Small-molecule inhibitors of protein-protein interactions: progressing toward the reality

Abstract

The past 20 years have seen many advances in our understanding of protein-protein interactions (PPIs) and how to target them with small-molecule therapeutics. In 2004, we reviewed some early successes; since then, potent inhibitors have been developed for diverse protein complexes, and compounds are now in clinical trials for six targets. Surprisingly, many of these PPI clinical candidates have efficiency metrics typical of "lead-like" or "drug-like" molecules and are orally available. Successful discovery efforts have integrated multiple disciplines and make use of all the modern tools of target-based discovery-structure, computation, screening, and biomarkers. PPIs become progressively more challenging as the interfaces become more complex, i.e., as binding epitopes are displayed on primary, secondary, or tertiary structures. Here, we review the last 10 years of progress, focusing on the properties of PPI inhibitors that have advanced to clinical trials and prospects for the future of PPI drug discovery.

Figure 1

PPI can be classified by whether one side of the interface consists of a primary (linear) protein sequence (green), a single region of secondary structure (such as an alpha helix, yellow), or multiple sequences requiring tertiary structure (red). There are fewer examples of small-molecule inhibitors of PPI as the interface becomes more complex (from primary, to secondary, to tertiary epitopes).Structures shown are BRDt/histone (green, 2WP1), MDM2/p53 (yellow, 1YCR), and IL-2/IL-2Ra (red, 1Z92).

Figure 2

Peptide-like inhibitors of PPI with primary epitopes. A) SAR1 118 (lifitegrast) inhibits binding of LFA1 (CD11a/CD18) to its ligand ICAM. The mechanism either involves binding directly to the ICAM site in the I-domain of CD11a (Keating et al., 2006) or allosteric inhibition through binding to the I-like domain in CD18 (Shimaoka et al., 2003). B) X-ray structure of a cIAP1/XIAP chimera (white surface) bound to GDC-0152 (green sticks; PDB: 3UW4) and overlaid with SMAC peptide (magenta cartoon; PDB: 1G73). Chemical structures of SMAC mimetics in clinical trials.

Figure 3

Small-molecule inhibitors of PPI with primary epitopes. A) Crystal structure of BRD4 bromodomain (white surface) bound to (+)-JQ1 (green sticks, PDB: 3MXF) overlaid with acetylated histone peptide (magenta cartoon, PDB: 2WP1). Clinical compounds or their closest published analogs are shown below. B) Crystal structure of the dimerization interface of HIV integrase (white and cyan surface) bound to compound 16 (green sticks, PDB: 4NYF) with overlaid epitope from LEDGF (magenta, PDB: 2B4J). Compound 16 is a precursor to the clinical compound BI 224436. C) Von-Hippel Lindau (VHL) protein (white surface) with bound inhibitor compound 51 (green sticks, PDB: 4B9K). The central hydroxyproline mimics the binding of a peptide derived from HIF1α (PDB: 4AJY, not shown).

Figure 4

BCL-2/BCL-xL and MDM2 interfaces contain secondary epitopes. A) Structure of BCL-2 (white surface) bound to ABT-199 (green sticks, PDB: 4MAN) with overlaid BAX BH3 peptide (magenta cartoon, PBD: 2XA0). Chemical structures of selected BCL-2 and BCL-xL inhibitors. B) Structure of MDM2 (white surface) bound to RG-7112 (green sticks, PDB: 4IPF) with overlaid p53 peptide (magenta cartoon, PDB: 1YCR). Chemical structures of compounds in clinical testing or their closest published analogs.

Figure 5

Preclinical examples of inhibitors of PPI with secondary epitopes. A) Crystal structure of menin (white surface) bound to MIV-6R (green sticks, PDB: 4OG8) with MLL peptide overlaid (magenta cartoon, PDB: 3U85). Structures of MLL inhibitors MIV-6R and MIV 2-2. B) Crystal structures of PDK-1, showing the PIF-tide binding site bound with Tethered activator (JS30, green sticks, PDB: 3OTU) or inhibitor (1F8, magenta sticks, 3ORX). JS30 pushes the C-helix into a catalytically competent conformation. Chemical structure of noncovalent PIF-tide inhibitor PS210. C) Structure of OHM1, which binds to CBP at the HIF1α peptide-binding site.

Figure 6

Small-molecule inhibitors of PPI with tertiary epitopes. A) Structure of IL-2 (white surface) bound to SP4206 (green sticks, PDB: 1PY2). B) Structure of transactivation domain of E2 protein from HPV11 (white surface) bound to BILH 434 (green sticks, PDB: 1R6N).