Background: Protein–protein interactions dominate molecular recognition in biologic systems. One major challenge for drug discovery arises from the very large surfaces that are characteristic of many protein–protein interactions. Objectives: To identify ‘drug-like’ small molecule leads capable of modulating protein–protein interactions based on common protein-recognition motifs, such as α-helices, β-strands, reverse-turns and polyproline motifs for example. Overview: Many proteins/peptides are unstructured under physiologic conditions and only fold into ordered structures on binding to their cellular targets. Therefore, preorganization of an inhibitor into its protein-bound conformation reduces the entropy of binding and enhances the relative affinity of the inhibitor. Accordingly, this review describes a general strategy to address the challenge based on the ‘privileged structure hypothesis’ [Che, PhD thesis, Washington University, 2003] that chemical templates capable of mimicking surfaces of protein-recognition motifs are potential privileged scaffolds as small-molecule inhibitors of protein–protein interactions. The authors highlight recent advances in the design of privileged scaffolds targeting reverse-turn and helical recognition. Conclusions: Privileged scaffolds targeting common protein-recognition motifs are useful to help elucidate the receptor-bound conformation and to provide non-peptidic, bioavailable substructures suitable for optimization to modulate protein–protein interactions.