Chemical Platforms for Non-Extant Ribosomal Chemistry: Synthetic Efforts Towards Ribosome-Assisted Polyketide-Polypeptide Products
Date of Award
Fall 2023
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Chemistry
First Advisor
Miller, Scott
Abstract
Polyketide-polypeptide hybrids are an interesting class of natural products, which share features from two tremendously pharmaceutically relevant classes: polyketides (i.e., erythromycin, geldanamycin) and polypeptides (i.e., penicillin, vancomycin). In nature, these products are generally synthesized from methods involving non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) working in concert. Further, these products are often co- and/or post-synthetically modified in a controlled fashion by additional enzymes to add further complexity. Recapitulating this process biochemically is difficult and accessing these molecules using total synthesis methods is tedious at best. In this work, an alternative synthetic approach is explored to access these structures by reimagining the ribosome as a templated polymerization machine.The ribosome is a molecular machine that synthesizes proteins from amino acids in a sequence-specific fashion. It has been said that this process, translation, is perhaps the greatest example of controlled polymer synthesis known to scientists to date. To create its complex polymers, the ribosome facilitates amide bond formation. There are no reports of the ribosome facilitating any other bond forming reaction in nature. Herein, we explore the synthesis of novel amino acid-like ribosomal inputs, which could introduce novel chemical reactivity to the ribosome. We report that an α-thio acid bearing a malonyl-containing side chain can be synthesized. This novel ribosomal input can be used to perform an intramolecular decarboxylative Claisen, reminiscent of PKSs, to form a polyketide backbone in a peptide model system in biomimetic conditions. Further, we report that derivatives of an α-thio acid and an α-hydroxy acid containing a β-amine side chain, can be synthesized and loaded onto tRNA using Flexizyme- mediated conditions. In silico analysis of this system reveals that in-ribosome native chemical ligation is possible from these ribosomal inputs to generate polypeptides with β-backbones. These advances demonstrate that synthetic intervention of ribosomal inputs can lead to diverse products in a “bottom-up” fashion. Further, in nature, polyketides and polypeptides undergo post-translational (or synthetic) modification (PTM) and transformations which generate aromatic rings are common. We report that an amino acid with a malonyl residue can be loaded onto tRNA and successfully translated and extended by wild type ribosomes to form a β-keto amide on the N-terminus of the polypeptide chain. We then demonstrated that this diketide can be transformed to quinoline products using a Friedländer reaction and studied the intrinsic atroposelectivity of this transformation in congested peptide environments. Additionally, as glycosylation is the most common protein PTM, we report the chemoselective S-GlcNAcylation of cysteine using glycosyl fluorides in aqueous conditions. These advances showcase our ability to modify peptide products in a “top- down” fashion. Combined with our “bottom-up” approaches, a platform is envisioned to synthesize increasingly diverse polyketide-polypeptide hybrid products.
Recommended Citation
Dilworth, Diondra, "Chemical Platforms for Non-Extant Ribosomal Chemistry: Synthetic Efforts Towards Ribosome-Assisted Polyketide-Polypeptide Products" (2023). Yale Graduate School of Arts and Sciences Dissertations. 1198.
https://elischolar.library.yale.edu/gsas_dissertations/1198
