Structural analysis and inhibition capacity of dioscorin protein yam: Theoretical study by molecular docking and dynamic simulations

Abstract

AbstractProteases such as trypsins in the gut of Spodoptera frugiperda are responsible for breaking down dietary proteins into amino acids necessary for insect growth and development. In this study, we characterized the insecticidal potential of dioscorin, the storage protein of yam (Dioscorea alata), using molecular docking and molecular dynamics simulations to determine the interactions between trypsin enzymes and the protein inhibitor dioscorin. To achieve this, we used the three‐dimensional structures of the trypsin‐like digestive enzymes of S. frugiperda, a pest of corn and cotton, as receptors or target molecules. We performed protein–protein docking using Cluspro software, estimation of the binding free energy, and information on the dynamic and time‐dependent behavior of dioscorin–trypsin complexes using the NAMD package. Our computational analysis showed that dioscorin can bind to the digestive trypsins of S. frugiperda, as confirmed by the affinity energy values (−1022.4 to −1236.9), stability of the complexes during the simulation trajectory, and binding free energy values between −57.3 and −66.9 kcal/mol. Additionally, dioscorin uses two reactive sites to bind trypsin, but the largest contribution to the interaction energy is made by amino acid residues between amino acid backbone positions 8–14 by hydrogen bonds, hydrophobic, and Van der Waals (VdW) interactions. VdW is the energy that makes the greatest contribution to the binding energy. Collectively, our findings demonstrate, for the first time, the binding capacity of the yam protein dioscorin to the digestive trypsin of S. frugiperda. These promising results suggest a possible bioinsecticide action of dioscorin.