Discovery and biosynthesis of bacterial drimane-type sesquiterpenoids from Streptomyces clavuligerus

• Dongxu Zhang,
• Wenyu Du,
• Xingming Pan,
• Xiaoxu Lin,
• Fang-Ru Li,
• Qingling Wang,
• Qian Yang,
• Hui-Min Xu and
• Liao-Bin Dong

Beilstein J. Org. Chem. 2024, 20, 815–822, doi:10.3762/bjoc.20.73

• significant in industrial applications, renowned for its production of diverse natural products with chemical structures and bioactivities, such as cephamycin C, clavulanic acid, and isopenicillin N [22][23][24]. Genomic sequencing of S. clavuligerus has revealed 48 potential secondary metabolite BGCs, and

• our analysis indicated that 16 of them are potential terpene-producing BGCs, indicative of its extensive capacity for diverse metabolite production [25]. In our large-scale fermentation of S. clavuligerus, aimed at uncovering novel bacterial terpenoids, we observed that specific culture conditions are

• crucial for metabolite production. Different culture media can lead to the biosynthesis of varied compounds. Specifically, in this study, S. clavuligerus was cultivated in two terpene favored media, XTM and YMS [26][27], resulting in three drimenol (1) congeners from the extracts: 3β-hydroxydrimenol (2

Methodology for awakening the potential secondary metabolic capacity in actinomycetes

• Shun Saito and
• Midori A. Arai

Beilstein J. Org. Chem. 2024, 20, 753–766, doi:10.3762/bjoc.20.69

• , and the associated undiscovered secondary metabolite biosynthesis genes are called “silent” genes. This review outlines several approaches to further activate the metabolic potential of actinomycetes. Keywords: actinomycete; co-culture; heat shock metabolites (HSMs); secondary metabolites; silent

• considered to have been completely characterized. This may be because the number of discovered compounds is small compared to the number of secondary metabolite biosynthesis genes harbored by actinomycetes [26][27][28]. For example, in Streptomyces avermitilis, 38 secondary metabolite biosynthetic gene

• identified. These as yet undiscovered secondary metabolite biosynthesis genes are called “silent genes”, because they are either not expressed or their expression levels are low under normal culture conditions. A number of studies have reported methods to activate these genes, and many new compounds have

Genome mining of labdane-related diterpenoids: Discovery of the two-enzyme pathway leading to (−)-sandaracopimaradiene in the fungus Arthrinium sacchari

• Fumito Sato,
• Terutaka Sonohara,
• Shunta Fujiki,
• Akihiro Sugawara,
• Yohei Morishita,
• Taro Ozaki and
• Teigo Asai

Beilstein J. Org. Chem. 2024, 20, 714–720, doi:10.3762/bjoc.20.65

• Information File 1). The constructed plasmid was introduced into A. oryzae to give the transformant AO-AsGGS/AsCPS/AsPS. We then analyzed the metabolite of this transformant by GC–MS. By comparing the metabolites extracted from A. oryzae NSAR1, we identified compound 1 as a product (Figure 3A and Figure S2 in

New variochelins from soil-isolated Variovorax sp. H002

• Jabal Rahmat Haedar,
• Aya Yoshimura and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2024, 20, 692–700, doi:10.3762/bjoc.20.63

• , including soil-isolated plant pathogens. Results and Discussion Isolation and structure elucidation In this study, we explored the secondary metabolite potential of the soil-isolated Variovorax sp. H002, domesticated from the Medicinal Plant Garden of the Faculty of Pharmaceutical Sciences, Hokkaido

Chemical and biosynthetic potential of Penicillium shentong XL-F41

• Ran Zou,
• Xin Li,
• Xiaochen Chen,
• Yue-Wei Guo and
• Baofu Xu

Beilstein J. Org. Chem. 2024, 20, 597–606, doi:10.3762/bjoc.20.52

• stimulating the production of a greater number of metabolite peaks, as shown in Figure 1. Scaled-up fermentation allowed us to isolate and characterize two new indole terpene alkaloids, shentonins A and B (1 and 2), a new fatty acid 3, and nine previously identified compounds 4–12, among which were gram

