A 1,6-ring closure mechanism for (+)-δ-cadinene synthase?

Discovery of a terpene synthase synthesizing a nearly non-flexible eunicellane reveals the basis of flexibility

Eunicellane diterpenoids, containing a typical 6,10-bicycle, are bioactive compounds widely present in marine corals, but rarely found in bacteria and plants. The intrinsic macrocycle exhibits innate structural flexibility resulting in dynamic conformational changes. However, the mechanisms controlling flexibility remain unknown. The discovery of a terpene synthase, MicA, that is responsible for the biosynthesis of a nearly non-flexible eunicellane skeleton, enable us to propose a feasible theory about the flexibility in eunicellane structures. Parallel studies of all eunicellane synthases in nature discovered to date, including 2Z-geranylgeranyl diphosphate incubations and density functional theory-based Boltzmann population computations, reveale that a trans-fused bicycle with a 2Z-configuration alkene restricts conformational flexibility resulting in a nearly non-flexible eunicellane skeleton. The catalytic route and the enzymatic mechanism of MicA are also elucidated by labeling experiments, density functional theory calculations, structural analysis of the artificial intelligence-based MicA model, and mutational studies.

Understanding mechanisms of terpene synthases using substrate analogs

Terpene synthases (TS) transform achiral prenyl substrates into elaborate hydrocarbon scaffolds with multiple stereocenters through a series of cyclization reactions and carbon skeleton rearrangements. The reactions involve high-energy carbocation intermediates that must be stabilized by the enzyme along the pathway to the desired products. A variety of substrate analogs have been used to investigate TS mechanism. This article will focus on a class of analogs which strategically replace hydrogen atoms with fluorine to inhibit the generation of specific carbocation intermediates. We will explore the synthesis and use of the analogs to study TS mechanism.

Production of non-natural terpenoids through chemoenzymatic synthesis using substrate analogs

Chemoenzymatic synthesis of non-natural terpenes using the promiscuous activity of terpene synthases allows for the expansion of the chemical space of terpenoids with potentially new bioactivities. In this report, we describe protocols for the preparation of a novel aphid attractant, (S)-14,15-dimethylgermacrene D, by exploiting the promiscuity of (S)-germacrene D synthase from Solidago canadensis and using an engineered biocatalytic route to convert prenols to terpenoids. The method uses a combination of five enzymes to carry out the preparation of terpenoid semiochemicals in two steps: (1) diphosphorylation of five or six carbon precursors (prenol, isoprenol and methyl-isoprenol) catalyzed by Plasmodium falciparum choline kinase and Methanocaldococcus jannaschii isopentenyl phosphate kinase to form DMADP, IDP and methyl-IDP, and (2) chain elongation and cyclization catalyzed by Geobacillus stearothermophilus (2E,6E)-farnesyl diphosphate synthase and S. canadensis (S)-germacrene D synthase to produce (S)-germacrene D and (S)-14,15-dimethylgermacrene D. Using this method, new non-natural terpenoids are readily accessible and the approach can be adopted to produce different terpene analogs and terpenoid derivatives with potential novel applications.

Expanding the terpene biosynthetic code with non-canonical 16 carbon atom building blocks

Humankind relies on specialized metabolites for medicines, flavors, fragrances, and numerous other valuable biomaterials. However, the chemical space occupied by specialized metabolites, and, thus, their application potential, is limited because their biosynthesis is based on only a handful of building blocks. Engineering organisms to synthesize alternative building blocks will bypass this limitation and enable the sustainable production of molecules with non-canonical chemical structures, expanding the possible applications. Herein, we focus on isoprenoids and combine synthetic biology with protein engineering to construct yeast cells that synthesize 10 non-canonical isoprenoid building blocks with 16 carbon atoms. We identify suitable terpene synthases to convert these building blocks into C₁₆ scaffolds and a cytochrome P450 to decorate the terpene scaffolds and produce different oxygenated compounds. Thus, we reconstruct the modular structure of terpene biosynthesis on 16-carbon backbones, synthesizing 28 different non-canonical terpenes, some of which have interesting odorant properties.

