Discovery and mechanism of novel anticoagulant peptides from Larimichthys crocea based on in silico, molecular docking, molecular dynamics, and in vitro analysis

Abstract

Fish is rich in protein and is an ideal raw material for the preparation of bioactive peptides. This study effectively identified 21 bioactive peptides from Larimichthys crocea protein using a combination of bioinformatics and in vitro evaluation. Molecular docking and molecular dynamics simulations (MD) showed that six of the peptides could strongly bind to the active center of thrombin through hydrogen bonding and hydrophobic interactions (binding energies are −7.2 to −8.5 kcal/mol), thereby displaying significant anticoagulant potential. These peptides were further demonstrated to have significant anticoagulant activity in vitro experiments with half-maximal inhibitory concentration (IC₅₀) ranging from 0.47 ± 0.14 to 9.33 ± 0.12 mM. The activity may be closely related to the β-sheet and random coil conformations they contains. Furthermore, molecular docking with coagulation factors also revealed that these peptides might precisely regulate the intrinsic coagulation pathway by prolonging the activated partial thromboplastin time (APTT) by 2–3 times (p < 0.05) through blocking Factor IXa (FIXa) activity. This work provides new strategies for the anticoagulant evaluation and inhibitory mechanism of food-derived bioactive peptides.