One ring to bind them all" - Fication of promising G-quadruplex ligands by screening of cyclophane-type macrocycles (original) (raw)
Related papers
2010
Macrocyclic scaffolds are particularly attractive for designing selective G-quadruplex ligands essentially because, on one hand, they show a poor affinity for the "standard" B-DNA conformation and, on the other hand, they fit nicely with the external G-quartets of quadruplexes. Stimulated by the pioneering studies on the cationic porphyrin TMPyP4 and the natural product telomestatin, follow-up studies have developed, rapidly leading to a large diversity of macrocyclic structures with remarkablequadruplex binding properties and biological activities. In this review we summarize the current state of the art in detailing the three main categories of quadruplex-binding macrocycles described so far (telomestatin-like polyheteroarenes, porphyrins and derivatives, polyammonium cyclophanes), and in addressing both synthetic issues and biological aspects.
Selective Recognition of G-Quadruplex Telomeric DNA by a Bis(quinacridine) Macrocycle
Journal of the American Chemical Society, 2003
The interaction of G-quadruplex DNA with the macrocyclic compound BOQ1, which possesses two dibenzophenanthroline (quinacridine) subunits, has been investigated by a variety of methods. The oligonucleotide 5′-A(GGGT2A)3G3, which mimics the human telomeric repeat sequence and forms an intramolecular quadruplex, was used as one model system. Equilibrium binding constants measured by biosensor surface plasmon resonance (SPR) methods indicate a high affinity of the macrocycle for the quadruplex conformation (K > 1 × 10 7 M-1) with two equivalent binding sites. The affinity of BOQ1 for DNA duplexes is at least 1 order of magnitude lower. In addition, the macrocycle is more selective than the monomeric control compound (MOQ2), which is not able to discriminate between the two DNA structures (K duplex ≈ Kquadruplex ≈ 10 6 M-1). Strong binding of BOQ1 to G4 DNA sequences was confirmed by fluorometric titrations with a tetraplex-forming oligonucleotide. Competition dialysis experiments with a panel of different DNA structures, from single strands to quadruplexes, clearly established the quadruplex binding specificity of BOQ1. Fluorescence resonance energy transfer (FRET) Tm experiments with a doubly labeled oligonucleotide also revealed a strong stabilization of the G4 conformation in the presence of BOQ1 (∆Tm) +28°C). This ∆Tm value is one of the highest values measured for a G-quadruplex ligand and is significantly higher than observed for the monomer control compounds (∆Tm) +10-12°C). Gel mobility shift assays indicated that the macrocycle efficiently induces the formation of G-tetraplexes. Strong inhibition of telomerase was observed in the submicromolar range (IC 50) 0.13 µM). These results indicate that macrocycles represent an exciting new development opportunity for targeting DNA quadruplexes.
Heterocyclic Dications as a New Class of Telomeric G-Quadruplex Targeting Agents
Current Pharmaceutical Design, 2012
Small molecules that can induce and stabilize G-quadruplex DNA structures represent a novel approach for anti-cancer and anti-parasitic therapy and extensive efforts have been directed towards discovering lead compounds that are capable of stabilizing quadruplexes. The purpose of this study is to explore conformational modifications in a series of heterocyclic dications to discover structural motifs that can selectively bind and stabilize specific G-quadruplexes, such as those present in the human telomere. The G-quadruplex has various potential recognition sites for small molecules; however, the primary interaction site of most of these ligands is the terminal tetrads. Similar to duplex-DNA groove recognition, quadruplex groove recognition by small molecules offers the potential for enhanced selectivity that can be developed into a viable therapeutic strategy. The compounds investigated were selected based on preliminary studies with DB832, a bifuryl-phenyl diamidine with a unique telomere interaction. This compound provides a paradigm that can help in understanding the optimum compound-DNA interactions that lead to quadruplex groove recognition. DNA recognition by the DB832 derivatives was investigated by biophysical experiments such as thermal melting, circular dichroism, mass spectrometry and NMR. Biological studies were also performed to complement the biophysical data. The results suggest a complex binding mechanism which involves the recognition of grooves for some ligands as well as stacking at the terminal tetrads of the human telomeric G-quadruplex for most of the ligands. These molecules represent an excellent starting point for further SAR analysis for diverse modes of quadruplex recognition and subsequent structure optimization for drug development.
