Bovine pancreatic trypsin inhibitor and soybean Kunitz trypsin inhibitor: Differential effects on proteases and larval development of the soybean pest Anticarsia gemmatalis (Lepidoptera: Noctuidae)

Barros, Rafael de Almeida; Meriño‐Cabrera, Yaremis; Castro, José Severiche; Silva, Neilier Rodrigues da; Oliveira, João Vitor Aguilar de; Schultz, Halina; Andrade, Rafael Júnior de; Ramos, Humberto Josué de Oliveira; Oliveira, Maria Goreti de Almeida

doi:10.1016/j.pestbp.2022.105188

Cited by 1 publication

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“…On the other hand, in silico tools have recently become an unavoidable approach for the optimization of protein–protein complexes and the design of new molecules from the study of the interaction between these proteins related to pest management (de Almeida Barros, Meriño‐Cabrera, Severiche Castro, da Silva Junior, de Oliveira, et al, 2022; de Almeida Barros, Meriño‐Cabrera, Severiche Castro, da Silva Júnior, Schultz, et al, 2022; de Almeida Barros et al, 2021; Halim et al, 2022; Machado et al, 2020; Meriño‐Cabrera, de Oliveira Mendes, et al, 2020; Meriño‐Cabrera, Severiche Castro, et al, 2020; Meriño‐Cabrera, et al, 2022). Using tools such as molecular modeling of proteins, which allows us to determine the three‐dimensional (3D) structure of the sequences of receptors and ligands such as yam disocorins; protein–protein molecular docking, to determine the affinity site and energy of the inhibitor to the digestive enzymes of interest; and study of the interface using software such as Pymol and Discovery, which allow exploring inhibitory residues that bind to the active site of the enzyme and/or potential to reduce enzyme activity (hot‐spot residues), which would be expensive and slowly by experimental methods (Childers & Daggett, 2017); In addition, molecular dynamics (MD) simulations are performed to analyze the stability of the protein–protein complex and the free binding energy in aqueous solution estimation, allowing to understand several underlying biological phenomena, such as enzyme inhibition (Patel & Ytreberg, 2018).…”

Section: Introductionmentioning

confidence: 99%

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

Severiche‐Castro,

Wilches Diaz,

Combariza Montañez

et al. 2023

Arch Insect Biochem Physiol

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Proteases 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.

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