Tenacibactins K–M, cytotoxic siderophores from a coral-associated gliding bacterium of the genus Tenacibaculum

• Yasuhiro Igarashi,
• Yiwei Ge,
• Tao Zhou,
• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku and
• Agus Trianto

Beilstein J. Org. Chem. 2022, 18, 110–119, doi:10.3762/bjoc.18.12

• . Microorganism Strain C16-1 was isolated from a stony coral Favia sp. purchased from an aquarium vendor in Nagasaki, Japan, according to the method described previously [40]. The strain was identified as a member of the genus Tenacibaculum on the basis of 99.4% similarity in the 16S rRNA gene sequence (1455

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

• HPLC analysis was done on a Shimadzu Prominence UFLC system composed of a DGU-20A3R degasser, an SPD-20A UV detector, and an LC-20AD pump, which is connected to a C-R8A Chromatopac data processor. Microorganism Strain RD010705 was obtained from NBRC. The strain was identified as a member of the genus

Nomimicins B–D, new tetronate-class polyketides from a marine-derived actinomycete of the genus Actinomadura

• Zhiwei Zhang,
• Tao Zhou,
• Taehui Yang,
• Keisuke Fukaya,
• Enjuro Harunari,
• Shun Saito,
• Katsuhisa Yamada,
• Chiaki Imada,
• Daisuke Urabe and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2194–2202, doi:10.3762/bjoc.17.141

• , Institute for Chemical Research, Kyoto University. Molecular structures were visualized using Maestro 12.3 software package. ECD spectra were visualized using GaussView 6.0.16 and Microsoft Excel 2019. Microorganism Actinomadura sp. AKA43 was isolated from a sea water sample collected from Sagami Bay at a

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

• -B24674, which revealed the presence of a fluorinase gene, suggesting that the microorganism could produce fluorinated compounds from fluoride ion. This was confirmed by 19F NMR of culture supernatant after the bacterium was grown in medium containing 2 mM fluoride ion. Furthermore, because of the large

The preparation and properties of 1,1-difluorocyclopropane derivatives

• Kymbat S. Adekenova,
• Peter B. Wyatt and
• Sergazy M. Adekenov

Beilstein J. Org. Chem. 2021, 17, 245–272, doi:10.3762/bjoc.17.25

• smooth hydrolysis. Wang et al. reported the enantioselective biotransformations of geminally difluorinated cyclopropanecarbonitriles and amides in 2004 [77]. They transformed gem-difluorocyclopropane derivatives with the help of a soil microorganism, Rhodococcus sp. AJ270, which provided a very effective

Nocarimidazoles C and D, antimicrobial alkanoylimidazoles from a coral-derived actinomycete Kocuria sp.: application of ¹J_C,H coupling constants for the unequivocal determination of substituted imidazoles and stereochemical diversity of anteisoalkyl chains in microbial metabolites

• Md. Rokon Ul Karim,
• Enjuro Harunari,
• Amit Raj Sharma,
• Naoya Oku,
• Kazuaki Akasaka,
• Daisuke Urabe,
• Mada Triandala Sibero and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 2719–2727, doi:10.3762/bjoc.16.222

• 7.27) and carbon atoms (δC 77.0) as internal standards for other compounds. HRESITOFMS spectra were recorded on a Bruker micrOTOF focus mass spectrometer. An Agilent HP1200 system equipped with a diode array detector was used for analysis and purification. Microorganism The coral sample Mycedium sp

4-Hydroxy-3-methyl-2(1H)-quinolone, originally discovered from a Brassicaceae plant, produced by a soil bacterium of the genus Burkholderia sp.: determination of a preferred tautomer and antioxidant activity

• Dandan Li,
• Naoya Oku,
• Yukiko Shinozaki,
• Yoichi Kurokawa and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1489–1494, doi:10.3762/bjoc.16.124

• spectrometer. Chemiluminescence was measured on a Molecular Devices SpectraMax M2 microplate reader. Microorganism Burkholderia sp. 3Y-MMP was isolated from a soil sample collected in Toyama, central Japan, in June 2015 by a procedure similar to that described in [46]. One mM of ZnCl2, instead of CoCl2, was

A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium

• Shun Saito,
• Kota Atsumi,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Naoya Oku,
• Md. Rokon Ul Karim,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97

• obtained on a Bruker AVANCE 500 spectrometer in DMSO-d6 or CDCl3, and referenced to the residual solvent signals (δH 2.50, δC 39.5 for DMSO-d6; δH 7.26, δC 77.2 for CDCl3). HRESITOFMS spectra were recorded on a Bruker micrOTOF spectrometer. Microorganism Pseudosporangium sp. RD062863 was obtained from NBRC

Opening up connectivity between documents, structures and bioactivity

• Christopher Southan

Beilstein J. Org. Chem. 2020, 16, 596–606, doi:10.3762/bjoc.16.54

• -P” (DARCP). This is shown schematically in Figure 1. The entity specifications can be adapted to different use-cases. For example, the substitution of “P” with target “T” can be used where “T” is a cell or a microorganism. Another example would be where an SAR series can be represented as a

Two antibacterial and PPARα/γ-agonistic unsaturated keto fatty acids from a coral-associated actinomycete of the genus Micrococcus

• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku,
• Nobuyasu Matsuura,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 297–304, doi:10.3762/bjoc.16.29

• . Microorganism Strain C5-9 was collected from a stony coral, Catalaphyllia sp., obtained from an aquarium vendor in Osaka, Japan. A piece of the coral specimen (ca. 1 g) was surface-sterilized by washing with 70% ethanol, followed by rinsing with sterile natural seawater. The coral piece was homogenized by

Pigmentosins from Gibellula sp. as antibiofilm agents and a new glycosylated asperfuran from Cordyceps javanica

