Bacterial Cytochrome P450-Mediated Biosynthesis of Non-Symmetrical Diketopiperazine Dimers: Discovery, Catalysis, and Structure

Abstract

The simplest cyclic peptide is composed of two amino acids and forms a 2,5- diketopiperazine (DKP). Diketopiperazine containing natural products can be found from eukaryotic, fungal, and bacterial sources and are present in a diverse array of scaffolds. DKPs are most commonly biosynthesized by non-ribosomal peptide synthetases (NRPS) modules condensing two amino acids into a DKP upon offloading by a thioesterase. Recently a new class of enzymes, cyclodipeptide synthases (CDPS) have been identified as capable of synthesizing DKPs from tRNA charged amino acid precursors. Since this discovery, there has been a dramatic rise in the identification and characterization of CDPS containing gene clusters, and some classic natural products have been ascribed to these clusters, including albonoursin and bicyclomycin. The subject of this thesis is the study of a cyclodipeptide synthase containing gene clusters which also harbor a cytochrome P450 which oxidatively dimerizes DKP monomers into topologically complex dimers with exquisite selectivity. These enzymes catalyze a C–H functionalization reaction and transform an sp2 hybridized C–H bond into a C–C or C–N bond. We discovered a series of unique cytochromes, NznB, NascB, and homologues NascB-S1868, and NascB-F5053 all of which catalyze reactions novel site- stereo- and chemoselectivity. Chapter 1 discusses the synthetic and biosynthetic literature regarding diketopiperazine dimers. In the Chapters 2 and 3, these cytochromes are characterized biochemically using native and non-native substrates in in vitro and in vivo biocatalytic reactions demonstrating their synthetic utility, and Chapter 4 interrogates the structure and mechanism of the dimerization reaction of NascB-F5053. Chapter 5 discusses the future directions and applications of these cytochromes.