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

• antibiotic activity towards Gram-negative bacteria. An NNG degrading heme enzyme, called NnlA, has recently been discovered in the genome of Variovorax sp. strain JS1663 (Vs NnlA). Evidence is presented that NnlA and therefore, NNG degradation activity is widespread. To achieve this objective, we

• NnlA cannot degrade the NNG analog 2-nitroaminoethanol. The combined data strongly suggest that NnlA enzymes specifically degrade NNG and are found in diverse bacteria and environments. These results imply that NNG is also produced in diverse environments and NnlA may act as a detoxification enzyme to

• nitramine. An enzyme, N-nitroglycine lyase A (NnlA), from the bacterium Variovorax sp. strain JS1663 (Vs NnlA) was recently shown to degrade NNG. This strain was enriched from sludge from the Holston Army Ammunition Plant using selective growth media containing NNG as the only carbon and nitrogen source [20

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

• calidoustene C, DrtB from Aspergillus calidoustus functions as a dual-functional enzyme, comprising two domains: a HAD-like hydrolase domain fused with a terpene cyclase domain. Initially, FPP is cyclized into the drimenyl diphosphate in a class II terpene cyclase manner, which is then processed by the

• with literature data [29]. This marks the first discovery of natural DMTs from bacteria, surpassing previous findings of bacterial DMSs which focused only on the enzyme itself without reporting natural DMT or exploring associated BGCs [17]. Additionally, while drimentines, bacterial meroterpenoids

• utilizing the EFI-genome neighborhood tool (EFI-GNT), sequence alignment, and manual BLAST analysis [33]. Leveraging our previous discovery of SsDMS from Streptomyces showdoensis, we identified a homologous terpene cyclase (sclav_p0068) in S. clavuligerus. This enzyme shares a 50% sequence similarity with

Synthesis and characterization of water-soluble C₆₀–peptide conjugates

• Yue Ma,
• Lorenzo Persi and
• Yoko Yamakoshi

Beilstein J. Org. Chem. 2024, 20, 777–786, doi:10.3762/bjoc.20.71

• and nonionic polymer, poly(vinylpyrrolidone) (PVP) [25] and applied these to several in vitro biological assays to report DNA photocleavage [26] and related ROS generation [27][28], antimicrobial photoactivity [29], chondrogenesis-promoting activity [30][31], photocytotoxicity [32][33], and GST enzyme

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

• Zeeck and co-workers in the early 2000s, is a method in which the target bacteria are cultured under various conditions (medium composition, temperature, pH, oxygen supply, light quality and quantity, addition of precursors and enzyme inhibitors, etc.) and all metabolites obtained from them are analyzed

Research progress on the pharmacological activity, biosynthetic pathways, and biosynthesis of crocins

• Zhongwei Hua,
• Nan Liu and
• Xiaohui Yan

Beilstein J. Org. Chem. 2024, 20, 741–752, doi:10.3762/bjoc.20.68

• extracting crocins include ultrasound-assisted extraction (UAE), supercritical fluid extraction, enzyme-linked extraction, and microwave-assisted extraction. Among these methods, the UAE exhibits a higher extraction yield [23][24]. Recently, Fiorito et al. developed a technique that utilizes cost-effective

• carotenoids, while NCEDs cleave the 11,12-double bond [89]. Rubio et al. identified four CCDs, CsCCD1a, CsCCD1b, CsCCD4a, and CsCCD4b, from C. crocus. The expression patterns of CsCCD4a and CsCCD4b were associated with the accumulation of β-ionone during stigma development. However, no enzyme involved in

• enzyme activity was lower than CsCCD2 [2][92]. BoCCD4-3 from Bixa orellana was revealed to cleave various carotenoids, lycopene (5), β-carotene (6), and zeaxanthin (7), to form crocetin dialdehyde (8) by in vitro assay [93][94]. In contrast, CsCCD2, BdCCD4.1, and BdCCD4.3 could only cleave zeaxanthin (7

