Design and Identification of Dual-Target AChE/GSK-3β Inhibitors for Alzheimer’s Disease Through Structure-Based Pharmacophore Modelling, Virtual Screening, and RDKit-Based Lead Optimization

Author

Mrs. Tamilarasi G, Ajin TS, Hameedhash R, Archana A, Priya M, Srimathi D

Abstract

 Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder in which cholinergic deficit, amyloid-β aggregation, tau hyperphosphorylation, neuroinflammation and oxidative stress act as an interconnected network, limiting the benefit of single-target drugs such as donepezil and memantine. This study applied a multi-target-directed ligand (MTDL) strategy to identify small molecules capable of inhibiting both acetylcholinesterase (AChE; PDB 4EY7, reference ligand donepezil) and glycogen synthase kinase-3β (GSK-3β; PDB 1Q5K, reference ligand AR-A014418).Ligands were prepared using Meeko, while protein preparation, visualization, and complex generation were performed using UCSF ChimeraX. Docking was conducted using AutoDock Vina, followed by protein–ligand interaction analysis using ChimeraX, BIOVIA Discovery Studio, and PLIP and the resulting ligand-interaction coordinates were used to build a four-point dual-target pharmacophore in Pharmit, combining the GSK-3β hinge (Val135) and hydrophobic (Val110, Tyr134) features with an AChE aromatic anchor (Tyr86). Screening of the ZINC, Mcule and MolPort libraries returned 500 hits, from which five candidates with complementary AChE/GSK-3β binding were shortlisted . The synthetically accessible lead Z636067564 was modified using RDKit to generate benzimidazole and p-cresol analogues. The benzimidazole analogue showed balanced dual-target docking scores (GSK-3β −8.166 kcal/mol; AChE −10.544 kcal/mol), zero Lipinski, GSK or PAINS violations, and a favourable synthetic accessibility score of 2.0, and was selected for experimental synthesis. High predicted hERG and hepatotoxicity probabilities for both analogues indicate that further structural optimisation and experimental validation are required.

Keywords

Alzheimer's disease; multi-target-directed ligand (MTDL); acetylcholinesterase; glycogen synthase kinase-3β; pharmacophore modelling; molecular docking; virtual screening; ADMET

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References

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