Research Project
2068378
The long-range objective of this proposal is to identify and optimize synthetic ligands to essential proteins of the HIV lifecycle that will serve as structural leads for protein-structure based design and development of novel therapeutic agents active against HIV. It is proposed that a new NCDDG be established which integrates the complementary scientific strengths of Agouron Pharmaceuticals, Inc., Selectide Corporation and Nexagen. The methodological bases of this cooperative agreement are recently discovered powerful technologies for rapidly generating and screening of small peptide and RNA ligands which bind to selected target molecules. These ligand selection methods are to be combined with the rigorous structural determination and analysis of the binding mode by x-ray crystallography of the ligand-protein complex. In the first phase, this approach will be applied to the isolated RNase H domain of HIV-1 reverse transcriptase. This domain is involved in critical interactions with both protein and nucleic acids macromolecules, and its three-dimensional structure is available. Binding of a high-affinity ligand that would interfere with these interactions is expected to block virus replication. Towards this goal, the Selectide technology will be used to create large libraries comprised of millions of synthetic peptides generated via a novel random synthesis technique which produces single peptide entities on individual solid phase beads. Nexagen's approach of exponential enrichment from a large library of random sequences will be applied for selection of RNA-based ligands. Using both methodologies, the accessible surface of the RNase H domain will be systematically explored for potential binding sites. Once peptides and oligoribonucleotides with suitable binding properties are identified they will be provided for structural studies, which will enable detailed quantitative analysis of the binding interaction in the three-dimensional context of the ligand-receptor complex. This analysis will form the basis for the elaboration of the ligand into a suitable drug lead. In the second phase, the experience with generation and analysis of high- affinity ligands will be applied to other essential HIV-encoded proteins currently studied at Agouron as antiviral targets. The additional potential of these ligands to facilitate crystallization will be explored. It is expected that the combined effort of the Agouron, Selectide and Nexagen scientific teams will bring new structural information and provide insight for design of novel antiviral agents.