Substrate specificity of a ketosynthase domain involved in bacillaene biosynthesis

• Zhiyong Yin and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2024, 20, 734–740, doi:10.3762/bjoc.20.67

• glutamate decarboxylase, and incubated with BaeJ-KS2. Substrate binding was demonstrated through 13C NMR analysis of the products against the background of various control experiments. Keywords: bacillaene; biosynthesis; enzyme mechanisms; isotopes; trans-AT polyketide synthases; Introduction Polyketides

• only for the incorporation of one extender unit [2][3]. Although enzyme domains with various specialised catalytic functions can be found as integral part of polyketide synthases, three domain types are fundamental to their biosynthesis, resembling the same logic as observed for fatty acid biosynthesis

• agreement with the presence of a double bond between C22 and C23 in 1. A contrasting picture was obtained through deletion of the TE domain that resulted in off-loading of all premature intermediates from the PKS [16], possibly catalysed by a proofreading AT-like enzyme encoded in the bae cluster [17

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

• cyclization and hydrolytic activities that are not easily predictable, related mechanism studies indicated that the pre-reaction states of the enzyme and substrate are critical for selectivity [15][16]. Thus, both the mutation of key residues in the active pocket and the addition of a nonionic detergent can

• increase the ratio of intramolecular nucleophilic attack, resulting in macrocyclic products via preorganization of substrate and enzyme in an active conformation [17][18]. Chemoenzymatic strategies, which merge practical enzymatic transformations with modern organic synthetic methods to increase the

• efficiency of synthetic approaches, have already shown a growing influence in the synthesis of bioactive natural products, pharmaceutical components, and other valuable molecules with the development of microbial genetics and enzyme engineering [19][20][21][22]. The comprehensive investigation of TE domains

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

• TCs subsequently catalyze the second cyclization to construct the polycyclic scaffold of natural products [5]. In plants, two independent αβγ tri-domain TCs, ent-CPP synthase (CPS) and ent-kaurene synthase (KS), are often used for this conversion [6], and a single bifunctional enzyme that successively

• catalyzes these reactions is also known [7]. Bacteria also use two enzyme systems for the biosynthesis of LRDs, but the domain organization of the corresponding TCs is different from those of plant enzymes. In bacteria, the class II enzymes with βγ domains and the class I enzyme with a single α domain are

• Aspergillus oryzae and biochemical characterization of recombinant enzymes unveiled a fungal two-enzyme pathway to isopimaradiene, which is unprecedented for fungal LRDs. Results and Discussion To explore the fungal LRDs, we searched our in-house database by BLAST using known fungal bifunctional TCs such as

Production of non-natural 5-methylorsellinate-derived meroterpenoids in Aspergillus oryzae

• Jia Tang,
• Yixiang Zhang and
• Yudai Matsuda

Beilstein J. Org. Chem. 2024, 20, 638–644, doi:10.3762/bjoc.20.56

• instead of the C-4′ carbonyl group (Figure 2C). It is unlikely that 8 is the direct product of InsA7; thus, we hypothesized that an endogenous enzyme in A. oryzae is responsible for the reduction, with an enoylreductase first reducing the C-2′/C-3′ double bond of 7 and the resulting product undergoing

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

• methyltransferase near BGC 7.3, suggesting its involvement in adding a methoxy group at the C16 position of compound 1. From these key enzyme genes, we propose a hypothetical biosynthetic pathway (Figure 5). Compounds 1 and 2 are hypothesized to be synthesized from a tryptophan precursor via a shared biosynthetic

• a ring-opening rearrangement. Alternatively, it is proposed that the ring-opening rearrangement precedes the methyl modification at the oxygen atom of the succinimide ring. We aim to confirm the initial step of this pathway, where tryptophan and DMAPP are catalyzed by the enzyme ShnA to form a

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

• the individual enzyme activities is lacking. In this study, we verify the activity for one enzyme in this pathway. We show that Hyg17 is a myo-inositol dehydrogenase that has a unique substrate scope when compared to other myo-inositol dehydrogenases. Furthermore, we analyze sequences from the protein

