Alzheimer’s Disease (AD) is one of the significant diseases of the aging population and affects Central Nervous System dominantly. Blood-brain-barrier permeation is a substantial complication in developing CNS drugs, and it is considered challenging with minimal success rates. Although Glycogen synthase kinase-3β (GSK-3β) is an attractive disease-modifying target for AD, there is no single GSK-3β inhibitor in clinical trials for AD. Here we performed structure-based virtual screening on the Chembridge CNS-Set library compounds. 10 hits were identified based on interaction, binding energy, and dock score. These 10 chosen compounds showed a potential ADME profile and were then investigated for in vitro kinase inhibitory activity against GSK-3β and other AD-related kinases. Among these, the molecule 7114202 showed 48% GSK-3β inhibition while showing selectivity over other AD-related kinases. Molecular dynamic simulations of apoenzyme, co-crystallized molecule, and 7114202 validated the Lys85, Val135, Leu188, Asp200 located in the active site of enzyme plays a significant role for GSK-3β complex formation with inhibitors, and they are responsible for activity and selectivity. The in vitro studies also revealed a potent and selective Casein Kinase 1ε (CK1ε) inhibitor 7774767 with IC50 5.10 µM.