Enzyme evolution in fungal indole alkaloid biosynthesis

Metabolome insights into nutrients and glucosinolates in broccoli and lacinato kale

To elucidate differences in nutritional components and glucosinolates between broccoli and lacinato kale leaves, and to promote consumption of broccoli and kale leaves for human nutrition, food development, and by-product utilisation, this study used UPLC-MS/MS and HPLC for both qualitative and quantitative analyses of their metabolome and glucosinolate profiles. In broccoli leaves, 11 glucosinolates were identified, notably including high concentrations of glucoraphanin, glucobrassicin, and neoglucobrassicin. In contrast, lacinato kale leaves contained seven glucosinolates, with glucoraphasatin being the most abundant. Moreover, our analysis revealed 644 metabolites, 87 of which were differentially expressed between these crucuiferous vegetables. These findings not only offer new insights into nutritional value but also highlight their potential as plant chassis for the biosynthesis of valuable products, thereby broadening food diversity and improving by-product utilisation.

Engineering a Biosynthetic Pathway to Produce (+)-Brevianamides A and B

The privileged fused-ring structure comprising the bicyclo[2.2.2]diazaoctane (BDO) core is prevalent in diketopiperazine (DKP) natural products that exhibit potent and diverse biological activities. Typically, only low yields of these compounds can be extracted from native fungal producing strains and accessing them diastereoselectively remains challenging using available synthetic routes. BDO-containing DKPs including (+)-brevianamides A 5 and B 6 are assembled via multi-enzyme biosynthetic pathways incorporating non-ribosomal peptide synthetases, prenyltransferases, flavin monooxygenases, cytochromes P450 and isomerases. To simplify access to this class of alkaloids, we designed an engineered biosynthetic pathway in Escherichia coli, composed of six enzymes sourced from different kingdoms of life. The pathway includes a cyclodipeptide synthase from Streptomyces sp. CMB-MQ030 (NascA), cyclodipeptide oxidase from Streptomyces sp. F5123 (DmtD2/DmtE2), prenyltransferase from Aspergillus sp. MF297-2 (NotF), flavin-dependent monooxygenase from Penicillium brevicompactum (BvnB), and kinases from Shigella flexneri and Thermoplasma acidophilum (PhoN and IPK). Cultivated in glycerol media supplemented with prenol, the engineered E. coli strain produces 5.3 mg/L of (-)-dehydrobrevianamide E 4, which undergoes a previously reported lithium hydroxide rearrangement cascade to yield 5 and 6, with a combined 70% yield and a 94:6 diastereomeric ratio. Additionally, titers of 4 were increased to 20.6 mg/L by enhancing NADPH pools in the engineered strain. Overall, our study combines de novo biosynthetic pathway engineering and chemical synthesis approaches to generate complex indole alkaloids.

Modeling Possible Biogenetic Pathways to the Isomeric Pyrano[2,3-g]indole and Pyrano[3,2-f]indole Cores of Certain Prenylated Indole Alkaloids Using Gold(I)-Catalyzed Intramolecular Hydroarylation Reactions

A significant subset of the so-called prenylated indole alkaloids (PIAs) contains an angularly fused pyrano[2,3-g]indole core, while a smaller number embody the isomeric and linearly fused pyrano[3,2-f]indole one. In an effort to probe the capacities of intramolecular hydroarylation (IMHA) reactions to allow for the selective formation of one or other of these motifs, a series of 6-((2-methylbut-3-yn-2-yl)oxy)-1H-indoles varying in the nature of the substituents at C1-C3 was prepared and subjected to reaction with a range of gold(I) catalysts. In every instance, preferential (but not exclusive) formation of the angularly fused pyrano[2,3-g]indole isomer was observed. This was so even as the C2 and C3 substituents increasingly resembled those associated with key members of the PIA family of natural products. These IMHA protocols have been deployed in the total syntheses of the natural products (±)-1, (±)-2, (±)-3, (±)-4, 25, and 26. The possible biosynthetic implications of these studies are discussed.