Cloning and functional characterization of three sesquiterpene synthase genes from Chamaecyparis formosensis Matsumura

Terpene synthase (TPS) analysis may contribute to a better understanding of terpenoids biosynthesis and the evolution of phylogenetic taxonomy. Chamaecyparis formosensis Matsumura is an endemic and valuable conifer of Taiwan. Its excellent wood quality, fragrance, and durability make it become the five precious conifers in Taiwan. In this study, three sesquiterpene synthase genes that belong to the TPS-d2 clade were isolated and characterized through in vitro reaction of recombinant protein and in vivo reaction of Escherichia coli heterologous expression system. The main product of Cf-GerA was germacrene A using GC/MS analysis, while the product of Cf-Aco and Cf-Gor were identified as acora-4(14),8-diene and (5R,6R,10S)-α-gorgonene by using NMR analysis. These are the first reported enzymes that biosynthesize acora-4(14),8-diene and (5 R,6 R,10 S)-α-gorgonene. Both sesquiterpene synthases may isomerize the farnesyl pyrophosphate substrate to nerolidyl pyrophosphate for further cyclization. Cf-Aco may catalyze 1,6-cyclization of nerolidyl cation while Cf-Gor may catalyze through an uncharged intermediate, isogermacrene A.

Skipped dienes in natural product synthesis

Covering: 2000-2020The 1,4-diene motif, also known as a skipped diene, is widespread across various classes of natural products including alkaloids, fatty acids, terpenoids, and polyketides as part of either the finalized structure or a biosynthetic intermediate. The prevalence of this nonconjugated diene system in nature has resulted in numerous encounters in the total synthesis literature. However, skipped dienes have not been extensively reviewed, which could be attributed to overshadowing by the more recognized 1,3-diene system. In this review, we aim to highlight the relevance of skipped dienes in natural products through the lens of total synthesis. Subjects that will be covered include nomenclature, structural properties, prevalence in natural products, synthetic strategies and the future direction of the field.

Ten undescribed cadinane-type sesquiterpenoids from Eupatorium chinense

Ten undescribed cadinane-type sesquiterpenes (1-10) were isolated from the whole plant of Eupatorium chinense. Their planar structures were mainly elucidated by extensive analysis of spectroscopic data and DFT NMR calculations. The absolute configurations of 1, 2, and 3 were determined by TDDFT ECD calculations while those of compounds 4-7 and 9 were confirmed by single crystal X-ray diffraction experiments. Compounds 2 and 3 are a pair of C-10 epimers, compounds 4 and 5 a pair of C-1 epimers, and compounds 9 and 10 a pair of compounds isomerized at both C-1 and C-10. A possible biosynthetic pathway for these new sesquiterpenes was proposed.

Taxonomic Insights and Its Type Cyclization Correlation of Volatile Sesquiterpenes in Vitex Species and Potential Source Insecticidal Compounds: A Review

Sesquiterpenes (SS) are secondary metabolites formed by the bonding of 3 isoprene (C5) units. They play an important role in the defense and signaling of plants to adapt to the environment, face stress, and communicate with the outside world, and their evolutionary history is closely related to their physiological functions. This review considers their presence and extensively summarizes the 156 sesquiterpenes identified in Vitextaxa, emphasizing those with higher concentrations and frequency among species and correlating with the insecticidal activities and defensive responses reported in the literature. In addition, we classify the SS based on their chemical structures and addresses cyclization in biosynthetic origin. Most relevant sesquiterpenes of the Vitex genus are derived from the germacredienyl cation mainly via bicyclogermacrene and germacrene C, giving rise to aromadrendanes, a skeleton with the highest number of representative compounds in this genus, and 6,9-guaiadiene, respectively, indicating the production of 1.10-cyclizing sesquiterpene synthases. These enzymes can play an important role in the chemosystematics of the genus from their corresponding routes and cyclizations, constituting a new approach to chemotaxonomy. In conclusion, this review is a compilation of detailed information on the profile of sesquiterpene in the Vitex genus and, thus, points to new unexplored horizons for future research.

Predicting enzymatic reactions with a molecular transformer

The use of enzymes for organic synthesis allows for simplified, more economical and selective synthetic routes not accessible to conventional reagents. However, predicting whether a particular molecule might undergo a specific enzyme transformation is very difficult. Here we used multi-task transfer learning to train the molecular transformer, a sequence-to-sequence machine learning model, with one million reactions from the US Patent Office (USPTO) database combined with 32 181 enzymatic transformations annotated with a text description of the enzyme. The resulting enzymatic transformer model predicts the structure and stereochemistry of enzyme-catalyzed reaction products with remarkable accuracy. One of the key novelties is that we combined the reaction SMILES language of only 405 atomic tokens with thousands of human language tokens describing the enzymes, such that our enzymatic transformer not only learned to interpret SMILES, but also the natural language as used by human experts to describe enzymes and their mutations.

