Chemical structure metagenomics of microbial natural products: surveying nonribosomal peptides and beyond

• Thomas Ma and
• John Chu

Beilstein J. Org. Chem. 2024, 20, 3050–3060, doi:10.3762/bjoc.20.253

• metagenomics uses genetically tractable model organisms, such as Escherichia coli or Streptomyces albus, to express DNA extracted from the environment and then screen for the phenotype of interest [23][24]. This approach was used to identify BGCs that produce antibiotics, pigments, compounds that alter the

N-Glycosides of indigo, indirubin, and isoindigo: blue, red, and yellow sugars and their cancerostatic activity

• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 2840–2869, doi:10.3762/bjoc.20.240

• , indirubin, and isoindigo which can be regarded as blue, red, and yellow sugars, respectively. Review Indigo-N-glycosides (blue sugars) In 2002, Laatsch and Maskey reported the isolation of the akashins A, B and C, indigo-N-glycosides, from terrestric Streptomyces (Scheme 2) [17][18]. These natural products

Photoredox-catalyzed intramolecular nucleophilic amidation of alkenes with β-lactams

• Valentina Giraldi,
• Giandomenico Magagnano,
• Daria Giacomini,
• Pier Giorgio Cozzi and
• Andrea Gualandi

Beilstein J. Org. Chem. 2024, 20, 2461–2468, doi:10.3762/bjoc.20.210

• well known as a potent β-lactamase inhibitor [33][34]. It is produced by the filamentous bacterium Streptomyces clavuligerus, but in low yield. Various clavams 2–5 have been identified (Figure 2B), either through isolation as natural metabolites or obtained by synthetic methods [35][36][37][38][39][40

Natural resorcylic lactones derived from alternariol

• Joachim Podlech

Beilstein J. Org. Chem. 2024, 20, 2171–2207, doi:10.3762/bjoc.20.187

• Talaromyces flavus [49], T. pinophilus [227], Penicillium verruculosum [228], P. simplicissimum [229], and a further unidentified P. sp. [228][230], from Streptomyces verticillus [228], Coleophoma sp. [231], Ulocladium sp. [210], Botryosphaeria dothidea [232], and from a Pleosporales sp. [233]. As one of the

Allostreptopyrroles A–E, β-alkylpyrrole derivatives from an actinomycete Allostreptomyces sp. RD068384

• Marwa Elsbaey,
• Naoya Oku,
• Mohamed S. A. Abdel-Mottaleb and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2024, 20, 1981–1987, doi:10.3762/bjoc.20.174

• metabolites, and most of them are pyrroloterpenes from Streptomyces (Figure 1 and Figure S54 in Supporting Information File 1). Examples include pyrrolostatin [12] and its congener geranylpyrrol A [13], bearing a carboxylic group at the C2 and a geranyl group at the C4 position of the pyrrole ring, and their

• of β-alkylpyrrole, bearing a pentyl chain on the pyrrolyldipyrromethene core [16]. Similarly, α-alkylpyrroles are limited to a handful examples including α-pyrrolosesquiterpenes [17][18][19], undecylprodigiosin [16] from Streptomyces, and fungus-derived pyrrol-2-ylpolyenes [20]. In 2017

• and carboxyl functionalities. Furthermore, a β-alkyl substitution is not very common in pyrrolic secondary metabolites. The most related metabolites to 1–5 are the reported alkylpyrroles from a marine sponge Oscarella lobularis [7] and pyrroloterpenes from Streptomyces [12][13][14][15], although the

Chemo-enzymatic total synthesis: current approaches toward the integration of chemical and enzymatic transformations

• Ryo Tanifuji and
• Hiroki Oguri

Beilstein J. Org. Chem. 2024, 20, 1693–1712, doi:10.3762/bjoc.20.151

• macrolactonization catalyzed by two massive PKS modules exemplifies a refined and innovative method in chemo-enzymatic synthesis. Tylactone (4), a 16-membered macrolactone, was isolated from a Streptomyces fradiae mutant and characterized as the aglycone of the macrolide antibiotic tylosin (Scheme 7) [69]. Since the

• 1970s, the biosynthetic pathway of 4 has been investigated through isotope labelling and analysis of metabolites from S. fradiae mutants [70][71][72][73]. Heterologous production of 4 was also achieved by expression of elucidated biosynthetic gene cluster from S. fradiae in Streptomyces venezuelae [74

