Molecular dynamics simulation for screening phytochemicals as α-amylase inhibitors from medicinal plants

Abstract

Diabetes mellitus (DM) is a complicated metabolic disorder with several enzymes, including α-amylase and α-glycosidase. The α-amylase is responsible for postprandial glucose levels; therefore, inhibiting its activity is helpful in diabetes management. Hence, to find natural inhibitors of α-amylase, we have prepared a 257 phytochemical library from selected medicinal plants with antidiabetic activity and conducted a virtual screening and molecular dynamics study. Seventy-nine phytochemicals were screened out of 257 phytochemicals based on binding energy, ranged from −10.1 kcal mol−1 to −7.6 kcal mol−1. The binding energies of screened compounds were lower or equal to the reference molecule (−7.6 kcal mol−1). The binding affinity of six screened phytochemicals was re-scored by X-SCORE. These phytochemicals were subjected to ADMET and Drug-likeness analysis. After screening docking and drug-likeness analysis, six phytochemicals viz., Shahidine, Epicatechin, Quercetin, Isocolumbin, Ellagic acid, Luteolin and a reference molecule (Acarbose) were subjected to Molecular dynamics (MD) simulation to analyze the stability of the docked protein-ligand complex. The values of root mean square deviation, RMSF, RG, SASA, H-Bond, the interaction energy of all protein-ligand complexes were calculated after 30 ns of MD simulation. The results of screened complexes revealed good stability as compared to reference Acarbose. Pharmacophore features of the screened phytochemicals and α-amylase inhibitors showed many common pharmacophore features. Based on finding the screened phytochemicals, e.g. Shahidine, Epicatechin, Quercetin, Isocolumbin, Ellagic acid, and Luteolin, may be used as a potential inhibitors against α-amylase. These phytochemicals could be optimized and synthesized to develop potential drugs to manage and treat diabetes, targeting α-amylase. Communicated by Ramaswamy H. Sarma.