Enhancing G-Quadruplex Binding: Rational Design and Biophysical Evaluation of Dimeric Ligands

G-quadruplexes (G4s) are non-canonical nucleic acid structures formed by guanine-rich sequences. Within the human genome, beyond telomeres, G4 motifs have also been found in promoters, implying a potential role in gene regulation that could be achieved through interactions with small-molecule ligands. In this field, anthraquinone represented a privileged scaffold for the design of G4-targeting molecules. Additionally, emerging evidence proved that compounds bearing two aromatic cores can offer enhanced affinity and selectivity toward G4s due to cooperative binding in a tweezer-like fashion. This study reports the rational design and synthesis of anthraquinone-based building blocks conceived to generate a dimeric ligand connected through a flexible polyethylene glycol (PEG) linker to potentially recognize G4 as molecular tweezers. The interaction of the synthesized compounds with G4 structures has been investigated by biophysical techniques, including fluorescence thermal shift assays, electrospray ionization-mass spectrometry and circular dichroism (CD) spectroscopy, supported by molecular modeling studies. Finally, cytotoxicity assays were performed to evaluate the antiproliferative effects of the new ligands.