ZNL0325, a Pyrazolopyrimidine-Based Covalent Probe, Demonstrates an Alternative Binding Mode for Kinases

Zhengnian Li, Wenchao Lu, Tyler S. Beyett, Scott B. Ficarro, Jie Jiang, Jason Tse, Audrey Yong-Ju Kim, Jarrod A. Marto, Jianwei Che, Pasi A. Jänne, Michael J. Eck, Tinghu Zhang, and Nathanael S. Gray

Journal of Medicinal Chemistry 2024-5
DOI: 10.1021/acs.jmedchem.3c01891

The pyrazolopyrimidine (PP) heterocycle is a versatile and widely deployed core scaffold for the development of kinase inhibitors. Typically, a 4-amino-substituted pyrazolopyrimidine binds in the ATP-binding pocket in a conformation analogous to the 6-aminopurine of ATP. Here, we report the discovery of ZNL0325 which exhibits a flipped binding mode where the C3 position is oriented toward the ribose binding pocket. ZNL0325 and its analogues feature an acrylamide side chain at the C3 position which is capable of forming a covalent bond with multiple kinases that possess a cysteine at the αD-1 position including BTK, EGFR, BLK, and JAK3. These findings suggest that the ability to form a covalent bond can override the preferred noncovalent binding conformation of the heterocyclic core and provides an opportunity to create structurally distinct covalent kinase inhibitors.