Structure-Based Design of Potent Selective Nanomolar Type-II Inhibitors of Glycogen Synthase Kinase-3β

Area of Science:

• Medicinal Chemistry
• Computational Drug Design
• Neuroscience

Background:

• Glycogen synthase kinase 3 beta (GSK-3β) is a key target for neurodegenerative diseases.
• Developing selective GSK-3β inhibitors is challenging due to the lack of structural data for certain conformations.
• Type-II inhibitors offer a promising avenue for targeting kinases.

Purpose of the Study:

• To present the in silico design, screening, and in vitro validation of novel GSK-3β type-II inhibitors.
• To explore a computational modeling approach for designing inhibitors targeting the DFG-out conformation.
• To evaluate the potential of these inhibitors in cellular models of neuroprotection.

Main Methods:

• Computational modeling including adapted DOLPHIN, Prime loop refinement, induced-fit docking, and molecular dynamics.
• Virtual screening of the ZINC database (Biogenics subset).
• In vitro isolated enzyme assays and ex vivo cell-based assays (SH-SY5Y cell lines).

Main Results:

• Initial virtual screening identified two low micromolar GSK-3β inhibitors.
• Structure-activity relationship studies on analogues led to five potent nanomolar inhibitors, including compound 23 (IC50 = 0.087 μM).
• Compound 23 demonstrated >100-fold increased potency over Phase I compounds and selectivity against homologous kinases.
• Ex vivo studies showed promising neuroprotective effects against tau hyperphosphorylation at low micromolar concentrations.

Conclusions:

• The in silico design and validation strategy successfully identified potent and selective GSK-3β type-II inhibitors.
• Type-II inhibitor design represents a viable strategy for developing clinically effective GSK-3β inhibitors.
• These findings suggest potential therapeutic applications in neurodegenerative diseases.