• Hyg17 sequences with other members of the oxidoreductase family and inositol dehydrogenases and discuss specialized genome mining approaches using these sequences to identify new natural product biosynthetic clusters. Results and Discussion Hyg17 enzyme activity We found that Hyg17 formed inclusion

• (Figure 2b). Although this is consistent with native myo- and scyllo-dehydrogenases LcIDH1 and LcIDH2 from Lactobacillus casei [12], there have been reports of a genetically engineered NAD-specific dehydrogenase that has been converted to an efficient NADP-dependent enzyme [14]. Next, we determined the

Recent developments in the engineered biosynthesis of fungal meroterpenoids

• Zhiyang Quan and
• Takayoshi Awakawa

Beilstein J. Org. Chem. 2024, 20, 578–588, doi:10.3762/bjoc.20.50

• for the design of biosynthetic machineries to produce a variety of bioactive meroterpenoids. Keywords: αKG-dependent dioxygenases; enzyme engineering; fungal meroterpenoids; synthetic biology; terpene cyclases; Introduction Meroterpenoids are complex natural products with intricate skeletal

• resulting cation intermediate at C-4' to induce an acyl shift, forming the steroid-like structure of 7 with a 6-6-6-5 ring (Figure 2). Swapping terpenoid cyclases in heterologous expression systems A search of the genome database for Trt1-homolog CYCs revealed the enzyme AusL (41% identity with Trt1) in

• Aspergillus nidulans, within the same phylogenetic clade. Expression of this enzyme in place of Trt1 resulted in the formation of the 6-6-6-6-membered ring protoaustinoid A (8) (Figure 2) [9]. In addition, the expression of the cyclase AdrI (38% identity with Trt1) from Penicillium chrysogenum produced the 6

Synthesis and biological profile of 2,3-dihydro[1,3]thiazolo[4,5-b]pyridines, a novel class of acyl-ACP thioesterase inhibitors

• Jens Frackenpohl,
• David M. Barber,
• Guido Bojack,
• Birgit Bollenbach-Wahl,
• Ralf Braun,
• Rahel Getachew,
• Sabine Hohmann,
• Kwang-Yoon Ko,
• Karoline Kurowski,
• Bernd Laber,
• Rebecca L. Mattison,
• Thomas Müller,
• Anna M. Reingruber,
• Dirk Schmutzler and
• Andrea Svejda

Beilstein J. Org. Chem. 2024, 20, 540–551, doi:10.3762/bjoc.20.46

• the release of fatty acids from the plastids to the endoplasmic reticulum, where they are utilized for the synthesis of acyl lipids that are essential components for various physiological and defensive processes [3][4][5][6]. As this enzyme target does not exist in other kingdoms, structure–activity

• binding affinity to enzyme targets, e.g., acyl-ACP thioesterases, belonging to the protein family of FATs, was demonstrated by using co-crystallization, fluorescence-based thermal shift assays, and chemoproteomics techniques [3]. Likewise, methiozolin (2) is a recently assigned FAT inhibitor that has

• ]pyridines that showed promising inhibition of the plant-specific enzyme FAT, we explored the selective late-stage conversion into the corresponding 2,3-dihydro[1,3]thiazolo[4,5-b]pyridines via different reduction methods. Noteworthy, substituted 2,3-dihydro[1,3]thiazolo[4,5-b]pyridines had remained almost

Development of a chemical scaffold for inhibiting nonribosomal peptide synthetases in live bacterial cells

• Fumihiro Ishikawa,
• Sho Konno,
• Hideaki Kakeya and
• Genzoh Tanabe

Beilstein J. Org. Chem. 2024, 20, 445–451, doi:10.3762/bjoc.20.39

• groups of compounds 14a–e yielded the desired ʟ-Phe-AMS derivatives 4, 5, and 7. We first determined the binding affinities of ʟ-Phe-AMS derivatives 4–9 for the A-domain of GrsA using a previously developed competitive enzyme-linked immunosorbent assay technique for A-domains in NRPSs [14], which allowed

