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bioRxiv · 10.1101/2024.05.12.593776

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

Bashore, F. M.·Min, S. M.·Chen, X.·Howell, S.·Rinderle, C. H.·Morel, G.·Silvaroli, J. A.·Wells, C. I.·Bunnell, B. A.·Drewry, D.·Pabla, N. S.·Ultanir, S. K.·Bullock, A. N.·Axtman, A. D.
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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.

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Bashore, F. M., Min, S. M., Chen, X., Howell, S., Rinderle, C. H., Morel, G., Silvaroli, J. A., Wells, C. I., Bunnell, B. A., Drewry, D., Pabla, N. S., Ultanir, S. K., Bullock, A. N., Axtman, A. D.. 2024-05-14. Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2. https://doi.org/10.1101/2024.05.12.593776

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