Challenges and discoveries in the total synthesis of complex polyketide natural products

The biosynthetic logic and enzymatic machinery of approved fungi-derived pharmaceuticals and agricultural biopesticides

Covering: 2000 to 2023The kingdom Fungi has become a remarkably valuable source of structurally complex natural products (NPs) with diverse bioactivities. Since the revolutionary discovery and application of the antibiotic penicillin from Penicillium, a number of fungi-derived NPs have been developed and approved into pharmaceuticals and pesticide agents using traditional "activity-guided" approaches. Although emerging genome mining algorithms and surrogate expression hosts have brought revolutionary approaches to NP discovery, the time and costs involved in developing these into new drugs can still be prohibitively high. Therefore, it is essential to maximize the utility of existing drugs by rational design and systematic production of new chemical structures based on these drugs by synthetic biology. To this purpose, there have been great advances in characterizing the diversified biosynthetic gene clusters associated with the well-known drugs and in understanding the biosynthesis logic mechanisms and enzymatic transformation processes involved in their production. We describe advances made in the heterogeneous reconstruction of complex NP scaffolds using fungal polyketide synthases (PKSs), non-ribosomal peptide synthetases (NRPSs), PKS/NRPS hybrids, terpenoids, and indole alkaloids and also discuss mechanistic insights into metabolic engineering, pathway reprogramming, and cell factory development. Moreover, we suggest pathways for expanding access to the fungal chemical repertoire by biosynthesis of representative family members via common platform intermediates and through the rational manipulation of natural biosynthetic machineries for drug discovery.

Stereoselective Synthesis of Secondary and Tertiary Boronic Esters via Matteson Homologation

Matteson homologations of chiral boronic esters with lithium dichlorocarbenoids and various nucleophiles proved to be a useful method for the synthesis of functionalized polyketides in a highly stereoselective fashion. Via repeated homologation steps, only 1,2-anti- and 1,3-syn-configured products were obtained. Homologation with substituted carbenoids followed by reaction with carbon nucleophiles resulted in configurationally inverted products and tertiary boronic esters in a highly stereoselective fashion. This approach significantly expands the potential of the Matteson reaction.

Methanotrophs as a reservoir for bioactive secondary metabolites: Pitfalls, insights and promises

Methanotrophs are potent natural producers of several bioactive secondary metabolites (SMs) including isoprenoids, polymers, peptides, and vitamins. Cryptic biosynthetic gene clusters identified from these microbes via genome mining hinted at the vast and hidden SM biosynthetic potential of these microbes. Central carbon metabolism in methanotrophs offers rare pathway intermediate pools that could be further diversified using advanced synthetic biology tools to produce valuable SMs; for example, plant polyketides, rare carotenoids, and fatty acid-derived SMs. Recent advances in pathway reconstruction and production of isoprenoids, squalene, ectoine, polyhydroxyalkanoate copolymer, cadaverine, indigo, and shinorine serve as proof-of-concept. This review provides theoretical guidance for developing methanotrophs as microbial chassis for high-value SMs. We summarize the distinct secondary metabolic potentials of type I and type II methanotrophs, with specific attention to products relevant to biomedical applications. This review also includes native and non-native SMs from methanotrophs, their therapeutic potential, strategies to induce silent biosynthetic gene clusters, and challenges.

Thioester Capture Strategy for the Identification of Nonribosomal Peptide and Polyketide Intermediates

Nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are multi-domainal megasynthases. While they are capable of generating a structurally diverse array of metabolites of therapeutic relevance, their mere size and complex nature of their assembly (intermediates are tethered and enzyme bound) make them inherently difficult to characterize. In order to facilitate structural characterization of these metabolites, a thioester capture strategy that enables direct trapping and characterization of the thioester-bound enzyme intermediates was developed. Specifically, a synthetic Biotin-Cys agent was designed and utilized, enabling direct analysis by LCMS/MS and NMR spectroscopy. In the long term, the approach might facilitate the discovery of novel scaffolds from cryptic biosynthetic pathways, paving the way for the development of drug leads and therapeutic initiatives.

Enzyme-Catalyzed Spiroacetal Formation in Polyketide Antibiotic Biosynthesis

A key step in the biosynthesis of numerous polyketides is the stereospecific formation of a spiroacetal (spiroketal). We report here that spiroacetal formation in the biosynthesis of the macrocyclic polyketides ossamycin and oligomycin involves catalysis by a novel spiroacetal cyclase. OssO from the ossamycin biosynthetic gene cluster (BGC) is homologous to OlmO, the product of an unannotated gene from the oligomycin BGC. The deletion of olmO abolished oligomycin production and led to the isolation of oligomycin-like metabolites lacking the spiroacetal structure. Purified OlmO catalyzed complete conversion of the major metabolite into oligomycin C. Crystal structures of OssO and OlmO reveal an unusual 10-strand β-barrel. Three conserved polar residues are clustered together in the β-barrel cavity, and site-specific mutation of any of these residues either abolished or substantially diminished OlmO activity, supporting a role for general acid/general base catalysis in spiroacetal formation.

