Polyketides and Non-ribosomal Peptides

Although many of these highly sought-after natural products are, in principle, available from sources in nature, obtaining sufficient quantities to characterise their potential therapeutic activity is often difficult [6]. Moreover, efficient chemical synthesis of these complex compounds is extremely challenging. Investigating the biosynthetic mechanisms responsible for such attractive compounds has allowed the chanistry of polyketide-producing enzymes to be harnessed for the production of novel, biochemically bioactive natural products [7, 8]. 

This thesis reports efforts to better understand the enzymology of key proteins involved in polyketide biosynthesis, and how understanding the specificity of these enzymes can assist the discovery of novel natural products. 

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Polyketide and non-ribosomal peptides produced by bacteria and fungi often attain the conformations that establish biological activity by cychzation constraints introduced by tailoring enzymes. This includes heterocychzation of cysteines, serines and threonines in non-ribosomal peptides. The second cychzation constraint is macrocychzation in polyketides, such as the above-mentioned antibiotic erythromycin and the antitumor epothilones. Regio- and stereospecific macrocychzation usuaUy occurs at the end of the polyketide and non-ribosomal peptide assembly hnes during chain release by thioesterase domains [49]. However, in the case of antibiotics of the ansamycin class, like the antitubercular drug rifamycin, the final... 

Staunton J, Wilkinson B (2001). Combinatorial biosynthesis of polyketides and non-ribosomal peptides. Curr. Opin. Chem. Biol. 5 159-164. 

Polyketide synthases, fatty acid synthases, and non-ribosomal peptide synthetases are a structurally and mechanistically related class of enzymes that catalyze the synthesis of biopolymers in the absence of a nucleic acid or other template. These enzymes utilize the common mechanistic feature of activating monomers for condensation via covalently-bound thioesters of phosphopantetheine prosthetic groups. The information for the sequence and length of the resulting polymer appears to be encoded entirely within the responsible proteins. 

Silakowski, B., Nordsiek, G., Kunze, B., Blocker, H., and MUller, R. (2001). Novel features in a combined polyketide synthase/non-ribosomal peptide synthetase The myxalamid biosynthetic gene cluster of the myxobacterium Stigmatella aurantiaca Sgal5. Chem. Biol. 8, 59-69. 

Tlie sequential reactions in elongating acyl transfers in the synthesis of polyketide natural products and non-ribosomal peptide antibiotics such as erythromycin, rapamycin, epotliilone, lovastatin, penicillins, cyclosporin and vancomycin resemble molecular solid-state assembly lines. Such multimodular enzymes may be utilized in combinatorial biosynthesis by way of reprogramming for the manufacture of unnaUiral analogs of natural products. 

Cane D E, Walsh C T (1999). The parallel and convergent universes of polyketide synthases and non-ribosomal peptide synthases. Chem. Biol. 6 R319-325. 

The marine bacterium Salinospora tropica elaborates the 205 proteasome inhibitor salinosporamide A (SalA 38), which contains an unusual and pharmacologically important chloroethyl side chain (Scheme 45.15a). The gene cluster for SalA biosynthesis was sequenced and revealed polyketide synthase-non-ribosomal peptide synthase (PKS-NEIPS)... 

For example, proteinogenic and non-proteinogerhc amino acids in l- and n-config-uration are assembled in non-ribosomal peptides. (3) Decorating enzymes can add sugar moieties to the peptide or polyketide backbone resulting in complex structures like the glycosylated antibiotic vancomycin. 

Unlike primary metabolites, the genes that regulate the formation of the enzymes of seeondary metaboUte biosynthesis are often clustered. In several eases the loei of these genes have been determined. This has considerable sig-nifieanee in the control of secondary metabolite biosynthesis. The genes that eode for several important polyketide pathways such as those leading to the aflatoxins and the statins have been identified. Similar work has also been reported for penicillin biosynthesis and some non-ribosomal peptides as well as terpenoid pathways such as that leading to the gibberellins. 

The past decade has seen an explosion in our understanding of enzyme pathways through which natural products are produced [6, 7]. For example, linear non-ribosomal peptide (NRP), polyketide (PK), and terpenoid (terpene) scaffolds are usually assembled from amino acids (isopenicillin) [8], acyl-CoAs (erythromycin) [9], and pentenyl pyrophosphates (artemisinin), respectively [10] (Scheme 8.1). These... 

The third type of modularity, the multi-catalytic enzymes using substrate channelling, are of particular interest for synthetic applications. Prominent members are the fatty acid synthases, the polyketide synthases and the non-ribosomal peptide synthases l42-44 . in these large proteins, a number of catalytic domains is combined with accessory domains and allows the catalysis of an entire pathway by a single polypeptide chain. Multi-catalytic enzymes frequently use a swinging arm , which is covalently attached to the intermediary product of one reaction step, and is subsequently able to present this molecule to the next catalytic domain for further... 

Fig. 5.2 Organization of polyketide synthases (PKSs). (A) The type I erythromycin PKS (DEBS) which catalyzes the biosynthesis of 6-dEB. The PKS consists of three polypeptides, DEBSl, DEBS2, and DEBS3, each possessing two modules. (B) The type I epothilone PKS consists of six polypeptides EpoA, EpoB [a non-ribosomal peptide synthase (NRPS)], EpoC, EpoD (possessing four modules), EpoE (possessing two modules), and EpoF. (C) The type II actinorhodin PKS con-...

An enormous range of medically important polyketide and peptide natural products assembled by modular polyketide synthases (PKSs), non-ribosomal peptide synthases (NRPSs) and mixed PKS/NRPS systems have macrocyclic structures, including the antibiotics erythromycin (PKS) and daptomycin (NRPS), the immunosuppressants cyclosporin (NRPS) and rapamycin (PKS/NRPS), and the antitumor agent epothilone (PKS/NRPS). PKSs and NRPSs are large, multifunctional proteins that are organized into sets of fnnc-tional domains termed modules. The order of modules corresponds directly to the seqnence of monomers in the product. Synthetic intermediates are covalently tethered by thioester linkages to a carrier protein domain in each module. The thiol tether on each carrier domain is phosphopantetheine, which is attached to a conserved serine residne in the carrier protein in a post-translational priming reaction catalyzed by a phosphopantetheinyltransferase. 

C.T. Walsh, R.V.O. Brien, C. Khosla, Nonproteinogenic amino acid building blocks for non-ribosomal peptide and hybrid polyketide scaffolds. Angew. Chem. Int. Ed. 52, 7098-7124 (2013)... 

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