Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in a Series of Thermolysin Inhibitors

In lead optimization, open, solvent-exposed
protein pockets are
often disregarded as prospective binding sites. Because of bulk-solvent
proximity, researchers are instead enticed to attach charged polar
groups at inhibitor scaffolds to improve solubility and pharmacokinetic
properties. It is rarely considered that solvent effects from water
reorganization in the first hydration shell of protein–ligand
complexes can have a significant impact on binding. We investigate
the thermodynamic fingerprint of thermolysin inhibitors featuring
terminal charged ammonium groups that are gradually pulled from a
distal, solvent-exposed position into the flat, bowl-shaped S2′ pocket. Even for the most remote attachment, costs
for partial desolvation of the polar group next to the protein–solvent
interface are difficult to compensate by interactions with the protein
or surrounding water molecules. Through direct comparison with hydrophobic
analogues, a significant 180-fold affinity loss was recorded, which
questions popular strategies to attach polar ligand-solubilizing groups
at the exposed terminus of substituents accommodated in flat open
pockets.