Proteome-wide target profiling of α-helix mimetics

The dysregulation of protein–protein interactions (PPIs) in disease states is well established, yet they are challenging to target, owing to the large surface area and featureless nature of protein binding interfaces. For targeting helix-mediated interactions, α-helix mimetics present a promising strategy. These are versatile small molecule scaffolds, capable of mimicking the hotspot residues on an α-helix. A wide range of such scaffolds have been reported, yet their target protein selectivity in the context of a whole proteome requires further exploration. Here, we report the affinity-based protein profiling of three structurally distinct classes of α-helix mimetics, N-substituted oligobenzamides, pyrrolopyrimidines, and oxopiperazines. This represents the first direct cross-comparison of different helix mimetic scaffolds, revealing significant differences in proteome-wide selectivity.