CF · Catalytic foldamers from dynamic combinatorial libraries using high-throughput methods

Catalytic foldamers from dynamic combinatorial libraries using high-throughput methods

The complexity, and specificity of natural enzymes is beyond what has been achieved by chemists in aqueous medium. However, one strategy is to synthesize foldamers, folded oligomers, that are stabilized through intramolecular interactions. The overall structure of foldamers resembles proteins and therefore provides an opportunity to explore the basic principles of how enzymes gain their activity and specificity. Traditionally, covalent-based foldamers require tedious synthetic efforts to fold only into a limited number of confirmations, typically secondary structures (e.g. helices). The host lab had previously discovered a new system to generate foldamers with more complex folds from simple building blocks using dynamic covalent chemistry. The system relies on the building block reacting with itself to form a library of macrocycles. Since the system is dynamic, these macrocycles can exchange and form larger or smaller sized rings. However, (in some instances) a single large macrocycle (foldamer) can emerge from the library and is stabilized by the fold that is dissimilar to any secondary folds known. Therefore, this system provides an opportunity to combine complex folding and catalysis with minimal effort and design. However, due to the “minimal design” of the fold, high-throughput screens for foldamer formation of simple building block sequences bearing catalytic motifs and catalytic activity were required to identify hit active foldamers. There were two points of importance to this project. The first comes from a fundamental perspective, as uncovering the basic principles connecting a folded molecule to its function (i.e. catalysis) from a bottom-up approach will aid in the synthesis of de novo life. Often times, a fold is carefully engineered into the molecule giving rise to predicted catalytic activity. However, through the use of dynamic combinatorial chemistry in this project, we can discover new folds and new catalytic potential. This new catalytic activity can then be integrated into a larger system that contains other characteristics of life, such as compartmentalization. This added level of complexity takes us one step closer to de novo life. The second point of importance is from a practical perspective. By discovering new folds and hence new functions through a less resource intensive method via systems chemistry, there is the possibility of discovering foldamer-based catalysts that can be used in an industrial setting. However, the development of new technologies was not a primary goal within the time frame of this project. The overall aim was to develop high-throughput screening methods to quickly identify catalytic foldamers that emerge from dynamic combinatorial libraries. To reach this goal, four objectives have been identified: 1. Synthetically integrate catalytic motifs into building block structure This action was fully completed. A full suite of building block structures bearing catalytic motifs were synthesized. 2. High-throughput assay development and initial screen of foldamer formation and catalysis This action was fully completed. The screening for foldamer formation within a DCL were conducted in 96-well plates and libraries that produced (nearly) a single species were analysed further to determine foldamer size. These libraries were screened for catalytic activity with fluorescent-based assays. 3. High-throughput optimization of mixed building block catalytic foldamers This action was partially completed. Although mixing of building block libraries were conducted in the hopes of improving catalytic activity, it was not conducted through a high-throughput manner nor did the mixed building block foldamers improve catalytic activity. 4. Characterization of catalytic foldamers by NMR spectroscopy and X-ray crystal structures This action was partially completed. Hit foldamers from action 2 were characterized by NMR spectroscopy but X-ray crystal structures were only partially obtained (with low resolution).

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