Mechanisms for radical reactions initiating from N-hydroxyphthalimide esters

• Carlos R. Azpilcueta-Nicolas and
• Jean-Philip Lumb

Beilstein J. Org. Chem. 2024, 20, 346–378, doi:10.3762/bjoc.20.35

• -derived NHPI esters has found application in the total synthesis of natural products, including the plant metabolite denobilone A and the highly oxidized dibenzocyclooctadiene lignans heteroclitin J and kadsulignan E [55]. Activation via charge-transfer complex formation Under conditions where oxidative

Discovery of unguisin J, a new cyclic peptide from Aspergillus heteromorphus CBS 117.55, and phylogeny-based bioinformatic analysis of UngA NRPS domains

• Sharmila Neupane,
• Marcelo Rodrigues de Amorim and
• Elizabeth Skellam

Beilstein J. Org. Chem. 2024, 20, 321–330, doi:10.3762/bjoc.20.32

• those from UngA’ regardless of which two amino acids were condensed. Conclusion In this study unguisins B and J were isolated from A. heteromorphus CBS 117.55 which has not been extensively investigated for secondary metabolite production. A BGC encoding the unguisins was identified by genome mining

Identification of the p-coumaric acid biosynthetic gene cluster in Kutzneria albida: insights into the diazotization-dependent deamination pathway

• Seiji Kawai,
• Akito Yamada,
• Yohei Katsuyama and
• Yasuo Ohnishi

Beilstein J. Org. Chem. 2024, 20, 1–11, doi:10.3762/bjoc.20.1

• vigorously used to search for novel compounds in recent years due to the rapid improvement of DNA sequence technologies and computational approaches to analyze BGCs [1][3]. Our research group previously identified the secondary metabolite-specific nitrous acid biosynthetic pathway, named ANS (aspartate

• gene sets on heterologous expression plasmids to construct S. albus-cma. The tipA promoter was used for gene expression. B) Metabolite analysis of S. albus-cma. UV chromatograms at 310 nm are shown. The production yield of 6 was decreased in S. albus-cma ∆cmaG. Several metabolites produced by S. albus

Intermediates and shunt products of massiliachelin biosynthesis in Massilia sp. NR 4-1

• Till Steinmetz,
• Blaise Kimbadi Lombe and
• Markus Nett

Beilstein J. Org. Chem. 2023, 19, 909–917, doi:10.3762/bjoc.19.69

• ) using a 1 dm cuvette. For this, samples were dissolved in 1 mL methanol. Cultivation and extraction of Massilia sp. NR 4-1 For metabolite production, the strain was grown in 5 L Erlenmeyer flasks containing 1.5 L of modified R2A medium: 0.5 g/L yeast extract, 0.5 g/L proteose peptone, 0.5 g/L casamino

Enolates ambushed – asymmetric tandem conjugate addition and subsequent enolate trapping with conventional and less traditional electrophiles

• Péter Kisszékelyi and
• Radovan Šebesta

Beilstein J. Org. Chem. 2023, 19, 593–634, doi:10.3762/bjoc.19.44

• war against resistant bacteria strains. The tricyclic diterpene fungal metabolite (+)-pleuromutilin was isolated in 1951 [104]. Since then it has served as a starting point for developing new antibiotics, including semisynthetic derivatives effective against Gram-positive or even both types of

Strategies to access the [5-8] bicyclic core encountered in the sesquiterpene, diterpene and sesterterpene series

• Cécile Alleman,
• Charlène Gadais,
• Laurent Legentil and
• François-Hugues Porée

Beilstein J. Org. Chem. 2023, 19, 245–281, doi:10.3762/bjoc.19.23

• . Further functionalization steps finally furnished (+)-ophiobolin A (8). In the fusicoccanes family, cotylenol (50), the aglycon of cotylenin A (131) (see section 3.1), is a fungal metabolite which displays various interesting biological activities [28]. For example, it expresses a moderate cytotoxicity

