4.8.10. Molecular Docking

Molecular docking studies were carried out in order to identify the top hit phytoconstituents present in the aerial part extract of *A. aspera* (ethyl acetate fraction) and flower part of *C. gigantea* (ethyl acetate fraction) [65]. The three-dimensional (3D) crystal structure of target proteins (PDB: 7LD8, 4Q4N, 5XE2, 4LJ1, 1TQ8, 4CHG, 5WZ4, 2JAX, 5SV2, 6L2A) was retrieved from RCSB PDB and refined before performing molecular docking. Binding sites/pockets were determined by using CASTp 3.0 server, which examined the geometric and topological properties of the protein structures, including surface pockets, interior cavities and cross channels, as they are fundamentally important for the proteins to carry out their functions. The GC-MS analyzed phytoconstituents (as ligand) were downloaded from PubChem database. The compound structures unavailable in PubChem database were drawn by ChemBioDraw Ultra 14.0 [66]. For the receptor preparation, the water molecules and co-crystallized ligands were removed from the PDB file and polar hydrogens were added. The receptor protein (target) was transformed from pdb format into pdbqt format using in-house protocol [67]. In molecular docking was performed by InstaDock. Results were evaluated from the log files via Python script [68]. The blind docking mechanism was used to explore the binding site(s) in the protein structures. PyMOL was used to visualize protein-ligand interactions. The receptor-ligand complex was prepared by Discovery Studio and 2D interaction of docked conformations was analyzed to understand the ligand binding amino acid residues [69]. The best-fitting conformation related to the binding affinity of the ligand-receptor complex was identified, while keeping the receptor as a rigid entity and ligand as flexible. The top 10 hits showing strong binding affinity to the binding sites were selected.
