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K. Gobalan*, S. Ahamed John


Molecular Modeling Study and Computer Aided Drug Design of Peptide deformylase (PDF) is essential in a variety of pathogenic bacteria but it is not required forcytoplasmic protein synthesis in eukaryotes, which makes this enzyme an attractive target for developing novel antibiotics. Because PDF inhibitors are one of the most promising classes of antibacterial agents discovered to date, we designed a series of PDF inhibitors and we predicted their biological activities using molecular simulation methods. The Docking simulations of PDF inhibitors with the ligand binding pocket of PDF have been carried out.The binding conformations and binding affinities of these inhibitors have been obtained using the flexible docking protocol FlexX. Calculations performed for test compounds suggested that FlexX can reproduce the bindingconformation of the crystal structure. Moreover, the predicted binding affinities have a good correlation with the biological activities of these inhibitors, thus allowing us to determine the interaction model of PDF inhibitors. A series of designed inhibitors have been docked to the PDF model and the computed docking scores have been used as a reference standard to evaluate the activities of these inhibitors. The results presented in this paper show that several of our designed compounds are promising PDF inhibitors.

Keywords: Molecular Modeling: Peptide deformylase; PDF; inhibitors; molecular docking; quantitative structure–activity relationships; QSAR; FlexX.

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