Combining the best of both worlds: radical-based divergent total synthesis

• Kyriaki Gennaiou,
• Antonios Kelesidis,
• Maria Kourgiantaki and
• Alexandros L. Zografos

Beilstein J. Org. Chem. 2023, 19, 1–26, doi:10.3762/bjoc.19.1

• meroterpenoids. This class of compounds possesses versatile bioactivities, ranging from anticancer and anti-HIV to antifungal properties, with minor modifications on the decoration of either the hydroquinone or the terpene part of the secondary metabolite [34]. The group applied a semisynthetic plan starting

Synthetic study toward tridachiapyrone B

• Morgan Cormier,
• Florian Hernvann and
• Michaël De Paolis

Beilstein J. Org. Chem. 2022, 18, 1741–1748, doi:10.3762/bjoc.18.183

• metabolite tridachiapyrone B is related to tridachiapyrone A (Scheme 1c). As the 1,3-cyclohexadiene motif of the latest is oxidized into 2,5-cyclohexadienone, it is assumed that tridachiapyrone B arises from the ring opening of the epoxide (tridachiapyrone C) of tridachiapyrone A. To our knowledge, the

Navigating and expanding the roadmap of natural product genome mining tools

• Friederike Biermann,
• Sebastian L. Wenski and
• Eric J. N. Helfrich

Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178

• ). Moreover, since these assembly line-like pathways follow the same biosynthetic principle, they often form hybrids with other biosynthetic assembly line-like pathways [21]. Prominent examples of the usage of pHMMs are the original algorithm of the antibiotics & Secondary Metabolite Analysis Shell (antiSMASH

• secondary metabolite biosynthetic enzymes are distant paralogs of enzymes involved in primary metabolism [63][71]. These NP biosynthetic enzymes are hypothesized to have undergone significant sequence and selectivity changes while still operating based on the same reaction mechanism (e.g., fatty acid

• EvoMining is a signature sequence independent concept and instead uses phylogenetic analysis of primary metabolite biosynthetic enzymes, it remains a “hard-coded” sequence similarity-based approach that uses phylogenetic analysis instead of pHMMs for BGC detection [63][71]. Machine learning-based genome

Using UHPLC–MS profiling for the discovery of new sponge-derived metabolites and anthelmintic screening of the NatureBank bromotyrosine library

• Sasha Hayes,
• Aya C. Taki,
• Kah Yean Lum,
• Joseph J. Byrne,
• Merrick G. Ekins,
• Robin B. Gasser and
• Rohan A. Davis

Beilstein J. Org. Chem. 2022, 18, 1544–1552, doi:10.3762/bjoc.18.164

• clusters) and subjected to reversed-phase C18 HPLC (MeOH/H2O/0.1%TFA) which led to the purification of the new metabolite, 5-debromopurealidin H (1) as its TFA salt along with the major previously reported metabolite, ianthesine E (2) (Figure 2). Comparison of the 1D NMR, MS and specific rotation data for

• compound 2 with literature values [15] identified this metabolite as ianthesine E, which had been previously identified from a Pseudoceratina sp. specimen collected from the Great Barrier Reef. 5-Debromopurealidin H and ianthesine E corresponded to peaks one and two in the UHPLC–MS trace, respectively

New triazole-substituted triterpene derivatives exhibiting anti-RSV activity: synthesis, biological evaluation, and molecular modeling

• Elenilson F. da Silva,
• Krist Helen Antunes Fernandes,
• Denise Diedrich,
• Jessica Gotardi,
• Marcia Silvana Freire Franco,
• Carlos Henrique Tomich de Paula da Silva,
• Ana Paula Duarte de Souza and
• Simone Cristina Baggio Gnoatto

