM1 of respectively casein kinase 2 and cyclin-dependent kinase 1 dedicated inhibitors. In turn, the structure with CX-6258 demonstrates a binding mode of a potent, selective inhibitor of PIM1, PIM2, PIM3 and Flt-3 kinases. The consequences of our findings for future inhibitor development are discussed.

Figure 1

Chemical structures of inhibitors used in the study. (A) CX-4945 (B) Ro-3306 (C) CX-6258.

Figure 2

Binding mode of CX-4945 at the active site of PIM1. (A) Detailed binding mode and quality of PIM1 co-crystal structure. Electron density defining the inhibitor (SA Fo-Fc omit map contoured at 3σ level) is shown as grey mesh. (B) Comparison of the interactions guiding the affinity of CX-4945 at the binding sites of PIM1 (green) and CK2α (blue). Corresponding residues are labeled with PIM1 (on top) and equivalent CK2α residue in parentheses. (A,B) The protein is shown in cartoon representation and the compound as sticks. Protein residues forming direct and water mediated hydrogen bonds are shown in stick model, thick and thin respectively. Water molecules are depicted as purple spheres. Hydrogen bonds are shown as black dashed lines.

Figure 3

Interactions guiding the recognition of Ro-3306 at the active site of PIM1. Representations, color coding and labeling scheme same as in Fig. 2, save that the bottom panel depicts comparison of the binding mode of Ro-3306 at PIM1 (green) and CDK2 (blue) active sites.

Figure 4

The binding mode of CX-6258 at the active site of PIM1. (A) Detailed binding mode and quality of PIM1 co-crystal structure. Electron density defining the inhibitor (SA Fo-Fc omit map contoured at 2.5σ level) is shown as grey mesh. Representations and color coding scheme same as in Fig. 2, save that the bottom panel depicts comparison of the binding mode of CX-6258 and AMP-PNP to PIM1. Magnesium atoms are depicted as orange spheres.