Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein–Ligand Complexes

Multipolar interactions involving
fluorine and the protein backbone
have been frequently observed in protein–ligand complexes.
Such fluorine–backbone interactions may substantially contribute
to the high affinity of small molecule inhibitors. Here we found that
introduction of trifluoromethyl groups into two different sites in
the thienopyrimidine class of menin–MLL inhibitors considerably
improved their inhibitory activity. In both cases, trifluoromethyl
groups are engaged in short interactions with the backbone of menin.
In order to understand the effect of fluorine, we synthesized a series
of analogues by systematically changing the number of fluorine atoms,
and we determined high-resolution crystal structures of the complexes
with menin. We found that introduction of fluorine at favorable geometry
for interactions with backbone carbonyls may improve the activity
of menin–MLL inhibitors as much as 5- to 10-fold. In order
to facilitate the design of multipolar fluorine–backbone interactions
in protein–ligand complexes, we developed a computational algorithm
named FMAP, which calculates fluorophilic sites in proximity to the
protein backbone. We demonstrated that FMAP could be used to rationalize
improvement in the activity of known protein inhibitors upon introduction
of fluorine. Furthermore, FMAP may also represent a valuable tool
for designing new fluorine substitutions and support ligand optimization
in drug discovery projects. Analysis of the menin–MLL inhibitor
complexes revealed that the backbone in secondary structures is particularly
accessible to the interactions with fluorine. Considering that secondary
structure elements are frequently exposed at protein interfaces, we
postulate that multipolar fluorine–backbone interactions may
represent a particularly attractive approach to improve inhibitors
of protein–protein interactions.