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Small-molecule inhibitors of protein–protein interactions: progressing towards the dream

Key Points

  • Protein–protein interactions represent a large and important class of targets for human therapeutics.

  • However, developing small-molecule antagonists of protein–protein interactions is challenging, owing to issues such as the general lack of small-molecule starting points for drug design, the typical flatness of the interface, the difficulty of distinguishing real from artefactual binding, and the size and character of typical small-molecule libraries.

  • This article uses examples to describe general strategies in the development of small molecule antagonists of protein–protein interactions. Two types of antagonists are described: those that bind directly to the 'hot spot'of a protein–protein interface — a region that has a major contribution to high-affinity binding — and those that bind at allosteric sites distal from the protein–protein interface.

  • Finally, characteristics of programmes that have successfully identified small-molecule antagonists of protein–protein interactions are discussed. A high degree of validation is recommended for antagonists of protein–protein interactions owing to the nature of these targets, and a series of steps for validating and characterizing a new series of antagonists are presented.

Abstract

Protein–protein interactions have a key role in most biological processes, and offer attractive opportunities for therapeutic intervention. Developing small molecules that modulate protein–protein interactions is difficult, owing to issues such as the lack of well-defined binding pockets. Nevertheless, there has been important progress in this endeavour in recent years. Here, we use illustrative examples to discuss general strategies for addressing the challenges inherent in the discovery and characterization of small-molecule inhibitors of protein–protein interactions.

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Figure 1: Structures of unliganded IL-2, and Ro26-4550 bound to IL-2.
Figure 2: Small-molecule inhibitors of interleukin-2.
Figure 3: Protein and small-molecule ligands for B7-1.
Figure 4: Structure of BCL-XL (surface representation) bound to a sixteen-residue peptide derived from BAK (ribbon representation)79.
Figure 5
Figure 6: Mechanism of inhibition of LFA1 by small molecules.
Figure 7: Allosteric inhibitors of LFA1.
Figure 8: Small-molecule allosteric antagonists of inducible nitric oxide synthase.
Figure 9

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Acknowledgements

All images derived from X-ray crystallography data were prepared using Pymol (Delano Scientific, Belmont, California, USA).

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M.R.A. and J.A.W. are employed by Sunesis Pharmaceuticals, which uses proprietary target-directed fragment discovery technologies.

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DATABASES

LocusLink

B7-1

B7-2

BAK

BCL2

BCL-XL

CTLA4

ICAM1

IL-2

IL-2R

iNOS

LFA1

MDM2

NGF

p53

p75NTR

TRKA

Glossary

ALLOSTERIC PROTEIN

A protein containing two or more topologically distinct binding sites that interact functionally with each other.

SURFACE PLASMON RESONANCE

A method for measuring binding interactions between a surface-immobilized molecule and a solution-phase analyte. The technology measures changes in refractive index caused by a change in mass at the surface.

ANTIGEN-PRESENTING CELL

An immune system cell that takes up antigens, processes them, and presents them to T cells, which are then stimulated to mount an immune response.

APOPTOSIS

Programmed cell death.

ISOTHERMAL CALORIMETRY

A method for measuring the change in heat that occurs when a protein–ligand complex is formed. From these data, the thermodynamic parameters for the interaction can be determined.

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Arkin, M., Wells, J. Small-molecule inhibitors of protein–protein interactions: progressing towards the dream. Nat Rev Drug Discov 3, 301–317 (2004). https://doi.org/10.1038/nrd1343

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