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Anticoagulants are very important for the treatment and prevention of thrombotic disorders. The use of conventional anticoagulants like heparin and warfarin can cause bleeding complications. To find safer anticoagulant therapy agents, the development of isolation of new anticoagulant compounds has shifted towards natural sources. Bioactive peptides can be considered a better alternative because of their therapeutic potential in the treatment of various diseases. Several peptide molecules have been shown to inhibit the cytochrome P450 (CYP) 2C9 enzyme as a natural anticoagulant, such as bioactive peptides produced by yellowfin sole (Limanda aspera) and bioactive peptides in blue mussel (Mytilus edulis). This study aims to identify and evaluate the interactions that occur between peptide molecules with the cytochrome P450 (CYP) 2C9 enzyme using protein-peptide docking methods. Bioactive peptide sequencing was modeled using the PEP-FOLD software. The best conformation was chosen for an interaction study against the macromolecule of cytochrome P450 (CYP) 2C9 enzyme using PatchDock software. Further observations were made of interactions formed using BIOVIA Discovery Studio 2020 software. Based on the results of protein-peptide docking, the yellowfin sole peptide molecule has a good affinity against the macromolecule of cytochrome P450 (CYP) 2C9 enzyme, with an ACE score of −2527.01 kJ / mol. Therefore, the bioactive peptide is predicted to be used as a candidate for the cytochrome P450 (CYP) 2C9 enzyme inhibitor.

Anticoagulants are very important for the treatment and prevention of thrombotic disorders. The use of conventional anticoagulants like heparin and warfarin can cause bleeding complications. To find safer anticoagulant therapy agents, the development of isolation of new anticoagulant compounds has shifted towards natural sources. Bioactive peptides can be considered a better alternative because of their therapeutic potential in the treatment of various diseases. Several peptide molecules have been shown to inhibit the cytochrome P450 (CYP) 2C9 enzyme as a natural anticoagulant, such as bioactive peptides produced by yellowfin sole (Limanda aspera) and bioactive peptides in blue mussel (Mytilus edulis). This study aims to identify and evaluate the interactions that occur between peptide molecules with the cytochrome P450 (CYP) 2C9 enzyme using protein-peptide docking methods. Bioactive peptide sequencing was modeled using the PEP-FOLD software. The best conformation was chosen for an interaction study against the macromolecule of cytochrome P450 (CYP) 2C9 enzyme using PatchDock software. Further observations were made of interactions formed using BIOVIA Discovery Studio 2020 software. Based on the results of protein-peptide docking, the yellowfin sole peptide molecule has a good affinity against the macromolecule of cytochrome P450 (CYP) 2C9 enzyme, with an ACE score of −2527.01 kJ / mol. Therefore, the bioactive peptide is predicted to be used as a candidate for the cytochrome P450 (CYP) 2C9 enzyme inhibitor.

Anticoagulants are very important for the treatment and prevention of thrombotic disorders. The use of conventional anticoagulants like heparin and warfarin can cause bleeding complications. To find safer anticoagulant therapy agents, the development of isolation of new anticoagulant compounds has shifted towards natural sources. Bioactive peptides can be considered a better alternative because of their therapeutic potential in the treatment of various diseases. Several peptide molecules have been shown to inhibit the cytochrome P450 (CYP) 2C9 enzyme as a natural anticoagulant, such as bioactive peptides produced by yellowfin sole (Limanda aspera) and bioactive peptides in blue mussel (Mytilus edulis). This study aims to identify and evaluate the interactions that occur between peptide molecules with the cytochrome P450 (CYP) 2C9 enzyme using protein-peptide docking methods. Bioactive peptide sequencing was modeled using the PEP-FOLD software. The best conformation was chosen for an interaction study against the macromolecule of cytochrome P450 (CYP) 2C9 enzyme using PatchDock software. Further observations were made of interactions formed using BIOVIA Discovery Studio 2020 software. Based on the results of protein-peptide docking, the yellowfin sole peptide molecule has a good affinity against the macromolecule of cytochrome P450 (CYP) 2C9 enzyme, with an ACE score of −2527.01 kJ / mol. Therefore, the bioactive peptide is predicted to be used as a candidate for the cytochrome P450 (CYP) 2C9 enzyme inhibitor.

Modeling protein-peptide interactions remains a significant challenge for docking programs due to the inherent highly flexible nature of peptides, which often adopt different conformations whether in their free or bound forms. We present here a protocol consisting of a hybrid approach, combining the most frequently found peptide conformations in complexes with representative conformations taken from molecular dynamics simulations of the free peptide. This approach intends to broaden the range of conformations sampled during docking. The resulting ensemble of conformations is used as a starting point for information-driven flexible docking with HADDOCK. We demonstrate the performance of this protocol on six cases of increasing difficulty, taken from a protein-peptide benchmark set. In each case, we use knowledge of the binding site on the receptor to drive the docking process. In the majority of cases where MD conformations are added to the starting ensemble for docking, we observe an improvement in the quality of the resulting models.