Bioorganic & Medicinal Chemistry Letters, 2012
Keywords: G-quadruplex Duplex DNA Ligands NCI Diversity Set High throughput screen FRET-based assay Drug-likeness a b s t r a c t Thirteen compounds with diverse chemical structures have been identified as selective telomeric G-quadruplex-binding ligands through screening the NCI Diversity Set II, the NCI Natural Products Set II and the NCI Mechanistic Diversity Set libraries containing a total of 2307 members against a human telomeric G-quadruplex using a FRET-based DNA melting assay. These compounds show significant selectivity towards a telomeric G-quadruplex compared to duplex DNA, fall within a molecular weight range of 327-533, and are generally consistent with the Lipinski Rule of Five for drug-likeness. Thus they provide new chemical scaffolds for the development of novel classes of G-quadruplex-targeting agents.
Ligand Binding to Tandem G Quadruplexes from Human Telomeric DNA
ChemBioChem, 2008
Ligand-induced stabilization of intramolecular telomeric G quadruplexes produced in the single-stranded overhang of the human telomere has become an attractive strategy for the development of anticancer drugs. [1] Several distinct solution conformations of human telomeric G quadruplexes have been elucidated in the presence of sodium [2] and potassium [3] cations. The K +-form, hybrid-type G-quadruplex structure has been considered to be a physiologically relevant conformation of the human telomeric sequence, and thus, can be specifically targeted by G-quadruplex-interactive, small-molecule A C H T U N G T R E N N U N G drugs. [3a, b] Recently, a beads-on-a-string model was proposed for the telomeric overhang, in which every four consecutive Grich repeats adopt an individual G-quadruplex structure, and two G-quadruplex units are connected by one TTA linker. [3a, c, 4] Ligand binding to the G quadruplex has mostly been investigated on telomere sequences producing a single G quadruplex, but few studies of ligand binding to beads-on-a-string G quadruplexes have been reported. To gain insight into the beads-on-a-string model and the nature of ligand binding, we undertook the polymerase stop assay on human telomere sequences of three to eight repeats (Table S1 in the Supporting Information) with TMPyP4, a G-quadruplex-interactive ligand, [5] and sanguinarine (Scheme 1), a natural isoquinoline alkaloid. The results described in this paper confirm the beads-on-astring structure of telomeric overhang and suggest a mode of ligand binding between tandem G-quadruplex beads. These observations should be taken into account for structure-based design of anticancer drugs targeting human telomeric DNA. Sanguinarine is a natural isoquinoline alkaloid isolated from the North American herb bloodroot (Sanguinaria canadensis). It was approved by the FDA in 2003 to be added to oral cleansing products as an antibacterial agent. Sanguinarine also possesses potent anticancer activity. [6] We have previously reported its DNA-binding activity and distinct sequence selectivity to double-stranded DNA, [7] which was proposed to be one of the molecular mechanisms of its anticancer activity. The structural similarity of sanguinarine with berberine, another isoquinoline alkaloid possessing G-quadruplex-binding activity, [8] prompted us to speculate that sanguinarine is probably a G-quadruplex binder. In this communication, we report its binding to the A C H T U N G T R E N N U N G telomeric overhang using DNA polymerase stop assays. [9] DNA templates Tem-3 and Tem-4 (Table S1), which contains three and four human telomeric repeats dA C H T U N G T R E N N U N G (TTAGGG), respectively, were employed, and TMPyP4 was used as the reference compound in the assay. [5, 9a, 10] Neither TMPyP4 nor sanguinarine blocked DNA synthesis on Tem-3, because an intramolecular Gquadruplex structure could not form with three human telomeric repeats on Tem-3 (Figure 1). In contrast, both sanguinarine and TMPyP4 produced paused bands in DNA synthesis on Tem-4. The position of the paused bands was the same for the two ligands. For each ligand, a series of concentration-dependent paused bands appeared at the beginning of the G-quadruplex-forming site, that is, the first site of G-rich repeats in Tem-4 (from 3' to 5'). In the presence of 3 mm TMPyP4, the polymerase reaction was totally suppressed to give no elongation of the primer. The tight binding of sanguinarine and TMPyP4 to the K +-form hybrid-type G-quadruplex structure was clearly indicated from the large increase in the melting temperature (DT m
Journal of Medicinal Chemistry, 2013
Nowadays, it has been demonstrated that DNA G-quadruplex arrangements are involved in cellular aging and cancer, thus boosting the discovery of selective binders for these DNA secondary structures. By taking advantage of available structural and biological information on these structures, we performed a high throughput in silico screening of commercially available molecules databases by merging ligand-and structure-based approaches by means of docking experiments. Compounds selected by the virtual screening procedure were then tested for their ability to interact with the human telomeric G-quadruplex folding by circular dichroism, fluorescence spectroscopy, and photodynamic techniques. Interestingly, our screening succeeded in retrieving a new promising scaffold for G-quadruplex binders characterized by a psoralen moiety.
