Natural
compounds are an important class of potent drug molecules
including some retrospectively found to act as stabilizers of protein–protein
interactions (PPIs). However, the design of synthetic PPI stabilizers
remains an understudied approach. To date, there are limited examples
where cooperativity has been utilized to guide the optimization of
a PPI stabilizer. The 14-3-3 scaffold proteins provide an excellent
platform to explore PPI stabilization because these proteins mediate
several hundred PPIs, and a class of natural compounds, the fusicoccanes,
are known to stabilize a subset of 14-3-3 protein interactions. 14-3-3
has been reported to negatively regulate the p65 subunit of the NF-κB
transcription factor, which qualifies this protein complex as a potential
target for drug discovery to control cell proliferation. Here, we
report the high-resolution crystal structures of two 14-3-3 binding
motifs of p65 in complex with 14-3-3. A semisynthetic natural product
derivative, DP-005, binds to an interface pocket of the p65/14-3-3
complex and concomitantly stabilizes it. Cooperativity analyses of
this interaction, and other disease relevant 14-3-3-PPIs, demonstrated
selectivity of DP-005 for the p65/14-3-3 complex. The adaptation of
a cooperative binding model provided a general approach to characterize
stabilization and to assay for selectivity of PPI stabilizers.