Structural insight in understanding the impact of mutation at position 88 and 94 of DNA gyrase A of Mycobacterium tuberculosis in developing resistance against delafloxacin.

Abstract

DNA gyrase is a target for treating tuberculosis caused by Mycobacterium tuberculosis. Many cases of antibiotic resistance have been reported due to different point mutations in the Chain A of DNA gyrase. Based on literature information on drug-resistance related study for DNA gyrase, we generated 4 different mutant models 3ILW_G88A, 3ILW_G88C, 3ILW_D94G, and 3ILW_D94H by inserting two mutations at each position 88 and 94 in DNA gyrase chain A. Antibiotics Clinafloxacin, Gatifloxacin, Moxifloxacin, Sitafloxacin, Prulifloxacin, Besifloxacin, Delafloxacin, Ozenoxacin were docked with 3ILW_wild to understand their stability, binding affinity, and interaction pattern with the wild-type DNA gyrase (3ILW_wild). Delafloxacin has shown more stable and favorable binding interaction with the 3ILW_wild (BFE, -8.6 kcal/mol). Docking of Delafloxacin with four mutant models (3ILW_G88A, 3ILW_G88C, 3ILW_D94G, and 3ILW_D94H) was performed to understand the impact of these mutations on binding stability and interaction. A complete loss of binding interaction with Ser118 and Pro119 was observed in mutant complexes as compared to 3ILW_wild, suggesting the role of these residues in developing resistance. Molecular dynamics simulations over 100 ns were carried out for the complex of Delafloxacin with 3ILW_wild and four mutant models. Parameters like RMSD, RMSF, radius of gyration, H-bond, and solvent-accessible surface area revealed that the mutant models are more rigid and less flexible as compared to wild-type DNA gyrase, which in turn results in loss of some interactions. 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 due to reduced binding affinity with delafloxacin. This study explains the structural changes and mechanism behind the resistance against Delafloxacin, and may also guide the structural changes required in existing Delafloxacin or other antibiotics to develop new therapeutics to overcome the issue of resistance.