Expanding the number of 'druggable' targets: non-enzymes and protein-protein interactions

Abstract

Following sequencing and assembly of the human genome, the preferred methods for identification of new drug targets have changed dramatically. Modern tactics such as genome-wide association studies (GWAS) and deep sequencing are fundamentally different from the pharmacology-guided approaches used previously, in which knowledge of small molecule ligands acting at their cellular targets was the primary discovery engine. A consequence of the 'target-first, pharmacology-second' strategy is that many predicted drug targets are non-enzymes, such as scaffolding, regulatory or structural proteins, and their activities are often dependent on protein-protein interactions (PPIs). These types of targets create unique challenges to drug discovery efforts because enzymatic turnover cannot be used as a convenient surrogate for compound potency. Moreover, it is often challenging to predict how ligand binding to non-enzymes might affect changes in protein function and/or pathobiology. Thus, in the postgenomic era, targets might be strongly implicated by molecular biology-based methods, yet they often later earn the designation of 'undruggable'. Can the scope of available targets be widened to include these promising, but challenging, non-enzymes? In this review, we discuss advances in high-throughput screening (HTS) technology and chemical library design that are emerging to deal with these challenges.

Figure 1

Nonenzyme targets present unique challenges to drug discovery. Classic enzyme targets have well-defined active sites and many have clear allosteric sites, which make attractive binding regions for orthosteric and allosteric inhibitors. In contrast, most non-enzymes lack obvious binding pockets or they are involved in protein-protein interactions that involve larger, more diffuse contact areas.

Figure 2

Selected biophysical methods for ligand discovery. A: Ligand-induced changes in chemical shifts of a ¹H, ¹⁵N HSQC spectrum of a protein target suitable for NMR-based screening indicate binding. Fluorescent spots on a small molecule microarray indicate the presence of a fluorescently labeled protein bound to the immobilized ligands. B: Differential scanning fluorimetry measures changes in the melting temperature (T_m) of a protein target induced by ligand binding. Similarly, hydrogen-deuterium exchange can measure changes in stability to chemical denaturation due to small molecule binding. C: The mixed-solvent molecular dynamics method may be used for both binding site identification and the construction of a pharmacophore.

Figure 3

A: Diversity-oriented synthesis uses sequences of modular, complexity-generating reactions to build compound libraries of diverse scaffolds (figure adapted from [87]). B: Focused libraries of natural product-inspired scaffolds and cyclic peptides may be useful for lead generation against non-enzymes and protein-protein interactions. C: Fragment-based screening enables the evolution of low-affinity, high-efficiency binders into high affinity leads.