Molecular Docking
The 3D structure in SDF format was acquired from PubChem data according
to the CAS number (60-33-3) of the small molecule metabolite linoleic
acid, and the structure was imported into ChemBio3D Ultra 14.0 for
energy minimization. The Minimum RMS Gradient was set to 0.001, and the
small molecule metabolite was saved in mol2 format. The protein
long-chain acyl-CoA synthetase 1 (ACSL1) that interacts with the small
molecule metabolite linoleic acid was identified from the database
STITCH (http://stitch.embl.de/). Downloaded the protein structure of
ACSL1 from the Uniprot database, and the protein structure was processed
to remove protein crystal water, original ligand, etc on PyMOL2.3.0
platform. The optimized small molecules and protein structures were
imported into AutodockTools-1.5.6 software for hydrogenation, charge
calculation, charge distribution, and saved as ”pdbqt” format as ligands
for molecular docking. POCASA 1.1 was used to predict protein binding
sites, and the interaction mode analysis of molecular docking results
were completed by PyMOL2.3.0 software.