PDBsum entry 2k4l

DNA

PDB id: 2k4l

Contents

DNA/RNA

Ligands

PZD ×2

PDB id:

2k4l

Name:

DNA

Title:

Solution structure of a 2:1c2-(2-naphthyl)pyrrolo[2,1-c][1, 4]benzodiazepine (pbd) DNA adduct: molecular basis for unexpectedly high DNA helix stabilization.

Structure:

5'-d( Dap Dap Dtp Dcp Dtp Dtp Dtp Dap Dap Dap Dgp Dap Dtp D t)-3'. Chain: a, b. Engineered: yes

Source:

Synthetic: yes. Other_details: the 14-mer nucleotide sequence aatctttaaagatt was synthesised using an applied biosystems DNA synthesizer. The DNA sequence was purified by reversed-phase hplc at room temperature. The duplex was formed by annealing in phosphate buffer.

NMR struc:

10 models

Authors:

D.Antonow,T.Barata,T.C.Jenkins,G.N.Parkinson,P.W.Howard,D.E.Thurston, M.Zloh

Key ref:

D.Antonow et al. (2008). Solution structure of a 2:1 C2-(2-naphthyl) pyrrolo[2,1-c][1,4]benzodiazepine DNA adduct: molecular basis for unexpectedly high DNA helix stabilization. Biochemistry, 47, 11818-11829. PubMed id: 18925745

Date:

13-Jun-08 Release date: 28-Oct-08

DNA/RNA chains

A-A-T-C-T-T-T-A-A-A-G-A-T-T 14 bases

A-A-T-C-T-T-T-A-A-A-G-A-T-T 14 bases

Biochemistry 47:11818-11829 (2008)

PubMed id: 18925745

Solution structure of a 2:1 C2-(2-naphthyl) pyrrolo[2,1-c][1,4]benzodiazepine DNA adduct: molecular basis for unexpectedly high DNA helix stabilization.

D.Antonow, T.Barata, T.C.Jenkins, G.N.Parkinson, P.W.Howard, D.E.Thurston, M.Zloh.

ABSTRACT

The naturally occurring pyrrolo[2,1- c][1,4]benzodiazepine (PBD) monomers such as sibiromycin, anthramycin, and tomaymycin form stable covalent adducts with duplex DNA at purine-guanine-purine sites. A correlative relationship between DNA-binding affinity, as measured by enhanced thermal denaturation temperature of calf thymus DNA ( T m), and cytotoxicity is well documented for these naturally occurring compounds and a range of synthetic analogues with sibiromycin having the highest Delta T m value (16.3 degrees C), reflecting favorable hydrogen-bonding interactions between the molecule and DNA bases. We report here that, surprisingly, the structurally simple synthetic C2-(2-naphthyl)-substituted pyrrolo[2,1- c][1,4]benzodiazepine monomer ( 5) has a Delta T m value (15.8 degrees C) similar to that of sibiromycin and significantly higher than the values for either anthramycin (13.0 degrees C) or tomaymycin (2.6 degrees C). 5 also has similar cytotoxic potency to sibiromycin which is widely regarded as the most potent naturally occurring PBD monomer. To investigate this, we have used NMR in conjunction with molecular dynamics to study the 2:1 adduct formed between 5 and the DNA duplex d(AATCTTTAAAGATT) 2. In contrast to the hydrogen-bonding interactions which predominate in the case of sibiromycin and anthramycin adducts, we have shown that the high binding affinity of 5 is due predominantly to hydrophobic (van der Waals) interactions. The high-resolution 2D NOESY, TOCSY, and COSY data obtained have also allowed unequivocal determination of the orientation of the PBD molecule (A-ring toward 3'-end of covalently bound strand), the stereochemistry at the C11 position of the PBD (C11 S), and the conformation of the C2-naphthyl ring which extends along the floor of the minor groove thus optimizing hydrophobic interactions with DNA. These results provide opportunities for future drug design in terms of extending planar hydrophobic groups at the C2 position of PBDs to maximize binding affinity.