2K4L

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.

Summary for 2K4L

• Entry DOI: 10.2210/pdb2k4l/pdb
• NMR Information: BMRB: 15613
• Descriptor: 5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DAP*DAP*DAP*DGP*DAP*DTP*DT)-3', (11aS)-7,8-dimethoxy-2-naphthalen-2-yl-1,10,11,11a-tetrahydro-5H-pyrrolo[2,1-c][1,4]benzodiazepin-5-one (2 entities in total)
• Functional Keywords: pyrrolo[2, 1-c][1, 4]benzodiazepine, pbd, dna adduct, dna
• Total number of polymer chains: 2
• Total formula weight: 9328.54

Authors

Antonow, D.,Barata, T.,Jenkins, T.C.,Parkinson, G.N.,Howard, P.W.,Thurston, D.E.,Zloh, M. (deposition date: 2008-06-13, release date: 2008-10-28, Last modification date: 2024-05-01)

Primary citation

Antonow, D.,Barata, T.,Jenkins, T.C.,Parkinson, G.N.,Howard, P.W.,Thurston, D.E.,Zloh, M.
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, 2008

PubMed 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.

PubMed: 18925745
DOI: 10.1021/bi801225q

Experimental method

SOLUTION NMR