Unveiling the Antimicrobial Phytoconstituents of Cyperus difformis L.: Comprehensive Metabolite Identification via LC-MS/MS and Molecular Networking Coupled with Target-Specific In Silico Validation

The Cyperus genus (Cyperaceae) has been extensively utilized in traditional medicine systems worldwide, primarily for its gastrointestinal, anti-inflammatory, and neuroprotective properties. Biochemically, Cyperus species are rich in flavonoids, phenolic acids, sesquiterpenes, and alkaloids. The phytochemical profiling of Cyperus difformis aerial parts and rhizome extracts via LC-ESI-qTOF-MS/MS and GNPS molecular networking identified 68 metabolites, dominated by flavonoids (35 compounds, including C-O-glycosides of luteolin, apigenin, and chrysoeriol), phenolics (8), lipids (10), nitrogenous compounds (9), and miscellaneous constituents. Antimicrobial assays revealed significant activity, particularly in the rhizome extract, which exhibited superior inhibition against Candida albicans (surpassing fluconazole) and Staphylococcus aureus, with MIC values comparable to standard antibiotics (ciprofloxacin/amphotericin B). Molecular docking highlighted chrysoeriol glycosides (e.g., chrysoeriol-7-O-rutinoside, ΔG = −9.87 kcal/mol) and phospholipids (e.g., PC 16:0/18:0, ΔG = −10.95 kcal/mol) as potent binders to DNA gyrase B and CYP51B targets. These compounds formed stable complexes via hydrogen bonding (e.g., with ASP512/ARG1033 in gyrase) and hydrophobic interactions, rationalizing the observed bioactivity and supporting traditional uses against infections.