G-Quadruplexes as Targets for Drug Design

Summary

Principal Investigator: L H Hurley
Abstract: The overall objective of the research described in this proposal is to bring a small molecule therapeutic agent into phase 1 clinical trails for treatment of cancers that depend upon c-Myc overexpression for growth. The specific aims are (1) structural characterization of the i-motif(s) in the NHE 1111 of the c-Myc promoter and its complex(es) with TMPyP4, (2) to determine the conformational state of the NHE 1111 element that exists in a short linear duplex DMA molecule, in a supercoiled plasmid state, and in vivo, and then to determine how binding of TMPyP4 affects the structure of these forms, (3) to establish in vitro biochemical and cell-based screens to identify small molecules that interact specifically with the i-motif structure in the silencer element of the c-Myc promoter, (4) To discover and optimize new i-motif-interactive compounds using structure-based approaches for virtual screening of compound libraries, de novo design, and follow-up optimization of active lead molecules, and (5) in vivo and in vitro evaluation and subsequent preclinical development. We have recently uncovered a novel mechanism for silencing of gene expression involving secondary DMA structures that is amenable to small molecule targeting to specifically modulate gene expression. Our recent results show that the i-motif in the NHE 1111 element is the druggable target for modulation of c-Myc gene expression. Proof of principle already exists in vitro and in vivo using a cationic porphyrin. High-field NMR and footprinting techniques will be used to determine the structure of the DNA element and its drug complexes in cell-free, in vitro biochemical, and in vivo systems. Structure-based design and high through-put screening methods will be used to identify small molecule drug leads. In vitro and in vivo evaluation will be carried out to evaluate these leads prior to preclinical development and phase 1 clinical trials carried out in collaboration with Cylene Pharmaceuticals.
Funding Period: 2002-07-01 - 2008-06-30
more information: NIH RePORT

Top Publications

  1. pmc The C-terminus of nucleolin promotes the formation of the c-MYC G-quadruplex and inhibits c-MYC promoter activity
    Veronica Gonzalez
    College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
    Biochemistry 49:9706-14. 2010
  2. pmc NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III(1)
    Thomas S Dexheimer
    College of Pharmacy, University of Arizona, Tucson, Arizona 85721, USA
    Mol Cancer Ther 8:1363-77. 2009
  3. pmc Biochemical techniques for the characterization of G-quadruplex structures: EMSA, DMS footprinting, and DNA polymerase stop assay
    Daekyu Sun
    Department of Pharmacology, College of Pharmacy, University of Arizona, Tucson, AZ, USA
    Methods Mol Biol 608:65-79. 2010
  4. pmc Identification and characterization of nucleolin as a c-myc G-quadruplex-binding protein
    Veronica Gonzalez
    College of Pharmacy, University of Arizona, Tucson, Arizona 85721, USA
    J Biol Chem 284:23622-35. 2009
  5. pmc A direct and nondestructive approach to determine the folding structure of the I-motif DNA secondary structure by NMR
    Jixun Dai
    College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, USA
    J Am Chem Soc 131:6102-4. 2009
  6. pmc The importance of negative superhelicity in inducing the formation of G-quadruplex and i-motif structures in the c-Myc promoter: implications for drug targeting and control of gene expression
    Daekyu Sun
    College of Pharmacy, University of Arizona, Tucson, Arizona 85721, USA
    J Med Chem 52:2863-74. 2009
  7. pmc The proximal promoter region of the human vascular endothelial growth factor gene has a G-quadruplex structure that can be targeted by G-quadruplex-interactive agents
    Daekyu Sun
    BIO5 Institute, Room 102, 1657 East Helen Street, Tucson, AZ 85721, USA
    Mol Cancer Ther 7:880-9. 2008
  8. pmc Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions
    Yong Qin
    College of Pharmacy, 1703 E Mabel, University of Arizona, Tucson, AZ 85721, USA
    Biochimie 90:1149-71. 2008
  9. pmc A novel G-quadruplex-forming GGA repeat region in the c-myb promoter is a critical regulator of promoter activity
    SunMi L Palumbo
    Arizona Cancer Center, University of Arizona, 1515 N Campbell Ave, Tucson, AZ 85724 5024, USA
    Nucleic Acids Res 36:1755-69. 2008
  10. pmc Characterization of the G-quadruplexes in the duplex nuclease hypersensitive element of the PDGF-A promoter and modulation of PDGF-A promoter activity by TMPyP4
    Yong Qin
    College of Pharmacy, 1703 E Mabel, University of Arizona, Tucson, Arizona 85721, USA
    Nucleic Acids Res 35:7698-713. 2007

