Molecular Docking for MAO Binding Affinity

The binding of ligands to MAO-A and MAO-B could be quantitatively measured by using MM-GBSA combined with MD simulation.^{41 (link)} For each molecular species, apo and holo, the G_bind (binding free energy) was calculated by using the following equation:
The different components (G_R+L, G_R, and G_L) required for the free energy calculation of the apo and holo states are given in eqn (v). In the MM/GBSA and MM/PBSA methods, each free energy term in eqn (v) is calculated using the following equation:
In eqn (vi), E_bond, E_vdw, and E_elec are the bond energies, van der Waals, and electrostatic energy, including the dihedral bonds and angles, G_PB and G_SA. TS_S represents the solvation energy corresponding to the polar and non-polar contributions, including absolute energy and solute entropy. The optimized parameters and MIEC model, as proposed recently, work for calculating the free energies between protein–protein interfaces,^{42–45 (link)} but here we utilized the MM-PBSA.py method using interior solute and exterior solvent values as constant^{46 (link)} to calculate the free energy.