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.

Keywords: Binding free energy; DNA gyrase A; Drug resistance; Electrostatic interaction; Mutation; Quinolone.

© 2025. The Author(s), under exclusive licence to Springer Nature B.V.

DNA拓扑异构酶是治疗由结核分枝杆菌引起的肺结核的靶点。由于DNA拓扑异构酶A链中不同位置的点突变，已经报道了许多抗生素耐药病例。基于有关DNA拓扑异构酶抗药性研究的文献信息，我们在DNA拓扑异构酶A链88和94位引入两个突变，生成了四个不同的突变模型3ILW_G88A、3ILW_G88C、3ILW_D94G和3ILW_D94H。通过将抗生素克拉氟喹、加替沙星、莫西沙星、西他沙星、普卢利沙星、贝斯沙星、德拉沙星、欧森沙星与野生型DNA拓扑异构酶（3ILW_wild）进行对接，以了解它们的稳定性、结合亲和力以及与野生型DNA拓扑异构酶的相互作用模式。德拉沙星显示出与3ILW_wild更稳定且更有利的结合相互作用（结合自由能，-8.6 kcal/mol）。将德拉沙星与四个突变模型进行对接，以了解这些突变对结合稳定性及相互作用的影响。与野生型相比，在突变复合物中观察到丝氨酸118和脯氨酸119完全失去了结合互作，这表明了这两个残基在耐药性发展中的作用。我们对德拉沙星与3ILW_wild以及四个突变模型的复合体进行了为期100 ns的分子动力学模拟。参数如RMSD、RMSF、回转半径、氢键和可及表面积显示，突变模型比野生型DNA拓扑异构酶更为刚性且不那么灵活，这导致一些互作的损失。值得注意的是，在DNA拓扑异构酶A链94位的突变更显著地增加了德拉沙星结合亲和力降低所引起的耐药性的可能性。这项研究解释了德拉沙星耐药性背后的结构变化及机制，并可能为改进现有德拉沙星或其他抗生素的结构以开发新的治疗手段提供指导，从而克服耐药性问题。

关键词：结合自由能；DNA拓扑异构酶A；药物抗性；静电相互作用；突变；喹诺酮类。