Genetically Encoded Systems for the Selection of Synthetic Molecules

Selection-based approaches to molecular discovery offer much higher throughput and simpler infrastructure requirements compared with screening methods, but typically require an information-encoding molecule that can be readily amplified and decoded, such as DNA. While the in vitro or in vivo selection of proteins and nucleic acids is made possible by their genetic encoding and by biosynthetic machinery that uniquely translates DNA sequences into corresponding RNA or protein molecules, nature does not provide corresponding encoding and translation machinery for synthetic molecules.;The desire to apply selection methodology to synthetic structures led to the development of DNA-templated synthesis, a technique which enables the synthesis of DNA-encoded synthetic-polymer and small-molecule libraries that can be subjected to in vitro selection for binding or bond formation with a target of interest.;In Chapter Two of this thesis, we expand the capabilities of DNA-templated synthesis to generate diversely functionalized DNA-encoded synthetic polymers. These results lay the groundwork for the in vitro selection of side-chain-functionalized synthetic polymers with novel catalytic or binding properties.;In Chapters Three, Four and Five, we describe the in vitro selection of a DNA-templated small-molecule macrocycle library against protein targets of biomedical interest. Analysis of the selection results by high-throughput DNA sequencing led to the discovery and development of potent and selective inhibitors of Src kinase and insulin-degrading enzyme. These findings validate that DNA-templated synthesis coupled with in vitro selection and high-throughput DNA sequencing enables the efficient discovery of novel bioactive small molecules. Furthermore, the discovered enzyme inhibitors offer new and promising scaffolds to serve as biochemical probes or pharmacological inhibitors.