An Orthogonal Supramolecular Approach toward Protein Binding and Protein Sensing Using Dendrimers as Scaffolds for the Noncovalent Assembly of Binding and Sensing Groups

Abstract

Inhibiting unwanted protein–protein interactions (PPIs) by targeting extensive protein binding surfaces presents a significant challenge. Macro-ligands offer a promising approach, but traditional covalent functionalization strategies often suffer from synthetic complexity, particularly in controlling the spatial arrangement of binding moieties. This study introduces a new method for macro-ligand design based on the noncovalent, modular self-assembly of functional units within an inert dendrimer scaffold. Although these units are embedded within the dendrimer in a random arrangement, they are mobile and free to move. As such, when a target protein is introduced, these binding units can undergo a self-organization process to optimize their spatial distribution and maximize cooperative interactions with the protein’s binding surface. This dynamic process is controlled by the protein, as it guides and controls the formation of its own optimized macromolecular ligand. When sensor units are combined and included in the assembly process, real-time monitoring and quantification of binding can be detected and quantified. This study details the synthetic methodology employed for the preparation of the component parts and their self-assembly into dendrimer complexes. Subsequent binding assays using cytochrome-c as the target protein, and associated dendrimer complexes, exhibited binding affinities in the nanomolar (nM) range.