Alzheimer’s and D2M are the metabolic syndromes that are interlinked due to interaction of regulatory proteins or enzymes such as AchE and BchE. The function of AchE and BchE relies on specific regulation on its expression and localization in biological systems has been proved experimentally, and the interaction study and docking with virtual ligands has been conducted in the present work. Prediction of the binding of a ligand to a target protein is important in computational drug design and discovery. Alzheimer’s and D2M are the metabolic syndromes that are interlinked due to interaction of regulatory proteins such as AchE and BchE. Docking has been made for the energy minimized ligands with the AchE (2X8B.pdb) and BchE (2XMB.pdb) proteins using docking softwares such as AutoDock, Hex and iGemDock. Docking results predicted that Huperzine and Galanthamine have better drug activity with AchE protein. Docking results also predicted that Dibucaine and propionyl thiocholine have better drug activity with BchE.