Unlocking the potential of protein-derived peptides to target G-quadruplex DNA: from recognition to anticancer activity

• Published in: Nucleic acids research 2024-07, Vol.52 (12), p.6748-6762
• Main Authors: Merlino, Francesco, Marzano, Simona, Zizza, Pasquale, D'Aria, Federica, Grasso, Nicola, Carachino, Alice, Iachettini, Sara, Biroccio, Annamaria, Fonzo, Silvia Di, Grieco, Paolo, Randazzo, Antonio, Amato, Jussara, Pagano, Bruno
• Format: Article
• Language: English
• Subjects: Antineoplastic Agents - chemistry; Antineoplastic Agents - pharmacology; Cell Line, Tumor; Cell-Penetrating Peptides - chemistry; Cell-Penetrating Peptides - pharmacology; Chemical Biology and Nucleic Acid Chemistry; DNA - chemistry; DNA - metabolism; G-Quadruplexes - drug effects; Humans; Ligands; Peptides - chemistry; Peptides - pharmacology; Protein Binding; Shelterin Complex - chemistry; Shelterin Complex - metabolism
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkae471

Noncanonical nucleic acid structures, particularly G-quadruplexes, have garnered significant attention as potential therapeutic targets in cancer treatment. Here, the recognition of G-quadruplex DNA by peptides derived from the Rap1 protein is explored, with the aim of developing novel peptide-based G-quadruplex ligands with enhanced selectivity and anticancer activity. Biophysical techniques were employed to assess the interaction of a peptide derived from the G-quadruplex-binding domain of the protein with various biologically relevant G-quadruplex structures. Through alanine scanning mutagenesis, key amino acids crucial for G-quadruplex recognition were identified, leading to the discovery of two peptides with improved G-quadruplex-binding properties. However, despite their in vitro efficacy, these peptides showed limited cell penetration and anticancer activity. To overcome this challenge, cell-penetrating peptide (CPP)-conjugated derivatives were designed, some of which exhibited significant cytotoxic effects on cancer cells. Interestingly, selected CPP-conjugated peptides exerted potent anticancer activity across various tumour types via a G-quadruplex-dependent mechanism. These findings underscore the potential of peptide-based G-quadruplex ligands in cancer therapy and pave the way for the development of novel therapeutic strategies targeting these DNA structures.