Flow Biocatalysis: A Challenging Alternative for the Synthesis of APIs and Natural Compounds

Biocatalysts represent an efficient, highly selective and greener alternative to metal catalysts in both industry and academia. In the last two decades, the interest in biocatalytic transformations has increased due to an urgent need for more sustainable industrial processes that comply with the principles of green chemistry. Thanks to the recent advances in biotechnologies, protein engineering and the Nobel prize awarded concept of direct enzymatic evolution, the synthetic enzymatic toolbox has expanded significantly. In particular, the implementation of biocatalysts in continuous flow systems has attracted much attention, especially from industry. The advantages of flow chemistry enable biosynthesis to overcome well-known limitations of “classic” enzymatic catalysis, such as time-consuming work-ups and enzyme inhibition, as well as difficult scale-up and process intensifications. Moreover, continuous flow biocatalysis provides access to practical, economical and more sustainable synthetic pathways, an important aspect for the future of pharmaceutical companies if they want to compete in the market while complying with European Medicines Agency (EMA), Food and Drug Administration (FDA) and green chemistry requirements. This review focuses on the most recent advances in the use of flow biocatalysis for the synthesis of active pharmaceutical ingredients (APIs), pharmaceuticals and natural products, and the advantages and limitations are discussed.

Synthetic biology, combinatorial biosynthesis, and chemo‑enzymatic synthesis of isoprenoids

Isoprenoids are a large class of natural products with myriad applications as bioactive and commercial compounds. Their diverse structures are derived from the biosynthetic assembly and tailoring of their scaffolds, ultimately constructed from two C5 hemiterpene building blocks. The modular logic of these platforms can be harnessed to improve titers of valuable isoprenoids in diverse hosts and to produce new-to-nature compounds. Often, this process is facilitated by the substrate or product promiscuity of the component enzymes, which can be leveraged to produce novel isoprenoids. To complement rational enhancements and even re-programming of isoprenoid biosynthesis, high-throughput approaches that rely on searching through large enzymatic libraries are being developed. This review summarizes recent advances and strategies related to isoprenoid synthetic biology, combinatorial biosynthesis, and chemo-enzymatic synthesis, focusing on the past 5 years. Emerging applications of cell-free biosynthesis and high-throughput tools are included that culminate in a discussion of the future outlook and perspective of isoprenoid biosynthetic engineering.

Methyl-Shifted Farnesyldiphosphate Derivatives Are Substrates for Sesquiterpene Cyclases

New sesquiterpene backbones are accessible after biotransformation of presilphiperfolan-8β-ol synthase (BcBOT2), a fungal sesquiterpene synthase, with non-natural farnesyldiphosphates in which methyl groups are shifted by one position toward the diphosphate terminus. One of the macrocycles formed, a new germacrene A derivative, undergoes a Cope rearrangement to iso-β-elemene. Three of the new terpenoids show olfactoric properties that range from an intense peppery note to a citrus, ozone-like, and fruity scent.

Nerylneryl diphosphate is the precursor of serrulatane, viscidane and cembrane-type diterpenoids in Eremophila species

BACKGROUND

Eremophila R.Br. (Scrophulariaceae) is a diverse genus of plants with species distributed across semi-arid and arid Australia. It is an ecologically important genus that also holds cultural significance for many Indigenous Australians who traditionally use several species as sources of medicines. Structurally unusual diterpenoids, particularly serrulatane and viscidane-types, feature prominently in the chemical profile of many species and recent studies indicate that these compounds are responsible for much of the reported bioactivity. We have investigated the biosynthesis of diterpenoids in three species: Eremophila lucida, Eremophila drummondii and Eremophila denticulata subsp. trisulcata.

RESULTS

In all studied species diterpenoids were localised to the leaf surface and associated with the occurrence of glandular trichomes. Trichome-enriched transcriptome databases were generated and mined for candidate terpene synthases (TPS). Four TPSs with diterpene biosynthesis activity were identified: ElTPS31 and ElTPS3 from E. lucida were found to produce (3Z,7Z,11Z)-cembratrien-15-ol and 5-hydroxyviscidane, respectively, and EdTPS22 and EdtTPS4, from E. drummondii and E. denticulata subsp. trisulcata, respectively, were found to produce 8,9-dihydroserrulat-14-ene which readily aromatized to serrulat-14-ene. In all cases, the identified TPSs used the cisoid substrate, nerylneryl diphosphate (NNPP), to form the observed products. Subsequently, cis-prenyl transferases (CPTs) capable of making NNPP were identified in each species.

CONCLUSIONS

We have elucidated two biosynthetic steps towards three of the major diterpene backbones found in this genus. Serrulatane and viscidane-type diterpenoids are promising candidates for new drug leads. The identification of an enzymatic route to their synthesis opens up the possibility of biotechnological production, making accessible a ready source of scaffolds for further modification and bioactivity testing.