• utilizing Streptomyces venezuelae DHS316, developed by the same group, mediated the desosaminylation of 4 at C5 and afforded M-4365 G1 (80) in 70% yield [87]. For further oxidative modifications, they prepared the fusion proteins Tyll-RhFRED and JuvD-RhFRED, comprising P450 monooxygenases (TylI, JuvD) with

Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry

• Maria-Paula Schröder,
• Isabel P.-M. Pfeiffer and
• Silja Mordhorst

Beilstein J. Org. Chem. 2024, 20, 1652–1670, doi:10.3762/bjoc.20.147

• demonstrated. OlvSA, an O-MT encoded in the olv cluster from Streptomyces olivaceus NRRL B-3009 (Figure 5), is involved in the biosynthesis of the class I lanthipeptide OlvA(BCSA). It catalyses the conversion of a highly conserved ʟ-aspartate to ʟ-isoaspartate by methylation of a side chain carboxylate group

• [RMSD: 8.152 Å (109 to 109 atoms)], demonstrating the structural diversity among O-MTs (Figure 5). Streptomyces bottropensis produces various bottromycins, including bottromycin A2 (Figure 4) [79]. The precursor peptide consists of an N-terminal core and a rare C-terminal follower region. The

• CsrA, which is a promising target for new anti-infective compounds. However, drug development is hampered by poor cellular uptake [86][87]. In the biosynthesis of cypemycin in Streptomyces sp. OH-4156, CypM adds two methyl groups to the N-terminal alanine residue. Cypemycin has a very narrow activity

Computation-guided scaffold exploration of 2E,6E-1,10-trans/cis-eunicellanes

• Zining Li,
• Sana Jindani,
• Volga Kojasoy,
• Teresa Ortega,
• Erin M. Marshall,
• Khalil A. Abboud,
• Sandra Loesgen,
• Dean J. Tantillo and
• Jeffrey D. Rudolf

Beilstein J. Org. Chem. 2024, 20, 1320–1326, doi:10.3762/bjoc.20.115

• system and the C2–C3 alkene, are instilled by these terpene synthases. Four types of eunicellane synthases are known (Figure 1B). The first eunicellane synthase identified, Bnd4 from the biosynthesis of benditerpenoic acid in Streptomyces sp. (CL12-4) [5], forms a cis-eunicellane named benditerpetriene

• (1) [6]. In 1, the C2–C3 and C6–C7 alkenes are E-configured, with the latter alkene configuration being conserved in all known eunicellane cyclization mechanisms. The first trans-eunicellane synthase, AlbS from the biosynthesis of albireticulone in Streptomyces albireticuli [10], was also identified

Cofactor-independent C–C bond cleavage reactions catalyzed by the AlpJ family of oxygenases in atypical angucycline biosynthesis

• Jinmin Gao,
• Liyuan Li,
• Shijie Shen,
• Guomin Ai,
• Bin Wang,
• Fang Guo,
• Tongjian Yang,
• Hui Han,
• Zhengren Xu,
• Guohui Pan and
• Keqiang Fan

Beilstein J. Org. Chem. 2024, 20, 1198–1206, doi:10.3762/bjoc.20.102

• analysis of the alp gene cluster from Streptomyces ambofaciens revealed AlpG as the homolog of JadH. The N-terminal His6-tagged construct of AlpG was expressed and purified to homogeneity in E. coli (Figure S2, Supporting Information File 1). The purified AlpG displayed a light yellow color, and the

A Diels–Alder probe for discovery of natural products containing furan moieties

• Alyssa S. Eggly,
• Namuunzul Otgontseren,
• Carson B. Roberts,
• Amir Y. Alwali,
• Haylie E. Hennigan and
• Elizabeth I. Parkinson

Beilstein J. Org. Chem. 2024, 20, 1001–1010, doi:10.3762/bjoc.20.88

• products, methylenomycin furan (MMF) hormones, and MMF derivatives. Moreover, the molecular probe has been tested in crude supernatants of various Streptomyces strains and enables identification of MMFs. Keywords: Diels–Alder reaction; furans; methylenomycin furan hormones; natural products; reactivity

• . Natural products with furan moieties can also be signaling hormones. Methylenomycin furans (MMFs) are naturally occurring secondary metabolites that are produced by Streptomyces coelicolor, a soil dwelling bacterium. These molecules are important as they induce the production of the antibiotic

