Fragment based lead discovery of small molecule inhibitors for the EPHA4 receptor tyrosine kinase

• Published in: European journal of medicinal chemistry 2012, Vol.47 (1), p.493-500
• Main Authors: van Linden, Oscar P.J., Farenc, Carine, Zoutman, Willem H., Hameetman, Liesbeth, Wijtmans, Maikel, Leurs, Rob, Tensen, Cornelis P., Siegal, Gregg, de Esch, Iwan J.P.
• Format: Article
• Language: English
• Subjects: Adenosine Triphosphate - metabolism; Antineoplastic agents; Binding Sites; Biological and medical sciences; Cancer; Computational Biology; Crystallization; Docking; Drug Discovery - methods; EPH receptor; EPHA4; Ephrin; Fragment; General aspects; In silico; Inhibition; Kinase; Medical sciences; Models, Molecular; Pharmacology. Drug treatments; Pharmacophore; Protein Conformation; Protein Kinase Inhibitors - chemistry; Protein Kinase Inhibitors - pharmacology; Receptor, EphA4 - antagonists & inhibitors; Receptor, EphA4 - chemistry; Receptor, EphA4 - metabolism; Screening; Small Molecule Libraries - chemistry; Small Molecule Libraries - pharmacology
• ISSN: 0223-5234; 1768-3254
• DOI: 10.1016/j.ejmech.2011.11.020

The in silico identification, optimization and crystallographic characterization of a 6,7,8,9-tetrahydro-3 H-pyrazolo[3,4- c]isoquinolin-1-amine scaffold as an inhibitor for the EPHA4 receptor tyrosine kinase is described. A database containing commercially available compounds was subjected to an in silico screening procedure which was focused on finding novel, EPHA4 hinge binding fragments. This resulted in the identification of 6,7,8,9-tetrahydro-3 H-pyrazolo[3,4- c]isoquinolin-1-amine derivatives as EPHA4 inhibitors. Hit exploration yielded a compound with 2 μM (IC 50) affinity for the EPHA4 receptor tyrosine kinase domain. Soaking experiments into a crystal of the EPHA4 kinase domain gave a 2.11Å X-ray structure of the EPHA4 – inhibitor complex, which confirmed the binding mode of the scaffold as proposed by the initial in silico work. The results underscore the strength of fragment based in silico screening as a tool for the discovery of novel lead compounds as small molecule kinase inhibitors. [Display omitted] ► In silico screening used to identify hinge binding fragments. ► Characterization of novel EPHA4 inhibitors. ► Hit exploration yielded a compound with 2 μM (IC 50) affinity for EPHA4. ► Soaking into a crystal of EPHA4 confirmed the binding mode.