Systematic comparison of competitive and allosteric kinase inhibitors reveals common structural characteristics

Allosteric and ATP-competitive kinase inhibitors act by distinct mechanisms and are expected to have high and low kinase selectivity, respectively. This also raises the question whether or not these different types of inhibitors might be structurally distinct. To address this question, we have assembled data sets of currently available competitive and allosteric kinase inhibitors confirmed by X-ray crystallography and systematically compared these compounds on the basis of different structural criteria. Many competitive and allosteric inhibitors were found to contain the same or similar substructures and a subset of allosteric inhibitors was found to share core structures with ATP site-directed inhibitors. In some instances, small chemical modifications of common cores were found to yield either allosteric or competitive inhibitors. Hence, these different categories of inhibitors with distinct mechanisms of action were often structurally related and represented much more of a structural continuum than discrete states. Additional target annotations were frequently identified for competitive inhibitors, but were rare for allosteric inhibitors. As a part of this study, our collection of kinase inhibitors and the associated information are made freely available to enable further assessment of chemical modifications that distinguish similar kinase inhibitors with distinct mechanisms of action.

Mapping Biological Activities to Different Types of Molecular Scaffolds: Exemplary Application to Protein Kinase Inhibitors

Scaffolds were originally introduced to delineate core structures of active compounds. They are also used to assess the ability of computational methods to identify structurally diverse active compounds. Biological activities of compound series are often mapped to scaffolds. This is done to better understand activity distributions over different structural classes or search for core structures of compounds that are preferentially active against target families of interest. Herein, we describe in detail how such scaffold activity profiles are generated and compare profiles for differently defined scaffolds. As an exemplary application, scaffolds of currently available kinase inhibitors covering the human kinome are analyzed.