Proximity-Induced Saccharide Binding to Protein Active Site within a Confined Cavity of Coordination Cages

Abstract

Enhancing protein-ligand affinity is crucial for regulating protein function; however, redesigning ligand molecules often requires extensive trial and error. In this study, we demonstrate proximity-induced ligand binding to a protein’s active site by confining it within coordination cages, thereby enabling precise control of protein activity. Co-encapsulation within the confined cavity of the cage brings lysozyme and a low-affinity saccharide into close proximity, resulting in a 10³-fold decrease in the apparent dissociation constant of the monosaccharide. The significant enhancement of the saccharide binding to lysozyme's active site effectively inhibited its enzymatic activity. NMR studies confirmed the formation of lysozyme–saccharide complexes through enhanced weak interactions, which are otherwise unobservable, facilitated by the confined cavity. This cage confinement strategy thus offers a novel approach for ligand-based functional control of native proteins, eliminating the need for elaborate ligand design and protein engineering.