Fe^II Metallohelices Stabilize DNA G‐Quadruplexes and Downregulate the Expression of G‐Quadruplex‐Regulated Oncogenes

Abstract

DNA G‐quadruplexes (G4s) have been identified within the promoter regions of many proto‐oncogenes. Thus, G4s represent attractive targets for cancer therapy, and the design and development of new drugs as G4 binders is a very active field of medicinal chemistry. Here, molecular biophysics and biology methods were employed to investigate the interaction of chiral metallohelices with a series of four DNA G4s (hTelo, c‐myc, c‐kit1, c‐kit2) that are formed by the human telomeric sequence (hTelo) and in the promoter regions of c‐MYC and c‐KIT proto‐oncogenes. We show that the investigated water‐compatible, optically pure metallohelices, which are made by self‐assembly of simple nonpeptidic organic components around FeII ions and exhibit bioactivity emulating the natural systems, bind with high affinity to G4 DNA and much lower affinity to duplex DNA. Notably, both enantiomers of a metallohelix containing a m‐xylenyl bridge (5 b) were found to effectively inhibit primer elongation catalyzed by Taq DNA polymerase by stabilizing G4 structures formed in the template strands containing c‐myc and c‐kit2 G4‐forming sequences. Moreover, both enantiomers of 5 b downregulated the expression of c‐MYC and c‐KIT oncogenes in human embryonic kidney cells at mRNA and protein levels. As metallohelices also bind alternative nucleic acid structures, they hold promise as potential multitargeted drugs.

Dinuclear nickel(ii) supramolecular helicates down-regulate gene expression in human cells by stabilizing DNA G-quadruplexes formed in the promoter regions

“…A closer examination of the data on the binding affinity of the metallo-supramolecular helicates investigated in this study to G4 DNA obtained by FRET melting, FID, and DNA Taq polymerase stop assays reveals some inconsistency. Interestingly, a similar inconsistency between the results obtained using FRET melting, FID, and DNA Taq polymerase footprinting assays (when the binding affinity of the ligands towards DNA G4s was examined) was already observed in our earlier work 40 and also much earlier by other authors. 39 The observation that some FRET data are not perfectly consistent with the FID data could be at least partly explained similarly as in our recent work 40 by the differences in experimental conditions between FRET and FID assays and different binding modes of the ligands.…”

“…Interestingly, a similar inconsistency between the results obtained using FRET melting, FID, and DNA Taq polymerase footprinting assays (when the binding affinity of the ligands towards DNA G4s was examined) was already observed in our earlier work 40 and also much earlier by other authors. 39 The observation that some FRET data are not perfectly consistent with the FID data could be at least partly explained similarly as in our recent work 40 by the differences in experimental conditions between FRET and FID assays and different binding modes of the ligands. As far as the Taq Polymerase stop assay is concerned, the structure of G4 itself (hybrid vs. parallel vs. antiparallel) plays a major role in the inhibition of replication.…”

“…Overall, the values of SIs were quite low in comparison with the recently studied Fe( ii ) metallohelices from P. Scott, having SIs above 30 and the highest SI towards c-myc G4 equal to 62. 40 On the other hand, TMPyP4, a well-known G4 binder, is poorly selective towards DNA G4s 39 and despite that it inhibits expression of G4-mediated genes. 41…”

“…Excellent DNA G4 binders have DC 50 values around 0.5 µM and lower. 39 Titrations were carried out in three different concentrations of potassium ions (40,80, and 160 mM) to explore the influence of electrostatic interactions on the binding of cylinders to G4 DNA. Inspection of results presented in bar graphs in Fig.…”

Metallohelix vectors for efficient gene delivery via cationic DNA nanoparticles

“…Conversely, the reappearance of the band for plasmid DNA was observed for DNA condensed by 1 at the concentrations of Na + , K + and Mg 2+ as low as 100, 50 and 6 mM, respectively. It is in agreement with our previous report showing that the binding of 1 to double-stranded (ds) DNA was more weakened by the increased ionic strength than the binding of 2 and 3 ( 42 ). It suggests that the binding of 1 to ds DNA is more dependent on the electrostatic interactions.…”