Previously, Dr. Elder and his colleagues used comparative modeling of FIV and HIV aspartyl proteinases (PRs) to identify specific amino acid residues that interact with the substrate binding pocket in a unique fashion in each protease. They have discovered that HIV protease and FIV protease are very similar structurally but that each has certain unique characteristics which result in strongly preferential homologous gag substrate cleavage. The hypothesis behind the proposed work is that an in-depth understanding of both the similarities and the differences between two distantly related lentiviral proteases will promote development of protease inhibitors that may be efficacious against both FIV and HIV proteases but at that same time, relatively homologous resistance-proof. To explore this hypothesis, Dr. Elder and his colleagues will focus on substrate binding pocket interactions. They will use site-directed mutagenesis to replace FIV-specific residues with HIV-specific residues, both alone and in combinations predicted to be interactive in the three-dimensional structure. Mutant proteases will be expressed in bacteria, purified, refolded. These mutant proteases will be biochemically defined as to their substrate specificities using both natural and synthetic peptide substrates and as to the kinetics of their inhibition by a panel of previously defined HIV protease inhibitors. Interesting mutants will be placed in the context of infectious virus, and examined in cell culture for their potential to be inhibited by, or develop resistance to, known protease inhibitors during virus passage. Where appropriate, the three-dimensional structure of interesting mutant proteases can be examined by Dr. Alex Wlodawer.
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