Nature-driven approaches to non-natural terpene analogues

The reactions catalysed by terpene synthases belong to the most complex and fascinating cascade-type transformations in Nature.

1 H-NMR and GC for detection of adulteration in commercial essential oils of Cymbopogon ssp

INTRODUCTION

Essential oils of Cymbopogon nardus and C. winterianus have fungicidal, bactericidal, and insect repellent activities. In addition, they are components of fragrances, cosmetics, and household products. The growing demand for essential oils has intensified adulteration practices of such products.

OBJECTIVES

To evaluate the authenticity and quality of citronella commercial essential oils based on chemical composition [by gas chromatography mass spectrometry (GC-MS)] and the contents of its major constituents [by ¹ H-NMR, and gas chromatography with a flame ionisation detector using internal standardisation (GC-IS)].

MATERIALS AND METHODS

The chemical composition of essential oil was determined by GC-MS. Major components were quantified by ¹ H-NMR and the results compared to those obtained by GC-IS.

RESULTS

The adulteration of oils was verified by GC and ¹ H-NMR. In the pure oils, the results obtained by ¹ H-NMR were similar to those obtained by GC-IS for most of the oils. However, in adulterated oils, signal overlap prevented the quantification of citronellol and geraniol by NMR. Importantly, due to dilution with dipropylene glycol it was not possible to quantify citronellal using ¹ H-NMR. However, for both pure and adulterated oils, GC-IS method proved successful in quantifying notable constituents.

CONCLUSION

All the methods used proved efficient in detecting adulteration. However, whilst GC-IS provided quantification of constituents of interest, both in pure and adulterated oils, their quantification by NMR was only possible in non-adulterated samples. None of the oils evaluated presented a composition within the threshold established by British Pharmacopoeia quality standards.

Harnessing enzyme plasticity for the synthesis of oxygenated sesquiterpenoids

8-Methoxy-γ-humulene, (E)-8-methoxy-β-farnesene, 12-methoxy-β-sesquiphellandrene and 12-methoxyzingiberene can be synthesised in amorphadiene synthase-catalysed reactions from 8- and 12-methoxyfarnesyl diphosphates due to the highly plastic yet tightly controlled carbocationic chemistry of this sesquiterpene cyclase.

Pushing the limits of concertedness. A waltz of wandering carbocations

Among the array of complex terpene-forming carbocation cyclization/rearrangement reactions, the so-called "triple shift" reactions are among the most unexpected. Such reactions involve the asynchronous combination of three 1,n-shifts into a concerted process, e.g., a 1,2-alkyl shift followed by a 1,3-hydride shift followed by a second 1,2-alkyl shift. This type of reaction so far has been proposed to occur during the biosynthesis of diterpenes and the sidechains of sterols. Here we describe efforts to push the limits of concertedness in this type of carbocation reaction by designing, and characterizing with quantum chemical computations, systems that could couple additional 1,n-shift events to a triple shift leading, in principle to quadruple, pentuple, etc. shifts. While our designs did not lead to clear-cut examples of quadruple, etc. shifts, they did lead to reactions with surprisingly flat energy surfaces where more than five chemical events connect reactants and plausible products. Ab initio molecular dynamics simulations demonstrate that the formal minima on these surfaces interchange on short timescales, both with each other and with additional unexpected structures, allowing us a glimpse into a very complex manifold that allows ready access to great structural diversity.

Silent catalytic promiscuity in the high-fidelity terpene cyclase δ-cadinene synthase

Aza-analogues of carbocations inhibit δ-cadinene synthase: 1,6-cyclisation.

δ-Cadinene synthase (DCS) is a high-fidelity sesquiterpene synthase that generates δ-cadinene as the sole detectable organic product from its natural substrate (E,E)-FDP. Previous work with this enzyme using substrate analogues revealed the ability of DCS to catalyse both 1,10- and 1,6-cyclisations of substrate analogues. To test whether this apparent promiscuity was an artefact of alternate substrate use or an inherent property of the enzyme, aza analogues of the proposed α-bisabolyl cation intermediate were prepared since this cation would be formed after an initial 1,6-cyclisation of FDP. In the presence of 250 μM inorganic disphosphate both (R)- and (S)-aza-bisaboyl cations were potent competitive inhibitors of DCS (K_i = 2.5 ± 0.5 mM and 3.44 ± 1.43 μM, respectively). These compounds were also shown to be potent inhibitors of the 1,6-cyclase amorpha-4,11-diene synthase but not of the 1,10-cyclase aristolochene synthase from Penicillium roquefortii, demonstrating that the 1,6-cyclase activity of DCS is most likely an inherent property of the enzyme even when the natural substrate is used and not an artefact of the use of substrate analogues.