Application of Vinyl Nucleophiles in Matteson Homologations

The Matteson homologation with vinyl nucleophiles was found to be a versatile tool for the synthesis of highly substituted and functionalized allyl boronic esters. High yields and stereoselectivities are obtained with sterically demanding alkyl boronic esters and/or Grignard reagents. With the application of such vinyl Matteson homologations, the polyketide fragment of lagunamide B is synthesized.

Stereochemical Control via Chirality Pairing: Stereodivergent Syntheses of Enantioenriched Homoallylic Alcohols

We report herein the development of stereodivergent syntheses of enantioenriched homoallylic alcohols using chiral nonracemic α-CH₂ Bpin-substituted crotylboronate. Chiral phosphoric acid (S)-A-catalyzed asymmetric allyl addition with the reagent gave Z-anti-homoallylic alcohols with excellent enantioselectivities and Z-selectivities. When the enantiomeric acid catalyst (R)-A was utilized, the stereoselectivity was completely reversed and E-anti-homoallylic alcohols were obtained with high E-selectivities and excellent enantioselectivities. By pairing the chirality of the boron reagent with the catalyst, two complementary stereoisomers of chiral homoallylic alcohols can be obtained selectively from the same boron reagent. DFT computational studies were conducted to probe the origins of the observed stereoselectivity. These reactions generate highly enantioenriched homoallylic alcohol products that are valuable for rapid construction of polyketide structural frameworks.

Unusual Rearrangement-Remercuration Reactions of Allylic Silanols

We present the first examples of rearrangement reactions of allylic silanol substrates into linear ketone and 5-membered cyclic silanediol organomercurial products. Both reactions are mediated by Hg(OTf)₂ but differ in the use of base, solvent, and temperature. The substrate scope of both transformations was explored, and the product organomercurials were shown to be valuable synthons. Mechanistic studies suggest that both products are the result of a series of transformations, cascading in one pot. DFT analysis provides a basis for understanding the rearrangement of a 6-endo intermediate into the 5-exo cyclic silanediol product.

Total synthesis of apratoxin A and B using Matteson's homologation approach

Apratoxin A and B, two members of an interesting class of marine cyclodepsipeptides are synthesized in a straightforward manner via Matteson homologation. Starting from a chiral boronic ester, the polyketide fragment of the apratoxins was obtained via five successive homologation steps in an overall yield of 27% and very good diastereoselectivity. This approach is highly flexible and should allow modification also of this part of the natural products, while previous modifications have been carried out mainly in the peptide fragment.

Mild C-C Bond Formation via Lewis Acid Catalyzed Oxetane Ring Opening with Soft Carbon Nucleophiles

Mild oxetane opening by soft carbon nucleophiles has been developed for efficient C-C bond formation. In the presence of LiNTf₂ or TBSNTf₂ as catalyst, silyl ketene acetals were found to be effective nucleophiles to generate a wide range of highly oxygenated molecules, which are key substructure in natural products like polyketides. Furthermore, intramolecular oxetane opening by a styrene-based carbon nucleophile via a Prins-type process was also achieved with Sc(OTf)₃ as catalyst, leading to efficient formation of the useful 2,3-dihydrobenzo[b]oxepine skeleton.

A Straightforward Synthesis of Polyketides via Ester Dienolate Matteson Homologation

Application of ester dienolates as nucleophiles in Matteson homologations allows for the stereoselective synthesis of highly substituted α,β-unsaturated δ-hydroxy carboxyl acids, structural motifs widespread found in polyketide natural products. The protocol is rather flexible and permits the introduction of substituents and functionalities also at those positions which are not accessible by the commonly used aldol reaction. Therefore, this ester dienolate Matteson approach is an interesting alternative to the "classical" polyketide syntheses.

Development of α,α-Disubstituted Crotylboronate Reagents and Stereoselective Crotylation via Brønsted or Lewis Acid Catalysis

The development of α,α-disubstituted crotylboronate reagents is reported. Chiral Brønsted acid-catalyzed asymmetric aldehyde addition with the developed E-crotylboron reagent gave (E)-anti-1,2-oxaborinan-3-enes with excellent enantioselectivities and E-selectivities. With BF₃·OEt₂ catalysis, the stereoselectivity is reversed, and (Z)-δ-boryl-anti-homoallylic alcohols are obtained with excellent Z-selectivities from the same E-crotylboron reagent. The Z-crotylboron reagent also participates in BF₃·OEt₂-catalyzed crotylation to furnish (Z)-δ-boryl-syn-homoallylic alcohols with good Z-selectivities. DFT computations establish the origins of observed enantio- and stereoselectivities of chiral Brønsted acid-catalyzed asymmetric allylation. Stereochemical models for BF₃·OEt₂-catalyzed reactions are proposed to rationalize the Z-selective allyl additions. These reactions generate highly valuable homoallylic alcohol products with a stereodefined trisubstituted alkene unit. The synthetic utility is further demonstrated by the total syntheses of salinipyrones A and B.

