The long-term goal of our program is to advance the knowledge of RNA-ligand interactions and to apply the principles uncovered to the design, synthesis and discovery of new antiretroviral agents. The guiding hypothesis is that small molecules that target viral-specific RNA sites and prevent the formation of key RNA-protein and RNA-RNA complexes are promising candidates for antiretroviral drug discovery.
The specific aims of this proposal are: (1) Develop rapid assays for the discovery of potent and specific viral RNA binders. To complement our Rev-RRE assay, we will develop a rapid assay for identifying high affinity and selective Tat-TAR inhibitors. We will also develop a fluorescence-based assay for the discovery of HIV DIS binders. (2) Design and synthesize RNA-selective ligands. We will conjugate """"""""RNA-friendly"""""""" scaffolds (e.g., functionalized beta-and gamma-peptides, conformationally-constrained amino- and guanidine-glycosides) to sequence- and structure-selective elements (e.g., nucleobase analogs, RNA-selective intercalators, cis-Pt) to provide new families of potent and selective viral RNA binders. (3) Determine affinity and selectivity to HIV RNA sites. We will assess the Rev-RRE and Tat-TAR inhibitory activity as well as DIS affinity of all binders using the novel assays. (4) Evaluate anti HIV activity. Most promising binders will be evaluated for: (a) their ability to interfere with viral replication in HIV-1 infected cells, (b) their toxicity, and (c) their potential site(s) of interference. The rapid emergence of resistant viral strains necessitates the development of novel strategies for anti-HIV drug design. Small molecules that target pivotal viral RNA sites, and can specifically prevent the formation of key regulatory RNA-protein and RNA-RNA complexes, are proposed as promising candidates for antiretroviral drug development. Our integrated approach brings together organic synthesis, chemical diversity, novel solution and solid-phase assays, systematic structure-activity relationship studies, as well as in vivo anti-HIV tests, toxicity evaluation and mechanistic studies. It will yield new families of effective and specific binders that target key HIV-1 RNA sites. Potent and specific effectors of essential regulatory events will significantly advance the development of highly active antiretroviral agents.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
3R01AI047673-07S1
Application #
7276881
Study Section
AIDS Discovery and Development of Therapeutics Study Section (ADDT)
Program Officer
Miller, Roger H
Project Start
2000-05-01
Project End
2008-04-30
Budget Start
2006-08-01
Budget End
2007-04-30
Support Year
7
Fiscal Year
2006
Total Cost
$57,496
Indirect Cost
Name
University of California San Diego
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
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Staple, David W; Venditti, Vincenzo; Niccolai, Neri et al. (2008) Guanidinoneomycin B recognition of an HIV-1 RNA helix. Chembiochem 9:93-102
Tam, Victor K; Kwong, Denise; Tor, Yitzhak (2007) Fluorescent HIV-1 Dimerization Initiation Site: design, properties, and use for ligand discovery. J Am Chem Soc 129:3257-66
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Srivatsan, Seergazhi G; Tor, Yitzhak (2007) Fluorescent pyrimidine ribonucleotide: synthesis, enzymatic incorporation, and utilization. J Am Chem Soc 129:2044-53