Retracted Article: Synthesis of deuterated isopentyl pyrophosphates for chemo-enzymatic labelling methods: GC-EI-MS based 1,2-hydride shift in epicedrol biosynthesis

A sesquiterpene epicedrol cyclase mechanism was elucidated based on the gas chromatography coupled to electron impact mass spectrometry fragmentation data of deuterated (²H) epicedrol analogues. The chemo-enzymatic method was applied for the specific synthesis of 8-position labelled farnesyl pyrophosphate and epicedrol. EI-MS fragmentation ions compared with non-labelled and isotopic mass shift fragments suggest that the ²H of C6 migrates to the C7 position during the cyclization mechanism.

The cyclisation mechanism of epicedrol cyclase elucidated based on GC-EI-MS fragmentation of specific deuterated (²H) epicedrol analogues. The chemo-enzymatic method was applied for the synthesis 8-position-²H-farnesyl pyrophosphate synthesis.

Identification of sesquiterpene synthases from the Basidiomycota Coniophora puteana for the efficient and highly selective β-copaene and cubebol production in E. coli

Background

Terpenes are an important and extremely versatile class of secondary metabolites that are commercially used in the pharmaceutical, food and cosmetics sectors. Genome mining of different fungal collections has revealed the genetic basis for a steadily increasing number of putative terpene synthases without any detailed knowledge about their biochemical properties. The analysis and research of this rich genetic source provides a precious basis for the advancing biotechnological production of an almost endless number of valuable natural metabolites.

Results

Three annotated terpene synthases from the little investigated Basidiomycota Coniophora puteana were studied in this work. For biochemical characterization, the heterologous expression in E. coli was conducted leading to the identification of two sesquiterpene synthases capable of the highly selective generation of β-copaene and cubebol. These compounds are commercially used as food and flavor additives. The new enzymes show the highest reported product selectivity for their main compounds and therefore represent the first exclusive synthases for β-copaene (62% product selectivity) and cubebol (75% product selectivity) generation. In combination with an optimized heterologous microbial production system, we obtained product titers of 215 mg/L β-copaene and 497 mg/L cubebol.

Conclusion

The reported product selectivity and our generated terpene titers exceed all published biotechnological data regarding the production of β-copaene and cubebol. This represents a promising and economic alternative to extraction from natural plant sources and the associated complex product purification.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-1010-z) contains supplementary material, which is available to authorized users.

Sesquiterpene Synthase-Catalysed Formation of a New Medium-Sized Cyclic Terpenoid Ether from Farnesyl Diphosphate Analogues

Terpene synthases catalyse the first step in the conversion of prenyl diphosphates to terpenoids. They act as templates for their substrates to generate a reactive conformation, from which a Mg2+ -dependent reaction creates a carbocation-PPi ion pair that undergoes a series of rearrangements and (de)protonations to give the final terpene product. This tight conformational control was exploited for the (R)-germacrene A synthase- and germacradien-4-ol synthase-catalysed formation of a medium-sized cyclic terpenoid ether from substrates containing nucleophilic functional groups. Farnesyl diphosphate analogues with a 10,11-epoxide or an allylic alcohol were efficiently converted to a 11-membered cyclic terpenoid ether that was characterised by HRMS and NMR spectroscopic analyses. Further experiments showed that other sesquiterpene synthases, including aristolochene synthase, δ-cadinene synthase and amorphadiene synthase, yielded this novel terpenoid from the same substrate analogues. This work illustrates the potential of terpene synthases for the efficient generation of structurally and functionally novel medium-sized terpene ethers.

Identification, Functional Characterization, and Seasonal Expression Patterns of Five Sesquiterpene Synthases in Liquidambar formosana

Terpenoids are a large group of important secondary metabolites that are involved in a variety of physiological mechanisms, and many are used commercially in the cosmetics and pharmaceutical industries. During the past decade, the topic of seasonal variation in terpenoid biosynthesis has garnered increasing attention. Formosan sweet gum ( Liquidambar formosana Hance) is a deciduous tree species. The expression of terpene synthase and accumulation of terpenoids in leaves may vary in different seasons. Here, four sesquiterpene synthases (i.e., LfTPS01, LfTPS02, LfTPS03, and LfTPS04) and a bifunctional mono/sesquiterpene synthase ( LfTPS05) were identified from Formosan sweet gum. The gene expression of LfTPS01, LfTPS02, and LfTPS03 showed seasonal diversification, and, in addition, expression of LfTPS04 and LfTPS05 was induced by methyl jasmonate treatment. The major products LfTPS01, LfTPS02, LfTPS04, and LfTPS05 are hedycaryol, α-selinene, trans-β-caryophyllene, α-copaene/δ-cadinene, and nerolidol/linalool, respectively. The data indicated that the sesquiterpenoid content in the essential oil of Formosan sweet gum leaves shows seasonal differences that were correlated to the sesquiterpene synthase gene expression.