Beilstein J. Org. Chem. 2022, 18, 1524–1531, doi:10.3762/bjoc.18.161

• ). One of the main known mechanisms of action of RBV is the depletion of intracellular GTP pools via the inhibition of cellular IMPDH induced by the 5-monophosphate metabolite of RBV [44]. Thus, our finding based on these results is that compound 8 may act similarly to IMPDH inhibitors and the active

• metabolite of RBV, leading to GTP depletion, since best poses achieved for the tested compound interact in an equivalent way as IMP and inhibitor MAD1 and in the same site of action, suggesting that compound 8 can be a bioisostere for IMPDH inhibitors that could be used to combat RSV infections. However

Synthesis of the biologically important dideuterium-labelled adenosine triphosphate analogue ApppI(d₂)

• Petri A. Turhanen

Beilstein J. Org. Chem. 2022, 18, 1466–1470, doi:10.3762/bjoc.18.153

• diester (ApppI(d2)) is described. ApppI has been reported to be an important mevalonate pathway metabolite, induced by nitrogen-containing bisphosphonates used for the treatment of several diseases related to the calcium metabolism, of which osteoporosis is the most well-known. The availability of ApppI

Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants

• Karan Malhotra and
• Jakob Franke

Beilstein J. Org. Chem. 2022, 18, 1289–1310, doi:10.3762/bjoc.18.135

• celastrol, a potent anti-obesity metabolite [42][43]. In two independent studies, transcriptome mining and functional studies in Nicotiana benthamiana were used to identify the CYPs CYP712K1, CYP712K2, CYP712K3, and CYP712K4 capable of oxidising friedelin (8) into polpunonic acid via an aldehyde

Vicinal ketoesters – key intermediates in the total synthesis of natural products

• Marc Paul Beller and
• Ulrich Koert

Beilstein J. Org. Chem. 2022, 18, 1236–1248, doi:10.3762/bjoc.18.129

• the desired α-carbonyl group. (−)-Preussochromone A In 2020, the Koert group disclosed the synthesis of (−)-preussochromone A (24), a fungal metabolite with a highly substituted tetrahydrothiopyrane core annulated to a chromenone [10]. The tetrahydrothiopyrane ring was closed by a Lewis-acid-promoted

• the cytotoxic metabolite (−)-aplaminal (96), which was isolated from the sea hare Aplysia kurodai [32]. The natural product is characterized by a triazabicyclo[3.2.1]octane, where each bridge possesses a nitrogen atom. The synthesis commenced with N-Boc-serine (93) which was converted to secondary

Synthesis of tryptophan-dehydrobutyrine diketopiperazine and biological activity of hangtaimycin and its co-metabolites

• Houchao Xu,
• Anne Wochele,
• Minghe Luo,
• Gregor Schnakenburg,
• Yuhui Sun,
• Heike Brötz-Oesterhelt and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 1159–1165, doi:10.3762/bjoc.18.120

• , People's Republic of China Institute of Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany 10.3762/bjoc.18.120 Abstract An improved synthesis for tryptophan-dehydrobutyrine diketopiperazine (TDD), a co-metabolite of the hybrid polyketide/non-ribosomal peptide

• ]. Another hangtaimycin co-metabolite in S. spectabilis [9] is tryptophan-dehydrobutyrine diketopiperazine (TDD, 4) that was already isolated several decades before the discovery of 1, and likewise reported to have no antibacterial activity [9]. The initially published structure was that of (E)-4 [9], but

• inactivity of 4 against bacteria was confirmed in this study, and also 2 is an inactive metabolite of S. spectabilis, while for 1 moderate growth retardation against A. baumannii and B. subtilis, and growth inhibition against PMBN-treated E. coli was observed. However, the low activity of 1 in these assays

Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity

• Jamshid Amiri Moghaddam,
• Huijuan Guo,
• Karsten Willing,
• Thomas Wichard and
• Christine Beemelmanns

