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G-quadruplex recognition by bis-indole carboxamides.

Jyotirmayee Dash1, Pravin S Shirude, Shankar Balasubramanian

  • 1Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW.

Chemical Communications (Cambridge, England)
|August 9, 2008
PubMed
Summary

Researchers designed novel small molecules, bis-indole carboxamides, that stabilize DNA G-quadruplex structures. These molecules show potential for targeting cancer-related genes like c-kit2 and c-myc.

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Area of Science:

  • Medicinal Chemistry
  • Chemical Biology
  • Molecular Oncology

Background:

  • DNA G-quadruplexes are non-canonical DNA structures found in gene promoter regions.
  • Stabilization of G-quadruplexes can regulate gene expression, offering therapeutic potential for diseases like cancer.
  • The promoters of oncogenes such as c-kit2 and c-myc are known to harbor G-quadruplex forming sequences.

Purpose of the Study:

  • To report the de novo design and synthesis of a novel class of small molecule scaffolds.
  • To investigate the potential of these scaffolds to stabilize DNA G-quadruplex sequences.
  • To evaluate the efficacy of these compounds against G-quadruplexes in the promoters of c-kit2 and c-myc.

Main Methods:

  • De novo design and chemical synthesis of bis-indole carboxamide derivatives.
  • Structural characterization of the synthesized compounds.
  • Assessment of G-quadruplex stabilization using biophysical techniques (e.g., FRET, CD spectroscopy).
  • Evaluation of the compounds' effect on c-kit2 and c-myc promoter activity.

Main Results:

  • Successful synthesis of a geometrically flexible bis-indole carboxamide and a constrained derivative.
  • Demonstrated high stabilization potential of these novel scaffolds for DNA G-quadruplex sequences.
  • Evidence of interaction with G-quadruplexes in the promoter regions of c-kit2 and c-myc.

Conclusions:

  • A novel class of small molecule scaffolds, bis-indole carboxamides, has been developed.
  • These compounds effectively stabilize DNA G-quadruplexes, particularly those in the c-kit2 and c-myc promoters.
  • This class of molecules holds promise as potential therapeutic agents for targeting cancer-associated gene expression.