Fine-tuning multiprotein complexes using small molecules

Abstract

Multiprotein complexes such as the transcriptional machinery, signaling hubs, and protein folding machines are typically composed of at least one enzyme combined with multiple non-enzymes. Often the components of these complexes are incorporated in a combinatorial manner, in which the ultimate composition of the system helps dictate the type, location, or duration of cellular activities. Although drugs and chemical probes have traditionally targeted the enzyme components, emerging strategies call for controlling the function of protein complexes by modulation of protein-protein interactions (PPIs). However, the challenges of targeting PPIs have been well documented, and the diversity of PPIs makes a "one-size-fits-all" solution highly unlikely. These hurdles are particularly daunting for PPIs that encompass large buried surface areas and those with weak affinities. In this Review, we discuss lessons from natural systems, in which allostery and other mechanisms are used to overcome the challenge of regulating the most difficult PPIs. These systems may provide a blueprint for identifying small molecules that target challenging PPIs and affecting molecular decision-making within multiprotein systems.

Figure 1. Multi-protein complexes are assembled from enzymes bound to multiple, non-enzyme partners through protein-protein interactions

The majority of protein complexes in biology share the common features of being assembled from protein-protein interactions (PPIs) between enzymes (red) and non-enzymes (white). These factors assemble into multi-protein systems that have emergent properties (e.g. biology not engendered by any individual component) and essential roles in molecular processes in the cell. To illustrate this idea, a few of the major protein complexes are shown.

Figure 2. Not all protein-protein interactions are created equal: some PPIs are harder to inhibit than others

(A) PPIs can be roughly categorized by their apparent affinity and the buried surface area involved in the contact. This type of analysis creates four major quadrants of interactions: strong and concise, strong and broad, weak and concise, and weak and broad. Examples of each type of interaction from the Protein Data Bank (PDB) are shown. Strong and concise: XIAP-SMAC (2JK7,1G73); strong and broad: IL-2-IL-2R (2ERJ); weak and concise: p53-CBP NRID complex (2L14); weak and broad: cadherin-8 homer dimer (1ZXK). (B) Multiple categories of PPIs are often found within a single complex, as illustrated by the Hsp70 system in which the four major types of PPIs are represented in interactions between Hsp70 and its associated partners: substrate (1DKY); TPR-domain protein (3Q49); nucleotide exchange factor (3C7N); J-domain (2QWN). (C) The p53 system is another example of a system in which multiple types of PPIs are found in the same complex. The repressor Mdmx(3DAC); p53 self-association(1PET); transcriptional coactivators (2K8F). (D) PPIs with known inhibitors were acquired from the 2P2IDB and TIMBAL data bases and the binding affinities (as reported in PDBbind (115)) and surface areas (as measured by InterProSurf (116)) of the PPI were determined. Placing these PPIs into categories revealed small molecules which targeted PPIs with smaller concise surface areas (<1,800 Ų) and relatively strong affinities (<1 ΔM) represent 68% of known PPI inhibitors.

Figure 3. Nature-inspired strategies for modulating difficult PPIs

Natural multi-protein systems use mechanisms such as allostery, PTMs, dynamics, and subcellular localization to control their assembly and disassembly. Small molecules have been found to access similar mechanisms, such as (A) allosteric regulation of the Sec61 translocon by cotransin, which blocks translocation of VCAM-1 without affecting VEGFR2, (B) conformational change in PKCε caused by Bim1, which allows binding to priming kinases, (C) altering microtubule dynamics with paclitaxel and vinblastin, and (D) membrane localization of Akt induced by the kinase inhibitor A-443654.