Abstract 1856: Targeting human telomeres by binding of epiberberine to telomeric G-quadruplex

Human telomeres play critical roles in cancer, aging, and genetic stability. Human telomeric DNA consists of tandem repeats of the sequence d(TTAGGG) and can form G-quadruplexes. G-quadruplexes are non-canonical DNA secondary structures formed in G-rich sequences, built upon the H-bonded G-tetrads and stabilized by monovalent cations such as K+ or Na+. Telomerase is a reverse transcriptase activated in 80-85% of human cancers. Small molecules that stabilize the telomeric G-quadruplex have been demonstrated to inhibit telomerase and disrupt telomere capping and maintenance, resulting in cancer cell apoptosis. Thus, the human telomeric G-quadruplex is considered an attractive target for anticancer drug development. G-quadruplexes formed in human telomeres are structurally polymorphic. The hybrid-2 G-quadruplex is the major form in the wild-type human telomeric DNA in the physiologically relevant K+ solution. Protoberberines are medicinal natural products with anticancer and anti-inflammatory activities. We show for the first time that a small molecule (epiberberine) specifically binds and induces the physiologically relevant hybrid-2 human telomeric G-quadruplex and converts other telomeric G-quadruplexes to the hybrid-2 structure, the first such small molecule reported. We determined the molecular structure of the 1:1 complex of epiberberine and hybrid-2 human telomeric G-quadruplex in K+ solution by NMR, which elucidates the molecular basis for this specific recognition. Epiberberine binding induces extensive rearrangement of the previously disordered 5′ flanking and loop segments to form an unprecedented four-layer binding pocket specific to the hybrid-2 human telomeric G-quadruplex. Epiberberine recruits the flanking (-1) adenine to form a “quasi-triad” intercalated between the external G-tetrad and a T:T:A triad, capped by a T:T base-pair. The crucial hydrogen-bonded pair is observed between epiberberine and the flanking (-1) adenine in the human telomeric sequences. This strong recognition determines the epiberberine’s ability to convert other human telomeric G-quadruplex structures to the hybrid-2 structure, regardless of the presence and types of monovalent cation in solution. The deep intercalation of epiberberine in this multi-layer binding pocket explains the significant fluorescence enhancement of epiberberine induced by human telomeric sequences in K+. Our study provides structural insights into rational design of small molecule drugs targeting the hybrid-2 G-quadruplex predominant in the human telomeres in physiologically relevant K+ solution. Furthermore, the human telomeric sequence is polymorphic in nature and various G-quadruplexes can exist in dynamic equilibrium, the discovery of epiberberine provides a potential means to study the specific protein interactions and biological functions of the hybrid-2 telomeric G-quadruplex. Citation Format: Clement Lin, Guanhui Wu, Kaibo Wang, Buket Onel, Saburo Sakai, Danzhou Yang. Targeting human telomeres by binding of epiberberine to telomeric G-quadruplex [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1856.