Molecular docking of wild type and predicted resistance causing mutant proteins with drugs

The X-ray crystal structures for wild type proteins katG (PDB ID: 1SJ2), pncA (PDB ID: 3PL1), gyrA (PDB ID: 4G3N (N-terminal) and 5BS8 (C-terminal)) and gyrB (PDB ID: 5BS8) were obtained from PDB⁴⁹. The mutant models for the resistance causing mutations were generated using Schrodinger software⁵⁰. The wild type and mutant models were then subjected to MD simulations to study the behavior of protein in the presence of external salts and solvents. The wild type and mutant proteins were preprocessed using Schrodinger’s Protein Preparation Wizard⁵¹, during which bond orders were corrected and hydrogen and disulfide bonds were added. The proteins were optimized at pH 7 using Propka⁵². The ligands used in the present study included drugs, isoniazid (PubChem CID: 3767), pyrazinamide (PubChem CID: 1046) and fluoroquinolones, ciprofloxacin (PubChem CID: 2764), moxifloxacin (PubChem CID: 152946) and ofloxacin (PubChem CID: 4583). LigPrep module was used for ligand preparation which generated energy minimized ligands using OPLS3 force field, possible tautomers and ionization states were created and the mistakes in the ligands were removed. The grid was created using Receptor Grid Generation module around the already predicted drug binding pocket and extra precision algorithm of Glide module was used to dock the ligands in the active site of the receptor. The docked protein-ligand complexes having lowest binding free energy values were taken for further investigation.