Designing dual binding site acetylcholinesterase inhibitors ……

The bis (7)-tacrine bound co-crystal structure of AChE enzyme (PDB ID: 2CKM)

was used to describe the binding pocket having a grid size of 10 Å. New AChEIs

were originated from a fragment “seed” structure based on the Genetic Algorithm

(GA) procedure, which runs under generational-replacement mode of LigBuilder

Software (Wang et al , 2000). To allow the growth of fragment seed into new

compounds the growing site must be defined in the seed structures. Two criteria

were taken into considering while defining the site, first the growth of compound

should not result in steric clashes with the amino acids in the active site and it

could grow towards the PAS. Each seed allowed to grow on the selected grow

points. We have selected different hydrogen atoms in all the 31 seeds as growing

points. GROW module was used to generate ligands based on its inbuilt fragment

library, which contains various molecular fragments as building-blocks to build

ligands. This library contains nearly 60 fragments, including most of the common

chemical groups and ring frameworks observed in organic compounds. We

allowed the molecules to grow up to 50 generations. The compounds generated

by GROW module were collected and used as an input for the PROCESS module.

New compounds generation

LigBuilder software was used to design new AChEIs by considering the structural

requirements of AChE enzyme active site (Wang et al , 2000). We generated 3097

new compounds by the GROW module of LigBuilder from 31 fragment seeds

as shown in Figure 1. For fragment growing, functional groups are added to the

initial detected seed fragment, guided by fragment binding orientation. Fragment

binding in the proximal regions in active site are obtained by deconstructing the

known AChEIs, which might be beneficial for improving the synthetic feasibility

of the new compounds. The bis(7)-tacrine bound co-crystal structure of AChE

enzyme (PDB ID: 2CKM) having resolution 2.15 Å is taken as a reference

structure for building the ligands (Pang et al , 1996). This structure is selected as

a target structure because bis (7)-tacrine was the first purposely designed potent

and selective dual binding site inhibitor of AChE enzyme by utilizing computer

modeling of ligand docking with the target proteins. This was done to identify low

affinity sites normally missed by X-ray crystallography and design bi-functional

analogs capable of simultaneous binding at the CS and PAS respectively (Pang

et al , 1996). Applying this strategy to 9-amino-1,2,3,4-tetrahydroacridine (THA)

or tacrine, a drug for AD, the alkylene linked bis-THA analogs were discovered.

These analogs were up to 10,000-fold more selective and 1,000-fold more potent

than THA in inhibiting AChE enzyme.

ADMET filtering

ADMET (absorption, distribution, metabolism, excretion, toxicity) properties of

the compounds at the early stages of the discovery are very important indicator for

Int. J. Bioinformatics and Biological Sci.: v.2 n.1&2, p. 111-126. March & June 2014

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