Structure‐Guided Design of an Interface‐Derived Inhibitor Peptide Against Spodoptera frugiperda Digestive Trypsins

ABSTRACT Spodoptera frugiperda is a major agricultural pest whose control requires safer and more sustainable alternatives. In this study, a rational in silico strategy was applied to design a bioinsecticidal peptide targeting digestive trypsin from S. frugiperda , using a functionally relevant interfacial region of the Dioscorin–trypsin complex as a structural template. Interface analysis allowed the identification of an 11‐residue oligopeptide designated as PEP‐11. Trypsin–peptide docking, pharmacophore profiling, and triplicate molecular dynamics simulations were performed to characterize its interaction with the trypsin model. Docking analysis revealed that PEP‐11 binds through a cooperative network of polar and hydrophobic interactions, supporting favorable molecular recognition. Molecular dynamics analyses showed that the trypsin–PEP‐11 complex remained stable throughout the 100 ns simulations, with limited structural deviations and flexibility mainly restricted to terminal and loop‐exposed regions. In addition, the radius of gyration and solvent‐accessible surface area remained stable, while intermolecular hydrogen bonds increased over time. MM/GBSA calculations yielded negative binding free energy values in all replicas, indicating energetically favorable binding. Overall, these results support the computational prioritization of PEP‐11 as an interface‐derived peptide candidate for future experimental evaluation, including enzymatic inhibition, selectivity, proteolytic stability, and bioactivity assays.