Metabolic Profiling and In Silico Evaluation of Cynodon dactylon Leaf Metabolites Targeting PINK1 Kinase

Cynodon dactylon (Bermuda grass) is a perennial medicinal grass widely distributed across tropical and subtropical regions and known for its antioxidant and anti-inflammatory properties. The present study aimed to identify bioactive metabolites from the leaves of C. dactylon and evaluate their potential interaction with PTEN-induced kinase 1 (PINK1), a crucial regulator of mitochondrial quality control implicated in neurodegenerative disorders, particularly Parkinson’s disease. GC–MS analysis identified a total of 95 phytochemicals, of which the top 20 metabolites were selected based on retention time and area percentage. These metabolites were subjected to virtual screening using PyRx, with ATP employed as the reference ligand. Among the screened metabolites, 5,8,11-eicosatrienoic acid was the high-affinity compound which predicted a binding affinity of −5.9 kcal/mol and forming two hydrogen bond interactions within the PINK1 active site. The docked complexes were further evaluated through a 100 ns molecular dynamics simulation in replicates that showed stable binding of the protein–ligand complex, as reflected by RMSD values, reduced residue fluctuations and stable radius of gyration and solvent-accessible surface area. These findings suggest that 5,8,11-eicosatrienoic acid from C. dactylon may act as a potential PINK1 modulator for Parkinson’s disease.