Beilstein J. Org. Chem. 2022, 18, 722–731, doi:10.3762/bjoc.18.72

• homogentisate and geranylgeranyl diphosphate [10][11]. Another intriguing Ptase, called AuaA, has been reported to catalyze the farnesylation of 2-methyl-4-hydroxyquinoline using farnesyl diphosphate (FPP), which results in the metabolite aurachin D [12][13]. Following up on our recent exploration of the

• , and a TIM barrel protein (EboE) [28]. While prior studies suggested that the enzymatic reactions carried out by EboA-E include the prenylation of an undetermined substrate by eboC (UbiA-297 homologue) and modifications of a polyhydroxylated aromatic metabolite, the enzymatic reactions carried out by

• of the enzymatic products: UHPLC-HESI-HRMS measurement was performed on a Dionex Ultimate3000 system combined with a Q-Exactive Plus mass spectrometer (Thermo Scientific) with a heated electrospray ion source (HESI). Metabolite separation was carried out by reversed-phase liquid chromatography at 40

Menadione: a platform and a target to valuable compounds synthesis

• Acácio S. de Souza,
• Ruan Carlos B. Ribeiro,
• Dora C. S. Costa,
• Fernanda P. Pauli,
• David R. Pinho,
• Matheus G. de Moraes,
• Fernando de C. da Silva,
• Luana da S. M. Forezi and
• Vitor F. Ferreira

Beilstein J. Org. Chem. 2022, 18, 381–419, doi:10.3762/bjoc.18.43

Amamistatins isolated from Nocardia altamirensis

• Till Steinmetz,
• Wolf Hiller and
• Markus Nett

Beilstein J. Org. Chem. 2022, 18, 360–367, doi:10.3762/bjoc.18.40

• been reported before. The isolated metabolite 5 represents the previously described siderophore amamistatin B [7], while compound 6 was before only known as a decomposition product of a synthetically prepared obafluorin derivative [8]. Results and Discussion To induce siderophore biosynthesis in N

• as eluent. Fractions that showed a color change in the CAS assay were pooled and subjected to semipreparative reversed-phase HPLC. This led to the isolation of six CAS active compounds (1–6; Figure 1). The major metabolite 1 (12 mg) was obtained as a slight reddish oil. High resolution (HR) ESIMS

Unsaturated fatty acids and a prenylated tryptophan derivative from a rare actinomycete of the genus Couchioplanes

• Shun Saito,
• Kanji Indo,
• Naoya Oku,
• Hisayuki Komaki,
• Masashi Kawasaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2939–2949, doi:10.3762/bjoc.17.203

• underexplored. However, in silico genome mining identified multiple secondary metabolite biosynthetic gene clusters in selected strains from minor actinomycetes genera, implying their comparable biosynthetic capacities to those of the already proven genera [19]. Encouraged by these reports, we examined the

• Micromonosporaceae first isolated in 1994 from a sandy soil in Japan [23], was set to be the next target. While the anti-SMASH-assisted genome mining [24] in C. caeruleus DSM 43634 revealed approximately 20 secondary metabolite biosynthetic gene clusters, only one compound, heptaene macrolide 67-121C, is known to

• unused carbon (δH 177.1, C-1) and the molecular formula. A NOESY correlation between H-11 and H-12 supported an E-configuration for the C-4/C-5 double bond. The established planar structure was identical to that of a fungal metabolite phialomustin B [26], for which specific rotation, enumerated 1H and

First total synthesis of hoshinoamide A

• Haipin Zhou,
• Zihan Rui,
• Yiming Yang,
• Shengtao Xu,
• Yutian Shao and
• Long Liu

Beilstein J. Org. Chem. 2021, 17, 2924–2931, doi:10.3762/bjoc.17.201

• , hoshinoamides A, B [11] and C [12], from a microbial metabolite of marine cyanobacterium Caldora penicillata (Figure 1). Hoshinoamides A and B showed potent activities against chloroquine-sensitive Plasmodium falciparum 3D7 with IC50 values of 0.52 and 1.0 μM, respectively. Hoshinoamide C inhibited the growth