Bispecific DNA-Peptide Probes for Targeting Receptor Pairs on Live Cells

: Chemical modification and nucleic acid self-assembly can be used to make protein receptor ligands form specific arrangements. While this property has been exploited extensively for probing of homomultivalent interactions in solution, on cells and viruses, there has been comparatively little attention paid to the exploration of heteromultivalent interactions. In this study, we investigated the use of readily assembable DNA duplexes as scaffolds for the DNA-programmed heterobivalency to target specific cell types. In contrast to previous bispecific agents, we leverage the potential of peptide-based high affinity binders of cell surface proteins used in diagnostics/therapeutics. Systematic spatial screening revealed the optimal distance between two (cyclo)peptides required for selectively recognizing cells expressing unique combinations of receptors. The VGFR2 / αVβ3 receptor system on HUVECs was tolerant to changes of the distance between two cyclopeptides (L and cyclo(-RGDfK-)) required that the distance exceeded approx. 65 Å distance. Of note, a different distance-affinity landscape was observed for recognition of EGFR and MET on A498 cells (through GE11 and bicyclic peptide GE-137). The DNA-programmed bispecific binders demonstrated specificity and efficient internalization into target cells. Nucleic acid hybridization with auristatin-loaded DNA enabled a selective targeting of cytotoxic payload. The distance-optimized bispecific DNA-peptide probes offers insights useful for developing targeted therapeutics in cancer therapy.