Deciphering the Electrostatic and Structural dynamics due to point Mutation in DNA gyrase leading to acquired Quinolone resistance in Mycobacterium tuberculosis

The structural bioinformatics analysis approach provides valuable information regarding the protein’s structure and function by analyzing the contribution of each and every amino acid residue present in its active site. Residue substitution in the active site has a profound effect on the protein’s shape, stability, binding affinity, charge distribution, etc. We inserted a mutation in the DNA gyrase protein's A chain (3ILW_wild) to understand the structural and electrical alternations, resulting in the formation of the 3ILW_G88A, 3ILW_G88C, 3ILW_D94G, and 3ILW_D94H mutant proteins. The molecular docking approach was applied to screen the best-interacting fourth-generation quinolone antibiotics and to elucidate their stability, binding affinity, and interaction pattern with the wild protein. The results of molecular docking studies suggested that delafloxacin (dfx) had the highest binding affinity with the DNA gyrase A chain and fits best at the active site. Mutant proteins were again docked with delafloxacin to monitor the effect of residue change on the protein’s properties. The results of the molecular docking approach were further validated by molecular dynamic simulation and binding free energy calculation studies. Molecular dynamics simulations over 100 ns were carried out for five protein systems. Parameters like RMSD, RMSF, radius of gyration, H-bond, and solvent-accessible area obtained from MD simulation studies revealed that the mutant proteins experienced greater rigidity and lesser structural fluctuations than the wild protein. Electrostatic investigation and comparison of BFE revealed that the electrostatic interactions were reduced, and this reduction directly affected the binding affinity of proteins and ligand molecules. Per-residue BFE decomposition and hydrogen bond analysis indicated that the reduced interaction was due to loss or gain of hydrophilic/hydrophobic or positively/negatively charged residues. It is worth noting that mutation at position 94 of DNA gyrase A has a very profound effect as it shows a positive contribution towards increased resistance and reduced binding affinity with delafloxacin.