The binding of Rev to a portion of viral RNA, called Rev Response Element (RRE) is a key event in the HIV-1 life cycle, since it regulates the expression of late stage viral proteins and the release of viral RNA into the cytosol. Blocking the Rev-RRE interaction has been shown to inhibit virus replication by preventing these late stage events from taking place. The currently known Rev-RRE inhibitors bind to RNA via ionic interactions (aminoglycosides, arginine derivatives) or by intercalation (heterocycles). The best inhibitors combine both approaches, leading to nanomolar inhibition. However, none of these inhibitors are likely to be developed into drugs, due to bioavailability issues. Hence, there is a great need for cell-permeable small molecular weight compounds that inhibit the Rev-RRE interaction at low concentrations. We plan to investigate whether bioavailable inhibitors of the HIV Rev-RRE interaction can be found using a combinatorial chemistry approach that is based on (a) click chemistry, (b) diversity analysis, (c) computational filtering for drug-likeness, and (d) incorporation of design elements that increase the potential for RNA binding.
The specific aims are as follows: 1. Create two in silico libraries of up to 50,000 compounds each based on the most reliable click chemistry reactions. Prioritize compound production based on diversity, drug-likeness and RNA-binding criteria. 2. Produce a library of 2,000 to 2,500 diverse and drug-like compounds based on [3+2] cycloaddition chemistry. 3. Produce a library of 1,500 to 2,000 drug-like compounds that are targeted against RRE. 4. Perform lead optimization with the goal of finding drug-like molecules that are strong inhibitors of Rev-RRE binding in the lower micromolar range.
| Marenchino, Marco; Armbruster, David W; Hennig, Mirko (2009) Rapid and efficient purification of RNA-binding proteins: application to HIV-1 Rev. Protein Expr Purif 63:112-9 |
| Pond, Stephanie J K; Ridgeway, William K; Robertson, Rae et al. (2009) HIV-1 Rev protein assembles on viral RNA one molecule at a time. Proc Natl Acad Sci U S A 106:1404-8 |
| Carlomagno, Teresa; Amata, Irene; Williamson, James R et al. (2008) NMR assignments of HIV-2 TAR RNA. Biomol NMR Assign 2:167-9 |
| Pljevaljcic, Goran; Millar, David P (2008) Single-molecule fluorescence methods for the analysis of RNA folding and ribonucleoprotein assembly. Methods Enzymol 450:233-52 |
| Edgcomb, Stephen P; Aschrafi, Angelique; Kompfner, Elizabeth et al. (2008) Protein structure and oligomerization are important for the formation of export-competent HIV-1 Rev-RRE complexes. Protein Sci 17:420-30 |
| Scott, Lincoln G; Hennig, Mirko (2008) RNA structure determination by NMR. Methods Mol Biol 452:29-61 |
| Hennig, Mirko; Scott, Lincoln G; Sperling, Edit et al. (2007) Synthesis of 5-fluoropyrimidine nucleotides as sensitive NMR probes of RNA structure. J Am Chem Soc 129:14911-21 |
| Hennig, Mirko; Munzarova, Marketa L; Bermel, Wolfgang et al. (2006) Measurement of long-range 1H-19F scalar coupling constants and their glycosidic torsion dependence in 5-fluoropyrimidine-substituted RNA. J Am Chem Soc 128:5851-8 |
