Exploiting Avidity Effects for the Discovery of Low Affinity Protein-Binding Fragments

Fragment-based drug discovery (FBDD) is a powerful approach
to
the development of pharmaceuticals and probe molecules and there is
broad interest in the development of new platforms for their discovery.
Here, we introduce a workflow in which low molecular weight organic
molecules displayed on the surface of TentaGel beads are exposed to
a multimeric, fluorescently labeled target protein. Using tetrameric
or dimeric protein targets, we show that beads that display even weak
ligands (KDs in the high μM to low
mM range) stably capture the protein due to avidity effects, thus
allowing a simple “pull-down” protocol to be employed
for fragment discovery. We also demonstrate that the platform is capable
of supporting a “fragment growth” screen, which is a
typical strategy to advance a fragment to a higher-affinity lead molecule.
This platform is inexpensive and requires no specialized infrastructure.