The Mutually Inspiring Biological and Chemical Synthesis of Fungal Bicyclo[2.2.2]diazaoctane Indole Alkaloids

Fungal indole alkaloids bearing a bicyclo[2.2.2]diazaoctane (BCDO) core structure are a fascinating family of natural products that exhibit a wide spectrum of biological activities. These compounds also display remarkable structural diversity, with many different diastereomers and enantiomers produced by specific fungal strains. The biogenesis of the unique BCDO moiety has long been proposed to involve an intramolecular [4+2] hetero-Diels-Alder (IMDA) reaction, but the exact mechanisms for this hypothetical transformation have remained elusive until recently. This review aims to summarize the whole history of synthetic and biosynthetic studies of fungal BCDO indole alkaloids, by covering the discovery, biomimetic syntheses, total syntheses, biosynthetic pathway elucidation, and biological activities of representative compounds. We highlight the mutual inspiration and corroboration between biological and synthetic chemists in exploring the intriguing biosynthetic mysteries of this family of natural products. We also provide perspectives and clues for the remaining biosynthetic problems.

Engineering a Biosynthetic Pathway for the Production of (+)-Brevianamides A and B in Escherichia coli

The privileged fused-ring system comprising the bicyclo[2.2.2]diazaoctane (BDO) core is prevalent in diketopiperazine (DKP) natural products with potent and diverse biological activities, with some being explored as drug candidates. Typically, only low yields of these compounds can be extracted from native fungal producing strains and the available synthetic routes remain challenging due to their structural complexity. BDO-containing DKPs including (+)-brevianamides A and B are assembled via multi-component biosynthetic pathways incorporating non-ribosomal peptide synthetases, prenyltransferases, flavin monooxygenases, cytochrome P450s and semi-pinacolases. To simplify access to this class of alkaloids, we designed an engineered biosynthetic pathway in Escherichia coli , composed of six enzymes sourced from different kingdoms of life. The pathway includes a cyclodipeptide synthase (NascA), a cyclodipeptide oxidase (DmtD2/DmtE2), a prenyltransferase (NotF), a flavin-dependent monooxygenase (BvnB), and kinases (PhoN and IPK). Cultivated in glycerol supplemented with prenol, the engineered E. coli strain produces 5.3 mg/L of (-)-dehydrobrevianamide E ( 4 ), which undergoes a terminal, ex vivo lithium hydroxide catalyzed rearrangement reaction to yield (+)-brevianamides A and B with a 46% yield and a 92:8 diastereomeric ratio. Additionally, titers of 4 were increased eight-fold by enhancing NADPH pools in the engineered E. coli strain. Our study combines synthetic biology, biocatalysis and synthetic chemistry approaches to provide a five-step engineered biosynthetic pathway for producing complex indole alkaloids in E. coli .

Abstract Figure

Biomimetic and Concise Total Syntheses of Prenylated and Bicyclo[2.2.2]diazaoctane-Containing Indole Alkaloids Including Taichunamide A, Notoamide N and Versicolamide B

Total syntheses of the title prenylated indole alkaloids together with seven others are reported. Biogenetic considerations have been employed in devising the reaction sequences leading to these targets with, in the opening stages, electrochemically-derived indole-3-carboxaldehyde 15 being subject to an aldol-type condensation reaction involving diketopiperazine derivative 19. This led, after prototopic shifts, intramolecular Diels-Alder cycloaddition and hydrolysis/deprotection steps, to the racemic forms of the bicyclo[2.2.2]diazaoctane-containing natural product stephacidin A (2) and its C6 epimer 3. Epoxidation of the last compound afforded, following rearrangement of the primary oxidation products, a mixture of (±)-taichunamide A [(±)-4] and (±)-versicolamide B [(±)-7]. Related protocols allowed for the conversion of (±)-stephacidin A [(±)-2] into (±)-notoamide B [(±)-5]. Analogous aldol condensation, nucleophilic reduction, and epoxidation steps led to the formation of (-)-notoamide E and its conversion into notoamide C as well as the indole fragmentation product amoenamide E. A late-stage chlorination reaction applied to (±)-stephacidin A provided access to the spirocyclic oxindole (±)-notoamide N [(±)-6].

