Identification of the Major Compounds from Ethanol Extract of Scoparia dulcis L. Leaves Based on LC-MS and Their Potential as Antibacterials Against Escherichia coli: A Study In Silico
DOI:
10.29303/jpm.v21i5.12049Published:
2026-10-23Downloads
Abstract
Bacterial infections remain a significant global health problem, particularly those caused by Escherichia coli, which is associated with various diseases such as diarrhea, urinary tract infections, and sepsis. The increasing prevalence of antibiotic resistance highlights the urgent need to explore alternative antibacterial agents derived from natural products. This study aims to identify the dominant compounds in the ethanol extract of Scoparia dulcis L. leaves using LC-MS and to evaluate their potential as antibacterial agents against E. coli via in silico molecular docking. The extraction was performed using the maceration method, followed by LC-MS analysis, which identified 104 secondary metabolites. Among these metabolites, flavonoids were identified as the dominant compound class, including apigenin, luteolin, acacetin, scutellarein, hispidulin, and ladanetin. Molecular docking was conducted using Autodock Vina against DNA gyrase (PDB ID: 1KZN) as the target protein. The docking protocol was validated by redocking the original ligand, yielding an RMSD value of 1.22 Å. Ligand-protein interactions were analyzed using Discovery Studio Visualizer to identify hydrogen bonds, π-interactions, and hydrophobic interactions. The docking results showed that all tested flavonoids exhibited lower binding affinity values than ciprofloxacin (-7.6 kcal/mol), with luteolin demonstrating the strongest interaction (-8.9 kcal/mol), followed by apigenin (-8.5 kcal/mol) and scutellarein (-8.4 kcal/mol). Visualization analysis revealed that these interactions played crucial roles in stabilizing ligand–protein interactions. Additionally, drug-likeness evaluation based on Lipinski’s Rule of Five indicated that the selected compounds possess favorable physicochemical properties, suggesting good membrane permeability and bioavailability. The novelty of this study lies in integrating LC-MS-based compound identification with molecular docking analysis, focusing specifically on the dominant flavonoids of Scoparia dulcis. These findings provide a scientific basis for developing flavonoid-based antibacterial agents targeting the DNA gyrase enzyme in E. coli.
Keywords:
Antibacterial Escherichia coli Flavonoids Molecular Docking Scoparia dulcis L.References
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