Targeting urinary tract infections: Anti-MDR efficacy of Syzygium aromaticum small molecules against uropathogenic Escherichia coli through in vitro and in silico approaches

Urinary tract infections (UTIs) are becoming increasingly challenging to treat owing to the emergence of multidrug-resistant (MDR) strains, including uropathogenic Escherichia coli (UPEC). Clove (Syzygiumaromaticum L.) has antimicrobial activity that can alter UPEC morphology and exhibit inhibitory effects. However, the mechanisms underlying the inhibition of specific small molecules remain largely unknown. This study aimed to explore the potential of small molecules in clove flower extract as anti-MDR UPEC agents using in vitro and in silico approaches. Extraction was performed using ethanol and n-hexane, yielding 27.44% and 9.9%, respectively. The ethanol extract exhibited inhibitory activity against MDR-UPEC, forming clear zones ranging from 11.07±0.32 (250 mg/mL) to 16.77±1.36 (1,000 mg/mL) in a disk diffusion assay. However, the combination of ethanol extract and ciprofloxacin resulted in antagonistic effects. GC-MS analysis of the ethanol extract identified 29 small molecules, which were subsequently analyzed using PASS Online, Lipinski’s Rule of Five, and molecular docking against target proteins PBP2 and AcrB. Three small molecules showed the potential to inhibit PBP2, and ten small molecules targeted AcrB. Spesifically, 8,14-Seco-3,19-epoxyandrostane-8,14-dione, 17-acetoxy-3β-methoxy-4,4-dimethyl-, Ethyl iso-allocholate and Estra-1,3,5(10)-trien-17β-ol show binding affinities of –7.9; –7.6; dan –8.0 kcal/mol to PBP2, and –9.3; –8.5; dan –8.6 kcal/mol to AcrB, respectively. These three small molecules are promising candidates for developing plant-based antibacterial agents against MDR UPEC.