Rational design of novel α-amylase inhibitor peptide derived from quinoa seed peptide with <i>in silico</i> approaches

Diabetes mellitus (DM) has become a global concern that is responsible for millions of deaths in the world. One alternative to combat diabetes is to inhibit α-amylase with a generally non-toxic peptide. Quinoa has been recognized as a source of bioactive peptides with promising α-amylase-inhibiting activity. However, the activity of the IQAEGGLT peptide from quinoa was still low. Therefore, the current study aims to modify the α-amylase inhibitory peptides from quinoa seeds to enhance their inhibitory activity using in silico approaches, followed by peptide activity assays and kinetic studies. A rational design approach involving mutations of multiple amino acids was used to improve the peptide’s binding affinity to the receptor. Molecular docking and MM/GBSA were performed to evaluate the effects of modifications. The molecular dynamics and MM/PBSA were performed to investigate the stability of peptide- α-amylase complexes. Modification increased the number of derivatized peptides (RQAEGRLT) interactions with α-amylase, with binding affinity increasing from −27.06 kcal/mol (parent peptide) to −59.06 kcal/mol in MM/GBSA calculation. The molecular dynamics study showed all complex exhibited relatively good stability with RQAEGRLT exhibited the best MM/PBSA binding affinity after simulation of −122.46 ± 23.75 kcal/mol, ∼2 fold higher than its parent (−55.72 ± 19.8 kcal/mol). A ∼ fourfold activity increase was showed by arginine derivative, from the IC50 values of 40.80 ± 0.10 μM (IQAEGGLT) to 9.75 ± 0.05 μM (RQAEGRLT). The CD showed the peptide exhibited a random coil structure that is effective to adjusting its structure in the interaction with receptor. The results showed that the derivative exhibited promising α-amylase inhibitory activity, suggesting it potential to combat diabetes.