| The powerful spectrum of synthesis of molecules either by chemical synthesis or by bio(technological) synthesis ranges from the synthesis of small molecules to the very large (bio)polymer molecules. The number of "biologics" (e.g. monoclonal antibodies, hormones etc.) as drugs is rapidly increasing. Concomitantly, interest in the design and molecular construction of molecules of "intermediate" size (ca 4000 > mw > ca 500) is rising, which also poses significant synthetic challenges. Their chemical synthesis is challenging because this size usually requires many different sophisticated steps, which have to be selective and high yielding in order to obtain substantial quantities of pure product. In addition, presently there are great opportunities to combine chemical synthesis and "bio(tech)" synthesis for example using ligation strategies. This will undoubtedly lead to the ultimate merging of different synthesis strategies, whereby the nature and complexity of the molecule determine how it will be synthesized in the quickest, efficient and most sustainable way. Finally, characterization and elucidation of 3D-structural aspects of these molecules remains a challenging task, since they are chemically highly functionalized and often still have considerable flexibility. In the chemical synthesis of biopolymers derived from peptides it is now possible to synthesize large linear sequences of (modified)peptides and peptide-peptidomimetic hybrids using stepwise synthesis, fragment coupling and ligation methods. In this way defined molecules of intermediate size containing many functional groups can be constructed. We now wish to use clever molecular approaches to control the shape and folding as well as the orientation of relative flexible parts of molecules of "intermediate" size in such a way that they will the mimic the essential structural features and properties of much larger molecules effectively using selectively addressable synthetic scaffolds in order to obtain functional protein mimics. In this "Scaffold induced Shape Control" (SSC) approach we will use the TriAzaCyclophane (TAC) and CycloTriVeratrylene (CTV) synthetic scaffolds. In the recent past we have successfully used the CTV-scaffold for the preparation of mimics of collagen having a triple helix. Here, the scaffolds will be especially used for proper positioning and alignment of functional peptide sequences of proteins ("epitopes") in order to effectively mimic the structure and function of these peptide sequences derived from the parent protein. Separated segments of the polypeptide chain of a protein representing a so-called discontinuous epitope may be mimicked by SSC, which so far is hardly possible. A very important direction using SSC is the mimicry of discontinuous epitopes present in proteins of disease causing organisms towards the development of synthetic vaccines. Complete proteins or the entire organism are often too pathogenic for vaccine purpose, so an adequate mimicry of discontinuous epitopes in a synthetic molecular construct is extremely attractive. We have designed and synthesized a successful TAC-scaffolded peptide vaccine that mimics the discontinuous B-cell epitopes present in the protein pertactin of the causitive organism of whooping cough and which leads to protection against this disease. Many protein-protein interactions involve the interactions of discontinuous peptide segments. A very prominent example is the interaction of HIV-gp120 with the CD4 receptor, which is one of the first steps in infection by HIV. Effective interference with this protein-protein interaction using a molecular construct based on SSC might prevent infection. Alternatively, this molecular construct can be used as a synthetic vaccine to generate protective antibodies against HIV-gp120. In our opinion the Holy Grail of mimicry of discontinuous epitopes is the effective mimicry of loops in the Complementarity-Determining Regions (CDRs) of the antigen binding sites of antibodies. This might lead to entirely "synthetic antibodies", which are even smaller than the smallest protein mimics of antibodies i.e. "nanobodies" presently available. "Small" might clearly be a advantageous property, since the molecular construct will then be less sensitive to degradation and can easier reach its site of interaction than the much larger available therapeutic antibodies. Chemical synthesis of the molecules might be easier, cheaper and lead to products without biological contaminants. An interesting target here is SSC mimicry of the CDRs of monoclonal antibody herceptin used in the treatment of breast cancer. |
