Scaffold mining of kinase hinge binders in crystal structure database

• Published in: Journal of computer-aided molecular design 2014-01, Vol.28 (1), p.13-23
• Main Authors: Xing, Li, Rai, Brajesh, Lunney, Elizabeth A.
• Format: Article
• Language: English
• Subjects: Animal Anatomy; Binders; Binding; Binding Sites; Chemistry; Chemistry and Materials Science; Computer Applications in Chemistry; Crystal structure; Crystallography, X-Ray; Databases, Protein; Hinges; Histology; Humans; Hydrogen Bonding; Inhibitors; Kinases; Morphology; Pharmaceutical sciences; Physical Chemistry; Protein Binding; Protein Conformation; Protein Kinase Inhibitors - chemistry; Protein Kinases - chemistry; Proteins; Scaffolds; Software
• ISSN: 0920-654X; 1573-4951
• DOI: 10.1007/s10822-013-9700-4

Protein kinases are the second most prominent group of drug targets, after G-protein-coupled receptors. Despite their distinct inhibition mechanisms, the majority of kinase inhibitors engage the conserved hydrogen bond interactions with the backbone of hinge residues. We mined Pfizer internal crystal structure database (CSDb) comprising of several thousand of public as well as internal X-ray binary complexes to compile an inclusive list of hinge binding scaffolds. The minimum ring scaffolds with directly attached hetero-atoms and functional groups were extracted from the full compounds by applying a rule-based filtering procedure employing a comprehensive annotation of ATP-binding site of the human kinase complements. The results indicated large number of kinase inhibitors of diverse chemical structures are derived from a relatively small number of common scaffolds, which serve as the critical recognition elements for protein kinase interaction. Out of the nearly 4,000 kinase-inhibitor complexes in the CSDb we identified approximately 600 unique scaffolds. Hinge scaffolds are overwhelmingly flat with very little sp3 characteristics, and are less lipophilic than their corresponding parent compounds. Examples of the most common as well as the uncommon hinge scaffolds are presented. Although the most common scaffolds are found in complex with multiple kinase targets, a large number of them are uniquely bound to a specific kinase, suggesting certain scaffolds could be more promiscuous than the others. The compiled collection of hinge scaffolds along with their three-dimensional binding coordinates could serve as basis set for hinge hopping, a practice frequently employed to generate novel invention as well as to optimize existing leads in medicinal chemistry.