Insights from Fragment Hit Binding Assays by Molecular Simulations

Novel bioactive molecules can be
rationally designed by growing
and linking small fragments. Because fragments are fast and promiscuous,
it is common to have contradictory hit results between different experimental
screening techniques. Here, we simultaneously determine fragment binding
poses, affinities, and kinetics on a focused library of 42 fragments
against the serine protease factor Xa using multimillisecond molecular
dynamics simulations. We predict experimental poses of 12 over 15
S1 crystal structures, and affinities are recovered for 4 out of 6.
A kinetic map of protein cavities is computed in terms of on- and
off-rates as well as insights into secondary ligand poses. The results
suggest that the approach can be useful to recapitulate discordant
fragment screening data.