Asymmetric Total Synthesis of (+)-Chuanxiongnolide L1 via a Stereoselective Oxidative Dearomatization/Diels-Alder Strategy

The first asymmetric total synthesis of chuanxiongnolide L1 was achieved in 16 steps and 1.9% overall yield by employing a bioinspired chiral auxiliary strategy. The key steps involving asymmetric oxidative dearomatization of chiral amino ether and subsequent asymmetric Diels-Alder reaction of the resulting masked chiral ortho-benzoquinone were adopted.

Aspertaichamide a, a novel cytotoxic prenylated indole alkaloid possessing a bicyclo[2.2.2]diazaoctane framework from a marine algal-derived endophytic fungus aspergillus taichungensis 299

Filamentous fungi belonging to the genus Aspergillus are prodigious producers of alkaloids, particularly prenylated indole alkaloids, that often exhibit structurally diversified skeletons and potent biological activities. In this study, five prenylated indole alkaloids possessing a bicyclo[2.2.2]diazaoctane core ring system, including a novel derivative, namely aspertaichamide A (1), as well as four known compounds, (+)-stephacidin A (2), sclerotiamide (3), (-)-versicolamide B (4), and (+)-versicolamide B (5), were isolated and identified from A. taichungensis 299, an endophytic fungus obtained from the marine red alga Gelidium amansii. The chemical structures of the compounds were elucidated by comprehensive NMR and HRESIMS spectroscopic analyses. In addition to the previously reported prenylated indole alkaloids, aspertaichamide A (1) was characterized as having an unusual ring structure with the fusion of a 3-pyrrolidone dimethylbenzopyran to the bicyclo[2.2.2]diazaoctane moiety, which was rare in these kinds of compounds. The absolute configuration of 1 was determined by TDDFT-ECD calculations. In vitro cytotoxic assays revealed that the novel compound 1 possessed selective cytotoxic activity against five human tumor cell lines (A549, HeLa, HepG2, HCT-116, and AGS), with IC50 values of 1.7-48.5 μM. Most importantly, compound 1 decreased the viability of AGS cells in a concentration-dependent manner with an IC50 value of 1.7 μM. Further studies indicated that 1 may induce AGS cells programmed cell death via the apoptotic pathway.

An NmrA-like enzyme-catalysed redox-mediated Diels-Alder cycloaddition with anti-selectivity

The Diels-Alder cycloaddition is one of the most powerful approaches in organic synthesis and is often used in the synthesis of important pharmaceuticals. Yet, strictly controlling the stereoselectivity of the Diels-Alder reactions is challenging, and great efforts are needed to construct complex molecules with desired chirality via organocatalysis or transition-metal strategies. Nature has evolved different types of enzymes to exquisitely control cyclization stereochemistry; however, most of the reported Diels-Alderases have been shown to only facilitate the energetically favourable diastereoselective cycloadditions. Here we report the discovery and characterization of CtdP, a member of a new class of bifunctional oxidoreductase/Diels-Alderase, which was previously annotated as an NmrA-like transcriptional regulator. We demonstrate that CtdP catalyses the inherently disfavoured cycloaddition to form the bicyclo[2.2.2]diazaoctane scaffold with a strict α-anti-selectivity. Guided by computational studies, we reveal a NADP+/NADPH-dependent redox mechanism for the CtdP-catalysed inverse electron demand Diels-Alder cycloaddition, which serves as the first example of a bifunctional Diels-Alderase that utilizes this mechanism.

