Study on the Binding of Five Plant-Derived Secondary Metabolites to G‑Quadruplexes

Chemical targeting of noncanonical secondary structures of DNA and RNA has emerged as a promising approach for therapeutic development. The most promising targets seem to be four-stranded structures in the G-rich regions of the genome, known as G-quadruplexes (G4s), which are associated with important regulatory regions including promoters. In this study, we tested and modeled the binding of five plant-derived secondary metabolites, known for their antiproliferative activity in vitro, to two G4s found in the human genome: the first at the c-Myc proto-oncogene and the second at the human telomere repeat region. Among the tested compounds, brucine exhibited the strongest interaction with both G4 sequences, while ellagic acid demonstrated binding efficacy comparable to that of brucine in the c-Myc sequence. Through molecular dynamics simulations and the Markov state model, we explored the binding modes of these ligands, elucidated the G4 stability in the bound state, and investigated the fluorescence quenching effect of thioflavin T (ThT) upon its displacement. The biological effects of these natural compounds were investigated in human cell lines, and the interaction with G4s was verified experimentally using a fluorescence displacement assay and CD spectroscopy. This study demonstrates the interaction of these natural compounds with the G4 structures and their implications for therapeutic targeting.