Bisindolylmaleimide Ligands Stabilize G-Quadruplex DNA Structure and Downregulate Gene Expression

G-Quadruplex (G4) structures play a pivotal role in diverse biological functions, including essential processes, such as telomere maintenance and gene regulation. G4 structures formed in functional regions of genomes are actively pursued toward therapeutics and are targeted by small-molecule ligands that alter their structure and/or stability. Herein, we report the synthesis of bisindolylmaleimide-based () ligands, which preferentially stabilize parallel G4 structures of and oncogenes over the telomeric G4 and duplex DNAs. The preferential stabilization of parallel G4s with ligands is further validated by the DNA polymerase stop assay, where stop products were only observed for templates containing the G4 sequence. Nuclear magnetic resonance (NMR) titration studies indicate that the lead ligand forms a 2:1 complex with G4 DNA with a of 38 ± 5 μM. The ligand stacks at the 5' and 3' quartets, with molecular modeling and dynamics studies supporting the proposed binding mode. The ligand is cytotoxic to HeLa cells and downregulates gene expression. Collectively, the results present bisindolylmaleimide scaffolds as novel and powerful G4 targeting agents.