Indole Alkaloids from Psychoactive Mushrooms: Chemical and Pharmacological Potential as Psychotherapeutic Agents

Neuropsychiatric diseases such as depression, anxiety, and post-traumatic stress represent a substantial long-term challenge for the global health systems because of their rising prevalence, uncertain neuropathology, and lack of effective pharmacological treatments. The approved existing studies constitute a piece of strong evidence whereby psychiatric drugs have shown to have unpleasant side effects and reduction of sustained tolerability, impacting patients' quality of life. Thus, the implementation of innovative strategies and alternative sources of bioactive molecules for the search for neuropsychiatric agents are required to guarantee the success of more effective drug candidates. Psychotherapeutic use of indole alkaloids derived from magic mushrooms has shown great interest and potential as an alternative to the synthetic drugs currently used on the market. The focus on indole alkaloids is linked to their rich history, their use as pharmaceuticals, and their broad range of biological properties, collectively underscoring the indole heterocycle as significant in drug discovery. In this review, we aim to report the physicochemical and pharmacological characteristics of indole alkaloids, particularly those derived from magic mushrooms, highlighting the promising application of such active ingredients as safe and effective therapeutic agents for the treatment of neuropsychiatric disorders.

Data Science-Driven Analysis of Substrate-Permissive Diketopiperazine Reverse Prenyltransferase NotF: Applications in Protein Engineering and Cascade Biocatalytic Synthesis of (-)-Eurotiumin A

Prenyltransfer is an early-stage carbon-hydrogen bond (C-H) functionalization prevalent in the biosynthesis of a diverse array of biologically active bacterial, fungal, plant, and metazoan diketopiperazine (DKP) alkaloids. Toward the development of a unified strategy for biocatalytic construction of prenylated DKP indole alkaloids, we sought to identify and characterize a substrate-permissive C2 reverse prenyltransferase (PT). As the first tailoring event within the biosynthesis of cytotoxic notoamide metabolites, PT NotF catalyzes C2 reverse prenyltransfer of brevianamide F. Solving a crystal structure of NotF (in complex with native substrate and prenyl donor mimic dimethylallyl S-thiolodiphosphate (DMSPP)) revealed a large, solvent-exposed active site, intimating NotF may possess a significantly broad substrate scope. To assess the substrate selectivity of NotF, we synthesized a panel of 30 sterically and electronically differentiated tryptophanyl DKPs, the majority of which were selectively prenylated by NotF in synthetically useful conversions (2 to >99%). Quantitative representation of this substrate library and development of a descriptive statistical model provided insight into the molecular origins of NotF's substrate promiscuity. This approach enabled the identification of key substrate descriptors (electrophilicity, size, and flexibility) that govern the rate of NotF-catalyzed prenyltransfer, and the development of an "induced fit docking (IFD)-guided" engineering strategy for improved turnover of our largest substrates. We further demonstrated the utility of NotF in tandem with oxidative cyclization using flavin monooxygenase, BvnB. This one-pot, in vitro biocatalytic cascade enabled the first chemoenzymatic synthesis of the marine fungal natural product, (-)-eurotiumin A, in three steps and 60% overall yield.

Halogenation in Fungi: What Do We Know and What Remains to Be Discovered?

In nature, living organisms produce a wide variety of specialized metabolites to perform many biological functions. Among these specialized metabolites, some carry halogen atoms on their structure, which can modify their chemical characteristics. Research into this type of molecule has focused on how organisms incorporate these atoms into specialized metabolites. Several families of enzymes have been described gathering metalloenzymes, flavoproteins, or S-adenosyl-L-methionine (SAM) enzymes that can incorporate these atoms into different types of chemical structures. However, even though the first halogenation enzyme was discovered in a fungus, this clade is still lagging behind other clades such as bacteria, where many enzymes have been discovered. This review will therefore focus on all halogenation enzymes that have been described in fungi and their associated metabolites by searching for proteins available in databases, but also by using all the available fungal genomes. In the second part of the review, the chemical diversity of halogenated molecules found in fungi will be discussed. This will allow the highlighting of halogenation mechanisms that are still unknown today, therefore, highlighting potentially new unknown halogenation enzymes.

