Rational drug design via intrinsically disordered protein

Despite substantial increases in research funding by the pharmaceutical industry, drug discovery rates seem to have reached a plateau or perhaps are even declining, suggesting the need for new strategies. Protein–protein interactions have long been thought to provide interesting drug discovery targets, but the development of small molecules that modulate such interactions has so far achieved a low success rate. In contrast to this historic trend, a few recent successes raise hopes for routinely identifying druggable protein–protein interactions. In this Opinion article, we point out the importance of coupled binding and folding for protein–protein signalling interactions generally, and from this and associated observations, we develop a new strategy for identifying protein–protein interactions that would be particularly promising targets for modulation by small molecules. This novel strategy, based on intrinsically disordered protein, has the potential to increase significantly the discovery rate for new molecule entities.

Introduction

The pharmaceutical industry is currently struggling to find promising new drug targets. Although research and development (R&D) spending has increased by an average of 8% (adjusted for inflation) each year for at least the past 35 years, and although the number of completed phase III clinical trials per year match or even exceed the R&D spending trend, the number of new molecule entities (NMEs) approved by the Food and Drug Administration (FDA; http://www.fda.gov) has not kept pace (Figure 1). For example, despite a twofold increase in R&D spending during the past decade (adjusted for inflation), the number of approved NMEs in 2004 increased just 10% compared with 1995, with no upward trend in the intervening years (Figure 1). By the end of 2005, 18 NMEs were approved for the year by the FDA (http://www.fda.gov/cder/rdmt/nmecy2005.htm), showing that 2005 was a particularly poor year for drug discovery – one of the two worst since before 1990 – and further showing the gradual decline in the five-year-average since a peak in the 1997–1998 period.

Current drug therapy uses ∼500 targets, less than 10% of a reasonable potential list [1]; membrane receptors (mostly G-protein coupled) and various enzymes account for ∼70% of the current drug molecule targets [2]. New approaches, including high-throughput screening, structure-based and fragment-based design, proteomics, microarrary analysis and systems biology, have not yielded the hoped-for increases in the discovery rates for NMEs, at least not to date, apparently due in significant measure to the failure to translate the new discoveries and understanding into new targets.

A major potential source of new drug targets is provided by the set of protein–protein interactions within a cell (http://www.nature.com/horizon/chemicalspace/background/protein.html). Upon environmental stimuli, the complex networks of protein–protein interactions generate a coordinated response; therefore, such interactions offer attractive targets for a generation of therapeutic intervention. However, the protein–protein interactions involved in cell signalling are transient and difficult to assay, which inherently hampers drug discovery efforts focused on the modulation of these interactions. Systems biology approaches are mapping out the protein interactome and an understanding of these results might help to identify the protein–protein interactions that appear to be particularly desirable drug targets [3]. A further complication is that kinetics is known to be of central importance in every drug design problem. The recent development of quantitative interaction network mapping is making this approach more powerful by including kinetics information [4]. Although the next step of finding drug molecules that modulate protein–protein interactions has not been generally successful in the past [5], recent promising examples are creating a new optimism in this arena 6, 7.

We at Molecular Kinetics noticed that for several of the protein–protein interactions that are being successfully blocked by small molecules one of the partners in each case undergoes a disorder-to-order transition upon binding to its structured complement. Although flexibility and rearrangement of side chains on the surface of a protein have been observed as a way for binding sites, or ‘hot spots’ to change shape to better fit small molecule ligands [8] through a mechanism that seems analogous to Koshland's induced fit [9], the importance of backbone flexibility coupled with a disorder-to-order transition upon binding has not received a mention in any of the current discussions on the modulation of protein–protein interactions by small molecule ligands. Although our concept of disorder-based modulation of protein–protein interactions currently suffers from a lack of extensive experimental support (because of the novelty of this field), one well-characterized example, the p53–MDM2 interaction, provides a useful illustration (for more discussion see below and 10, 11, 12, 13, 14, 15, 16, 17). Furthermore, the application of our computational tools revealed that the mechanisms where a small molecule can block the protein–protein interaction in which one partner undergoes disorder-to-order transition is likely to be applicable for the modulation of several additional protein–protein interactions such as tubulin polymerization and the formation of the Bcl2–BH3, Bcl-xL–BH3, XIAP–caspase-9, XIAP–caspase-3 and Rac–Trio complexes; however, the probable importance of intrinsic disorder in the druggable interactions was unmentioned [6]. The goals of this article are twofold: first, to show how this intrinsic backbone and side-chain disorder is important, perhaps even crucial, for the druggability of protein–protein interactions; and second, to use disorder knowledge to generalize from the current successes to identify, on a proteome-wide scale, the protein–protein interactions that are the most promising targets for therapeutic intervention. These analyses yield a cornucopia of new opportunities (Molecular Kinetics, patent pending) across a wide spectrum of diseases.