Modifications of diketopiperazines assembled by cyclodipeptide synthases with cytochrome P450 enzymes

Lauritz Harken,Shu-Ming Li

doi:10.1007/s00253-021-11178-1

Lauritz Harken, Shu-Ming Li

Open Access

https://doi.org/10.1007/s00253-021-11178-1

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Abstract

2,5-Diketopiperazines are the smallest cyclic peptides comprising two amino acids connected via two peptide bonds. They can be biosynthesized in nature by two different enzyme families, either by nonribosomal peptide synthetases or by cyclodipeptide synthases. Due to the stable scaffold of the diketopiperazine ring, they can serve as precursors for further modifications by different tailoring enzymes, such as methyltransferases, prenyltransferases, oxidoreductases like cyclodipeptide oxidases, 2-oxoglutarate-dependent monooxygenases and cytochrome P450 enzymes, leading to the formation of intriguing secondary metabolites. Among them, cyclodipeptide synthase-associated P450s attracted recently significant attention, since they are able to catalyse a broader variety of astonishing reactions than just oxidation by insertion of an oxygen. The P450-catalysed reactions include hydroxylation at a tertiary carbon, aromatisation of the diketopiperazine ring, intramolecular and intermolecular carbon-carbon and carbon-nitrogen bond formation of cyclodipeptides and nucleobase transfer reactions. Elucidation of the crystal structures of three P450s as cyclodipeptide dimerases provides a structural basis for understanding the reaction mechanism and generating new enzymes by protein engineering. This review summarises recent publications on cyclodipeptide modifications by P450s.Key Points• Intriguing reactions catalysed by cyclodipeptide synthase-associated cytochrome P450s• Homo- and heterodimerisation of diketopiperazines• Coupling of guanine and hypoxanthine with diketopiperazinesGraphical abstract

Highlights

Natural products derived from microbial, plant or animal organisms constitute the largest source for medicinal drugs, either in unmodified form or as chemically modified derivatives (Newman and Cragg 2020)
Two very similar biosynthetic gene clusters (BGCs) consisting of five genes were identified in Streptomyces monomycini NRRL B-24309 and Streptomyces varsoviensis NRRL B-3589
These genes code for four functional enzymes, i.e. cyclodipeptide synthases (CDPSs), CDO encoded by two genes, P450 and MT

Summary

Introduction

Natural products derived from microbial, plant or animal organisms constitute the largest source for medicinal drugs, either in unmodified form or as chemically modified derivatives (Newman and Cragg 2020). Mining of microbial genome sequences has strongly accelerated the elucidation process of biosynthetic pathways of known metabolites and revealed the presence of a large number of unknown biosynthetic gene clusters (BGCs). CDPs are assembled by either nonribosomal peptide synthetases (NRPSs) mostly in fungi or by cyclodipeptide synthases (CDPSs) mainly in bacteria. These two enzyme families differ in protein size and sequences and in substrates and reaction mechanisms. CDPSs consist only of 200–300 amino acids and hijack the activated aminoacyl-tRNAs from the ribosomal machinery for CDP formation (Fig. 1) (Gondry et al 2009, 2018; Moutiez et al 2017)

Modification of CDPs by tailoring enzymes

Modification by tailoring enzymes

Structural basis and reaction mechanisms

Conclusion