Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2

  • bioRxiv. 2024 May 14:2024.05.12.593776. doi: 10.1101/2024.05.12.593776.
Frances M Bashore  1 ,  Sophia M Min  1 ,  Xiangrong Chen  2 ,  Stefanie Howell  1 ,  Caroline H Rinderle  3 ,  Gabriel Morel  4 ,  Josie A Silvaroli  5 ,  Carrow I Wells  1 ,  Bruce A Bunnell  3 ,  David H Drewry  1  6 ,  Navjot S Pabla  5 ,  Sila K Ultanir  4 ,  Alex N Bullock  2 ,  Alison D Axtman  1
Affiliations
  • 1. Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • 2. Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK.
  • 3. Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA.
  • 4. Kinases and Brain Development Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
  • 5. Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210, United States of America.
  • 6. UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
PMID: 38798634 DOI: 10.1101/2024.05.12.593776
Abstract

Acylaminoindazole-based inhibitors of CDKL2 were identified via analyses of cell-free binding and selectivity data. Compound 9 was selected as a CDKL2 chemical probe based on its potent inhibition of CDKL2 enzymatic activity, engagement of CDKL2 in cells, and excellent kinome-wide selectivity, especially when used in cells. Compound 16 was designed as a negative control to be used alongside compound 9 in experiments to interrogate CDKL2-mediated biology. A solved co-crystal structure of compound 9 bound to CDKL2 highlighted key interactions it makes within its ATP-binding site. Inhibition of downstream phosphorylation of EB2, a CDKL2 substrate, in rat primary neurons provided evidence that engagement of CDKL2 by compound 9 in cells resulted in inhibition of its activity. When used at relevant concentrations, compound 9 does not impact the viability of rat primary neurons or certain breast Cancer cells nor elicit consistent changes in the expression of proteins involved in epithelial-mesenchymal transition.

Keywords
CDKL2; acylaminoindazole; chemical probe; cyclin dependent kinase-like 2; epithelial–mesenchymal transition; protein kinase.
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