Ruthenium-catalysed multicomponent synthesis of the 1,3-dienyl-6-oxy polyketide motif

Polyketide natural products are an important class of biologically active compounds. Although substantial progress has been made on the synthesis of repetitive polyketide motifs through the iterative application of a single reaction type, synthetic access to more diverse motifs that require more than one type of carbon-carbon bond connection remains a challenge. Here we describe a catalytic, multicomponent method for the synthesis of the privileged polyketide 1,3-dienyl-6-oxy motif. The method allows for the formation of two new carbon-carbon bonds and two stereodefined olefins. It generates products that contain up to three contiguous sp³ stereocentres with a high stereoselectivity in a single operation and can be used to generate chiral products. The successful development of this methodology relies on the remarkable efficiency of the ruthenium-catalysed alkene-alkyne coupling reaction between readily available vinyl boronic acids and alkynes to provide unsymmetrical 3-boryl-1,4-diene reagents. In the presence of carbonyl compounds, these reagents undergo highly diastereoselective allylations to afford the desired 1,3-dienyl-6-oxy motif and enable complex polyketide synthesis in a rapid and asymmetric fashion.

Total synthesis and biological evaluation of simplified aplyronine analogues as synthetically tractable anticancer agents

The aplyronines are a family of highly cytotoxic marine natural products with potential application in targeted cancer chemotherapy. To address the severe supply issue, function-oriented molecular editing of their macrolactone scaffold led to the design of a series of simplified aplyronine analogues. Enabled by a highly convergent aldol-based route, the total synthesis of four analogues was achieved, with a significant improvement in step economy versus previous compounds, and their cancer cell growth inhibition in the HeLa cell line was determined. The modular strategy presented offers a means for significantly shortening their chemical synthesis to facilitate the continued development of this promising class of anticancer agent.

Loss of Single-Domain Function in a Modular Assembly Line Alters the Size and Shape of a Complex Polyketide

The structural wealth of complex polyketide metabolites produced by bacteria results from intricate, highly evolved biosynthetic programs of modular assembly lines, in which the number of modules defines the size of the backbone, and the domain composition controls the degree of functionalization. We report a remarkable case where polyketide chain length and scaffold depend on the function of a single β-keto processing domain: A ketoreductase domain represents a switch between diverging biosynthetic pathways leading either to the antifungal aureothin or to the nematicidal luteoreticulin. By a combination of heterologous expression, mutagenesis, metabolite analyses, and in vitro biotransformation we elucidate the factors governing non-colinear polyketide assembly involving module skipping and demonstrate that a simple point mutation in type I polyketide synthase (PKS) can have a dramatic effect on the metabolic profile. This finding sheds new light on possible evolutionary scenarios and may inspire future synthetic biology approaches.

Diversification of polyketide structures via synthase engineering

Polyketide natural products possess diverse biological activities including antibiotic, anticancer, and immunosuppressive. Their equally varied and complex structures arise from head-to-tail condensation of simple carboxyacyl monomers. Since the seminal discovery that biosynthesis of polyketides such as the macrolide erythromycin is catalyzed by uncharacteristically large, multifunctional enzymes, termed modular type I polyketide synthases, chemists and biologists alike have been inspired to harness the apparent modularity of the synthases to further diversify polyketide structures. Yet, initial attempts to perform "combinatorial biosynthesis" failed due to challenges associated with maintaining the structural and catalytic integrity of large, chimeric synthases. Fast forward nearly 30 years, and advancements in our understanding of polyketide synthase structure and function have allowed the field to make significant progress toward effecting desired modifications to polyketide scaffolds in addition to engineering small, chiral fragments. This review highlights selected examples of polyketide diversification via control of monomer selection, oxidation state, stereochemistry, and cyclization. We conclude with a perspective on the present and future of polyketide structure diversification and hope that the examples presented here will encourage medicinal chemists to embrace polyketide synthetic biology as a means to revitalize polyketide drug discovery.

