Quantitative Characterization of the Binding and Unbinding of Millimolar Drug Fragments with Molecular Dynamics Simulations

A quantitative
characterization of the binding properties of drug
fragments to a target protein is an important component of a fragment-based
drug discovery program. Fragments typically have a weak binding affinity,
however, making it challenging to experimentally characterize key
binding properties, including binding sites, poses, and affinities.
Direct simulation of the binding equilibrium by molecular dynamics
(MD) simulations can provide a computational route to characterize
fragment binding, but this approach is so computationally intensive
that it has thus far remained relatively unexplored. Here, we perform
MD simulations of sufficient length to observe several different fragments
spontaneously and repeatedly bind to and unbind from the protein FKBP,
allowing the binding affinities, on- and off-rates, and relative occupancies
of alternative binding sites and alternative poses within each binding
site to be estimated, thereby illustrating the potential of long time
scale MD as a quantitative tool for fragment-based drug discovery.
The data from the long time scale fragment binding simulations reported
here also provide a useful benchmark for testing alternative computational
methods aimed at characterizing fragment binding properties. As an
example, we calculated binding affinities for the same fragments using
a standard free energy perturbation approach and found that the values
agreed with those obtained from the fragment binding simulations within
statistical error.