High-Throughput Molecular Docking Protocol

The AmpC campaign used the structure in PDB 1L2S, while the D₄ campaign used PDB 5WIU. In each, 45 matching spheres were calculated around and including the ligand atoms—a 26 μM thiophene carboxylate for AmpC and nemonapride for D₄ structures were prepared and AMBER united atom charges assigned^{14 (link)}. The magnitude of the partial atomic charges for five residues in AmpC were increased without changing the net residue charge⁵⁶ . For both targets, the low protein dielectric was extended into the binding site using pseudo-atom positions representing possible ligand docking sites, the radius was 1.0 Å and 2.0 Å for D₄ and AmpC respectively^{14 (link),54 ,60} . For the D₄ dopamine receptor, the desolvation volume of the site was also increased by similar atom positions, using a radius of 0.3 Å. This improved ligand charge-balance in benchmarking calculations, reducing the number of high-ranking dications. Energy grids representing the AMBER van der Waals potential⁶¹ , Poisson-Boltzmann electrostatic potentials using QNIFFT^{62 ,63} , and ligand desolvation from the occluded volume of the target for different ligand orientations⁵⁴ were calculated. Using DOCK3.7.2⁶⁴ , over 99 million and over 138 million library molecules were docked against AmpC and the D₄ dopamine receptor, respectively. Each library molecule was sampled in about 4054 and 3300 orientations and, on average, 280 and 479 conformations for AmpC and D₄, respectively, and were rigid-body minimized with a simplex minimizer. The throughput averaged 1 second per library compound.