Molecular modeling and quantum chemical calculation study of derived peptides from a Bowman-Birk inhibitor in complexes with trypsin

CONTEXT: Bowman-Birk inhibitors (BBIs) are cysteine-rich proteins that inhibit trypsin and chymotrypsin proteases. Derived from soybeans, these natural BBIs have been identified as potential anticarcinogenic agents. Recent studies of the black-eyed pea trypsin/chymotrypsin inhibitor (BTCI) demonstrated that peptides derived from the BBI family may retain their structure and inhibitory activity. Therefore, this study aimed to investigate the effects of solvent on BTCI-derived peptides and their inhibitory activity against trypsin. The results show that cyclic peptides exhibit reduced conformational flexibility, enhanced reactivity (narrower HOMO-LUMO gap), and LUMO localized at the disulfide bonds, in contrast to the linear peptide Ptry6. Non-covalent interactions were evaluated using the Independent Gradient Model based on Hirshfeld partitioning (IGMH). Molecular electrostatic potential maps and the IGMH confirmed that the cyclic architecture concentrates electropositive donor regions at key residues (Thr2, Lys3, Ser4, and Ile5), whereas Ptry6 displays only weak van der Waals contacts. Docking studies against trypsin showed strong hydrogen-bond and electrostatic interactions between cyclic peptides and residues involved in the catalytic mechanism. Predicted inhibition constants obtained from docking studies closely match experimental data. These findings suggest that electronic redistribution upon solvation governs peptide-trypsin affinity, highlighting Ptry9L as the most promising BTCI-derived inhibitor for further biotechnological development. METHODS: BTCI peptides were studied using quantum-chemical calculations and molecular docking. Three peptides-a cyclic nonapeptide in both L- and D-configurations (Ptry9L, Ptry9D) and a linear hexapeptide (Ptry6)-were optimized in vacuo and in implicit aqueous solvent using density functional theory at B3LYP-D3/Def2-SVP and B3LYP-D3/6-311+G(d,p) levels with D3 dispersion correction. Frontier molecular orbital analyses (HOMO-LUMO gaps and orbital localization) and IGMH revealed that the disulfide bond stabilizes cyclic peptides.