Molecular modeling, docking and dynamics studies of fenugreek () α-amylase.

α-Amylase catalyses the hydrolysis of glucosidic bonds in polysaccharides such as starch, glycogen and their degradation products. In the present study, the three-dimensional structure of fenugreek () α-amylase was determined using a homology modeling-based technique. The best predicted model was deposited in PMDB server with PMDB ID PM0084364. The phylogenetic tree was created using the UPGMA method with 8 homologous protein sequences, was utilized as the target protein. Alignment of the phylogenetic tree identified two primary functional groupings (A and B). α-Amylase from the target genome (Acc. No: GHNA01022531.1) was clustered with (Acc. No: XP003589186.1), (Acc. No: XP004499059.1), (Acc. No: XP020231823.1), (Acc. No: NP001316768.1) and (Acc. No: P17859.1), in group A cluster, while (Acc. No: Q40015) and (PDB ID: 3WN6) were in cluster B. The molecular dynamics simulations were performed to understand the molecular basis and mode of action of α-amylase. Additionally, a geometry-based molecular docking technique was used to evaluate potential binding interactions between the modeled structure of α-amylase and maltose. The results show that Trp, Glu, Arg, His, Tyr, Asp, Phe and Asp from α-amylase enzyme is involved in the binding to the substrate maltose. Our study provides a 3D model of α-amylase and aids in understanding the atomic level molecular underpinnings of the mechanism of α-amylase interaction with substrate maltose. Ca are essential for the stability of domain B since they are connected to it. Ca site ligands are Asp, Glu, Thr, Asp and Gly residues. HIGHLIGHTSIn analysis, gene prediction of α-amylase was carried from .Analysis of the structure of α-amylase was carried out using homology modelling.Calcium binding sites and their interactions with α-amylase were visualised using BIOVIA DISCOVERY STUDIO 2019.The molecular interaction between α-amylase and maltose was studied in using a molecular docking-based method.To give the required simulation parameters, RMSD, RMSF, and Total Energy were calculated using BIOVIA DISCOVERY STUDIO 2019.[Figure: see text]Communicated by Ramaswamy H. Sarma.