Abstract
The study of drug-receptor interactions has largely been framed in terms of the equilibrium thermodynamic binding affinity, an in vitro measure of the stability of the drug-receptor complex that is commonly used as a proxy measure of in vivo biological activity. In response to the growing realization of the importance of binding kinetics to in vivo drug activity we present a computational methodology for the kinetic characterization of drug-receptor interactions in terms of the encounter complex. Using trajectory data from multiple Brownian dynamics simulations of ligand diffusion, we derive the spatial density of the ligand around the receptor and show how it can be quantitatively partitioned into different basins of attraction. Numerical integration of the ligand densities within the basins can be used to estimate the residence time of the ligand within these diffusive binding sites. Simulations of two structurally similar inhibitors of Hsp90 exhibit diffusive binding sites with similar spatial structure but with different ligand residence times. In contrast, a pair of structurally dissimilar inhibitors of MDM2, a peptide and a small molecule, exhibit spatially distinct basins of attraction around the receptor, which in turn reveal differences in ligand orientational order. Thus, our kinetic approach provides microscopic details of drug-receptor dynamics that provide novel insight into the observed differences in the thermodynamic binding affinities for the two inhibitors, such as the differences in the entropic contributions to binding. The characterization of the encounter complex, in terms of the structure, topology, and dynamics of diffusive binding sites, offers a new perspective on ligand receptor interactions and the potential for greater insight into drug action. The method, which requires no prior knowledge of the bound state, is a first step toward the incorporation of ligand kinetics into in silica drug development protocols.