Elucidation of the Streptoazine Biosynthetic Pathway in Streptomyces aurantiacus Reveals the Presence of a Promiscuous Prenyltransferase/Cyclase

Heterologous expression of a three-gene cluster from Streptomyces aurantiacus coding for a cyclodipeptide synthase, a prenyltransferase, and a methyltransferase led to the elucidation of the biosynthetic steps of streptoazine C (2). In vivo biotransformation experiments proved the high flexibility of the prenyltransferase SasB toward tryptophan-containing cyclodipeptides for regular C-3-prenylation. Furthermore, their corresponding dehydrogenated derivatives prepared by using cyclodipeptide oxidases were also used for prenylation. This study provides an enzyme with high substrate promiscuity from a less explored group of prenyltransferases for potential use to generate prenylated derivatives.

Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins

Prenylated indole alkaloids featuring spirooxindole rings possess a 3R or 3S carbon stereocenter, which determines the bioactivities of these compounds. Despite the stereoselective advantages of spirooxindole biosynthesis compared with those of organic synthesis, the biocatalytic mechanism for controlling the 3R or 3S-spirooxindole formation has been elusive. Here, we report an oxygenase/semipinacolase CtdE that specifies the 3S-spirooxindole construction in the biosynthesis of 21R-citrinadin A. High-resolution X-ray crystal structures of CtdE with the substrate and cofactor, together with site-directed mutagenesis and computational studies, illustrate the catalytic mechanisms for the possible β-face epoxidation followed by a regioselective collapse of the epoxide intermediate, which triggers semipinacol rearrangement to form the 3S-spirooxindole. Comparing CtdE with PhqK, which catalyzes the formation of the 3R-spirooxindole, we reveal an evolutionary branch of CtdE in specific 3S spirocyclization. Our study provides deeper insights into the stereoselective catalytic machinery, which is important for the biocatalysis design to synthesize spirooxindole pharmaceuticals.

Flavoprotein monooxygenases: Versatile biocatalysts

Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.

Enzyme promiscuity and evolution in light of cellular metabolism

This Special Issue is composed of 10 reviews that delve into the intricacies behind enzyme promiscuity and evolution, an area that is of increasing interest in the biological research community. In particular, the reviews in this Special Issue explore enzyme promiscuity and evolution in the context of cellular metabolism, as discussed in this introductory Editorial. It is our hope that you enjoy these fascinating and informative reviews and we wish to thank the authors for their compelling contributions to The FEBS Journal. doi: 10.1111/febs.12650.

The FEBS Journal in 2021: a sharp reminder that science really matters

The FEBS Journal, a leading multidisciplinary journal in the life sciences, continues to grow in visibility and impact. Here, the Editor-in-Chief Seamus Martin discusses developments at the journal over the past year and the impact of the COVID-19 crisis on research activities.

Natural Products from Endophytic Fungi Associated with Rubiaceae Species

This review presents the chemical diversity and pharmacological properties of secondary metabolites produced by endophytic fungi associated with various genera of Rubiaceae. Several classes of natural products are described for these endophytes, although, this study highlights the importance of some metabolites, which are involved in antifungal, antibacterial, anti-protozoal activities; neurodegenerative diseases; cytotoxic activity; anti-inflammatory and antioxidant activity; and hyperglycemic control.

A unified strategy to reverse-prenylated indole alkaloids: total syntheses of preparaherquamide, premalbrancheamide, and (+)-VM-55599

A full account of our studies toward reverse-prenylated indole alkaloids that contain a bicyclo[2.2.2]core is described. A divergent route is reported which has resulted in the synthesis of preparaherquamide, (+)-VM-55599, and premalbrancheamide. An intramolecular Dieckmann cyclization between an enolate and isocyanate was used to forge the bicyclo[2.2.2]diazaoctane core that is characteristic of these molecules. The pentacyclic indole scaffold was constructed through a one-pot Hofmann rearrangement followed by Fischer indole synthesis. The utilization of our previously reported indole peripheral functionalization strategy also led to natural products including malbrancheamides B, C, stephacidin A, notoamides F, I and R, aspergamide B, and waikialoid A. Ultimately, the divergent route that we devised provided access to a wide range of prenylated indole alkaloids that are differently substituted on the cyclic amine core.