Histidine Focused Covalent Inhibitors Targeting Acetylcholinesterase: A Computational Pipeline for Multisite Therapeutic Discovery in Alzheimer’s Disease

Alzheimer’s
disease affects over 10% of individuals above
the age of 65, yet current treatments offer only limited and temporary
relief. Acetylcholinesterase, a key enzyme in neurotransmitter breakdown,
also contributes to disease progression by promoting β-amyloid
aggregation. While previous studies have focused on the catalytic
serine, a key proton transfer residue, His447 remains unexplored as
a potential covalent binding site. In this study, we aim to interrupt
the activation of Ser203 by covalently modifying His447, thereby shutting
down the entire catalytic process. Here, we reported a computational
pipeline to identify epoxide-based small molecules that covalently
engage His447 and modulate AChE activity. From a curated library of
>7,000 epoxides, three ligands (L5, L6, L7) were selected via covalent
docking, molecular dynamics simulations, and drug-likeness profiling.
Microsecond-scale simulations revealed stable binding across multiple
subsites, with L5 exhibiting the most consistent RMSD and compact Rg values. Covalent engagement of L5 and L6 induced
modest shifts in His447 (2.48 and 1.43 Å), whereas L7 maintained
apo-like geometry. Furthermore, ADMET predictions indicated favorable
profiles, with no cardiotoxicity risk. Our findings highlight His447
as a novel covalent target in AChE and support further in vivo investigation
of the specificity and inhibitory mechanisms of these ligands.