Conformational Analysis of the DFG-Out Kinase Motif and Biochemical Profiling of Structurally Validated Type II Inhibitors

• Published in: Journal of medicinal chemistry Vol. 58; no. 1; pp. 466 - 479
• Main Authors: Vijayan, R. S. K., He, Peng, Modi, Vivek, Duong-Ly, Krisna C., Ma, Haiching, Peterson, Jeffrey R., Dunbrack, Roland L., Levy, Ronald M.
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 08.01.2015
• Subjects: Allosteric Regulation; Allosteric Site; Amino Acid Motifs; Amino Acid Sequence; Biocatalysis - drug effects; Databases, Protein; Humans; Models, Molecular; Molecular Structure; Protein Binding; Protein Conformation; Protein Kinase Inhibitors - chemistry; Protein Kinase Inhibitors - metabolism; Protein Kinase Inhibitors - pharmacology; Protein Kinases - chemistry; Protein Kinases - metabolism; Protein Structure, Tertiary; Proteome - antagonists & inhibitors; Proteome - chemistry; Proteome - metabolism; Small Molecule Libraries - chemistry; Small Molecule Libraries - metabolism; Small Molecule Libraries - pharmacology
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/jm501603h

Structural coverage of the human kinome has been steadily increasing over time. The structures provide valuable insights into the molecular basis of kinase function and also provide a foundation for understanding the mechanisms of kinase inhibitors. There are a large number of kinase structures in the PDB for which the Asp and Phe of the DFG motif on the activation loop swap positions, resulting in the formation of a new allosteric pocket. We refer to these structures as “classical DFG-out” conformations in order to distinguish them from conformations that have also been referred to as DFG-out in the literature but that do not have a fully formed allosteric pocket. We have completed a structural analysis of almost 200 small molecule inhibitors bound to classical DFG-out conformations; we find that they are recognized by both type I and type II inhibitors. In contrast, we find that nonclassical DFG-out conformations strongly select against type II inhibitors because these structures have not formed a large enough allosteric pocket to accommodate this type of binding mode. In the course of this study we discovered that the number of structurally validated type II inhibitors that can be found in the PDB and that are also represented in publicly available biochemical profiling studies of kinase inhibitors is very small. We have obtained new profiling results for several additional structurally validated type II inhibitors identified through our conformational analysis. Although the available profiling data for type II inhibitors is still much smaller than for type I inhibitors, a comparison of the two data sets supports the conclusion that type II inhibitors are more selective than type I. We comment on the possible contribution of the DFG-in to DFG-out conformational reorganization to the selectivity.