Stabilization of c-KIT G-Quadruplex DNA Structures by the RNA Polymerase I Inhibitors BMH-21 and BA-41

Int J Mol Sci. 2019 Oct 4;20(19):4927. doi: 10.3390/ijms20194927.

Abstract

The stabilization of G-quadruplex DNA structures by small molecules with affinity to oncogene promoters has emerged as a promising anticancer strategy, due to a potential role in gene expression regulation. We explored the ability of BMH-21 (1) and its analogue BA-41 (2) to bind the G-quadruplex structure present in the c-KIT promoter by biophysical methods and molecular modeling. We provide evidence that both compounds interact with the c-KIT 21-mer sequence. The stable monomeric intramolecular parallel G-quadruplex obtained by the mutation of positions 12 and 21 allowed the precise determination of the binding mode by NMR and molecular dynamics studies. Both compounds form a complex characterized by one ligand molecule positioned over the tetrad at the 3'-end, stabilized by an extensive network of π-π interactions. The binding constants (Kb) obtained with fluorescence are similar for both complexes (around 106 M-1). Compound BA-41 (2) showed significant antiproliferative activity against a human lymphoma cell line, SU-DHL4, known to express substantial levels of c-KIT. However, the partial inhibition of c-KIT expression by Western blot analysis suggested that the interaction of compound 2 with the c-KIT promoter is not the primary event and that multiple effects provide a contribution as determinants of biological activity.

Keywords: CD; G-quadruplex; NMR spectroscopy; c-KIT; pyridoquinazolinone derivatives.

MeSH terms

  • Cell Line, Tumor
  • Cell Proliferation / drug effects
  • G-Quadruplexes*
  • Heterocyclic Compounds, 4 or More Rings / pharmacology*
  • Humans
  • Promoter Regions, Genetic
  • Proto-Oncogene Proteins c-kit / genetics*
  • Proto-Oncogene Proteins c-kit / metabolism
  • RNA Polymerase I / antagonists & inhibitors*

Substances

  • BMH-21
  • Heterocyclic Compounds, 4 or More Rings
  • Proto-Oncogene Proteins c-kit
  • RNA Polymerase I