Using prototype foamy virus integrase as a model for detailed structural studies of retroviral DNA integration

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To achieve productive infection, HIV must insert a DNA copy of its genome into a chromosome of a human cell. This process is orchestrated by integrase, an enzyme carried by the virus. Once integration is complete, the viral genome becomes a permanent resident in the cell. From there it will initiate production of new infectious particles or it might stay dormant and undetected for a long period of time. Integration is partly responsible for the persistence of HIV infection. Yet, the dependence of HIV on integration is also an exploitable weakness. A new class of antiretroviral drugs disrupts enzymatic activity of integrase taking advantage of this weakness to fight HIV. The main impediment to the development of these drugs, also known as integrase inhibitors, is our limited understanding of the structural aspects of HIV integration. In 2010 we determined the long-sought after three-dimensional structure of retroviral integrase bound to viral DNA ends. For these studies we chose to use IN derived from prototype foamy virus (PFV), which is much more soluble and active when removed from its natural environment compared to most of other retroviral INs. On the other hand, all retroviral integrase enzymes are very similar in their structural makeup. Therefore, although PFV is not a human pathogen, its integrase is an ideal model for experimentation as a proxy for HIV integrase. Crucially, it already allowed us to explain how HIV integrase inhibitors work. The current project aims use the unique biochemical properties of PFV integrase to understand the retroviral integration process down to a fine detail. Using X-ray crystallography as our main tool, we will determine three-dimensional structures of PFV integrase at various stages of the integration process. Furthermore, taking advantage of its similarity to HIV integrase, we will use it to understand how HIV can sometimes evade the action of integrase inhibiting drugs. We will also generate more structural information that drug developers will use to improve potency of integrase inhibitors. Our data will be of substantial value for drug discovery and development by both academic and private groups and will serve to reduce the costs and improve availability of the eventual treatments.