Designing dual binding site acetylcholinesterase inhibitors ……

taking the advantage of a large number of available crystal structures of AChE

enzyme with structurally diverse inhibitors. The 18 co-crystallized inhibitors of

the AChE enzyme from PDB were selected and dissected into 31 chemically

diverse and commercially available fragments with low molecular weight (≤ 300

Da). In the process of fragment generation by dissecting known co-crystallized

AChEIs, we have retained the spatial positions and orientations of fragments for

their 3D interactions with the AChE binding pocket. Hence, FBDD approaches

allow for a greater coverage of chemical space and generally produce higher

efficiency ligands. Its novelty lies in the fact that fragments obtained by chopping

different co-crystallized inhibitors of the AChE enzyme from PDB and their bio-

active conformations were used as building blocks for the generation of new dual

binding site leads against AChE enzyme.

materials and methods

An outline of fragment based approach used in the present study is schematically

depicted in Figure 1.

fragment generation

Compared to other de novo methods in FBDD, our strategy is unique to take

advantage of both i.e. the interaction information from the PDB and chemical

diversity for the generation of new dual binding site of AChEIs. In the first step,

known structurally diverse co-crystallized AChEIs were superimposed on the

bis (7)-tacrine bound co-crystal structure of AChE enzyme. Then other AChEIs

were deconstructed into small fragments according to predefined fragmentation

rules. The fragments that bound to the adjacent sites of the target protein were

then grown to create the desired and novel compounds. AChEIs with good AChE

inhibitory activities and structural diversity have fully probed and occupied almost

all regions in the active site. In addition, without any artificial modifications, the

generated component fragments will maintain their original spatial positions and

orientations.Thus,thefragmentbindingconformationsaremoreaccuratethanthose

predicted with fragment docking. We used structurally diverse 18 co-crystallized

inhibitors of the AChE enzyme. AChEIs within the co-crystallized structures

were superimposed onto the reference crystal structure used for the binding site

generation. Therefore, the binding conformations of these AChEIs were well-

aligned in the same dual binding site and extracted from the complex structures to

generate molecular fragments. These were further used as seeds to generate new

dual binding site AChEIs and their molecular structure are presented in Figure 2.

Compound deconstruction rules are also very important in fragment generation.

Retrosynthetic combinatorial analysis procedure (RECAP) is a classical method

that includes 11 fragmentation rules based on retrosynthetic chemistry knowledge

(Lewell et al , 1998). Correct fragments were generated by dissecting the aligned

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

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