In silico investigation of fenugreek-derived coumarin and its potential impact on human health

Coumarin is a naturally occurring small phytochemical found mainly in the Trigonella foenum-graecum (Fenugreek) with diverse therapeutic potential, but the molecular mechanisms of actions remain incompletely characterized. This study employed an integrated computational approach, combining network pharmacology, computational proteomics, molecular docking, and MD simulation to explore the network-level basis of coumarin multifunctional effects. Using STITCH and STRING databases, coumarin interacted directly with ten primary proteins, namely CYP2A6, NPY1R, CXCR4, MTRNR2L2, S1PR2, RGS6, TAS2R38, TAS2R30, TAS2R14, and TAS2R20 related to xenobiotic metabolism, GPCR-mediated signaling, immune system regulation, and sensory perception. The protein-protein interactions analysis revealed a closely connected hub of G-protein dependent proteins, underscoring the prominence of GPCR signaling networks associated with coumarin. The coordinated regulation of metabolic and immune pathways is also evident in the diverse transcriptional regulators of metabolic enzymes as well as chemokines related to the immune system. Pathway enrichment analysis indicates that the fenugreek-derived coumarin could have anti-inflammatory, metabolic regulatory and neuroprotective effects, via multi-target effects. Structure-based molecular docking analysis exhibited preferential binding energies at the several targets, and the CYP2A6-coumarin complex (-7.7 kcal/mol) showed the strongest binding of the several complexes were determined. Furthermore, molecular dynamics simulations (100 ns) validated the stability and flexibility of this complex, defined by persistent contacts with active sites conserve residues and low RMSD fluctuation over time. These findings are consistent with the biological probability of the predicted binding and highlighted the role of CYP2A6 in the coumarin metabolism. Collectively, these findings exhibited that coumarin showed its biological activity by network level polypharmacological mechanisms rather than the traditional single target activity, informing its diverse pharmacological properties via mechanism and providing a base for future experimental validation.