Small molecule/Nucleic acid affinity chromatography: application for the identification of telomerase inhibitors which target its key RNA/DNA heteroduplex

West, Corinna; Francis, Rawle; Friedman, Simon H.

doi:10.1016/s0960-894x(01)00553-4

Cited by 16 publications

(13 citation statements)

References 10 publications

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“…In this mixture, DNA is represented by poly(dA)·poly(dT), RNA by poly(rA)·poly(rU), hybrid I by poly(dA)·poly(rU) and hybrid II by poly(rA)·poly(dT). DNA:RNA hybrids are structures of profound biological importance and are an emerging target for drug design efforts ( 39 – 41 ). Results are shown in Figure 4 .…”

Section: Resultsmentioning

confidence: 99%

Sequence- and structural-selective nucleic acid binding revealed by the melting of mixtures

Shi

Chaires²

2006

Nucleic Acids Research

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A simple method for the detection of sequence- and structural-selective ligand binding to nucleic acids is described. The method is based on the commonly used thermal denaturation method in which ligand binding is registered as an elevation in the nucleic acid melting temperature (Tm). The method can be extended to yield a new, higher -throughput, assay by the simple expediency of melting designed mixtures of polynucleotides (or oligonucleotides) with different sequences or structures of interest. Upon addition of ligand to such mixtures at low molar ratios, the Tm is shifted only for the nucleic acid containing the preferred sequence or structure. Proof of principle of the assay is provided using first a mixture of polynucleotides with different sequences and, second, with a mixture containing DNA, RNA and two types of DNA:RNA hybrid structures. Netropsin, ethidium, daunorubicin and actinomycin, ligands with known sequence preferences, were used to illustrate the method. The applicability of the approach to oligonucleotide systems is illustrated by the use of simple ternary and binary mixtures of defined sequence deoxyoligonucleotides challenged by the bisanthracycline WP631. The simple mixtures described here provide proof of principle of the assay and pave the way for the development of more sophisticated mixtures for rapidly screening the selectivity of new nucleic acid binding compounds.

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Section: Resultsmentioning

confidence: 99%

Sequence- and structural-selective nucleic acid binding revealed by the melting of mixtures

Shi

Chaires²

2006

Nucleic Acids Research

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“…AM1 (CCT035764, diaminodimethylacridine or acridine yellow) inhibited HDAC activity, albeit with relatively low potency. This compound has a planar structure typically found in compounds that intercalate DNA and is known to inhibit telomerase by binding to the RNA/ DNA heteroduplex formed during the enzyme catalytic cycle (67). Aminoacridines, including compound AM1, are also inhibitors of protein kinase C (68).…”

Section: Discussionmentioning

confidence: 99%

A duplexed phenotypic screen for the simultaneous detection of inhibitors of the molecular chaperone heat shock protein 90 and modulators of cellular acetylation

Hardcastle

Tomlin

Norris

et al. 2007

Molecular Cancer Therapeutics

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Histone deacetylases (HDACs), histone acetyltransferases (HATs), and the molecular chaperone heat shock protein 90 (HSP90) are attractive anticancer drug targets. Highthroughput screening plays a pivotal role in modern molecular mechanism-based drug discovery. Cell-based screens are particularly useful in that they identify compounds that are permeable and active against the selected target or pathway in a cellular context. We have previously developed time-resolved fluorescence cell immunosorbent assays (TRF-Cellisas) for compound screening and pharmacodynamic studies. These assays use a primary antibody to the single protein of interest and a matched secondary immunoglobulin labeled with an europium chelate (Eu). The availability of species-specific secondary antibodies labeled with different lanthanide chelates provides the potential for multiplexing this type of assay. The approach has been applied to the development of a 384-well duplexed cell-based screen to simultaneously detect compounds that induce the co-chaperone HSP70 as a molecular marker of potential inhibitors of HSP90 together with those that modulate cellular acetylation (i.e., potential inhibitors of histone deacetylase or histone acetyltransferase activity). The duplexed assay proved reliable in high-throughput format and f64,000 compounds were screened. Following evaluation in secondary assays, 3 of 13 hits from the HSP70 arm were confirmed. Two of these directly inhibited the intrinsic ATPase activity of HSP90 whereas the third seems to have a different mechanism of action. In the acetylation arm, two compounds increased cellular acetylation, one of which inhibited histone deacetylase activity. A third compound decreased cellular histone acetylation, potentially through a novel mechanism of action. [Mol Cancer Ther 2007;6(3):1112 -22]

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“…Other approaches have attempted to modulate substrate/enzyme interaction, and/or inhibit dissociation of the enzyme from the substrate. 7,8 A number of molecules have been reported to bind to nontelomeric DRH duplexes such as ethidium derivatives, ellipticine, paramomycin, ribostamycin and neomycin (S1, ESI). [9][10][11][12][13] In 2010, Wheelhouse and co-workers reported a pyrimidine-connected bis-sulfane molecule (Figure 2) with a 20-fold preference for binding to a poly(dA)-poly(rU) hybrid duplex compared to an equivalent RNA fragment, a 3-fold preference over duplex DNA, and 7-fold preference over the alternative poly(rA)-poly(dT) hybrid sequence, in a competition dialysis assay.…”

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Methylene-linked bis-phenylbenzimidazoles – a new scaffold to target telomeric DNA/RNA hybrid duplex

et al. 2018

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We report a series of novel methylene-linked bis-phenylbenzimidazoles intercalators that stabilize telomeric DNA/RNA hybrid (tDRH) structures by up to 7.2 °C at a 1 μM ligand concentration while having negligible affinity for DNA/DNA duplexes, although with a low affinity for quadruplex DNA. We have used molecular modelling studies to rationalize this selectivity, concluding that the methylene spacer between the terminal benzimidazole and phenylene moieties plays a key role in facilitating the bis-intercalating process. This scaffold may be used to develop chemical tools or new therapeutics to selectively target the telomeric DNA/RNA duplex without affecting normal genomic DNA.

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Small molecule/Nucleic acid affinity chromatography: application for the identification of telomerase inhibitors which target its key RNA/DNA heteroduplex

Cited by 16 publications

References 10 publications

Sequence- and structural-selective nucleic acid binding revealed by the melting of mixtures

Sequence- and structural-selective nucleic acid binding revealed by the melting of mixtures

A duplexed phenotypic screen for the simultaneous detection of inhibitors of the molecular chaperone heat shock protein 90 and modulators of cellular acetylation

Methylene-linked bis-phenylbenzimidazoles – a new scaffold to target telomeric DNA/RNA hybrid duplex

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