Structure-Based Design of Novel Chk1 Inhibitors:  Insights into Hydrogen Bonding and Protein−Ligand Affinity

• Published in: Journal of medicinal chemistry 2005-06, Vol.48 (13), p.4332-4345
• Main Authors: Foloppe, Nicolas, Fisher, Lisa M, Howes, Rob, Kierstan, Peter, Potter, Andrew, Robertson, Alan G. S, Surgenor, Allan E
• Format: Article
• Language: English
• Subjects: Adenosine Triphosphate - metabolism; Antineoplastic agents; Binding Sites; Binding, Competitive; Biological and medical sciences; Checkpoint Kinase 1; Crystallography, X-Ray; Drug Design; Enzyme Inhibitors - chemical synthesis; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; General aspects; Humans; Hydrogen Bonding; Kinetics; Ligands; Medical sciences; Models, Molecular; Molecular Conformation; Pharmacology. Drug treatments; Protein Conformation; Protein Kinase Inhibitors - chemical synthesis; Protein Kinase Inhibitors - chemistry; Protein Kinase Inhibitors - pharmacology; Protein Kinases - chemistry; Protein Kinases - metabolism; Pyrimidines - chemical synthesis; Pyrimidines - chemistry; Pyrimidines - pharmacology
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/jm049022c

We report the discovery, synthesis, and crystallographic binding mode of novel furanopyrimidine and pyrrolopyrimidine inhibitors of the Chk1 kinase, an oncology target. These inhibitors are synthetically tractable and inhibit Chk1 by competing for its ATP site. A chronological account allows an objective comparison of modeled compound docking modes to the subsequently obtained crystal structures. The comparison provides insights regarding the interpretation of modeling results, in relationship to the multiple reasonable docking modes which may be obtained in a kinase-ATP site. The crystal structures were used to guide medicinal chemistry efforts. This led to a thorough characterization of a pair of ligand−protein complexes which differ by a single hydrogen bond. An analysis indicates that this hydrogen bond is expected to contribute a fraction of the 10-fold change in binding affinity, adding a valuable observation to the debate about the energetic role of hydrogen bonding in molecular recognition.