Rational Design of a DNA‐Scaffolded High‐Affinity Binder for Langerin

Abstract

Binders of langerin could target vaccines to Langerhans cells for improved therapeutic effect. Since langerin has low affinity for monovalent glycan ligands, highly multivalent presentation has previously been key for targeting. Aiming to reduce the amount of ligand required, we rationally designed molecularly defined high‐affinity binders based on the precise display of glycomimetic ligands (Glc2NTs) on DNA‐PNA scaffolds. Rather than mimicking langerin's homotrimeric structure with a C3‐symmetric scaffold, we developed readily accessible, easy‐to‐design bivalent binders. The method considers the requirements for bridging sugar binding sites and statistical rebinding as a means to both strengthen the interactions at single binding sites and amplify the avidity enhancement provided by chelation. This gave a 1150‐fold net improvement over the affinity of the free ligand and provided a nanomolar binder (IC50=300 nM) for specific internalization by langerin‐expressing cells.

Combination of peptides with biological, organic, and inorganic materials for synergistically enhanced diagnostics and therapeutics

“…Another useful advantage of the peptide‐DNA conjugate approach is that one can precisely control the distance and orientation of peptides by scaffolding them on a DNA nanostructure. [ 37 ] The Seitz group showed that the hybridization of peptide‐DNA conjugates and DNA templates based on Watson‐Crick base pairing is a facile and effective method to make peptides displayed on a nanostructure with a defined spatial arrangement, which was achieved by controlling the molecular structure of the peptide‐DNA conjugates and/or the length of spacer nucleotides in the DNA templates. [ 38 ] The hybrid structure exhibited significantly different target binding affinity and selectivity according to the interpeptide distance and orientation, which demonstrated that this approach is a promising strategy to maximize the target binding capability of peptides in a multivalent interaction.…”

High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody

“…These DNA-based nano-scaffolds can precisely position other molecular species (such as aptamers, proteins, peptides, small molecules, or carbohydrates), with a resolution spanning length scales ranging from a few nanometers to hundreds of nanometers or more. Examples of multivalent constructs built from oligonucleotides vary in complexity, from simple homo-and hetero-oligomers on a DNA duplex [4][5][6] to highly complex, stoichiometrically-defined presentation of ligands in 2D and 3D space using DNA origami nanostructures, designed to probe the effect of ligand spacing on biological activity 7,8 .…”