Solution Structure of a 2:1 Quindoline–c-MYC G-Quadruplex: Insights into G-Quadruplex-Interactive Small Molecule Drug Design

Abstract

Unimolecular parallel-stranded G-quadruplex structures are found to be prevalent in gene promoters. The nuclease hypersensitivity element III1 (NHE III1) of the c-MYC promoter can form transcriptionally active and silenced forms and the formation of DNA G-quadruplex structures has been shown to be critical for c-MYC transcriptional silencing. The solution structure of a 2:1 quindoline–G-quadruplex complex has been solved and shows unexpected features, including the drug-induced reorientation of the flanking sequences to form a new binding pocket. While both 3’ and 5’ complexes show overall similar features, there are identifiable differences which emphasize the importance of both stacking and electronic interactions. For the first time we describe the importance of the shape of the ligand as well as the two flanking bases in determining drug binding specificity. These structures provide important insights for the structure-based rational design of drugs that bind to unimolecular parallel G-quadruplexes commonly found in promoter elements.

NMR spectroscopy of G-quadruplexes

“…A recent NMR study shows the stacking of two molecules of quindoline at the two ends of a propeller-type MYC promoter G-quadruplex, where the NOE-driven computed structure of the complex indirectly suggests the formation of a hydrogen bond between the ligand and a flanking base (Fig. 11B) [78].…”

“…Before this work, full isotopic labels had already been used for resonance assignments, but only limited to a few studies [74]. The affordability of this low-enrichment approach make unambiguous assignments routinely available in different laboratories [35,38,53,59,[75][76][77][78][79].…”

“…11. G-quadruplex-ligand complexes elucidated using NMR spectroscopy: Anticancer (A) TMPyP4 and (B) quindoline ligands bound to intramolecular G-quadruplexes and (C) distamicyn A (derivative 3) ligands bound to a tetrameric G-quadruplex [44,78,179]. Anti and syn guanine bases are colored cyan and magenta, respectively; backbone and sugar, gray; O4 0 atoms, yellow; ligands, red.…”

Recognition of intermolecular G‐quadruplexes by full length nucleophosmin. Effect of a leukaemia‐associated mutation

“…Oligonucleotides G4MYC (5 0 -TGGGGAGGGTGGGGAGGGTGGG-GAAGG) [12], G4Pu22 (5 0 -TGAGGGTGGGTAGGGTGGGTAA) [17], and G4Pu24I (5 0 -TGAGGGTGGIGAGGGTGGGGAAGG) [15] (purchased from GenScript USA Inc) are related to the c-Myc promoter sequence. To facilitate G-quadruplex formation, the oligonucleotides were resuspended in 20 mM Hepes, 100 mM KCl, pH 7.5 and annealed by heating at 95°C for 5 min, and slowly cooling down at room temperature overnight.…”

Interactions of ruthenium complexes containing indoloquinoline moiety with human telomeric G-quadruplex DNA

“…Indoloquinoline and its derivatives, a relatively rare group alkaloids in nature, which has been used as an antimalarial drug in Central and Western Africa for centuries, have also been reported to be a kind of efficient G-quadruplex binder [24][25][26][27]. They have been found to interact preferentially to intramolecular G-qudruplex and inhibit telomerase activity in human K562 cells and SW620 cells, which have induced a cessation of cell growth and shortening of telomere length [24].…”