• been five natural MMFs isolated and characterized, with all of the MMFs being isolated from Streptomyces coelicolor W75 (Figure 1B). These compounds are 2,3,4-trisubstituted furans, and all five contain a carboxylic acid at the three position and a hydroxymethyl group at the four position. They differ

Enhancing structural diversity of terpenoids by multisubstrate terpene synthases

• Min Li and
• Hui Tao

Beilstein J. Org. Chem. 2024, 20, 959–972, doi:10.3762/bjoc.20.86

• of TSs have been discovered in bacteria [32][33]. VenA from Streptomyces venezuelae ATCC 15439 was characterized as a promiscuous class I TS that converts 3 to geraniol (24.2% yield), 4 to seven sesquiterpenes (24.6% yield), and 5 to four diterpenes (31.2% yield), with venezuelaene A (35, Figure 3b

• ) from Cryptosporangium arvum, and germacrene A synthase (SmTS6) from Streptomyces mobaraensis were chosen to convert four FPP analogs 72–75, which not only generated several new terpenoids (76–79), but also revealed the cyclization mechanisms of selected TSs [40] (Figure 6a). Similarly, two GGPP

• methyltransferase (IPPMT) from Streptomyces monomycini. Notably, polymethylated C41, C42, and C43 carotenoids were produced by combining the endogenous terpene biosynthesis pathway and IPPMT, demonstrating the potential of this approach to expand the terpene structural space [52]. In addition to methylation of the

Confirmation of the stereochemistry of spiroviolene

• Yao Kong,
• Yuanning Liu,
• Kaibiao Wang,
• Tao Wang,
• Chen Wang,
• Ben Ai,
• Hongli Jia,
• Guohui Pan,
• Min Yin and
• Zhengren Xu

Beilstein J. Org. Chem. 2024, 20, 852–858, doi:10.3762/bjoc.20.77

• proposing a reasonable cyclization mechanism [5]. Spiroviolene (1, Figure 1) was identified by Dickschat and co-workers as a nascent cyclization product of spiroviolene synthase (SvS), the coding gene of which was cloned from Streptomyces violens NRRL ISP-5597 [6]. Its unique spiro-fused linear triquinane

• for GGPP production. Also, we have cloned the SvS-coding gene directly from Streptomyces violens CGMCC 4.1786 (= NRRL ISP-5597) into pET28a to give pET28a-svs. The resultant two plasmids were then co-transformed into commercially available E. coli BL21(DE3) for diterpene production. Spiroviolene could

Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria

• Kara A. Strickland,
• Brenda Martinez Rodriguez,
• Ashley A. Holland,
• Shelby Wagner,
• Michelle Luna-Alva,
• David E. Graham and
• Jonathan D. Caranto

Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75

• /bjoc.20.75 Abstract Linear nitramines (R–N(R′)NO2; R′ = H or alkyl) are toxic compounds, some with environmental relevance, while others are rare natural product nitramines. One of these natural product nitramines is N-nitroglycine (NNG), which is produced by some Streptomyces strains and exhibits

• , the physiological function of its substrate NNG. This compound is one of the few known nitramine natural products and the only one produced by bacteria instead of fungi [22]. Its only known natural sources are strains of Streptomyces bacteria [23][24]. The abundance and distribution of these NNG

• possibility is that NNG has several physiological functions and fates. For example, a natural product nitronate intermediate was recently shown to have two fates within Streptomyces achromogenes var. streptozoticus NRRL 3125 [46]. This nitronate intermediate was shown to be O-methylated to form O

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

• biosynthetic pathways for DMTs have been primarily elucidated in fungi, with identified P450s only acting on the B ring. In this study, we isolated and characterized three bacterial DMTs, namely 3β-hydroxydrimenol (2), 2α-hydroxydrimenol (3), and 3-ketodrimenol (4), from Streptomyces clavuligerus. Through

• analogs. This discovery not only broadens the known chemical diversity of DMTs from bacteria, but also provides new insights into DMT biosynthesis in bacteria. Keywords: bacterial terpenoid; cytochrome P450s; drimane-type sesquiterpenoid; Streptomyces clavuligerus; terpenoid biosynthesis; Introduction

• associated with DMT biosynthesis have been identified in bacteria, the corresponding natural DMTs have not been discovered [17]. In this study, we isolated and characterized three drimenol congeners (2–4) from Streptomyces clavuligerus (Figure 2a). In the genome of S. clavuligerus, we identified a cav

