Our fundamental goal is to improve methods of designing anti-HIV drugs which have maximum interactions with cytoplasmic HIV viral nucleic acids (high activity) and minimum interactions with host cell chromosomal DNA (low toxicity) by two broad approaches: molecular targeting - drugs that selectively bind to HIV derived nucleic acids in the cell cytoplasm due to structural and dynamic differences between viral and host nucleic acids, and compartmentalization drugs with bulky groups that will interact strongly with viral nucleic acids and exploit the size dependence of partitioning of molecules into the nucleus. The basic ideas for molecular targeting of anti-HlV drugs follow: (i) by using a range of sophisticated techniques, including advanced NMR and molecular graphics-modeling methods, binding of existing compounds to specific secondary structural features of RNA can be enhanced and new compounds can be designed that specifically interact with viral RNA: (ii) since the DNA and RNA synthesis of the host cell occurs in the nucleus, the replicative metabolism of the HIV virus can be selectively disrupted. Viral RNA has a complex secondary structure (stacked single-strands, hairpin double-helical sections, and duplexed regions with unmatched or mismatched bases). Many of the regions with unusual secondary structural features represent critical control regions for the conversion of viral RNA into the proviral DNA and the very attractive targets for the design of anti-HIV drugs. Binding studies will be conducted for all new synthetic compounds to compare their affinity for RNA relative to a standard chromatin preparation. More detailed kinetics, NMR and computer modeling studies will be conducted on the most active compounds which bind strongly to specific secondary structural features of RNA but which bind weakly to chromatin. Based on these studies, new compounds will be designed with the aid of molecular modeling methods. These new compounds should have significantly enhanced affinity for the viral RNA. The basic idea for drug compartmentalization in the cytoplasm where important metabolic processes of viral nucleic acids can be disrupted is that bulky molecules pass quite slowly from the cell cytoplasm into the cell nucleus where many toxic processes can occur. A range of molecules will be designed with bulky substituents situated to maintain or actually enhance binding to viral RNA. Partition coefficients for all new compounds will be determine and adjusted in synthetic procedures such that the potential drugs achieve good cytoplasmic concentrations. Passage of these bulky molecules into the nucleus of a standard cell line will be monitored by fluorescence microscopy to evaluate the correlation between size and transport into the nucleus.
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