Structural Basis for Telomeric G-Quadruplex Targeting by Naphthalene Diimide Ligands

Abstract

The folding of the single-stranded 3' end of the human telomere into G-quadruplex arrangements inhibits the overhang from hybridizing with the RNA template of telomerase and halts telomere maintenance in cancer cells. The ability to thermally stabilize human telomeric DNA as a four-stranded G-quadruplex structure by developing selective small molecule compounds is a therapeutic path to regulating telomerase activity and thereby selectively inhibit cancer cell growth. The development of compounds with the necessary selectivity and affinity to target parallel-stranded G-quadruplex structures has proved particularly challenging to date, relying heavily upon limited structural data. We report here on a structure-based approach to the design of quadruplex-binding ligands to enhance affinity and selectivity for human telomeric DNA. Crystal structures have been determined of complexes between a 22-mer intramolecular human telomeric quadruplex and two potent tetra-substituted naphthalene diimide compounds, functionalized with positively charged N-methyl-piperazine side-chains. These compounds promote parallel-stranded quadruplex topology, binding exclusively to the 3' surface of each quadruplex. There are significant differences between the complexes in terms of ligand mobility and in the interactions with quadruplex grooves. One of the two ligands is markedly less mobile in the crystal complex and is more quadruplex-stabilizing, forming multiple electrostatic/hydrogen bond contacts with quadruplex phosphate groups. The data presented here provides a structural rationale for the biophysical (effects on quadruplex thermal stabilization) and biological data (inhibition of proliferation in cancer cell lines and evidence of in vivo antitumor activity) on compounds in this series and, thus, for the concept of telomere targeting with DNA quadruplex-binding small molecules.

Strategies for the Synthesis of Functional Naphthalene Diimides

“…[25,39] In addition, core-substituted NDI chromophores found applications as pH or metal-ion sensors, [40] for the sensitization of singlet oxygen, [41] and for interaction with G-quadruplex DNA. [42] In addition to heteroatom nucleophiles, numerous carbon nucleophiles were introduced in the form of organometallic compounds in transition-metal-catalyzed C À C cross-coupling reactions with NDI derivatives. Thus, appropriately coupled di- [26a, 43] and tetrasubstituted [44] NDI derivatives could be obtained by Suzuki, Stille, or Sonogashira coupling.…”

A DNA structural alphabet provides new insight into DNA flexibility

“…All B-to-A conformers occur in duplexes, but they can also occur in quadruplexes (BA13 in PDB entry 3sc8; Collie et al, 2012) or joints of Holliday junctions (BA05 in PDB entry 1p4e; Chen & Rice, 2003). Most of them (NtC BA01-BA10) can be characterized as BI-to-A, while conformers that describe a transition between BII and A forms (BA13-BA17) are much rarer.…”

Assessment of gene promoter G-quadruplex binding and modulation by a naphthalene diimide derivative in tumor cells

“…To date, a diverse array of G-4 stabilizing compounds has been identified (17,18). Among them, numerous tri-and tetra-substituted naphthalene diimides (NDIs) have shown high affinity for telomeric G-4s and good antiproliferative activity in different experimental human tumor models (19)(20)(21)(22)(23)(24).…”