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

• actinomycetes. Secondary metabolites produced by actinomycetes, representing a class of compounds with a diverse chemical space, have promising potential as sources of bioactive substances [10]. Due to his discovery of streptomycin from Streptomyces griseus, Waksman was awarded the Nobel Prize in Physiology and

• Medicine in 1952 [11]. Ōmura, who discovered avermectin from Streptomyces avermitilis, received the same award in 2015 [12]. While there are many such brilliant achievements, researchers are finding it increasingly difficult to isolate novel compounds from secondary metabolites produced by actinomycetes

• secondary metabolites from actinomycetes of the genus Streptomyces due to the prominence of species of this genus in surface soils and the difficulty of isolating members of other genera from natural environments. For this reason, actinomycetes other than those of the genus Streptomyces are referred to as

Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization

• Senze Qiao,
• Zhongyu Cheng and
• Fuzhuo Li

Beilstein J. Org. Chem. 2024, 20, 721–733, doi:10.3762/bjoc.20.66

• understanding of the acidic lipopeptide structure–activity relationship (Scheme 4b). Surugamide B The cyclic octapeptides surugamides were isolated from several Streptomyces sp. and shown to be cathepsin B inhibitors [56][57][58]. According to a biosynthetic viewpoint, the corresponding modules consist of four

• biocatalytic cyclization, a crucial feature for the chemoenzymatic synthesis of macrolides and PKS/NRPS hybrids. The pikromycins Methymycin (20) and pikromycin (21) are 12- and 14-membered macrolide antibiotics both isolated from Streptomyces venezuelae ATCC15439. The Kang lab reported the total synthesis of

• macrolactonization, leading to the formation of tylactone (39) in 69% yield. Furthermore, the Streptomyces strain S. venezuelae DHS316 [76] performed an in vivo glycosylation resulting in M-4365 G1 (50) in 15 linear steps and 4.6% overall yield from commercial resources. With regio- and stereoselective C–H

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A

• Michael O. Akintubosun and
• Melanie A. Higgins

Beilstein J. Org. Chem. 2024, 20, 589–596, doi:10.3762/bjoc.20.51

• was discovered in the 1950s and is produced by the soil bacterium Streptomyces hygroscopicus [1]. It has broad spectrum antibiotic activity, antitreponemal activity against the pathogen that causes swine dysentery, and selective activity against the spirochete that causes Lyme disease [1][2][3]. It

• Cloning, expression, and purification Streptomyces leeuwenhoekii NRRL B-24963 [28] was used as a template to amplify the hyg17 (GenBank CQR59633) with the primers 5’-GTTAGCCATATGACGGTCGCCGTCGTGGGC-3’ and 5’-GTAATGCTCGAGCGGCGCCACCGGCACCGA-3’. hyg17 was cloned into pTip-QC1 [10] using NdeI and XhoI

A new analog of dihydroxybenzoic acid from Saccharopolyspora sp. KR21-0001

• Rattiya Janthanom,
• Yuta Kikuchi,
• Hiroki Kanto,
• Tomoyasu Hirose,
• Arisu Tahara,
• Takahiro Ishii,
• Arinthip Thamchaipenet and
• Yuki Inahashi

Beilstein J. Org. Chem. 2024, 20, 497–503, doi:10.3762/bjoc.20.44

• actinomycetes, with 70% from Streptomyces and the rest from rare actinomycetes (non-Streptomyces) [5]. Rare actinomycetes are defined as actinomycete strains with low isolation rates when compared with the isolation of Streptomyces [6]. Currently, the discovery of new natural compounds is focusing on rare

• Rare actinomycetes are excellent sources of novel bioactive compounds, since they are less explored for secondary metabolites than the more common strains of Streptomyces [19][20]. The compounds from this group often have unique structures that may exhibit novel biological activities and could be

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

• [4]. To further understand the role of the ANS pathway in secondary metabolism, we recently identified the BGC for avenalumic acid (ava cluster, see the lower right corner of Figure 1B for its structure) by genome mining targeting the ANS pathway in Streptomyces sp. RI-77, and revealed its entire

• on an ava cluster-related BGC in Kutzneria albida JCM 3240. We showed that this BGC is involved in p-coumaric acid biosynthesis by heterologous expression in Streptomyces albus J1074 and several in vitro biochemical experiments using recombinant proteins. CmaA6 was shown to catalyze the diazotization

