Cited by 508Cancer, Hypoxia, and MetabolismHeterocyclic Compound Synthesis and BioactivityKruppel-like factors research

The DOI matches its Crossref record; 55 of the 55 references it cites were found in a registry or an index; 3 of the 30 sources its claims cite were checked for support.

Echinomycin, a small-molecule inhibitor of hypoxia-inducible factor-1 DNA-binding activity.

Open access

Published version of a preprint

Abstract

The identification of small molecules that inhibit the sequence-specific 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-1alpha and HIF-1beta proteins containing the basic-helix-loop-helix and PAS domains. Expressed recombinant HIF-1alpha and HIF-1beta 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 small-molecule 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-1alpha and HIF-1beta proteins to a HRE sequence but not binding of the corresponding proteins to activator protein-1 (AP-1) or nuclear factor-kappaB (NF-kappaB) 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-kappaB 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.

Overview

AI snapshot

Written from the paper’s full text.

TL;DR

Echinomycin (NSC-13502) was identified from a HIF-1-targeted compound screen as a sequence-specific DNA-binding inhibitor that blocks HIF-1 binding to hypoxia-responsive elements and reduces HIF-1-dependent transcription in U251 cells. It appears to act by binding DNA rather than by lowering HIF-1α protein, with selectivity over AP-1 and NF-κB in the assays used.

Key findings

  • Of 128 active compounds from an NCI 140,000-compound HIF-1 cell-based screen, 20 inhibited HIF-1 DNA-binding activity by more than 50% at 10 µM; 12 of those also inhibited AP-1 and/or NF-κB binding, leaving 8 with relative HIF-1 selectivity.
  • NSC-13502 dose-dependently inhibited recombinant HIF-1α/HIF-1β DNA binding in ELISA, with nearly complete inhibition at 320 nM, and in EMSA it did not inhibit AP-1 or NF-κB binding up to 10 µM.
  • In ChIP assays, 0.5 µM NSC-13502 abolished HIF-1 binding to the VEGF promoter HRE but did not affect c-Fos binding to the cyclin D1 promoter or p65 binding to the ICAM-1 promoter; HIF-1α protein levels were not reduced.
  • NSC-13502 inhibited hypoxic luciferase induction in U251-HRE cells with an EC50 of about 1.2 nM, blocked the roughly 5-fold hypoxic increase in VEGF mRNA (P < 0.01), and in microarray profiling 14 of 17 hypoxia-induced HIF-1 target genes were inhibited more than 3-fold.

Methods

  • Recombinant truncated HIF-1α bHLH-PAS (amino acids 1–389) and HIF-1β bHLH-PAS (amino acids 1–475) proteins were expressed and used in a 96-well DNA-binding ELISA and EMSA with HRE, mutant HRE, AP-1, NF-κB, and E-box oligonucleotides; 128 compounds were screened at 10 µM.
  • U251, U251-HRE, U251-pGL3, and MCF-7 cells were cultured under normoxia or 1% O2 hypoxia; assays included ChIP for VEGF, cyclin D1, and ICAM-1 promoters, Western blotting, luciferase reporter measurement, real-time PCR for VEGF, DNA thermal melting and ethidium bromide displacement, SRB viability, and oligonucleotide microarray analysis of about 11,000 genes.
  • Main analyses compared dose-dependent inhibition, competition and supershift controls, promoter binding specificity, reporter activity, mRNA expression, and global gene-expression changes.

