Cholinesterase inhibitors (ChE-Is) are the standard of therapy for treatment of patients with Alzheimer’s disease (AD) and are the only class of drugs approved by the Food and Drug Administration (FDA) for treatment of this condition. In this paper we used the new approach utilizing cheminformatics tools such as CORINA, Yet Another Scientific Artificial Reality Application (YASARA), and molecular docking program to identify binding affinity and mechanism of interaction between the ChE-Is with the target proteins. This approach should be helpful to understand the selectivity of the given drug molecule in the treatment of Alzheimer’s disease.