Total Synthesis, Stereochemical Revision, and Biological Assessment of Iriomoteolide-2a

Iriomoteolide-2a is a marine macrolide metabolite isolated from a cultured broth of the benthic dinoflagellate Amphidinium sp. HYA024 strain. This naturally occurring substance was reported to show remarkable cytotoxic activity against human cancer cell lines HeLa and DG-75 and in vivo antitumor activity against murine leukemia P388 cell line. Herein, the total synthesis, stereochemical revision, and biological assessment of iriomoteolide-2a are reported in detail. Total synthesis of the proposed structure 1 of iriomoteolide-2a featured a late-stage convergent assembly of three components by a Suzuki-Miyaura coupling, an esterification, and a ring-closing metathesis. However, the NMR data of synthetic 1 were not identical to those of the natural product. Careful analysis of the NMR data of the authentic material and synthesis/NMR analysis of appropriately designed model compounds led to consideration of four possible stereoisomers 2-5 as candidates for the correct structure. Accordingly, total syntheses of 2-5 were achieved by taking advantage of the convergent strategy, and comparison of the NMR spectra of synthetic 2-5 with those of the natural product led to the conclusion that 5 shows the correct relative configuration of iriomoteolide-2a. The absolute configuration of this natural product was finally established through chiral HPLC analysis of synthetic 5/ent-5 with the authentic sample. The antiproliferative activity of the synthetic compounds was assessed against HeLa and A549 cells to show that, in contrast to expectation, synthetic 5 and ent-5 were only marginally active in these cell lines. This work clearly underscores the vital role of total synthesis in the establishment of the structure and biological activity of natural products.

Toward the total synthesis of patellazole B: synthesis of an advanced C1-C25 fragment corresponding to the macrocyclic skeleton

The patellazoles are a family of complex marine macrolides that exhibit potent cytotoxicity against cancer cell lines. However, despite extensive characterisation efforts, their full stereochemical assignment has remained elusive. We report our approach towards the synthesis-enabled structural elucidation of patellazole B (4), a 24-membered macrolide with 16 stereocentres and a signature thiazole-containing side chain. Our plan hinges upon isolating the unknown stereocentres into a single C20-C25 fragment to facilitate the flexible assembly of various possible diastereomers of an advanced C1-C25 fragment. Towards this end, a highly convergent and modular synthesis of one candidate diastereomer 37, corresponding to the patellazole B macrocyclic skeleton, has been achieved based on the strategic application of stereocontrolled aldol methodology, combined with Suzuki and Heck cross-coupling reactions.

A counterintuitive stereochemical outcome from a chelation-controlled vinylmetal aldehyde addition leads to the configurational reassignment of phormidolide A

Detailed NMR spectroscopic comparisons of a series of synthetic C10–C23 fragments with a known derivative of phormidolide A resulted in the configurational reassignment of seven of its 11 stereocentres.

Acyltransferases as Tools for Polyketide Synthase Engineering

Polyketides belong to the most valuable natural products, including diverse bioactive compounds, such as antibiotics, anticancer drugs, antifungal agents, immunosuppressants and others. Their structures are assembled by polyketide synthases (PKSs). Modular PKSs are composed of modules, which involve sets of domains catalysing the stepwise polyketide biosynthesis. The acyltransferase (AT) domains and their “partners”, the acyl carrier proteins (ACPs), thereby play an essential role. The AT loads the building blocks onto the “substrate acceptor”, the ACP. Thus, the AT dictates which building blocks are incorporated into the polyketide structure. The precursor- and occasionally the ACP-specificity of the ATs differ across the polyketide pathways and therefore, the ATs contribute to the structural diversity within this group of complex natural products. Those features make the AT enzymes one of the most promising tools for manipulation of polyketide assembly lines and generation of new polyketide compounds. However, the AT-based PKS engineering is still not straightforward and thus, rational design of functional PKSs requires detailed understanding of the complex machineries. This review summarizes the attempts of PKS engineering by exploiting the AT attributes for the modification of polyketide structures. The article includes 253 references and covers the most relevant literature published until May 2018.

A synthesis-enabled relative stereochemical assignment of the C1-C28 region of hemicalide

Through synthesising both candidate diastereomers of a model C1-C28 fragment of the potent cytotoxic marine polyketide hemicalide, an assignment of the relative configuration between the C1-C15 and C16-C26 regions has been achieved. By detailed NMR comparisons with the natural product, the relative stereochemistry between these two 1,6-related stereoclusters is elucidated as 13,18-syn rather than the previously proposed 13,18-anti relationship. A flexible and modular strategy using an advanced C1-C28 ketone fragment 22 is outlined to elucidate the remaining stereochemical features and achieve a total synthesis.

Toward aplyronine payloads for antibody–drug conjugates: total synthesis of aplyronines A and D

We report an expedient total synthesis of aplyronines A and D, together with a linker-modified analogue for bioconjugation studies.