A clinical casein kinase 2 inhibitor, CX-4945 (silmitasertib),
shows significant affinity toward the DYRK1A and GSK3β kinases,
involved in down syndrome phenotypes, Alzheimer’s disease,
circadian clock regulation, and diabetes. This off-target activity
offers an opportunity for studying the effect of the DYRK1A/GSK3β
kinase system in disease biology and possible line extension. Motivated
by the dual inhibition of these kinases, we solved and analyzed the
crystal structures of DYRK1A and GSK3β with CX-4945. We built
a quantum-chemistry-based model to rationalize the compound affinity
for CK2α, DYRK1A, and GSK3β kinases. Our calculations
identified a key element for CK2α’s subnanomolar affinity
to CX-4945. The methodology is expandable to other kinase selectivity
modeling. We show that the inhibitor limits DYRK1A- and GSK3β-mediated
cyclin D1 phosphorylation and reduces kinase-mediated NFAT signaling
in the cell. Given the CX-4945’s clinical and pharmacological
profile, this inhibitory activity makes it an interesting candidate
with potential for application in additional disease areas.