Molecular mdelingThe chemical structures of inhibitors, shown in
Table 1 were designed using Hyperchem software (version 7, Hypercube Inc.). Conformational analysis of the desired compounds was performed through Semi-empirical molecular orbital calculations (PM3) method using HYPERCHEM software. The molecular structures were optimized using Polak-Ribiere (conjugate gradient) algorithm until the root mean square (RMS) gradient was 0.01 kcal mol
-1. Among all energy minima conformers, the global minimum of compounds were used in docking calculations and the resulted geometry was transferred into Autodock (version 4.2) program package, which was developed by Arthur J. Olson Chemometrics Group (12 (
link)). The structure of docked
N-phenyl substituent of phthalimide (1 (
link)-16 (
link)),
N-[3-methyl-(2-pyridinyl)] phthalimide (19) and
N-(3-amino-2-methylphenyl) succinimide (20) are shown in
Table 1.
DockingDocking calculations were performed using Autodock software (version 4.2). A model of Na channel open pore was used as a receptor. This open pore model was developed based on homology model of the crystal structures of K channels (11 (
link)). The model constructed by homology with potassium channel structures was reasonably successful in accounting for inner pore residue interactions with local anesthetics and anticonvulsant drugs like phenytoin. Desired compounds were docked into the active site as well as phenytoin which were acting as our reference drug and validation of our technique.
Docking was done using AutoDock4.2, in order to assign the perfect grid of each ligand, grid box values were obtained from trial and error and previous studies (13 (
link)-15 (
link)). Grid maps with 60×60×60 points were constructed and the grid point spacing was 0.375 Å (16 (
link)). The implementing Lamarckian Genetic Algorithm (LGA), considered as one of the best docking methods available in AutoDock, was adopted to perform the molecular docking studies. The parameters for LGA were defined as follows: a maximum number of 250,000 energy evaluations; a maximum number of generations of 27,000; and mutation and crossover rates of 0.02 and 0.8, respectively. Pseudo-Solis & Wets parameters were used for local search, and 300 iterations of Solis & Wets local search were imposed. Both Autogrid and Autodock computations were performed on Cygwin and ten independent docking runs were performed for each phthalimide. Final docked conformations were clustered using a tolerance of 1 A ˚ root mean square deviation (RMSD) and the docking log (dlg) files were analyzed using the AutoDock Tools, graphical user interface of Autodock. The docked conformations of each ligand were ranked into clusters based on the binding energy and the top ranked conformations were visually analyzed. Hydrogen bonding and hydrophobic interactions between docked potent agents and macromolecule were analyzed using Auto Dock Tools (version1.50).
