Software For Molecular Docking Essay

1346 words - 6 pages

Auto Dock
Auto Dock is an automated docking tool. It is designed to predict how small molecules, such as substrates, bind to a receptor of known 3D structures. Auto Dock actually consists of two main programs: one performs the docking of the ligand to a set of grids describing the target protein; and the other Auto Grid pre-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualized. A graphical user interface called Auto Dock Tools or ADT was utilized to generate grids, calculate dock score and evaluate the conformers.
RASMOL [Raster Display of Molecules] is a molecular graphics program intended for the structural visualization of proteins, nucleic acids and small biomolecules. The program reads in molecular coordinate files and interactively displays the molecule on the screen in variety of representations and color schemes.
The structure of β-ketoacyl-acyl carrier protein synthase (KAS) which is an essential target for novel antibacterial drug design was retrieved from PDB [10]. A comparative protein - ligand dock analysis was performed using 1HNJ to evaluate the algorithm and scoring function efficiency between Auto Dock 3.0 and experimental activities. The molecules selected for docking studies are from the selected article [11, 12]. The docking studies were done on ecKAS III (pdb id: 1HNJ) receptor. All these molecules as well as the bound ligand of the protein 1HNJ were docked by using the software Auto Dock and the score values are predicted. The protein ligand interactions were also studied. All molecules were drawn using ChemDraw Ultra 8.0 tool and energy minimized using Chem 3D Ultra 8.0 software. Automated docking was used to locate the appropriate binding orientations and conformations of various inhibitors into the 1HNJ binding pocket. To perform the task, the powerful genetic algorithm method implemented in the program AutoDock 3.017 was employed. Before docking the screened ligands in to the protein active site, the protein was prepared by deleting the substrate cofactor as well as the crystallographically observed water molecules and then protein was defined for generating the grid. Grid maps were generated by AutoGrid program.
Each grid was centered at the crystal structure of the corresponding 1HNJ. The grid dimensions were 60 A˚ X 60 A˚ X 60 A˚ with points separated by 0.375A˚. For all ligands, random starting positions, random orientations and torsions were used. During docking, grid parameters were specified for x, y and z axes as 38.808, 30.946 and 42.249 respectively.
Table 1: Docked scores of newly designed compounds

Compound R Auto Dock Score
(Kcal/mol) Ki (µM) No of H-bonds

1 CH2C6H5, -7.04 6.93 1
2 CH=CH-C6H5 -2.72 10.14* 3
Ki = inhibition constant
* in (mM)
Table 2: Lipinski properties of the docked ligands

Compound Molecular weight Log P H bond donor H bond acceptor Molar refractivity Number of criteria met

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