As part of a drug discovery group to develop anti-opportunistic infection agents that are targeted to DNA-protein complexes, Dr. Wilson has developed unfused aromatic dications that bind in the DNA minor groove. Two of these compounds are now entering clinical trials. An additional exciting discovery from the minor-groove research is that one of the new compounds, a diamidine with a phenyl-furan-benzimidazole ring system (DB293), binds to mixed AT/GC sequences in DNA as a dimer. Initial NMR, DNAse I footprinting, and surface plasmon resonance results clearly support the hypothesis that DB293 binds in the minor groove at specific GC containing sequences of DNA in a highly cooperative manner as a stacked dimer. Previous studies have suggested that such complexes are not possible with dications and neither of the symmetric analogs of DB293 bind significantly to GC sequences. This proposal is built around the hypothesis that DB293 recognizes both strands of DNA and provides a new paradigm for design of compounds for recognition of specific DNA sequences. Such a recognition motif would require reevaluation of ideas on the limits for small molecule-DNA recognition. The general goal of the proposed research is to fully characterize the dimer-DNA binding motif and to develop models that will allow us to extend the mode to additional DNA sequences. A complementary approach utilizing biophysical and synthetic methods will be used to thoroughly characterize the dimer recognition mechanism. Information on the initial dimer complexes will then be used to design, synthesize and characterize the DNA interaction of new compounds with modified and/or extended dimer-DNA sequence recognition capability.
Four specific aims will allow Dr. Wilson to achieve these goals:
Aim 1 : Determine the structural details of the DB293-dimer DNA complex by 2D NMR and x-ray methods if crystals can be obtained.
Aim 2 : Prepare analogs of DB293 and characterize their DNA interactions to determine what features of the molecular structure are essential for formation of the dimer motif.
Aim 3 : Modify the DB293-DNA dimer recognition sequence to determine what effect base pair changes have on dimer recognition and affinity.
Aim 4 : Use all of this information to define the dimer recognition rules for DB293.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
3R01GM061587-04S1
Application #
6891985
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Lewis, Catherine D
Project Start
2000-07-01
Project End
2005-02-28
Budget Start
2003-07-01
Budget End
2005-02-28
Support Year
4
Fiscal Year
2004
Total Cost
$65,475
Indirect Cost
Name
Georgia State University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
837322494
City
Atlanta
State
GA
Country
United States
Zip Code
30302
Munde, Manoj; Kumar, Arvind; Nhili, Raja et al. (2010) DNA minor groove induced dimerization of heterocyclic cations: compound structure, binding affinity, and specificity for a TTAA site. J Mol Biol 402:847-64
Lusvarghi, Sabrina; Murphy, Connor T; Roy, Subhadeep et al. (2009) Loop and backbone modifications of peptide nucleic acid improve g-quadruplex binding selectivity. J Am Chem Soc 131:18415-24
Lajiness, Jamie; Sielaff, Alan; Mackay, Hilary et al. (2009) Polyamide curvature and DNA sequence selective recognition: use of 4-aminobenzamide to adjust curvature. Med Chem 5:216-26
Nguyen, Binh; Neidle, Stephen; Wilson, W David (2009) A role for water molecules in DNA-ligand minor groove recognition. Acc Chem Res 42:11-21
Rahimian, Maryam; Miao, Yi; Wilson, W David (2008) Influence of DNA structure on adjacent site cooperative binding. J Phys Chem B 112:8770-8
Arafa, Reem K; Ismail, Mohamed A; Munde, Manoj et al. (2008) Novel linear triaryl guanidines, N-substituted guanidines and potential prodrugs as antiprotozoal agents. Eur J Med Chem 43:2901-8
Drewe, William C; Nanjunda, Rupesh; Gunaratnam, Mekala et al. (2008) Rational design of substituted diarylureas: a scaffold for binding to G-quadruplex motifs. J Med Chem 51:7751-67
Mackay, Hilary; Brown, Toni; Uthe, Peter B et al. (2008) Sequence specific and high affinity recognition of 5'-ACGCGT-3'by rationally designed pyrrole-imidazole H-pin polyamides: thermodynamic and structural studies. Bioorg Med Chem 16:9145-53
Wilson, W David; Tanious, Farial A; Mathis, Amanda et al. (2008) Antiparasitic compounds that target DNA. Biochimie 90:999-1014
Ismail, Mohamed A; Arafa, Reem K; Wenzler, Tanja et al. (2008) Synthesis and antiprotozoal activity of novel bis-benzamidino imidazo[1,2-a]pyridines and 5,6,7,8-tetrahydro-imidazo[1,2-a]pyridines. Bioorg Med Chem 16:683-91

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