A chemical probe for dark kinase Stk17b derives its potency and high selectivity through a unique P-Loop conformation

DOI: 10.1021/acs.jmedchem.0c01174

Authors: Alfredo Picado (Structural Genomics Consortium, University of North Carolina at Chapel Hill) , Apirat Chaikuad (Goethe University Frankfurt; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS)) , Carrow I. Wells (Structural Genomics Consortium, University of North Carolina at Chapel Hill) , Safal Shrestha (University of Georgia) , William J. Zuercher (Structural Genomics Consortium, University of North Carolina at Chapel Hill) , Julie E. Pickett (Structural Genomics Consortium, University of North Carolina at Chapel Hill) , Frank E. Kwarcinski (Luceome Biotechnologies) , Parvathi Sinha (Luceome Biotechnologies) , Chandi S. De Silva (Luceome Biotechnologies) , Reena Zutshi (Luceome Biotechnologies) , Shubin Liu (Structural Genomics Consortium, University of North Carolina) , Natarajan Kannan (University of Georgia) , Stefan Knapp (Goethe University Frankfurt; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS); German Translational Cancer Network (DKTK); Frankfurt Cancer Institute (FCI)) , David H. Drewry (Structural Genomics Consortium, University of North Carolina at Chapel Hill) , Timothy M. Willson (Structural Genomics Consortium, University of North Carolina)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Journal Of Medicinal Chemistry

State: Published (Approved)
Published: November 2020
Diamond Proposal Number(s): 442

Abstract: STK17B is a member of the death-associated protein kinase family and has been genetically linked to the development of diverse diseases. However, the role of STK17B in normal and disease pathology is poorly defined. Here, we present the discovery of thieno[3,2-d] pyrimidine SGC-STK17B-1 (11s), a high-quality chemical probe for this understudied “dark” kinase. 11s is an ATP-competitive inhibitor that showed remarkable selectivity over other kinases including the closely related STK17A. X-ray crystallography of 11s and related thieno[3,2-d]pyrimidines bound to STK17B revealed a unique P-loop conformation characterized by a salt bridge between R41 and the carboxylic acid of the inhibitor. Molecular dynamic simulations of STK17B revealed the flexibility of the P-loop and a wide range of R41 conformations available to the apo-protein. The isomeric thieno[2,3-d]pyrimidine SGC-STK17B-1N (19g) was identified as a negative control compound. The >100-fold lower activity of 19g on STK17B was attributed to the reduced basicity of its pyrimidine N1.

Journal Keywords: Assays; Inhibitors; Inhibition; Peptides and proteins; Selectivity

Subject Areas: Chemistry, Biology and Bio-materials, Medicine


Instruments: I02-Macromolecular Crystallography

Other Facilities: BESSY II; DESY