Green and sustainable approaches for the Friedel–Crafts reaction between aldehydes and indoles

• Periklis X. Kolagkis,
• Eirini M. Galathri and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2024, 20, 379–426, doi:10.3762/bjoc.20.36

• of green chemistry. Organocatalysis is the acceleration of chemical reactions with the use of small organic compounds, which do not contain any amounts of enzyme or inorganic elements [37][38][39]. The benefits of solid acid catalysis render them as an appealing choice, compared to their liquid

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

• biosynthesis by heterologous expression of the cma cluster and in vitro enzyme assays using recombinant Cma proteins. The ATP-dependent diazotase CmaA6 catalyzed the diazotization of both 3-aminocoumaric acid and 3-aminoavenalumic acid using nitrous acid in vitro. In addition, the high efficiency of the CmaA6

• recent studies [9][10][11][12][13][14]. Most of them belong to the adenylate-forming enzyme superfamily (ANL superfamily) and utilize ATP to activate nitrous acid by AMPylation, with the only exception being AzpL in alazopeptin biosynthesis, which is a membrane protein that catalyzes diazotization

• encoded by the cma cluster, we performed in vitro enzyme analyses using recombinant Cma proteins. First, we obtained recombinant CmaA1, holo-CmaA3, and CmaA6 by expressing the corresponding genes in Escherichia coli BL21(DE3) (Figure S4 in Supporting Information File 1). Note that holo-CmaA3 was obtained

Tying a knot between crown ethers and porphyrins

• Maksym Matviyishyn and
• Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

• cations. These molecules could serve as models for enzyme active centres and present intriguing catalytic features. Additionally, a separate and equally intriguing group of molecules that can be achieved by taking advantage of the hybrid porphyrin–crown ether compounds includes mechanically interlocked

Sulfur-containing spiroketals from Breynia disticha and evaluations of their anti-inflammatory effect

• Ken-ichi Nakashima,
• Naohito Abe,
• Masayoshi Oyama,
• Hiroko Murata and
• Makoto Inoue

Beilstein J. Org. Chem. 2023, 19, 1604–1614, doi:10.3762/bjoc.19.117

• the suppression of mRNA levels at high concentrations (>25 μM) of compound 7, anti-inflammatory effects occurred at lower concentrations without cytotoxicity. The production of IL-1β and IL-6 was also evaluated by an enzyme-linked immunosorbent assay (ELISA) using culture supernatants. The LPS

Unraveling the role of prenyl side-chain interactions in stabilizing the secondary carbocation in the biosynthesis of variexenol B

• Moe Nakano,
• Rintaro Gemma and
• Hajime Sato

Beilstein J. Org. Chem. 2023, 19, 1503–1510, doi:10.3762/bjoc.19.107

• group. However, such a large conformational change is unlikely to occur within the enzyme. Therefore, the Curtin–Hammett principle is not applicable to this system. To investigate the details of carbocations and hyperconjugations in the variexenol B biosynthetic pathway, we carried out a bond length

• computational models in the future. Furthermore, future research is expected to determine whether there is space in the enzyme active site for these prenyl side chains to fold and approach the reaction center, as seen in X-ray crystallographic analysis. Experimental All calculations were carried out using the

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

• studied. Several 2-methylisoborneol synthases have a proline-rich N-terminal domain of unknown function. The results presented here demonstrate that this domain leads to a reduced enzyme activity, in addition to its ability to increase long-term solubility of the protein. Furthermore, the substrate scope

• of the 2-methylisoborneol synthase was investigated through enzyme incubations with several substrate analogs, giving access to two C12 monoterpenoids. Implications on the stereochemical course of the terpene cyclisation by 2-methylisoborneol synthase are discussed. Keywords: biosynthesis; enzymes

