Rational design of k-casein peptides to modulate GSK-3B dynamics for Alzheimer's therapy

GSK-3β is an important therapeutic target in Alzheimer's disease due to its central role in tau hyperphosphorylation, and synaptic dysfunction. In this study, a κ-casein-derived peptide (LALTLPFLGA) was identified via HADDOCK and introduced to MD simulations for MM/PBSA per-residue analysis, revealing four unfavorable mutation sites (L12, L14, T15, F18). Using MCSM and ΔΔG-based substitution, a 48-peptide library was generated; 22 candidates satisfied toxicity/allergenicity filters. Docking and MD simulations prioritized four leads-PEP8, PEP36, PEP40, and PEP44-with PEP8 (- 89.1 kcal·mol⁻¹) and PEP44 (- 88.4 kcal·mol⁻¹) as top binders. These mutants, all carrying L12H/L14H substitutions, demonstrated stronger HADDOCK scores (- 89.1 to - 84.6 kcal/mol) compared with the template. Additionally, PEP8 carried F18→Asp, and T15→Leu/Ile developed affinity in other mutants. PEP8 established 21 contacts, followed by PEP44 (19), PEP40 (17), and PEP36 (15), indicating that larger interaction networks are vital for binding. PEP8 contacted with the ATP-binding pocket (Val135, Thr138, and Tyr134), whereas PEP44 contacted catalytic Asp200. MD results also showed reduced RMSD, slightly lower Rg/SASA, and tighter PCA clustering, exhibiting that PEP8 and PEP44 induced compaction and restricted conformational freedom, and possibly, hindering substrate binding. MMPBSA confirmed PEP44 and PEP8 as strongest complexes (- 188.482 and - 184.404 kJ/mol), governed by van der Waals and electrostatic contacts, while PEP36 suffered solvation penalties and PEP40 remained hydrophobic-driven. Together, our computational pipeline highlights PEP8 and PEP44 as promising κ-casein-derived inhibitors of GSK-3β, illustrating a rational design of food-derived peptides as potential multifunctional candidates for Alzheimer's disease.