Characterization of YcaO-Dependent Natural Product Biosynthetic Pathways

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 DESCRIPTION (provided by applicant): Our group has focused on the discovery, biosynthesis, and mode of action determination for novel natural products (NPs). It is beyond contestation that NPs, and simple derivatives thereof, have been the most historically significant source of drug leads for the pharmaceutical industry. Beyond their use in medicine, NPs have inspired generations of synthetic chemists and provided the chemical tools to unravel fundamental aspects of cell biology. Understanding what moieties of a NP give rise to a specific property enables the rational enhancement of target-binding potency, pharmacokinetic parameters, spectrum of activity, among others. Traditional synthetic approaches for establishing structure-activity relationships (SAR) are often intractable for synthetically challenging NP scaffolds. In contrast, a properly engineered biosynthetic route could represent an operationally preferable method to establish SAR and accelerate the introduction of drug leads. This project is comprised of three related, yet fully independent, specific aims. Each proposed aim targets a unique, architecturally-complex NP scaffold that originates from a ribosomal precursor peptide. For each tar- get, we aim to reconstitute the biosynthetic pathway in vitro and generate analogs for SAR purposes by mutation of the precursor peptide gene. The mechanistic characterization of key biosynthetic enzymes will also be evaluated. Aim I focuses on the thiazole-rich thiopeptide antibiotics, whose members inhibit different aspects of bacterial translation. The thiazoles are formed by the action of a cyclodehydratase, of which we have considerable expertise. Thiazole-forming cyclodehydratases belong to the cryptically named "YcaO" superfamily, which we have shown to utilize ATP in the phosphorylation of amide carbonyl oxygens. This direct amide backbone activation mechanism facilitates the cyclodehydration reaction. Thiopeptides are further defined by a central pyridine or dehydropiperidine macrocycle, arising from a predicted and chemically fascinating [4+2] cycloaddition of two dehydrated Ser residues, which this project will also fully characterize. Aim II targets the in vitro biosynthesis of thioviridamide, a thioamide-containing, apoptosis-activatin NP. Aim III is dedicated to the macroamidine- and thiazole-containing bottromycins, which represent an undeveloped class of bacterial translation inhibitor. All three of these biosynthetic gene clusters encode YcaO enzymes (two for bottromycin), which we implicate in roles beyond cyclodehydration. In the case of thioviridamide, the YcaO is predicted to be involved in thioamide formation while the YcaOs in bottromycin have suspected involvement in thiazole and macroamidine formation, all via an ATP-dependent amide carbonyl activation mechanism. This project will significantly advance our general understanding of NP biosynthesis and mechanistic enzymology, while also establishing the enzymatic tolerance of three NP pathways. Imparting additional chemical diversity into known NP scaffolds by our proposed heterologous and chemoenzymatic approaches holds enormous promise for revealing new drug leads and eventually expanding our pharmaceutical armamentarium.