Chemical Control Over Protein-Protein Interactions: Beyond Inhibitors

Abstract

Protein-protein interactions have become attractive drug targets and recent studies suggest that these interfaces may be amenable to inhibition by small molecules. However, blocking specific interactions may not be the only way of manipulating the extensive network of interacting proteins. Recently, several approaches have emerged for promoting these interactions rather than inhibiting them. Typically, these strategies employ a bifunctional ligand to simultaneously bind two targets, forcing their juxtaposition. Chemically "riveting" specific protein contacts can reveal important aspects of regulation, such as the consequences of stable dimerization or the effects of prolonged dwell time. Moreover, in some cases, entirely new functions arise when two proteins, which normally do not interact, are brought into close proximity with one another. Together with inhibitors, bifunctional molecules are part of a growing toolbox of chemical probes that can be used to reversibly and selectively control the interact-ome. Using these reagents, new insights into the dynamics of protein-protein interactions and their importance in biology are beginning to emerge. Future hurdles in this area lie in the development of robust synthetic platforms for rapidly generating compounds to meet the challenges of diverse protein-protein interfaces.

FK506-binding protein (FKBP) partitions a modified HIV protease inhibitor into blood cells and prolongs its lifetime in vivo

“…Carbodiimide-mediated coupling of 5 with an FKBPbinding group yielded the bifunctional compound 6. In this reaction, we took advantage of a well-known, synthetic ligand for FKBP (SLF) that has high affinity for FKBP (K d Ϸ1 to 10 nM) (27) but does not interface with calcineurin; thus, installing this group provides tight binding to FKBP without concurrent anticalcineurin activity (28)(29)(30). We refer to the bifunctional inhibitor as SLFavir because it incorporates chemical domains from both SLF and amprenavir.…”

Conditional Nuclear Import and Export of Yeast Proteins Using a Chemical Inducer of Dimerization

“…In this report, we have explored the versatility of a CIDbased system for controlling nucleocytoplasmic shuttling; however, replacing the NES or NLS with another address signal, such as a membrane localization sequence or an endoplasmic reticulum (ER) retention marker, could be used to expand this system [9,27]. In support of this idea, a myristoylation domain has been used to conditionally target a protein to the plasma membrane in a mammalian system [28] and fusions to membrane-bound proteins have been used to mislocalize targets in a system termed ''Anchors Away'' [29].…”

“…This method was adapted from work in mammalian models [5][6][7] and pioneering efforts by the Crabtree and Schreiber groups on chemical inducers of dimerization (CIDs; reviewed in [8][9][10]). CIDs are small, membrane-permeable molecules that bind to two proteins at the same time.…”

Targeting Prostate Cancer with Bifunctional Modulators of the Androgen Receptor

“…From this analysis, it is clear that the synthetic strategy yielded bifunctional ligands that retain a significantly high affinity for GR. Extrinsic recruitment of a designed coactivator enhances GR ligand efficacy FK506-binding proteins such as human FKBP1A bind with subnanomolar affinity to FK506, and the fact that this high-affinity interaction is retained, even when the macrolide is conjugated to other molecules, has made this pairing the basis for multiple successful small moleculemediated protein recruitment strategies (31 ). As a first approach, we designed and constructed a coactivator fusion protein consisting of a nuclear localization signal, the strong transcriptional activation domain of the herpes simplex virion protein 16 (VP16), and FKBP1A and examined its ability to modulate GR activity by monitoring the transcriptional output of a GR-stimulated reporter driven by a natural GR enhancer sequence.…”