Targeting GSK-beta with Peptide Inhibitors: A Rational Computational Strategy for Alzheimer's Disease Intervention

Abstract Glycogen synthase kinase-3 beta is a pivotal serine/threonine kinase implicated in Alzheimers disease (AD) pathogenesis, particularly through the hyperphosphorylation of tau protein and increased production of amyloid-beta (Abeta) peptides. This study investigates kappa casein-derived peptides as potential inhibitors of GSK-3beta. A peptide library of 42 sequences was generated from kappa casein and docking studies identified IP8 (LRFFVAPFPE) as the top candidate for binging to the previously approved inhibition site of GSK-3beta. Molecular dynamics (MD) simulations revealed that IP8 first three residues contributed unfavorably to binding, promoting the design of mutated peptides (MPs) MP27, MP31, and MP39. Of these, MP31 (HPDFVAPFPE) demonstrated the most stable interaction with GSK-3beta, exhibiting the most favorable binding score (-96.6) and interacting with 19 residues of the ATP-binding pocket of the enzyme. Structural analyses confirmed MP31 superior stability, with minimal RMSD deviations, and stable hydrogen bond formation. The results showed that peptide binding stabilizes GSK-3beta by reducing both domain-level dynamics and local side-chain flexibility, leading to a more structurally constrained enzyme. This dual stabilization of the backbone and side chains underscores the critical role of peptide interactions in modulating the conformational landscape of GSK-3beta and potentially obstructing substrate access or product release, which are crucial for enzyme activity. These results suggest that kappa casein-derived peptides, particularly MP31, could be promising therapeutic candidates for inhibiting GSK-3beta in AD.