AbstractBackgroundOne of the cruelest neurogenerative disorder is Alzheimer disease (AD) which majorly affects old aged humans. It initially affects a person’s ability to carry out daily functions and leads to death. Basically, many diverse factors are leading to neuronal cell death such as low level of acetylcholine, deposition of amyloid beta, aggregation of tau proteins, oxidative stress, neuro‐inflammation, excitotoxicity, genetic and heredity factors. Some of the recent reports also outline about AD and it was characterized by different hypothesis and are named as cholinergic hypothesis, amyloid hypothesis, tau hypothesis and others (oxidative stress and genetic). Therefore, the present study focused to identify a potential inhibitor to control the level of Alzheimer disease.MethodWe have selected two different databases (ZINC15 and DUNDEE) and four different enzymes (Acetylcholinesterase, Butyrylcholinesterase, β‐Secretase and Glycogen synthase kinase 3 beta) for the study and carried out the high throughput virtual screening (HTVS), molecular docking, molecular dynamics simulation and binding free energy calculation to understand the active site effects and its stability.ResultIn the AChE and BChE, the screened molecules are showing good binding with strong interactions; notably, π‐cationic interactions were observed between amine group of ligand and tyrosine, tryptophan residues of AChE. Whereas in the BChE, active site residue Glu197 is highly stable. The catalytic dyad residue Asp93 of BACE1 maintains their hydrogen bond and Asp133 of GSK3β also sustain the strong interactions during the MD simulation. Apart from this, the statistical parameters (RMSD, RMSF and Rg) of these complexes are acceptable.ConclusionIn‐silico based analyses demonstrate that all the selected molecules are forming strong hydrogen bonding with catalytic residues and these interactions are highly stable during the atomistic simulation with high affinity. This comparative study allows to understand binding affinity, stability of intermolecular interactions and molecular flexibility of the molecules in the active site of AChE/BChE enzymes. Computational understanding of unproven molecules may lead towards the developing against AD.