Rai Sumit Kumar, Singh Dev Bukhsh, Singh Satendra
Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, 211007, U. P, India.
Department of Biotechnology, Siddharth University, Kapilvastu, Siddharth Nagar, 272202, U.P, India.
J Biol Phys. 2025 Jun 10;51(1):21. doi: 10.1007/s10867-025-09686-6.
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.
DNA 回旋酶是治疗由结核分枝杆菌引起的结核病的一个靶点。由于DNA回旋酶A链中的不同点突变，已经报道了许多抗生素耐药病例。基于有关DNA回旋酶耐药性相关研究的文献信息，我们通过在DNA回旋酶A链的第88和94位各插入两个突变，生成了4种不同的突变模型3ILW_G88A、3ILW_G88C、3ILW_D94G和3ILW_D94H。将抗生素克林沙星、加替沙星、莫西沙星、西他沙星、普卢利沙星、贝西沙星、德拉氟沙星、奥泽沙星与3ILW_wild对接，以了解它们与野生型DNA回旋酶（3ILW_wild）的稳定性、结合亲和力和相互作用模式。德拉氟沙星与3ILW_wild显示出更稳定且有利的结合相互作用（结合自由能，-8.6千卡/摩尔）。将德拉氟沙星与四种突变模型（3ILW_G88A、3ILW_G88C、3ILW_D94G和3ILW_D94H）进行对接，以了解这些突变对结合稳定性和相互作用的影响。与3ILW_wild相比，在突变体复合物中观察到与Ser118和Pro119的结合相互作用完全丧失，这表明这些残基在耐药性形成中的作用。对德拉氟沙星与3ILW_wild和四种突变模型的复合物进行了超过100纳秒的分子动力学模拟。诸如均方根偏差（RMSD）、均方根波动（RMSF）、回转半径、氢键和溶剂可及表面积等参数表明，与野生型DNA回旋酶相比，突变模型更刚性且更不灵活，这反过来导致一些相互作用的丧失。值得注意的是，DNA回旋酶A链第94位的突变具有非常深远的影响，因为它由于与德拉氟沙星的结合亲和力降低而对耐药性增加有正向贡献。这项研究解释了对德拉氟沙星耐药背后的结构变化和机制，也可能指导现有德拉氟沙星或其他抗生素所需的结构变化，以开发新的治疗方法来克服耐药问题。