Limitations

  • The paper states that NSC-13502’s sequence specificity may not be limited to HIF-1; it also inhibited nuclear protein binding to an E-box oligonucleotide, the binding site for Myc/Max.
  • The paper states that in vivo feasibility and whether alternative dosing schedules could improve therapeutic potential remain to be established, and notes that earlier phase II clinical trials found minimal or no antitumor activity.
  • Evident from the text: most mechanistic evidence comes from cell-free DNA-binding assays and cultured U251/MCF-7 cells, with no in vivo tumor efficacy experiment reported here; ChIP used 0.5 µM while the luciferase EC50 was about 1.2 nM, indicating different potency across assay contexts.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1158/0008-5472.can-05-1235

Cites

55 of 55 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Verification

Claims the paper makes

43 Own result · 16 No full text of the sources · 11 Own interpretation · 2 Not checked yet · 1 Supported · 1 Supported so far

Show all 52 claims

  • Probably not a substantial claim. 9
  • It may state two separate claims as one. 17
22 of 22
  • The authors state this as an assumption.

    NSC-13502 inhibits HIF-1 DNA-binding activity in vitro by binding DNA in a sequence-specific fashion.

    “Results shown thus far indicate that NSC-13502 inhibits HIF-1, but not AP-1 or NF-nB, DNA-binding activity in vitro by binding DNA in a sequence-specific fashion.If this assumption were correct, a ChIP assay would show whether NSC-13502 inhibited endogenous HIF-1 DNA-binding activity in cultured cells.”
  • The paper relies on this without support.

    The core sequence of the HRE (5'-CGTG-3') is also present in the E-box (5'-CACGTG-3'), the DNA-binding site of the Myc/Max complex.

    “The core sequence of the HRE (5V -CGTG-3V) is also present in the E-box (5V-CACGTG-3V), which is the DNA-binding site of the Myc/Max complex, raising the possibility that NSC-13502 might also inhibit the binding of nuclear proteins to the E-box.”
  • The paper relies on this without support.

    The HRE recognized by HIF-1 contains the core sequence 5'-R(A/G)CGTG-3' and is present in promoters of HIF-1 target genes.

    “The DNA-binding site recognized by HIF-1, known as hypoxia-responsive element (HRE), contains the core sequence 5V -R(A/G)CGTG-3V , which is present in promoters of HIF-1 target genes.”
3 of 3

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Citations

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Metadata

Authors
Kong, D., Park, E. J., Stephen, A. G., Calvani, M., Cardellina, J. H., Monks, A., Fisher, R. J., Shoemaker, R. H., & Melillo, G.
Affiliations
  • Science Applications International Corporation (United States) (US)
  • National Cancer Institute (US)
Venue
Cancer Research
Published
2005-10-01
Volume
65
Issue
19
Pages
9047-9055
ISSN
  • 0008-5472 (ISSN-L)
  • 1538-7445
OpenAlex
W2144670533
Cited by
508
References
53
Citations by year
2026: 12 · 2025: 24 · 2024: 23 · 2023: 25 · 2022: 31 · 2021: 34 · 2020: 26 · 2019: 22 · 2018: 23 · 2017: 26 · 2016: 22 · 2015: 23 · 2014: 20 · 2013: 23 · 2012: 26
FWCI
7.64
Type
journal article
Language
en
Open access
Locations
  • Cancer Research (publishedVersion)
  • PubMed (publishedVersion)
  • Florence Research (University of Florence) (submittedVersion, other-oa)
Funders
  • National Institutes of Health (n01co12400-79-0-22, N01-CO-12400)
  • National Cancer Institute (N01CO12400)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer, Hypoxia, and Metabolism
  • Physical Sciences › Chemistry › Organic Chemistry › Heterocyclic Compound Synthesis and Bioactivity
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Kruppel-like factors research
Keywords
echinomycin, HIF-1, hypoxia response element, transcription factor-DNA binding, small molecule inhibitors, VEGF promoter, angiogenesis, tumor progression, metastasis, high-throughput screening
MeSH terms
Antibiotics, Antineoplastic, Breast Neoplasms, DNA, Neoplasm, Echinomycin, Enzyme-Linked Immunosorbent Assay, Glioma, Humans, Luciferases, Promoter Regions, Genetic, Recombinant Proteins, RNA, Messenger, Vascular Endothelial Growth Factor A, Cell Line, Tumor, Hypoxia-Inducible Factor 1

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