ORIGINAL RESEARCH 3D-pharmacophore model based virtual screening to identify dual-binding site and selective acetylcholinesterase inhibitors Shikhar Gupta • C. Gopi Mohan Received: 4 March 2010 / Accepted: 15 May 2010 Ó Springer Science+Business Media, LLC 2010 Abstract The formation of b-amyloid plaques in the brain is a key neurodegenerative event in Alzheimer’s disease (AD). Interestingly, research on acetylcholinester- ase (AChE) enzyme has increased due to findings sup- porting this enzyme involvement in the b-amyloid peptide fibril formation during AD pathogenesis. In this investi- gation, chemical features based 3D pharmacophore models were developed from structurally diverse xanthostigmine derivatives, known inhibitors of AChE enzyme, using 3D- QSAR pharmacophore generation module in Discovery Studio2.5 (DS2.5). The constructed pharmacophore models for AChE inhibitors was further cross-validated using test set and Cat-Scramble methodology. The best quantitative pharmacophore model Hypo1, was used for screening the chemical databases of small compounds including Specs, NCI, and IBScreen, to identify the new compounds that are presumably able to act as dual-binding site AChE inhibi- tors. The screened virtual hits were then subjected to the Lipinski’s rule of five, blood–brain barrier (BBB), PSA, LogS, percent human oral absorption, and toxicity analysis. Finally, 32 compounds were identified as potential leads against AChE enzyme, showing good estimated activities and promising ADMET properties. Molecular docking of these compounds using FlexX software showed catalytic and peripheral anionic binding site interactions, so called dual binding of the AChE enzyme. Docking study was also performed on butyrylcholinesterase in order to understand the compound selectivity. This study may assist in the discovery and design of novel dual binding site and selective AChE inhibitors with potent inhibitory activity. Keywords Acetylcholinesterase inhibitors Á Alzheimer’s disease Á Pharmacophore modelling Á Virtual screening Á Dual-binding site Introduction Alzheimer’s disease (AD), the most common form of neurodegenerative dementia, is associated with selective loss of cholinergic neurons and reduced levels of acetyl- choline neurotransmitter. AD is characterized by progres- sive loss of memory and impairment in cognition, which is becoming a serious threat to life expectancy for elderly people (Inestrosa et al., 2008; Butters et al., 1995). The main pathological changes in the AD brain are the for- mation of extracellular senile plaques consisting of aggre- gated amyloid-b-peptide (Ab) deposits and intracellular neurofibrillary tangles consisting of abnormally phosphor- ylated microtubule associated protein. In the past two decades, huge research effort has been done to understand the molecular pathogenesis of AD. However, the only symptomatic treatment proven to be effective to date is the use of cholinesterase inhibitors (ChEI) to augment sur- viving cholinergic activity by increasing the level of ace- tylcholine (Ach) within cholinergic synapses. Thus, out of the five FDA-approved drugs, four of them are primarily inhibitors of the enzyme acetylcholinesterase (donepezil, tacrine, rivastigmine, and galanthamine) have been laun- ched on the market for the symptomatic treatment of AD. Acetylcholinesterase (AChE; EC 3.1.1.7) and butyr- ylcholinesterase (BuChE; EC 3.1.1.8) enzymes are found in the central nervous system (CNS). AChE and BuChE S. Gupta Á C. Gopi Mohan (&) Centre for Pharmacoinformatics, National Institute of Pharmaceutical Education & Research (NIPER), S.A.S. Nagar, Phase X, Mohali 160062, Punjab, India e-mail: cmohan@niper.ac.in; TUcgopimohan@yahoo.comUT Med Chem Res DOI 10.1007/s00044-010-9373-7 MEDICINAL CHEMISTR Y RESEARCH