Novel Molecular Mechanism of Allicin-Mediated Inhibition of Bacterial Topoisomerase IV: A Combined Computational and Experimental Analysis

Abstract

Background/Objectives: Allicin, a bioactive compound from garlic, exhibits antibacterial activity by targeting bacterial proteins, including type II topoisomerases such as DNA gyrase and topoisomerase IV enzymes exclusive to prokaryotes. This study aimed to investigate the antibacterial effects of allicin and its inhibitory mechanism on topoisomerase IV using both in vitro and in silico approaches. Methods: In the in vitro experiments, the antibacterial activities of allicin, garlic extract, and ciprofloxacin were evaluated using agar diffusion, as well as determination of minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). In silico analyses included consensus sequence-based structural modeling, molecular docking, and molecular dynamics simulation of DNA gyrase and topoisomerase IV subunit A in the presence of allicin and ciprofloxacin. Results: In vitro results demonstrated that the allicin exhibited the most potent antibacterial activity (P ≤ 0.05), followed by garlic extract, while ciprofloxacin demonstrated relatively lower activity. Docking analysis revealed stronger interactions and higher binding affinity between allicin and topoisomerase IV compared to the other ligands. Molecular dynamics simulations further confirmed the enhanced stability of the allicin-topoisomerase IV complex. Additionally, genomic analysis was used to predict the conserved region of the protein and generate a refined structural model, which showed improved binding characteristics. Conclusion: These findings suggest that allicin is a promising inhibitor of bacterial topoisomerase IV and may serve as the basis for developing new antimicrobial agents.