Abstract:Cristatin A (1a/b), a prenylated dioxopiperazine alkaloid, has been shown to bind selectively to telomeric quadruplex DNA using a FRET-based DNA melting assay. Crucially, the molecule is more drug-like than most previously identified quadruplex-binding agents, and provides a unique chemical scaffold for future chemical biology and drug discovery studies.
“…It is also important to emphasize that FRET melting assay has been widely used to evaluate the stability of G-quadruplexes in the presence of various ligands, see Refs. 42 , 43 as examples. Figure 5 Inhibition of DNA synthesis catalyzed by ProtoScript II reverse transcriptase on the G-quadruplex containing HT4 RNA template (40 nM) at 42 °C in the presence of increasing concentrations (20–320 nM) of Λ-5b and Δ-5b .…”
RNA G-quadruplexes have been suggested to play key roles in fundamental biological processes and are linked to human diseases. Thus, they also represent good potential therapeutic targets. Here, we describe, using the methods of molecular biophysics, interactions of a series of biologically-active supramolecular cationic metallohelices with human telomeric RNA G-quadruplex. We demonstrate that the investigated metallohelices bind with a high affinity to human telomeric RNA G-quadruplex and that their binding selectivity considerably differs depending on the dimensions and overall shape of the metallohelices. Additionally, the investigated metallohelices inhibit DNA synthesis on the RNA template containing four repeats of the human telomeric sequence by stabilizing the RNA G-quadruplex structure. Collectively, the results of this study suggest that stabilization of RNA sequences capable of G-quadruplex formation by metallohelices investigated in this work might contribute to the mechanism of their biological activity.
“…It is also important to emphasize that FRET melting assay has been widely used to evaluate the stability of G-quadruplexes in the presence of various ligands, see Refs. 42 , 43 as examples. Figure 5 Inhibition of DNA synthesis catalyzed by ProtoScript II reverse transcriptase on the G-quadruplex containing HT4 RNA template (40 nM) at 42 °C in the presence of increasing concentrations (20–320 nM) of Λ-5b and Δ-5b .…”
RNA G-quadruplexes have been suggested to play key roles in fundamental biological processes and are linked to human diseases. Thus, they also represent good potential therapeutic targets. Here, we describe, using the methods of molecular biophysics, interactions of a series of biologically-active supramolecular cationic metallohelices with human telomeric RNA G-quadruplex. We demonstrate that the investigated metallohelices bind with a high affinity to human telomeric RNA G-quadruplex and that their binding selectivity considerably differs depending on the dimensions and overall shape of the metallohelices. Additionally, the investigated metallohelices inhibit DNA synthesis on the RNA template containing four repeats of the human telomeric sequence by stabilizing the RNA G-quadruplex structure. Collectively, the results of this study suggest that stabilization of RNA sequences capable of G-quadruplex formation by metallohelices investigated in this work might contribute to the mechanism of their biological activity.
“…This quadruplex was selected as it is one of the most studied structures, and a number of CD titration experiments with G-quadruplex-binding ligands have been reported [45], [51], [56], [67], [69]. The CD spectrum of the HT4 sequence showed the characteristic presence of mixed parallel and antiparallel structures with positive peaks around 295 nm and a negative peak around 240 nm (
Figure 5
).…”
Section: Resultsmentioning
confidence: 99%
“…To evaluate quadruplex versus duplex binding, we initially utilised a well-established FRET-based melting assay [55], [56], along with a control biaryl polyamide molecule KMR-04-12 ( 11 ,
Figure 3
), previously reported [55] to be highly selective for quadruplex versus duplex DNA. Despite evaluating the eight pyrrolobenzodiazepine compounds up to very high concentrations ( i.e.…”
The pyrrolo[2,1-c][1,4] benzodiazepines (PBDs) are a family of sequence-selective, minor-groove binding DNA-interactive agents that covalently attach to guanine residues. A recent publication in this journal (Raju et al, PloS One, 2012, 7, 4, e35920) reported that two PBD molecules were observed to bind with high affinity to the telomeric quadruplex of Tetrahymena glaucoma based on Electrospray Ionisation Mass Spectrometry (ESI-MS), Circular Dichroism, UV-Visible and Fluorescence spectroscopy data. This was a surprising result given the close 3-dimensional shape match between the structure of all PBD molecules and the minor groove of duplex DNA, and the completely different 3-dimensional structure of quadruplex DNA. Therefore, we evaluated the interaction of eight PBD molecules of diverse structure with a range of parallel, antiparallel and mixed DNA quadruplexes using DNA Thermal Denaturation, Circular Dichroism and Molecular Dynamics Simulations. Those PBD molecules without large C8-substitutents had an insignificant affinity for the eight quadruplex types, although those with large π-system-containing C8-substituents (as with the compounds evaluated by Raju and co-workers) were found to interact to some extent. Our molecular dynamics simulations support the likelihood that molecules of this type, including those examined by Raju and co-workers, interact with quadruplex DNA through their C8-substituents rather than the PBD moiety itself. It is important for the literature to be clear on this matter, as the mechanism of action of these agents will be under close scrutiny in the near future due to the growing number of PBD-based agents entering the clinic as both single-agents and as components of antibody-drug conjugates (ADCs).
“…The material obtained from A. auriculiformis was found to stabilize the G-quadruplex of telomeric DNA. 68 Other natural products that contain reverse prenylated Z-DTrp residues include the neoechinulins, which are exemplified by the neuroprotective agent neoechinulin A (31a, Fig. 23) 69 as well as neoechinulin B (31b), an inhibitor of infection by the H1N1 virus.…”
“…Essentially racemic 30 was also found in the leaves of Acacia auriculiformis in 2012 by Hasan, Thurston, and co-workers. 68 It is unclear if these variations in composition reflect differences in biosynthetic pathways between plant and fungal species, or if racemization occurred during two of the three isolation protocols. The material obtained from A. auriculiformis was found to stabilize the G-quadruplex of telomeric DNA.…”
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