• reactions with full length 2MIBS, domain A, domain B, and the combination of domains A + B (Figure 1A). Herein, the production of full length 2MIBS was normalised to 100%. Domain A alone did not yield any enzyme product, whereas domain B alone gave a strongly increased production of 1 (238 ± 4%). The

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

• ), geranylgeranyl pyrophosphate (GGPP) and geranylfarnesyl pyrophosphate (GFPP). Sesquiterpene synthases The enzyme from K. kofuensis (Table 1, entry 1) exhibited all highly conserved motifs required for functionality including the aspartate-rich motif (83DDAYCD) and the NSE triad (223NDIASYYKE, Figure S2

• , Supporting Information File 1). The closest characterised terpene synthase with an amino acid sequence identity of 25% is the (1(10)E,4E,6S,7R)-germacradien-6-ol synthase from Streptomyces pratensis [33]. The recombinant enzyme efficiently converted FPP into one sesquiterpene alcohol whose electron

• recently identified in which sesquiterpenes from bacteria showed an enantiomeric relationship to plant compounds [36]. The enzyme from K. kofuensis represents the first terpene synthase for the biosynthesis of 10 and was thus identified as Kutzneria kofuensis (+)-δ-Cadinol Synthase (KkdCS). A few closely

Enabling artificial photosynthesis systems with molecular recycling: A review of photo- and electrochemical methods for regenerating organic sacrificial electron donors

• Grace A. Lowe

Beilstein J. Org. Chem. 2023, 19, 1198–1215, doi:10.3762/bjoc.19.88

• tris buffer rather than phosphate [44]. Instead of using the regenerated NADH in a photocatalytic system, this team actually used an enzyme to consume the regenerated NADH and check its viability. Robert and co-workers recycled the NADH analogue 1,4-BNAH using different photosensitizers and cobalt

• that [CpRh(bpy)(H2O)]2+ could slowly produce formate, a key biocatalytic intermediate, in the absence of the enzymes but they validated their system by proving that overall the formate production and conversion to methanol by the biocatalytic enzyme cascade far outcompeted any side-reactions. Ishitani

Aromatic C–H bond functionalization through organocatalyzed asymmetric intermolecular aza-Friedel–Crafts reaction: a recent update

• Anup Biswas

Beilstein J. Org. Chem. 2023, 19, 956–981, doi:10.3762/bjoc.19.72

• antibacterial acitivity against resistant S. aureus strains. It is also an inhibitor of the enzyme peptide deformylases (PDFs). The synthesis comprised the reaction between the highly substituted hydroquinone 142 and dehydroalanine 143 in the presence of chiral phosphoric acid P7 as catalyst to prepare

Clauson–Kaas pyrrole synthesis using diverse catalysts: a transition from conventional to greener approach

• Dileep Kumar Singh and
• Rajesh Kumar

Beilstein J. Org. Chem. 2023, 19, 928–955, doi:10.3762/bjoc.19.71

• ], antiviral [11][12], antibacterial [13][14][15], antimalarial [16][17], anti-inflammatory [18][19], anti-oxidant [20][21][22], antifungal [23][24] and antibiotic [25][26] and as enzyme inhibitors [27][28]. Several pharmaceuticals, polymers and naturally occurring compounds, including heme, chlorophyll

• subsequent removal of MeOH, dehydration and aromatization affords N-substituted pyrroles 21. In 2013, Chatzopoulou [63] and co-workers reported a high-yielding Clauson–Kaas pyrrolyl-phenol synthesis using nicotinamide, which is a cheap and nontoxic catalyst and a vitamin and enzyme cofactor. The authors

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

• protein RS02200: FAAL: fatty acyl-AMP ligase; ACP: acyl carrier protein; KS: β-ketoacyl synthase; AT: acyltransferase; KR: ketoreductase; C: condensation; A: adenylation; MT: methyltransferase; PCP: peptidyl carrier protein. A discrete enzyme, the thiazolinyl imide reductase RS02195 (Red), catalyzes the