Structure-Based Design and Evaluation of Naphthalene Diimide G-Quadruplex Ligands As Telomere Targeting Agents in Pancreatic Cancer Cells

Abstract

Tetra-substituted naphthalene diimide (ND) derivatives with positively charged termini are potent stabilizers of human telomeric and gene promoter DNA quadruplexes and inhibit the growth of human cancer cells in vitro and in vivo. The present study reports the enhancement of the pharmacological properties of earlier ND compounds using structure-based design. Crystal structures of three complexes with human telomeric intramolecular quadruplexes demonstrate that two of the four strongly basic N-methyl-piperazine groups can be replaced by less basic morpholine groups with no loss of intermolecular interactions in the grooves of the quadruplex. The new compounds retain high affinity to human telomeric quadruplex DNA but are 10-fold more potent against the MIA PaCa-2 pancreatic cancer cell line, with IC50 values of ~10 nM. The lead compound induces cellular senescence but does not inhibit telomerase activity at the nanomolar dosage levels required for inhibition of cellular proliferation. Gene array qPCR analysis of MIA PaCa-2 cells treated with the lead compound revealed significant dose-dependent modulation of a distinct subset of genes, including strong induction of DNA damage responsive genes CDKN1A, DDIT3, GADD45A/G, and PPM1D, and repression of genes involved in telomere maintenance, including hPOT1 and PARP1.

A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer

“…One such compound (MM41: Fig. 1) has been characterised as a potent stabiliser of various quadruplex sequences and inhibitor of cell growth in a panel of cancer cell lines28. In particular it shows selectivity for several pancreatic cancer lines and its IC 50 value (the concentration required to inhibit cell growth by 50% in a 96 hr assay), is 10 nM in the MIA PaCa-2 pancreatic adenocarcinoma cell line.…”

Computational Methods to Study G-Quadruplex–Ligand Complexes

“…31 MMQ1 quinacridine-based ligand was described as an anti-cancer agent in 2007 by Hounsou et al 32 The G-quadruplex stabilising properties of the MMQ1 series were confirmed by Hou et al 33 and Gabelica et al 34 MM41 is a tetra-substituted naphthalenediimide derivative described first by Micco et al 35 as a potent stabilizer of human telomeric and gene promoter DNA quadruplexes and can inhibit the growth of human cancer cells in vitro and in vivo. Recently, Ohnmacht et al reported MM41's significant in vivo anti-tumour activity against the MIA PaCa-2 pancreatic cancer xenograft model.…”

Progress in Research on Small Molecules as Gene-targeted Drugs

“…For example, Fig. 3 presents interactions of small molecules with target genes and by molecular simulation technique [15,16]. …”