Concise synthesis of artemisinin from a farnesyl diphosphate analogue

Artemisinin is one of the most potent anti-malaria drugs and many often-lengthy routes have been developed for its synthesis. Amorphadiene synthase, a key enzyme in the biosynthetic pathway of artemisinin, is able to convert an oxygenated farnesyl diphosphate analogue directly to dihydroartemisinic aldehyde, which can be converted to artemisinin in only four chemical steps, resulting in an efficient synthetic route to the anti-malaria drug.

Nucleophilic Water Capture or Proton Loss: Single Amino Acid Switch Converts δ-Cadinene Synthase into Germacradien-4-ol Synthase

δ-Cadinene synthase is a sesquiterpene cyclase that utilises the universal achiral precursor farnesyl diphosphate (FDP) to generate predominantly the bicyclic sesquiterpene δ-cadinene and about 2 % germacradien-4-ol, which is also generated from FDP by the cyclase germacradien-4-ol synthase. Herein, the mechanism by which sesquiterpene synthases discriminate between deprotonation and reaction with a nucleophilic water molecule was investigated by site-directed mutagenesis of δ-cadinene synthase. If W279 in δ-cadinene synthase was replaced with various smaller amino acids, the ratio of alcohol versus hydrocarbon product was directly proportional to the van der Waals volume of the amino acid side chain. DCS-W279A is a catalytically highly efficient germacradien-4-ol synthase (kcat /KM =1.4×10-3  μm s-1 ) that produces predominantly germacradien-4-ol in addition to 11 % δ-cadinene. Water capture is not achieved through strategic positioning of a water molecule in the active site, but through a coordinated series of loop movements that allow bulk water access to the final carbocation in the active site prior to product release.

Structural and Chemical Biology of Terpenoid Cyclases

The year 2017 marks the twentieth anniversary of terpenoid cyclase structural biology: a trio of terpenoid cyclase structures reported together in 1997 were the first to set the foundation for understanding the enzymes largely responsible for the exquisite chemodiversity of more than 80000 terpenoid natural products. Terpenoid cyclases catalyze the most complex chemical reactions in biology, in that more than half of the substrate carbon atoms undergo changes in bonding and hybridization during a single enzyme-catalyzed cyclization reaction. The past two decades have witnessed structural, functional, and computational studies illuminating the modes of substrate activation that initiate the cyclization cascade, the management and manipulation of high-energy carbocation intermediates that propagate the cyclization cascade, and the chemical strategies that terminate the cyclization cascade. The role of the terpenoid cyclase as a template for catalysis is paramount to its function, and protein engineering can be used to reprogram the cyclization cascade to generate alternative and commercially important products. Here, I review key advances in terpenoid cyclase structural and chemical biology, focusing mainly on terpenoid cyclases and related prenyltransferases for which X-ray crystal structures have informed and advanced our understanding of enzyme structure and function.

An Efficient Chemoenzymatic Synthesis of Dihydroartemisinic Aldehyde

Artemisinin from the plant Artemisia annua is the most potent pharmaceutical for the treatment of malaria. In the plant, the sesquiterpene cyclase amorphadiene synthase, a cytochrome-dependent CYP450, and an aldehyde reductase convert farnesyl diphosphate (FDP) into dihydroartemisinic aldehyde (DHAAl), which is a key intermediate in the biosynthesis of artemisinin and a semisynthetic precursor for its chemical synthesis. Here, we report a chemoenzymatic process that is able to deliver DHAAl using only the sesquiterpene synthase from a carefully designed hydroxylated FDP derivative. This process, which reverses the natural order of cyclization of FDP and oxidation of the sesquiterpene hydrocarbon, provides a significant improvement in the synthesis of DHAAl and demonstrates the potential of substrate engineering in the terpene synthase mediated synthesis of high-value natural products.

