Ligand Density Docking Score Correlate Directionally to Experimental Retention studies
In a packed bed, the number of possible protein-ligand interaction sites will exceed one. Yet, for each given patch of resin with a specific ligand density, there is an optimal number of possible interactions and associated interaction energy. Data from the computational docking studies suggest that there is an optimal number of possible interactions at each ligand density. To address this assumption, the interaction energy for the agarose ligand complex was compared to experimentally determined retention data. From the retention studies, the capacity factor (k’) for mAb-1 was determined for the same ligand (Capto MMC) and at different ligand densities (low, medium, and high). Figure 5 indicates that there is a directional correlation between the experimentally determined values of k’ and the binding affinities determined in silico . As the ligand density increased the binding affinities increased and the k’ also increased. Figure 5A, shows that the calculated increase in in silico binding affinities for the agarose-ligand complex are greater than the baseline agarose interaction to the protein and higher than a single ligand docking.
To examine the effect of local perturbations and solvent components on binding affinity, we performed a droplet molecular dynamics simulation of the ligand binding site with a solvation shell ratio of 10 Å. Using droplet molecular dynamics simulation allowed for the exploration of dynamics near and around the docking site. This method was preferred over a solvation box because of the size and complexity of simulating a fully solvated antibody system. Constraints were applied to residues outside the solvation droplet to dampen out dynamics as we move outside the water droplet. Figure 6 shows that during the course of a 30 ns unconstrained atomistic molecular dynamics simulation (Insaidoo et al., 2011), the six-ligand agarose remained bound to the antibody with an average affinity of 18.26 (±1.05) kcal/mol. This value is very close to the original induced fit binding score for Capto MMC bound to mAb1 (19.08 kcal/mol), indicating that the binding interactions retained consistent.