Fig 4 Best docking solution of MEP into the open pocket (EVE): a(-MEP (leff); b(+)- MEP (right) Phe330 Phe330 The low RMSD and the consistency of calculated site consisting of some aromatic residues such as Trp84 and affinity with experimental activity indicated that the gold Phe330 method and parameter set were reasonable to reproduce the In order to explore the mechanism of action of MEP X-ray structure and could be extended to search and isomers on AChE and explain the reason of their differ- evaluate the binding poses of other AChE ds ences in activity, which is valuable for structure-based accordingly design of MEP derivatives with desired pharmacological On the other hand, comparison of the results of a specific properties, both S and R isomers of MEP were considered ligand from three conformations of AChe demonstrated for GOLD docking runs. ()-MEP and (+)-MEP were that the highest scoring pose was derived from the actual submitted to GOLd separately with the three gate gate conformation and indicated the lowest RMSD. Thus, conformations of AChE to consider the flexibility of the the experimental gate conformation of AChE complexed binding site of AChE with an unknown ligand could be predicted roughly by Fitness scores of the best solutions and detailed inter comparing the fitness score concluded from three gate action indices of both isomers are listed in Table 2.The conformations of achE hydrogen-bond (HB)interaction was evaluated by the dis tance between HB donor and acceptor atoms. The hydro phobic interaction was estimated according to the distance Predicted binding conformation of(-)-MEP between the centroid of aromatic or azepine cycle of MEP with achE and the centroid of the side train of the hydrophobic residue Trp84 or Phe330. Figs. 4, 5, 6 illustrated the binding maps The X-ray structure of AChE illustrated that the active site of (-)-MEP and (+)-MEP with the binding site of three of the enzyme was a deep and narrow gorge with such TcAChE conformations features [39]: a catalytic triad composed of residues The highest score of ()-MEP was found for the open Ser200, Glu327 and His440; a peripheral anionic site at pocket(IEVE), while that of (+)-MEP was found for the the entry centered by residue Trp279; and a hydrophobic closed one (lAC)(Table 2). Although the actual gate 5 Best docking solution of into the half-o T): a()-MEP (lefn); b(+)- Phes 30 Phe330The low RMSD and the consistency of calculated affinity with experimental activity indicated that the GOLD method and parameter set were reasonable to reproduce the X-ray structure and could be extended to search and evaluate the binding poses of other AChE ligands accordingly. On the other hand, comparison of the results of a specific ligand from three conformations of AChE demonstrated that the highest scoring pose was derived from the actual gate conformation and indicated the lowest RMSD. Thus, the experimental gate conformation of AChE complexed with an unknown ligand could be predicted roughly by comparing the fitness score concluded from three gate conformations of AChE. Predicted binding conformation of (−)-MEP with AChE The X-ray structure of AChE illustrated that the active site of the enzyme was a deep and narrow gorge with such features [39]: a catalytic triad composed of residues Ser200, Glu327 and His440; a peripheral anionic site at the entry centered by residue Trp279; and a hydrophobic site consisting of some aromatic residues such as Trp84 and Phe330. In order to explore the mechanism of action of MEP isomers on AChE and explain the reason of their differ￾ences in activity, which is valuable for structure-based design of MEP derivatives with desired pharmacological properties, both S and R isomers of MEP were considered for GOLD docking runs. (−)-MEP and (+)-MEP were submitted to GOLD separately with the three gate conformations of AChE to consider the flexibility of the binding site of AChE. Fitness scores of the best solutions and detailed inter￾action indices of both isomers are listed in Table 2. The hydrogen-bond (HB) interaction was evaluated by the dis￾tance between HB donor and acceptor atoms. The hydro￾phobic interaction was estimated according to the distance between the centroid of aromatic or azepine cycle of MEP and the centroid of the side train of the hydrophobic residue Trp84 or Phe330. Figs. 4, 5, 6 illustrated the binding maps of (−)-MEP and (+)-MEP with the binding site of three TcAChE conformations. The highest score of (−)-MEP was found for the open pocket (1EVE), while that of (+)-MEP was found for the closed one (1ACJ) (Table 2). Although the actual gate Fig. 4 Best docking solution of MEP into the open pocket (1EVE): a (−)-MEP (left); b (+)- MEP (right) Fig. 5 Best docking solution of MEP into the half-open pocket (1VOT): a (−)-MEP (left); b (+)- MEP (right) 394