Structural Basis for Telomeric\nG-Quadruplex Targeting\nby Naphthalene Diimide Ligands

Abstract

The folding of the single-stranded 3′ end of the\nhuman telomere\ninto G-quadruplex arrangements inhibits the overhang from hybridizing\nwith the RNA template of telomerase and halts telomere maintenance\nin cancer cells. The ability to thermally stabilize human telomeric\nDNA as a four-stranded G-quadruplex structure by developing selective\nsmall molecule compounds is a therapeutic path to regulating telomerase\nactivity and thereby selectively inhibit cancer cell growth. The development\nof compounds with the necessary selectivity and affinity to target\nparallel-stranded G-quadruplex structures has proved particularly\nchallenging to date, relying heavily upon limited structural data.\nWe report here on a structure-based approach to the design of quadruplex-binding\nligands to enhance affinity and selectivity for human telomeric DNA.\nCrystal structures have been determined of complexes between a 22-mer\nintramolecular human telomeric quadruplex and two potent tetra-substituted\nnaphthalene diimide compounds, functionalized with positively charged\nN-methyl-piperazine side-chains. These compounds promote parallel-stranded\nquadruplex topology, binding exclusively to the 3′ surface\nof each quadruplex. There are significant differences between the\ncomplexes in terms of ligand mobility and in the interactions with\nquadruplex grooves. One of the two ligands is markedly less mobile\nin the crystal complex and is more quadruplex-stabilizing, forming\nmultiple electrostatic/hydrogen bond contacts with quadruplex phosphate\ngroups. The data presented here provides a structural rationale for\nthe biophysical (effects on quadruplex thermal stabilization) and\nbiological data (inhibition of proliferation in cancer cell lines\nand evidence of <i>in vivo</i> antitumor activity) on compounds\nin this series and, thus, for the concept of telomere targeting with\nDNA quadruplex-binding small molecules.