G-quadruplexes (G4s), guanine-rich sequences that are able to fold up in polymorphous secondary structures, have received increasing attention in medicinal chemistry thanks to their occurrence in “hot” regions of the genome. Indeed, there is much evidence that G4s affect genomic instability, telomerase dysfunction, and behave as transcriptional repressor elements. Thus, targeting G4 structures has emerged as an alternative strategy for the potential treatment of several diseases. This chapter offers an overview of the critical role that the rational design of molecular ligands able to selectively interact, stabilize and cleave G4s, could play in drug discovery. Starting from natural products to more recent synthetic compounds, the key structural differences as well as the common features of each ligands sub-category have been compared to provide general directions in the development of more efficient and bioactive G4 ligands.
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