The affinity prediction of functional protein (MFG-E8) and oleic acid/ linoleic acid/ linolenic acid by molecular docking

MFG-E8 does not have a publicly available crystal structure, so Alphafold3 prediction was used. In this study, we employed a semi flexible docking method. Firstly, we downloaded the crystal structure of the target protein MFG-E8 from a protein database or modeled it using AlphaFold3. Then, we used Maestro computational software to prepare the structures of proteins and small molecules separately. During the protein preparation process, optimize the hydrogen bond network and minimize the energy of the protein system. Small molecule preparation: Generate three-dimensional structures and minimize energy, and generate multiple conformations (15) to increase the likelihood and accuracy of successful docking. Next, we use the sitemap module of Maestro software to predict the binding pocket of small molecules (default parameters) and generate a receiver grid file. Based on the predicted pocket location, size, and small molecule docking score, we determine the most likely binding pocket. The other parameters remained at their default values. During molecular docking, select the prepared grid file and small molecules in the small molecule docking ligand docking module for molecular docking. Based on the scoring of docking results and the rationality of small molecule binding conformation, the optimal binding mode is selected through comprehensive analysis and judgment. The docking results were visualized using Pymol software. The human sequence of MFG-E8 was submitted to the server along with oleic acid, and the generated computational model was used for molecular docking and MM-GBSA. Oleic acid combining pattern analysis: The binding mode of the three molecules is the same. The carboxyl group interacts with GLN314 through hydrogen bonding and with ARG377 through salt bridge interaction (also known as electrostatic interaction). The alkyl chain of the molecule occupies the hydrophobic pocket composed of MFG-E8 proteins PHE260, ASN274, ASN275, and ASN309. Linoleic acid combined with pattern analysis: The binding mode of the three molecules is the same. The carboxyl group interacts with GLN314 through hydrogen bonding and with ARG377 through salt bridge interaction (also known as electrostatic interaction). The alkyl chain of the molecule occupies the hydrophobic pocket composed of MFG-E8 proteins PHE260, ASN274, ASN275, and ASN309. Linolenic acid combined with pattern analysis: The binding mode of the three molecules is the same. The carboxyl group interacts with GLN314 through hydrogen bonding and with ARG377 through salt bridge interaction (also known as electrostatic interaction). The alkyl chain of the molecule occupies the hydrophobic pocket composed of MFG-E8 proteins PHE260, ASN274, ASN275, and ASN309.


Figure The affinity measurement of MFG-E8 protein and three types of fatty acids by molecular docking.