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.