A Chemometrics Approach to the Investigation of the Intraspecific Variability of the Volatile Oil of Eupatorium tremulum from Southern Brazil

Eupatorium tremulum is a South American shrub reported to cause cattle digestive intoxication, of which the volatile oil, mainly composed by bisabolane- and amorphane-type sesquiterpenoids, exhibits high quantitative variability. This report describes the application of chemometric tools for the identification of volatile compounds that characterize phenophasical changes in the plant. Preblooming, blooming, and postblooming specimens were paired-sampled and submitted to hydrodistillation and GC-MS analysis. Differential results were analyzed by orthogonal projection to latent structures-discriminant analysis (OPLS-DA), and the substances with different distribution in each phase were highlighted. Mean results between phases were submitted to factor analysis (FA), and correlations between the variables were demonstrated. Preblooming to blooming phase change was characterized by decreased levels of amorpha-4-en-7-ol (13) and epi-α-bisabolol (19) and increased amounts of amorpha-4,7(11)-diene (1). Blooming to postblooming change was characterized by decreases in 1, germacrene D (2), and β-bisabolene (4) and increases in 13 and 19. Finally, enhanced levels of 1, 4, and 2 reflected the change from the postblooming to the preblooming phase. FA revealed a strong correlation in the variability between the bisabolane hydrocarbons, possibly related to its common enzymatic origin. Another strong source of negative correlation showed bisabolane- and amorphane-type alcohols, on one side, and amorphane-type furans, on the other side, to occur in two alternative oxidation routes. Finally, 1 was strongly negatively correlated to its oxidized furan and ketofuran derivatives [verboccidentafuran (16) and 3-oxo-verboccidentafuran (23)] and additionally to a third compound, putatively identified as a biosynthetic intermediate between this hydrocarbon and the furans, amorpha-4,7(11)-dien-8-one (20).

Optimising Terpene Synthesis with Flow Biocatalysis

Sesquiterpenes are an important family of natural products, many of which exhibit important pharmaceutical and agricultural properties. They are biosynthesised from farnesyl diphosphate in sesquiterpene synthase catalysed reactions. Here, we report the development of a highly efficient segmented flow system for the enzyme-catalysed continuous flow production of sesquiterpenes. Design of experiment (DoE) methods were used to optimise the performance of the flow biocatalysis, and quantitative yields were achieved by using an operationally simple but highly effective segmented flow system.

Mechanism of Germacradien-4-ol Synthase-Controlled Water Capture

The sesquiterpene synthase germacradiene-4-ol synthase (GdolS) from Streptomyces citricolor is one of only a few known high-fidelity terpene synthases that convert farnesyl diphosphate (FDP) into a single hydroxylated product. Crystals of unliganded GdolS-E248A diffracted to 1.50 Å and revealed a typical class 1 sesquiterpene synthase fold with the active site in an open conformation. The metal binding motifs were identified as D(80)DQFD and N(218)DVRSFAQE. Some bound water molecules were evident in the X-ray crystal structure, but none were obviously positioned to quench a putative final carbocation intermediate. Incubations in H2(18)O generated labeled product, confirming that the alcohol functionality arises from nucleophilic capture of the final carbocation by water originating from solution. Site-directed mutagenesis of amino acid residues from both within the metal binding motifs and without identified by sequence alignment with aristolochene synthase from Aspergillus terreus generated mostly functional germacradien-4-ol synthases. Only GdolS-N218Q generated radically different products (∼50% germacrene A), but no direct evidence of the mechanism of incorporation of water into the active site was obtained. Fluorinated FDP analogues 2F-FDP and 15,15,15-F3-FDP were potent noncompetitive inhibitors of GdolS. 12,13-DiF-FDP generated 12,13-(E)-β-farnesene upon being incubated with GdolS, suggesting stepwise formation of the germacryl cation during the catalytic cycle. Incubation of GdolS with [1-(2)H2]FDP and (R)-[1-(2)H]FDP demonstrated that following germacryl cation formation a [1,3]-hydride shift generates the final carbocation prior to nucleophilic capture. The stereochemistry of this shift is not defined, and the deuteron in the final product was scrambled. Because no clear candidate residue for binding of a nucleophilic water molecule in the active site and no significant perturbation of product distribution from the replacement of active site residues were observed, the final carbocation may be captured by a water molecule from bulk solvent.

Enzymatic synthesis of natural (+)-aristolochene from a non-natural substrate

Aristolochene synthase from Penicillium roqueforti converts 7-methylene-FDP, a substrate the enzyme never encounters in nature, to the natural product (+)-aristolochene.

A method for investigating the stereochemical course of terpene cyclisations

The products of three bacterial terpene cyclases were characterised and the mechanisms of their formations were investigated using isotopic labellings.

The amino-terminal segment in the β-domain of δ-cadinene synthase is essential for catalysis

The β-domain of δ-cadinene synthase (DCS) directs desolvation of the active site.