Scientific Experts

  • Daekyu Sun
  • L H Hurley
  • Scot Ebbinghaus
  • Veronica Gonzalez
  • Thomas S Dexheimer
  • Yong Qin
  • Kexiao Guo
  • Vijay Gokhale
  • Evonne M Rezler
  • Jeyaprakashnarayanan Seenisamy
  • Jixun Dai
  • SunMi L Palumbo
  • Elizabeth White
  • Weijun Liu
  • W David Wilson
  • Sridevi Bashyam
  • Song Zuohe
  • Xiaohui Hu
  • Attila Ambrus
  • Steven S Carey
  • Lauren B Murata
  • Estelle M Maes
  • Andrzej Weichsel
  • Emmanuelle J Meuillet
  • William R Montfort
  • Danzhou Yang
  • Vijay M Gokhale
  • Yulia Krotova-Khan
  • Diana J Uribe
  • Regan M Memmott
  • Alan Pourpak
  • Kara Beetz-Rogers
  • Adam Siddiqui-Jain
  • Kazuo Shin-ya
  • Nicole Streiner
  • Mu Yong Kim
  • Hariprasad Vankayalapati

Detail Information

Publications18

  1. pmc The C-terminus of nucleolin promotes the formation of the c-MYC G-quadruplex and inhibits c-MYC promoter activity
    Veronica Gonzalez
    College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
    Biochemistry 49:9706-14. 2010
    ..Here we report that nucleolin's RNA binding domains 3 and 4, as well as the arginine-glycine-glycine (RGG) domain, are required to repress c-MYC transcription...
  2. pmc NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III(1)
    Thomas S Dexheimer
    College of Pharmacy, University of Arizona, Tucson, Arizona 85721, USA
    Mol Cancer Ther 8:1363-77. 2009
    ..Furthermore, this model provides a rationale for how the stabilization of the G-quadruplex or i-motif structures formed within the c-myc gene promoter region can inhibit NM23-H2 from activating c-myc gene expression...
  3. pmc Biochemical techniques for the characterization of G-quadruplex structures: EMSA, DMS footprinting, and DNA polymerase stop assay
    Daekyu Sun
    Department of Pharmacology, College of Pharmacy, University of Arizona, Tucson, AZ, USA
    Methods Mol Biol 608:65-79. 2010
    ....
  4. pmc Identification and characterization of nucleolin as a c-myc G-quadruplex-binding protein
    Veronica Gonzalez
    College of Pharmacy, University of Arizona, Tucson, Arizona 85721, USA
    J Biol Chem 284:23622-35. 2009
    ..Finally, we show that nucleolin binds to the c-myc promoter in HeLa cells, which indicates that this interaction occurs in vivo. In summary, nucleolin may induce c-myc G4 formation in vivo...
  5. pmc A direct and nondestructive approach to determine the folding structure of the I-motif DNA secondary structure by NMR
    Jixun Dai
    College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, USA
    J Am Chem Soc 131:6102-4. 2009
    ..Additionally, this method can be applied to the direct detection of the base-paired thymines that are involved in the capping structures...
  6. pmc The importance of negative superhelicity in inducing the formation of G-quadruplex and i-motif structures in the c-Myc promoter: implications for drug targeting and control of gene expression
    Daekyu Sun
    College of Pharmacy, University of Arizona, Tucson, Arizona 85721, USA
    J Med Chem 52:2863-74. 2009
    ....
  7. pmc The proximal promoter region of the human vascular endothelial growth factor gene has a G-quadruplex structure that can be targeted by G-quadruplex-interactive agents
    Daekyu Sun
    BIO5 Institute, Room 102, 1657 East Helen Street, Tucson, AZ 85721, USA
    Mol Cancer Ther 7:880-9. 2008
    ..Our results also provide further support for the idea that G-quadruplex structures may play structural roles in vivo and therefore might provide insight into novel methodologies for rational drug design...
  8. pmc Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions
    Yong Qin
    College of Pharmacy, 1703 E Mabel, University of Arizona, Tucson, AZ 85721, USA
