The proper filling of apolar pockets at
enzyme active sites is central for increasing binding activity and selectivity of hits and leads in medicinal chemistry. In our structure-based design approach toward the generation of potent
enzyme inhibitors, we encountered a variety of challenges in gaining suitable binding affinity from the occupation of such pockets. We summarize them here for the first time. A
fluorine scan of tricyclic
thrombin inhibitors led to the discovery of favorable orthogonal dipolar C-F...CO interactions. Efficient
cation-pi interactions were established in the S4 pocket of
factor Xa, another
serine protease from the blood coagulation cascade. Changing from mono- to bisubstrate inhibitors of
catechol O-methyltransferase, a target in the
L-Dopa-based treatment of
Parkinson's disease, enabled the full exploitation of a previously unexplored hydrophobic pocket. Conformational preorganization of a pocket at an
enzyme active site is crucial for harvesting binding affinity. This is demonstrated for two
enzymes from the nonmevalonate pathway of
isoprenoid biosynthesis, IspE and IspF, which are pursued as
antimalarial targets. Disrupting crystallographically defined water networks on the way into a pocket might cost all of the binding free enthalpy gained from its occupation, as revealed in studies with
tRNA-guanine transglycosylase, a target against
shigellosis. Investigations of the active site of
plasmepsin II, another
antimalarial target, showed that principles for proper apolar cavity filling, originally developed for synthetic host-guest systems, are also applicable to
enzyme environments.