The goal of this proposal is to use the structure of the gp41 subunit of the HIV-envelope glycoprotein to discover small molecule inhibitors of the membrane fusion activity of gp41. Evidence indicates that receptor and co- receptor binding by the gp120 subunit of HIV-1 ENV triggers a conformational change resulting in the membrane-fusion active conformation of the gp41 subunit. We and other have determined the x-ray structure of a soluble ectodomain of gp41, expressed in the absence of gp120, that provides an atomic model for the membrane-fusion active conformation of gp41. A novel feature of reported peptidic membrane-fusion inhibitors of HIV-1 is that they appear to target a transient state during the conformational change of gp41 into the double layered helical structure observed by crystallography. Therefore, inhibitors are not expected to bind the final structure seen by x-ray crystallography, but instead to a section of a core coiled-coil buried in that structure by the outer-layer helices. We propose both a structure-based design strategy and the design of a biased combinatorial library that should discover small molecule inhibitors that block the docking the outer-layer helices to the core coiled coil of gp41. An innovation we propose in order to study the bound state of inhibitors is to create stable inhibitor targets (not transient ones) by deleting small sections of the outer-layer helices, uncovering a targeted section of the core coiled coil. Bound inhibitors will then be visualized by x-ray crystallography, to allow refine of binding affinity.
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