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1

Molecular modelling of the interaction of carbocyclic analogues of netropsin and distamycin with d[CGCGAATTCGCG]2

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Bielawski K., Bielawska A., Bartulewicz D., Rozanski A.
Acta Biochimica Polonica
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2000
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tom 47
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nr 3
A molecular mechanics and molecular dynamics approach was used to examine the structure of complexes formed between the d(CGCGAATTCGCG)2 duplex and netropsin, distamycin, and four carbocyclic analogues of netropsin and distamycin (1-4). The resulting structures of the ligand-DNA model complexes and their energetics were examined. It is predicted that the compounds 1-4 should have a decreased affinity for the minor groove of AT-rich regions in comparison to netropsin and distamycin. From the energetic analysis it appears that van der Waals and electrostatic interactions are more important than specific hydrogen bonds in stabilizing the ligand-duplex complexes. We predict that compounds 1 and 2 are effectively isohelical with the DNA minor groove. The superior DNA-binding afforded by 1 and 2 in comparison to 3 and 4 results from their more effective penetration into the minor groove and smaller perturbation of molecular structure upon complex formation.
2

Molecular modelling, synthesis and antitumour activity of carbocyclic analogues of netropsin and distamycin - new carriers of alkylating elements

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Bartulewicz D., Markowska A., Wolczynski S., Dabrowska M., Rozanski A.
Acta Biochimica Polonica
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2000
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tom 47
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nr 1
A series of netropsin and distamycin analogues was synthesised and investigated by molecular modelling. The lowest-energy conformations of four carbocyclic lexitropsins, potential carriers of alkylating elements, were obtained using the HyperChem 4.0 program, and compared with the DNA-lexitropsin crystal structures from the Brookhaven National Laboratory Protein Data Bank. A method for synthesis of carbocyclic lexitropsins was elaborated, with the use of a nitro group or azobenzene as precursors for the aromatic amino group. The influence of methoxy group in ortho position with respect to amide groups on the activity of the new compounds was investigated. All of the compounds tested showed high antitumour activity in the standard cell line of mammalian tumour MCF-7.
3

New carbocyclic analogues of netropsin: synthesis and inhibition of topoisomerases

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Puckowska A., Bielawski K., Bielawska A., Rozanski A.
Acta Biochimica Polonica
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2002
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tom 49
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nr 1
A series of carbocyclic analogues of netropsin were synthesized and evaluated for their capacity to inhibit human topoisomerases I and II in vitro. The compounds are oligopeptides containing 1,4-di- and 1,2,5-trisubstituted benzene rings and unsubstituted N-terminal NH2 groups. Compounds 4-7 consist of two netropsin-like units linked by aliphatic (tetra- and hexamethylene) chains. In the topoisomerase I and II assay, the relaxation of pBR322 plasmid was inhibited by compounds 4-7 at 100 uM concentration.
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