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Affinity-Selected Bicyclic Peptide G-Quadruplex Ligands Mimic a Protein-like Binding Mechanism.

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Liu, Kim C 
Adhikari, Santosh 


The study of G-quadruplexes (G4s) in a cellular context has demonstrated links between these nucleic acid secondary structures, gene expression, and DNA replication. Ligands that bind to the G4 structure therefore present an excellent opportunity for influencing gene expression through the targeting of a nucleic acid structure rather than sequence. Here, we explore cyclic peptides as an alternative class of G4 ligands. Specifically, we describe the development of de novo G4-binding bicyclic peptides selected by phage display. Selected bicyclic peptides display submicromolar affinity to G4 structures and high selectivity over double helix DNA. Molecular simulations of the bicyclic peptide-G4 complexes corroborate the experimental binding strengths and reveal molecular insights into G4 recognition by bicyclic peptides via the precise positioning of amino acid side chains, a binding mechanism reminiscent of endogenous G4-binding proteins. Overall, our results demonstrate that selection of (bi)cyclic peptides unlocks a valuable chemical space for targeting nucleic acid structures.



G-Quadruplexes, Ligands, Molecular Dynamics Simulation, Peptides, Cyclic

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J Am Chem Soc

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American Chemical Society (ACS)


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Cancer Research Uk (None)
Engineering and Physical Sciences Research Council (EP/N035003/1)
Wellcome Trust (099232/Z/12/Z)
Cancer Research UK (18618)
Jesus College, Cambridge (Embiri- cos Scholarship) and the Herchel Smith studentship. The Balasubramanian group receives programme funding (C9681/A18618) and core funding (C14303/A17197) from Cancer Re- search UK, and an Investigator Award from the Wellcome Trust (099232/Z/12/Z). KR DJW received funding from the EPSRC (EP/N035003/1) and KR also received funding from the Cambridge Philosophical Society