AI–Driven Design of Miniproteins as Potential Allosteric Modulators

Allosteric modulation has emerged as a powerful strategy for achieving superior selectivity and safety in drug discovery and protein function regulation. Unlike highly conserved orthosteric sites, allosteric pockets are structurally diverse and less evolutionarily constrained, making them particularly amenable to be modulated by designed miniproteins. Miniproteins can provide extended binding interfaces and high affinity for shallow, dynamic, or cryptic regulatory surfaces that are often inaccessible to small molecules. Recent advances in artificial intelligence (AI) are transforming this field through deep learning–based structure prediction and generative modeling. These AI-driven approaches enable the identification of allosteric hotspots, characterization of conformational ensembles, and de novo} design of structured miniprotein binders. They are rapidly expanding the landscape of designing selective modulators across diverse allosteric targets, including GPCRs, receptor tyrosine kinases, nuclear receptors, ion channels, and protein–protein interfaces. This review summarizes state-of-the-art AI-driven computational methodologies for designing miniproteins as potential allosteric modulators and discusses their current challenges and future opportunities in allosteric drug discovery.