The overall goal of this project is the determination of the three-dimensional structures of biologically active natural products bound to their macromolecular (protein) receptors. The structures are useful in defining the structure of the natural product, elucidating the mechanism by which the natural product acts, and serving as the first stage of a structure-based drug design cycle. The projects that were examined during the last period include: 1. Peptidyl-palmitoyl thioesterase (PPT) and didemnin. Didemnin is currently in phase II clinical trial for cancer, but it s mode of action is not known. PPT is an important signaling protein. 2. Trypsin and aeruginosin 98B. Trypsin is a surrogate target for more clinically relevant serine proteases such as thrombin. Aeruginosin 98B is an interesting target for drug design since it contains none of the standard serine protease inhibitory motifs and might therefore be expected to be more selective. 3. Cyclohexadienyl dehydratase (CDT) and prephenic acid. CDT is a key enzyme in the synthesis of the aromatic amino acid phenylalanine. Since it occurs only in bacterial, fungi and plants, it could be an important target for the design of antibacterial, antifungal, or herbicidal agents. 4. FK506 binding protein (FKBP12), FK506 rapamycin associated protein (FRAP) and rapamycin analogs. This project began as a study on the mechanism of action of the immunosuppressive agent rapamycin and has evolved into a study of rapamycin and some of its analogs as chemical inducers of dimerization (CID). Basically a CID is a small molecule that will join two proteins, and in the case we ve studied most extensively, the complex is FKBP12-rapamycin-FRB. Since CIDs can be used to control biological processes, such as gene therapy, it s important to get away from the completely natural system in order to avoid wild type targets. We re working on developing rapamycin analogs that won t bind to wild type FKBP12 and/or FRB and proteins (FKBP12 and/or FRB) with compensatory mutations.
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