    Biochimie 90:1149-71. 2008
    ....
  9. pmc A novel G-quadruplex-forming GGA repeat region in the c-myb promoter is a critical regulator of promoter activity
    SunMi L Palumbo
    Arizona Cancer Center, University of Arizona, 1515 N Campbell Ave, Tucson, AZ 85724 5024, USA
    Nucleic Acids Res 36:1755-69. 2008
    ..Our findings show that the T:H:H:T G-quadruplex-forming region in the c-myb promoter is a critical cis-acting element and may repress c-myb promoter activity through MAZ interaction with G-quadruplexes in the c-myb promoter...
  10. pmc Characterization of the G-quadruplexes in the duplex nuclease hypersensitive element of the PDGF-A promoter and modulation of PDGF-A promoter activity by TMPyP4
    Yong Qin
    College of Pharmacy, 1703 E Mabel, University of Arizona, Tucson, Arizona 85721, USA
    Nucleic Acids Res 35:7698-713. 2007
    ..On the basis of these results, we have established that ligand-mediated stabilization of G-quadruplex structures within the PDGF-A NHE can silence PDGF-A expression...
  11. pmc Formation of pseudosymmetrical G-quadruplex and i-motif structures in the proximal promoter region of the RET oncogene
    Kexiao Guo
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
    J Am Chem Soc 129:10220-8. 2007
    ....
  12. ncbi Drug targeting of the c-MYC promoter to repress gene expression via a G-quadruplex silencer element
    Laurence H Hurley
    University of Arizona, College of Pharmacy, Tucson, AZ, USA
    Semin Oncol 33:498-512. 2006
    ..Furthermore, TMPyP4 has been shown to repress c-MYC expression, and this effect is mediated through the silencer element. Last, the in vivo activity of TMPyP4 in xenograph models is presented...
  13. pmc Deconvoluting the structural and drug-recognition complexity of the G-quadruplex-forming region upstream of the bcl-2 P1 promoter
    Thomas S Dexheimer
    College of Pharmacy, University of Arizona, Tucson, Arizona 85721, USA
    J Am Chem Soc 128:5404-15. 2006
    ....
  14. ncbi Binding of G-quadruplex-interactive agents to distinct G-quadruplexes induces different biological effects in MiaPaCa cells
    Weijun Liu
    College of Pharmacy, The University of Arizona, Tucson, Arizona 85724, USA
    Nucleosides Nucleotides Nucleic Acids 24:1801-15. 2005
    ..Our data suggest that binding of G-quadruplex-interactive agents to distinct G-quadruplexes could induce different biological effects in human cancer cells...
  15. pmc Facilitation of a structural transition in the polypurine/polypyrimidine tract within the proximal promoter region of the human VEGF gene by the presence of potassium and G-quadruplex-interactive agents
    Daekyu Sun
    College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
    Nucleic Acids Res 33:6070-80. 2005
    ....
  16. ncbi Telomestatin and diseleno sapphyrin bind selectively to two different forms of the human telomeric G-quadruplex structure
    Evonne M Rezler
    College of Pharmacy, The University of Arizona, 1703 East Mabel, Tucson, Arizona 85721, USA
    J Am Chem Soc 127:9439-47. 2005
    ..Thus, the biochemical and biological consequences of binding of ligands to G-quadruplex structures found in telomeres and promoter regions of certain important oncogenes go beyond mere stabilization of these structures...
  17. ncbi Design and synthesis of an expanded porphyrin that has selectivity for the c-MYC G-quadruplex structure
    Jeyaprakashnarayanan Seenisamy
    College of Pharmacy, The University of Arizona, 1703 East Mabel, Tucson, Arizona 85721, USA
    J Am Chem Soc 127:2944-59. 2005
    ..From this study, we have identified an expanded porphyrin that selectively binds with the c-MYC G-quadruplex in the presence of duplex DNA and other G-quadruplexes...