• . E. coli S17-1 was used for conjugation. Streptomyces albus J1074 was used for heterologous expression. Kutzneria albida JCM 3240 was purchased from the Japan Collection of Microorganisms. Enzymes used for DNA manipulation, including polymerase and restriction enzymes, were purchased from TaKaRa Bio

Secondary metabolites of Diaporthe cameroonensis, isolated from the Cameroonian medicinal plant Trema guineensis

• Bel Youssouf G. Mountessou,
• Élodie Gisèle M. Anoumedem,
• Blondelle M. Kemkuignou,
• Yasmina Marin-Felix,
• Frank Surup,
• Marc Stadler and
• Simeon F. Kouam

Beilstein J. Org. Chem. 2023, 19, 1555–1561, doi:10.3762/bjoc.19.112

• isolated from Streptomyces [30] and whose antimicrobial activity is probably related to the glutarimide moiety. In compound 1, the lack of this moiety, in addition to the fact that it has been isolated as a racemate could not lead to any beneficial property. As for compound 2, it is a diacetylated

Functions of enzyme domains in 2-methylisoborneol biosynthesis and enzymatic synthesis of non-natural analogs

• Binbin Gu,
• Lin-Fu Liang and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 1452–1459, doi:10.3762/bjoc.19.104

• diphosphate synthase (FPPS) and 2MIBS from Streptomyces coelicolor [26] (Scheme 1B). Crystal structures of both enzymes have been obtained [27][28] and allowed for a deep structure-based investigation of 2MIBS through site-directed mutagenesis [29]. The predicted amino acid sequences of 2MIBS homologs from

Functional characterisation of twelve terpene synthases from actinobacteria

• Anuj K. Chhalodia,
• Houchao Xu,
• Georges B. Tabekoueng,
• Binbin Gu,
• Kizerbo A. Taizoumbe,
• Lukas Lauterbach and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 1386–1398, doi:10.3762/bjoc.19.100

• . The first discovered example from this class is the fusicoccadiene (4) synthase from Phomopsis amygdali [8], and even triterpenes such as macrophomene (5) can be generated by these bifunctional enzymes [9]. After cloning of the gene for pentalenene (6) synthase from Streptomyces exfoliatus [10], many

• , revealing that the functions of still many terpene synthase homologs are unknown. Some of the largest branches in this tree represent the homologs of epi-isozizaene synthase from Streptomyces coelicolor [24], caryolan-1-ol synthase from Streptomyces griseus [25], selina-4(15),7(11)-diene synthase from

• Streptomyces pristinaespiralis [26], spiroviolene synthase from Streptomyces violens [27], micromonocyclol synthase from Micromonospora marina [28], α-amorphene synthase from Streptomyces viridochromogenes [29][30], epi-cubenol synthase from S. griseus [31], germacrene A synthase from M. marina [32], and 7-epi

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

Germacrene B – a central intermediate in sesquiterpene biosynthesis

• Houchao Xu and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 186–203, doi:10.3762/bjoc.19.18

• germacrene C synthase from Lycopersicon esculentum [32], the (+)-germacrene D synthase from Zingiber officinalis (17.1%) [33], the avermitilol synthase from Streptomyces avermitilis (5%) [34], and VoTPS1 from Valeriana officinalis [35]. For the bacterial selinadiene synthase (SdS) from Streptomyces

• of the δ-selinene synthase (ag4) from Abies grandis [66] and a product of several terpene synthases from C. sativa (CsTPS7, CsTPS8 and CsTPS22) [67], while 10 is the main product of the bacterial selinadiene synthase from Streptomyces pristinaespiralis [36][68]. It has recently been shown by a

Digyalipopeptide A, an antiparasitic cyclic peptide from the Ghanaian Bacillus sp. strain DE2B

• Adwoa P. Nartey,
• Aboagye K. Dofuor,
• Kofi B. A. Owusu,
• Anil S. Camas,
• Hai Deng,
• Marcel Jaspars and
• Kwaku Kyeremeh

Beilstein J. Org. Chem. 2022, 18, 1763–1771, doi:10.3762/bjoc.18.185

• the group have instilled fear in the scientists that may wish to investigate their potential. This has rendered the genera much less studied when compared to their Streptomyces counterparts in terms of bioprospecting for novel drug scaffolds. However, a substantial number of Bacillus species have