3.3. In Silico Modelling

For all compounds analyzed within this study, ionization states were generated at pH = 7.4 using Epik software. Ligprep software (under the default settings: generation of only one low energy ring conformation per ligand, retention of specified chiralities, and force field used OPLS2005) was applied for the generation of 3D structures (2.3.2. Docking protocol). All receptors have been centered on the ion zinc located inside the binding pocket. Grid box size was set to 25 × 25 × 25Å. All the docking calculations were run in Glide software at the SP level under the default settings (performing post-docking optimization, up to 100 steps during energy minimization, penalizing nonplanar conformation of amides, sampling ring conformations with energy window equal to 2.5 kcal·mol⁻¹ and sampling nitrogen inversion). Docking was carried out with one constraint: mandatory coordination of the zinc ion.