4.1.6. Molecular Docking

Molecular docking was employed to verify and understand the binding mode of 3–ESR2 interaction. The ESR2 structure was retrieved from the Protein Data Bank (PDB ID: 2QTU).

Binding modes and binding affinities of the evaluated compound within the binding site of the selected estrogen receptor ESR2 were calculated using the Autogrid 4.0 and Autodock 4.2 programs [48]

The docking calculations were then performed using the Lamarckian genetic algorithm (LGA) for ligand conformational searching to estimate the possible binding conformations of our indole derivative. During the docking process, a maximum of 150 different conformations was considered for compound 3. The conformer with the lowest binding free energy was used for further analysis.