Cheminformatic Discovery of Alternative Pathway C3 Pro-Convertase Inhibitors

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DESCRIPTION (provided by applicant): Although complement serves as a pillar of the innate immune system, inappropriate or uncontrolled levels of complement activation are a major contributor to a rapidly growing list of human inflammatory diseases. Yet even though therapeutic manipulation of the complement response would be tremendously important in the clinic, only a limited panel of FDA approved drugs and indications exist for specifically targeting an active component within the complement system. A major factor underlying this dearth of complement-targeted therapeutics is the large size of the proteins and complex nature of the molecular recognition events which underlie complement activity. This has made it very challenging for scientists to identify which specific points are most susceptible for therapeutic intervention. By contrast, the bacterial pathogen Staphylococcus aureus deploys an array of proteins that have been naturally selected and exquisitely optimized during the course of host/pathogen co-evolution to efficiently block fundamental events within the complement cascade - in particular formation of the multi-subunit AP C3 convertase that drives amplification of the complement response. As a consequence, molecules which mimic the activities of staphylococcal virulence proteins hold promise for complement-directed, anti-inflammatory therapeutics. We recently investigated the potential of using novel cheminformatic tools for identifying small molecules that bind the same C3b site as the SCIN family of S. aureus complement inhibitors. Although done on a pilot scale, this work strongly suggested that in silico methods are a viable means of screening for new chemotypes of drug-like compounds that specifically target functionally significant sites on C3b. In this investigation, our goal is to aply the same cheminformatic methods to screen a highly elaborated (~20 million) compound library and to identify small molecules that bind C3b sites with known roles in the initial step of AP C3 convertase formation. This step, which generates a structure known as the AP C3 pro-convertase, is the same point in the pathway that is disrupted by multiple families of secreted S. aureus complement inhibitors (including SCINs). Thus, we believe that formation of the AP C3 pro-convertase is a biologically validated target for pharmacological intervention in the complement-mediated inflammatory response. The research plan described in this application consists of three distinct specific aims. Each aim has a defined outcome that is based upon either preliminary studies directly relevant to this project or our previous experience in using similar methodologies. In the first aim, we will use cheminformatics to identify ~100 hit compounds that are likely binders at one of four target sites on C3b with known roles in AP C3 pro-convertase formation. Then, in the second aim, we will use established biochemical and functional tools to validate ~20 candidates that both bind C3b and inhibit AP activity. In the fina aim, we will use structural comparisons to identify the pharmacophores in these validated candidates and conduct a limited synthetic expansion of our most promising ~ 5 compound series. At the conclusion of this aim, we will have identified a single, non-toxic compound that will serve as our lead inhibitor of AP C3 pro-convertase assembly. As a consequence, this work will lay the foundation for future development of new classes of complement-targeted anti-inflammatory therapeutics.