Fluoroquinolone resistance in uropathogenic Escherichia coli (UPEC) poses a significant challenge in the treatment of urinary tract infections (UTIs), a major global health issue. As resistance rates rise, particularly in developing countries, there is an urgent need for novel derivatives. This study aims to explore fluoroquinolone resistance in UPEC isolates and identify potential lead compounds using in-silico methods to optimize fluoroquinolone derivatives that may overcome resistance. A retrospective observational study of 2,306 UTI cases was conducted at a tertiary care hospital in Nepal, with 167 samples showing significant bacterial growth. Molecular docking using AutoDock 4.2 assessed the binding affinities of 42 novel fluoroquinolone derivatives against E. coli DNA gyrase (PDB ID: 4KFG). Drug-protein interactions were analysed with Drug Discovery Studio, pharmacokinetics with SwissADME, and biological activity and toxicity predictions with PASS Online and ProTox-II. E. coli was identified in 64.7% of cases, with significant resistance to fluoroquinolones (levofloxacin: 83.33%, ofloxacin: 57.14%, ciprofloxacin: 32.67%). Novel derivatives SP9, SP12, and SP42 exhibited superior binding affinities (-11.9, -11.7, and -11.6 kcal/mol), and SP25 interacted with the highest number of amino acids compared to standard fluoroquinolones, forming multiple hydrogen bonds with key residues in DNA gyrase. These derivatives complied with Lipinski’s Rule of Five, suggesting favourable pharmacokinetics, though toxicity analysis revealed mutagenicity and other toxicities in SP9, SP12, and SP25. Considering fluoroquinolone resistance in E. coli at high levels, SP42 emerges as a promising candidate for future therapeutic development, while SP9, SP12, and SP25 require further optimization due to toxicity concerns.
