Allosteric Inhibition of Protein−DNA Complexes by Polyamide−Intercalator Conjugates

Fechter, Eric J.; Dervan, Peter B.

doi:10.1021/ja030125e

Cited by 67 publications

(52 citation statements)

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“…Hairpin polyamides and polyamideacridine conjugates have been shown to inhibit protein-DNA complexes in some cases (42,43). Recently, a synthetic pyrroleimidazole polyamide targeting the HRE site in the VEGF promoter has been described, which was designed to bind to the DNA sequence 5V-W TWCGW-3V (where W = A or T; ref.…”

Section: Resultsmentioning

confidence: 99%

Echinomycin, a Small-Molecule Inhibitor of Hypoxia-Inducible Factor-1 DNA-Binding Activity

et al. 2005

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The identification of small molecules that inhibit the sequencespecific binding of transcription factors to DNA is an attractive approach for regulation of gene expression. Hypoxia-inducible factor-1 (HIF-1) is a transcription factor that controls genes involved in glycolysis, angiogenesis, migration, and invasion, all of which are important for tumor progression and metastasis. To identify inhibitors of HIF-1 DNA-binding activity, we expressed truncated HIF-1A and HIF-1B proteins containing the basichelix-loop-helix and PAS domains. Expressed recombinant HIF-1A and HIF-1B proteins induced a specific DNA-binding activity to a double-stranded oligonucleotide containing a canonical hypoxia-responsive element (HRE). One hundred twenty-eight compounds previously identified in a HIF-1-targeted cell-based high-throughput screen of the National Cancer Institute 140,000 small-molecule library were tested in a 96-well plate ELISA for inhibition of HIF-1 DNA-binding activity. One of the most potent compounds identified, echinomycin (NSC-13502), a smallmolecule known to bind DNA in a sequence-specific fashion, was further investigated. Electrophoretic mobility shift assay experiments showed that NSC-13502 inhibited binding of HIF-1A and HIF-1B proteins to a HRE sequence but not binding of the corresponding proteins to activator protein-1 (AP-1) or nuclear factor-KB (NF-KB) consensus sequences. Interestingly, chromatin immunoprecipitation experiments showed that NSC-13502 specifically inhibited binding of HIF-1 to the HRE sequence contained in the vascular endothelial growth factor (VEGF) promoter but not binding of AP-1 or NF-KB to promoter regions of corresponding target genes. Accordingly, NSC-13502 inhibited hypoxic induction of luciferase in U251-HRE cells and VEGF mRNA expression in U251 cells. Our results indicate that it is possible to identify small molecules that inhibit HIF-1 DNA binding to endogenous promoters. (Cancer Res 2005; 65(19): 9047-55)

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Section: Resultsmentioning

confidence: 99%

Echinomycin, a Small-Molecule Inhibitor of Hypoxia-Inducible Factor-1 DNA-Binding Activity

et al. 2005

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“…The advantage of these synthetic approaches is the small size of the TF, which can facilitate both synthesis and cellular uptake. In addition, synthetic DBDs have demonstrated a high level of affinity, permitting not only regulation of targeted promoters but also specific competition with endogenous TFs (Chiang et al, 2000;Bremer et al, 2001;Coull et al, 2002;Ehley et al, 2002;Stanojevic and Young, 2002;Wurtz et al, 2002;Fechter and Dervan, 2003;Yang et al, 2003). DNA microarray experiments have shown that polyamides seem to be able to regulate a limited number of genes in lymphoid cells (Dudouet et al, 2003).…”

Section: Artificial Tf Designmentioning

confidence: 99%

Designing Transcription Factor Architectures for Drug Discovery

Blancafort¹,

Segal²,

Barbas³

2004

Mol Pharmacol

164

124

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Recent advances in the design, selection, and engineering of DNA binding proteins have led to the emerging field of designer transcription factors (TFs). Modular DNA-binding protein domains can be assembled to recognize a given sequence of a DNA in a regulatory region of a targeted gene. TFs can be readily prepared by linking the DNA-binding protein to a variety of effector domains that mediate transcriptional activation or repression. Furthermore, the interaction between the TF and the genomic DNA can be regulated by several approaches, including chemical regulation by a variety of small molecules.Genome-wide single target specificity has been demonstrated using arrays of sequence-specific zinc finger (ZF) domains, polydactyl proteins. Any laboratory today can easily construct polydactyl ZF proteins by linkage of predefined ZF units that recognize specific triplets of DNA. The potential of this technology to alter the transcription of specific genes, to discover new genes, and to induce phenotypes in cells and organisms is now being applied in the areas of molecular therapeutics, pharmacology, biotechnology, and functional genomics.

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“…The key feature to consider would be sequence selectivity based on the premise that pairing rules should be retained once the polyamide covalently binds to the intercalator. Polyamides covalently linked to acridine prevent major groove binding protein GCN4bZip protein 30) from simultaneously obeying the pairing rules. Polyamides covalently linked to camptothecin sitespecifically trap topoisomerase (Topo), resulting in cleavage at the trapped site.…”

Section: )mentioning

confidence: 99%