Polyketides, combinatorial biosynthetic

Because these genes are often arranged in clusters, this has allowed a combinatorial biosynthetic approach for the construction of diverse libraries of polyketides and nonribosomal peptides.388387 The use of E. coli as a production host whereby precursor supply and selected pathway enzymes are modified has resulted in respectable titers of targeted compounds as well as novel derivatives.388393... 

Given a wealth of natural chemical scaffolds for improved drug design, our ability to generate novel pharmaceuticals requires increased understanding of the biosynthetic processes that may lead to their discovery and production. Polyketide and nonribosomal peptide assembly offers enormous potential for development of combinatorial biosynthetic methods. The structural complexity of these natural products often prohibits practical chemical synthesis, which underscores the need for alternative means of accessing them in usable quantities. Research in this area requires in-depth knowledge of chemical,... 

Tlie development of combinatorial biosynthetic shategies, in which components of different polyketide patliways aie combined to generate new polyketides, has attracted interest as a new dmg discovery tool. Extension of previous approaches focused on combinations of different polyketide synthase components to inclusion of patliways that generate different polyketide staiter units provides an additional element of shiictural diversity. 

In this chapter, we will introduce an exciting class of natural product biosynthetic enzymes, the modular synthases, as well as their associated enzyme partners. We will discuss the use of metabolic engineering as a tool for small-molecule discovery and development, both through directed fermentation and combinatorial biosynthesis. In addition, we will review six classes of partner enzymes involved in the modification of polyketide (PK) and nonribosomal peptide (NRP) natural products. We believe that these enzymatic transformations hold great opportunities for synthetic chemists and will serve as the foundation for a new trend in both discovery and process chemistry. 

Manipulation of the biosynthetic pathways leading to natural compounds, so-called combinatorial biosynthesis, is presented in the third section, with particular attention paid to the opportunities arising from polyketide biosynthesis. Finally, combinatorial biotransformation of natural or synthetic compounds by means of isolated enzymes or whole microorganisms is presented in the fourth section. 

Polyketides (PKs) are a typical example of a large and diverse class of NPs that derive from several related biosynthetic pathways. Their stmctures contain repeating units iteratively assembled into a range of diverse chemical structures (Fig. 10.43). PKs can be taken as an example of the application of combinatorial biosynthesis as both the... 

Today, despite recent developments in combinatorial and other chemosynthetic strategies, flmgi and streptomycetes remain the most prolific sources of new candidate drugs and agrochemicals. Both phyla elaborate bicyclic, tricyclic and tetracyclic fused ring polyketides, however, a preliminary survey of isotopically labelled precursor incorporation studies has revealed a consistent difference in the modes of cyclisation by which their characteristic polybenzenoid metabolites are formed. These and subsequent observations (yide infra) provide the basis for a novel biosynthetic classification of microbial fused ring polyketides. 

In the simplest of terms, manipulation of polyketide and nonribosomal peptide components involves alteration of materials, tools, or both. From a chemical standpoint, modification of building blocks can ideally result in structures limited only by our imagination. Biologically, genetic control over biosynthetic machinery could allow, theoretically, for boundless reprogramming capabilities. Realistically, insight from both perspectives will be required as enzyme selectivity and reactivity can impede combinatorial prospects. 

Combinatorial biosynthesis is a contemporary approach with the ability not only to produce new natural product analogues but also to afford new drug candidates per se. This methodology involves the engineering of biosynthetic gene clusters in microorganisms. For example, the modification of bacterial polyketide synthases has led to production of some 200 new polyketides that do not occur naturally (43). 

Using these techniques (combinatorial biosynthesis) with streptomycetes, the polyketides have now been investigated, including not only the macrolides (e. g., erythromycin) but also polycyclic aromatic compounds (e.g., actinorhodin, tetracenomycins). The formation of hybrids can alter not only the size of the poly ketide skeleton, its stereochemistry or its functionality but also enzyme systems of the later steps of biosynthesis such as, e. g., oxygenases or glycosy Itrans-ferases. In practice major difficulties arise because each intermediate in the biosynthetic sequence is a substrate for the following enzyme thus if a changed substrate is not accepted by the respective enzyme the biosynthesis breaks down. 

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