2.5. Molecular Docking Protocol

The interactions of the lead compounds identified using our QSAR models with SERT, D2, and 5-HT1A receptors were predicted using molecular docking.

The 3D protein structures were imported from Protein Data Bank in the case of SERT (PDB ID: 6VRH [51]) and D2 (PDB ID:6CM4 [52]) receptors; the structure of the 5-HT1A receptor was imported from AlphaFold [53].

The molecular docking was performed using the CDOCKER algorithm [54] implemented in Biovia Discovery Studio v16.1.0.15350 (BIOVIA Dassault Systemes, San Diego, CA, USA).

The ligands were docked in the drug binding cavities according to the PDB files used [51,52]. In the case of 5-HT1A, the binding site was identified by similarity with the site of the D2 receptor [52]. The Docking protocol was applied as described in the study of Rao et al. [55].