PDBsum entry 4da3

DNA

PDB id: 4da3

Contents

DNA/RNA

Ligands

0DX

Metals

__K ×3

Waters ×26

PDB id:

4da3

Name:

DNA

Title:

Crystal structure of an intramolecular human telomeric DNA g- quadruplex 21-mer bound by the naphthalene diimide compound mm41.

Structure:

DNA (5'- d( Gp Gp Gp Tp Tp Ap Gp Gp Gp Tp Tp Ap Gp Gp Gp Tp Tp Ap Gp Gp G)- 3'). Chain: a. Engineered: yes

Source:

Synthetic: yes. Synthetic DNA. Organism_taxid: 32630. Other_details: DNA synthesized by standard phosphoramidite chemistry.

Resolution:

2.40Å R-factor: 0.244 R-free: 0.282

Authors:

G.W.Collie,S.Neidle

Key ref:

M.Micco et al. (2013). Structure-based design and evaluation of naphthalene diimide G-quadruplex ligands as telomere targeting agents in pancreatic cancer cells. J Med Chem, 56, 2959-2974. PubMed id: 23514618 DOI: 10.1021/jm301899y

Date:

12-Jan-12 Release date: 30-Jan-13

DNA/RNA chain

G-G-G-T-T-A-G-G-G-T-T-A-G-G-G-T-T-A-G-G-G 21 bases

DOI no: 10.1021/jm301899y

J Med Chem 56:2959-2974 (2013)

PubMed id: 23514618

Structure-based design and evaluation of naphthalene diimide G-quadruplex ligands as telomere targeting agents in pancreatic cancer cells.

M.Micco, G.W.Collie, A.G.Dale, S.A.Ohnmacht, I.Pazitna, M.Gunaratnam, A.P.Reszka, S.Neidle.

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.