Insights into protein kinase regulation and inhibition by large scale structural comparison

Abstract

Protein structure determination of soluble globular protein domains has developed into an efficient routine technology which can now be applied to generate and analyze structures of entire human protein families. In the kinase area, several kinase families still lack comprehensive structural analysis. Nevertheless, Structural Genomics (SG) efforts contributed more than 40 kinase catalytic domain structures during the past 4 years providing a rich resource of information for large scale comparisons of kinase active sites. Moreover, many of the released structures are inhibitor complexes that offer chemical starting points for development of selective and potent inhibitors. Here we discuss the currently available structural data and strategies that can be utilized for the development of highly selective inhibitors.

Fig. 1

Kinase architecture and available structural knowledge. (A) Kinase domain organization and structural elements that regulate kinase activity. The upper and lower lobe of the kinase catalytic domain is highlighted in yellow and green, respectively. Elements important for catalytic activity are highlighted and labelled. (B) Release of new kinase structures into the protein data bank (http://www.rcsb.org/pdb/home/home.do) by academic (red), industrial (green) and structural genomics groups (blue). Shown are only human crystal structures considering the date when the structure has been released for the first time. (C) Available crystal structures of kinase catalytic domains mapped onto the phylogenetic tree of the human kinome .

Fig. 2

Binding of Iodotubercidine to haspin and selectivity of the inhibitor. (A) Structural overview showing the structure of the haspin kinase domain in complex with iodotubercidine (pdb: 2vuw). The atypical activation segment of the kinase this kinase is highlighted in blue. The active site shown in the detailed view in B is indicated by a dashed square. (B) Detailed view of the haspin active site in complex with iodotubercidine. Residues interacting with the inhibitor are labelled and shown in stick representation. (C) Selectivity profile showing hits in a screen of 10 μM iodotubercidine against a representative set of 98 human kinases. Hits that showed T_m shifts of more than 10 °C, representing low nm hits are highlighted by large red spheres, T_m shifts 10 °C > T_m > 6 °C (representing > 100 nM to μM hits) are shown by smaller spheres and hits 6 °C > T_m > 4 °C (μM hits) are indicated by very small spheres. Targets with T_m shifts smaller than 4 °C are not shown.