G-quadruplexes as targets for drug design
Pharmacology & …, 2000
G-quadruplexes are a family of secondary DNA structures formed in the presence of monovalent cations that consist of four-stranded structures in which Hoogsteen base-pairing stabilizes G-tetrad structures. These structures are proposed to exist in vivo, although direct confirmatory evidence is lacking. Guanine-rich regions of DNA capable of forming G-quadruplex structures are found in a variety of chromosomal regions, including telomeres and promoter regions of DNA. In this review, we describe the design of three separate groups of G-quadruplex-interactive compounds and their interaction with G-quadruplex DNA. Using the first group of compounds (anthraquinones), we describe experiments that provide the proof of concept that a G-quadruplex is required for inhibition of telomerase. Using the second group of compounds (perylenes), we describe the structure of a G-quadruplex-ligand complex and its effect on the dynamics of formation and enzymatic unwinding of the quadruplex. For the third group of compounds (porphyrins), we describe the experiments that relate the biological effects to their interactions with G-quadruplexes.
Biochimie, 2008
We report here the details of G4-FID (G-quadruplex fluorescent intercalator displacement), a simple method aiming at evaluating quadruplex-DNA binding affinity and quadruplex-over duplex-DNA selectivity of putative ligands. This assay is based on the loss of fluorescence upon displacement of thiazole orange from quadruplexand duplex-DNA matrices. The original protocol was tested using various quadruplex-and duplex-DNA targets, and with a wide panel of G-quadruplex ligands belonging to different families (i.e. from quinacridines to metallo-organic ligands) likely to display various binding modes. The reliability of the assay is further supported by comparisons with FRET-melting and ESI-MS assays. that is not subjected to structural interconversion, the TBA (thrombin binding aptamer) . Finally, because quadruplex-vs. duplex-selectivity is a critical issue and because binding of both probe and ligand to duplex-DNA may be length-and sequence-dependent, we compare the results obtained with the 17-base pair duplex-DNA (dsl7) used in our initial work with a 26-bp duplex (ds26). G4-FID experiments reported herein were carried out with a set of 16 quadru-plex-ligands (from bisquinolinium to metallo-organic ligands) with two different QFOs (22AG , TBA ), in two different salt conditions (Na + , K + ) and with two different DNA control duplex-DNAs (dsl7 [31] and ds26 ).
Journal of Molecular Biology, 2008
Knowledge of the biologically relevant topology is critical for the design of drugs targeting quadruplex nucleic acids. We report here crystal structures of a G-quadruplex-selective ligand complexed with two human telomeric DNA quadruplexes. The intramolecular quadruplex sequence d[TAGGG (TTAGGG) 3 ] and the bimolecular quadruplex sequence d(TAGGGT-TAGGGT) were co-crystallized with a tetra-substituted naphthalene diimide quadruplex-binding ligand. The structures were solved and refined to 2.10and 2.20-Å resolution, respectively, revealing that the quadruplex topology in both structures is unchanged by the addition of the ligands, retaining a parallel-stranded arrangement with external double-chain-reversal propeller loops. The parallel topology results in accessible external 5′ and 3′ planar G-tetrad surfaces for ligand stacking. This also enables significant ligandinduced conformational changes in several TTA propeller loops to take place such that the loops themselves are able to accommodate bound drug molecules without affecting the parallel quadruplex topology, by stacking on the external TTA connecting loop nucleotides. Ligands are bound into the external TTA loop nucleotides and stack onto G-tetrad surfaces. These crystal structures provide a framework for further ligand development of the naphthalene diimide series to enhance selectivity and affinity.
Journal of Medicinal Chemistry, 2013
Recent findings have unambiguously demonstrated that DNA G-rich sequences can adopt a G-quadruplex folding in living cells, thus further validating them as crucial targets for anticancer therapy. Herein, to identify new potent G4 binders as antitumor drug candidates, we have targeted a 24-nt G4-forming telomeric sequence employing a receptorbased virtual screening approach. Among the best candidates, in vitro binding experiments allowed identification of three novel G4 ligands. Among them, the best compound features an unprecedented binding selectivity for the human telomeric DNA G-quadruplex with no detectable binding for other G4forming sequences present at different genomic sites. This behavior correlates with the detected ability to generate DNA damage response in tumor cells at the telomeric level and efficient antiproliferative effect on different tumor cell lines at low micromolar concentrations.