Modulating protein-protein interactions with small molecules: the importance of binding hotspots

Abstract

The modulation of protein-protein interactions (PPIs) by small drug-like molecules is a relatively new area of research and has opened up new opportunities in drug discovery. However, the progress made in this area is limited to a handful of known cases of small molecules that target specific diseases. With the increasing availability of protein structure complexes, it is highly important to devise strategies exploiting homologous structure space on a large scale for discovering putative PPIs that could be attractive drug targets. Here, we propose a scheme that allows performing large-scale screening of all protein complexes and finding putative small-molecule and/or peptide binding sites overlapping with protein-protein binding sites (so-called "multibinding sites"). We find more than 600 nonredundant proteins from 60 protein families with multibinding sites. Moreover, we show that the multibinding sites are mostly observed in transient complexes, largely overlap with the binding hotspots and are more evolutionarily conserved than other interface sites. We investigate possible mechanisms of how small molecules may modulate protein-protein binding and discuss examples of new candidates for drug design.

Fig. 1

Known cases of binding of small molecules to protein–protein interfaces with a comparison of the crystal structures of their protein–protein and protein–small-molecule complexes. (a) Small-molecule inhibitor of the ZipA–FtsZ PPI (PDB IDs: 1Y2G and 1F46). (b) A small molecule bound to adaptive IL2 and IL2R-alpha interface (PDB IDs: 1Z92 and 1M48). (c) Small molecule triggered Bax/Bak-mediated apoptosis in Bcl-2 proteins [Bcl-2, Bcl-x(L) and Bcl-w] (PDB IDs: 2BZW and 2YXJ). (d) A small molecule bound to the N-terminal transactivation domain of human papillomavirus type 11 E2 and inhibits its interaction with E1 (PDB IDs: 1TUE and 1R6N). (e) Small molecule inhibiting the p53–MDM2 to activate the p53 pathway in cancer cells (PDB IDs: 1RV1 and 1YCR). (f) A small-molecule inhibitor of tumor necrosis factor-alpha that promotes disassembly of this trimeric cytokine (PDB IDs: 1TNF and 2AZ5).

Fig. 2

Distribution of fraction of binding hotspots that overlap multibinding residues (dark gray) and that do not overlap multibinding residues (light gray).

Fig. 3

Distribution of fraction of conserved multibinding residues (dark gray) and of conserved non-multibinding residues (light gray). Conserved residues are defined as those with normalized entropy scores between 0.6 and 1.039.

Fig. 4

GO function distribution of 891 nonredundant protein chains (culled at 50% sequence identity) based on GO slim terms.

Fig. 5

Distribution of dissociation energies of protein dimers with and without multibinding sites at the protein–protein interfaces (red, dimers with multibinding sites; blue, all other dimers). Bandwidth (h) = 1.