Moonlighting Metals: Insights into Regulation of Cyclization Pathways in Fungal Δ(6) -Protoilludene Sesquiterpene Synthases

Fungal 1,11 cyclizing sesquiterpene synthases are product specific under typical reaction conditions. However, in vivo expression of certain Δ(6)-protoilludene synthases results in dual 1,11 and 1,10 cyclization. To determine the factors regulating this mechanistic variation, in-depth in vitro characterization of Δ(6)-protoilludene synthases was conducted. Divalent metal ions determine cyclization specificity and this product variability. Promiscuity in metal binding is mediated by secondary metal-binding sites away from the conserved D(D/E)XX(D/E) motif in sesquiterpene synthases. Phylogenetic analysis revealed a divergent evolution of Basidiomycota trans-humulyl cation producing sesquiterpene synthases, results that indicate a wider diversity in function than previously predicted. This study provides key insights into the function and evolution of 1,11 cyclizing fungal sesquiterpene synthases.

Draft genome of Omphalotus olearius provides a predictive framework for sesquiterpenoid natural product biosynthesis in Basidiomycota

The secondary metabolome of Basidiomycota represents a largely uncharacterized source of pharmaceutically relevant natural products. Terpenoids are the primary class of bioactive compounds isolated from mushrooms. The Jack O'Lantern mushroom Omphalotus olearius was identified 50 years ago as a prolific producer of anticancer illudin sesquiterpenoids; however, to date there have been exceptionally few studies into the biosynthesis of these important compounds. Here, we report the draft genome sequence of O. olearius, which reveals a diverse network of sesquiterpene synthases and two metabolic gene clusters associated with illudin biosynthesis. Characterization of the sesquiterpene synthases enabled a comprehensive survey of all currently available Basidiomycota genomes, thereby creating a predictive resource for terpenoid natural product biosynthesis in these organisms. Our results will facilitate discovery and biosynthetic production of unique pharmaceutically relevant bioactive compounds from Basidiomycota.

Mushroom hunting by using bioinformatics: application of a predictive framework facilitates the selective identification of sesquiterpene synthases in basidiomycota

The Basidiomycota fungi represent a diverse source of natural products, particularly the sesquiterpenoids. Recently, genome sequencing, genome mining, and the subsequent discovery of a suite of sesquiterpene synthases in Omphalotus olearius was described. A predictive framework was developed to facilitate the discovery of sesquiterpene synthases in Basidiomycota. Phylogenetic analyses indicated a conservation of both sequence and initial cyclization mechanisms used. Here, the first robust application of this predictive framework is reported. It was used to selectively identify sesquiterpene synthases that follow 1,6-, 1,10-, and 1,11-cyclization mechanisms in the crust fungus Stereum hirsutum. The successful identification and characterization of a 1,6- and a 1,10-cyclizing sesquiterpene synthase, as well as three 1,11-cyclizing Δ(6) -protoilludene synthases, is described. This study verifies the accuracy and utility of the predictive framework as a roadmap for the discovery of specific sesquiterpene synthases from Basidiomycota, and thus represents an important step forward in natural product discovery.

Efficient Terpene Synthase Catalysis by Extraction in Flow

Flowing enzymes: Continuous extraction of products enhances the enzymatic productivity of sesquiterpenes. Even unnatural substrates are tolerated leading to valuable unnatural target molecules in superior yields compared with batch protocols.

Natural sesquiterpenoids

This review covers the isolation, structural determination, synthesis and chemical and microbiological transformations of natural sesquiterpenoids. The literature from January to December 2012 is reviewed, and 471 references are cited.

Probing the mechanism of 1,4-conjugate elimination reactions catalyzed by terpene synthases

The reaction mechanisms of (E)-β-farnesene synthase (EBFS) and isoprene synthase (ISPS), enzymes that catalyze a formal regiospecific 1,4-conjugate elimination of hydrogen diphosphate from (E,E)-farnesyl and dimethylallyl diphosphate (FDP and DMADP) to generate the semiochemicals (E)-β-farnesene and isoprene, respectively, were probed with substrate analogs and kinetic measurements. The results support stepwise reaction mechanisms through analogous enzyme-bound allylic cationic intermediates. For EBFS, we demonstrate that the elimination reaction can proceed via the enzyme-bound intermediate trans-nerolidyl diphosphate, while for ISPS the intermediacy of 2-methylbut-3-enyl 2-diphosphate can be inferred from the product outcome when deuterated DMADPs are used as substrates. Possible implications derived from the mechanistic details of the EBFS-catalyzed reaction for the evolution of sesquiterpene synthases are discussed.

Chemoenzymatic synthesis of the alarm pheromone (+)-verbenone from geranyl diphosphate

The enzyme-guided asymmetric synthesis of (+)-verbenone from geranyl diphosphate in a simple two-step, one pot transformation highlights the potential of chemoenzymatic procedures for the generation of high-value terpenoids.