• Soleiman E. Helaly,
• Wilawan Kuephadungphan,
• Patima Phainuphong,
• Mahmoud A. A. Ibrahim,
• Kanoksri Tasanathai,
• Suchada Mongkolsamrit,
• Janet Jennifer Luangsa-ard,
• Souwalak Phongpaichit,
• Vatcharin Rukachaisirikul and
• Marc Stadler

Beilstein J. Org. Chem. 2019, 15, 2968–2981, doi:10.3762/bjoc.15.293

• formation of Staphylococcus aureus DSM1104. The lack of toxicity toward the studied microorganism and cell lines of pigmentosin B (2), as well as the antimicrobial effect of pigmentosin A (1), made them good candidates for further development for use in combination therapy of infections involving biofilm

• , as outlined in our recent publications [9][48]. The antibiofilm activity is expressed as MIC values, which is defined as the lowest concentration of substance that prevents biofilm formation of a target microorganism by at least 50%. Compounds that had shown inhibition of biofilm formation against

• incubated at 30 °C for 24 h. The MBC endpoint was defined as the lowest concentration of the compounds that killed microorganisms, where no visible growth of the microorganism tested was observed on the agar plates. The experimental procedures and the results are given in detail in Supporting Information

Two new aromatic polyketides from a sponge-derived Fusarium

• Mada Triandala Sibero,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Ocky K. Karna Radjasa,
• Agus Sabdono,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2019, 15, 2941–2947, doi:10.3762/bjoc.15.289

• Shimadzu UV-1800 (Shimadzu Corp., Kyoto, Japan). Microorganism Fusarium sp. KJMT.FP.4.3 was isolated from a sponge Xestospongia sp. collected from Karimunjawa National Park, Indonesia with the permission number 1096/T.34/TU/SIMAKSI/7/2017. This fungus was isolated using a surface sterilization method [14

Isolation and biosynthesis of an unsaturated fatty acid with unusual methylation pattern from a coral-associated bacterium Microbulbifer sp.

• Amit Raj Sharma,
• Enjuro Harunari,
• Tao Zhou,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2019, 15, 2327–2332, doi:10.3762/bjoc.15.225

• were recorded on a Bruker microTOF focus. Sodium [1-13C]acetate was purchased from Cambridge Isotope Laboratories, Inc., and ʟ-[methyl-13C]methionine from Sigma-Aldrich Co. LLC. Microorganism Strain C4-6 was isolated from a cultured stony coral (Porites sp.) obtained from an aquarium vendor in Nagasaki

Fluorine-containing substituents: metabolism of the α,α-difluoroethyl thioether motif

• Andrea Rodil,
• Alexandra M. Z. Slawin,
• Nawaf Al-Maharik,
• Ren Tomita and
• David O’Hagan

Beilstein J. Org. Chem. 2019, 15, 1441–1447, doi:10.3762/bjoc.15.144

• other areas of bioactives discovery research, to complement the widely used ROCF3 and RSCF3 groups and there is a clear similarity to the ‘polar lipophilic’ groups ROCF2H, and RSCF2H [26]. Experimental Microorganism growth Cunninghamella elegans DSM1908 was grown on Saboraud dextrose agar gel plates for

Protein–protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics

• Laura Carro

Beilstein J. Org. Chem. 2018, 14, 2881–2896, doi:10.3762/bjoc.14.267

• , respectively). A subsequent antibacterial screening showed that the lead pyrimidine 40 was also a moderate inhibitor of the growth of the Gram-positive pathogen B. subtilis and the Gram-negative microorganism E. coli. The same research group developed further SAR studies using compound 41 (Figure 9) as lead of

• described are conserved in prokaryotes but not present in eukaryotes, it may be feasible to develop inhibitors that selectively target the microorganism systems, and therefore avoiding mechanism-related side effects. However, these large sets of interactions remain poorly characterized and targeting them is

Latest development in the synthesis of ursodeoxycholic acid (UDCA): a critical review

• Fabio Tonin and
• Isabel W. C. E. Arends

Beilstein J. Org. Chem. 2018, 14, 470–483, doi:10.3762/bjoc.14.33

• of 12-dehydroxylase producing microorganism (Clostridium perfringens ATCC 19574) was patented in 1976 [55]. However, the presence and the expression of a protein that can catalyse this reaction were never confirmed in other papers. The putative molecular mechanism for the C12 dehydroxylation is still

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

• Marco Russo,
• Daniele La Corte,
• Annalisa Pisciotta,
• Serena Riela,
• Rosa Alduina and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2751–2763, doi:10.3762/bjoc.13.271

• tests in order to assess their interaction with a model plasmid DNA (pUC19) and to evaluate whether they may influence the internalization of exogenous DNA in bacterial systems, in particular the Gram-negative model microorganism Escherichia coli. Results and Discussion Polarimetric behavior of AmCDs A

18-Hydroxydolabella-3,7-diene synthase – a diterpene synthase from Chitinophaga pinensis

• Jeroen S. Dickschat,
• Jan Rinkel,
• Patrick Rabe,
• Arman Beyraghdar Kashkooli and
• Harro J. Bouwmeester

Beilstein J. Org. Chem. 2017, 13, 1770–1780, doi:10.3762/bjoc.13.171

• ]. Recently, the first terpene synthases were reported from a eukaryotic soil microorganism, the social amoeba Dictyostelium discoideum [4][5]. With respect to bacterial enzymes, many terpene synthases have been identified and their products have been structurally characterised (reviewed in [6], following

Biosynthetic origin of butyrolactol A, an antifungal polyketide produced by a marine-derived Streptomyces

• Enjuro Harunari,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2017, 13, 441–450, doi:10.3762/bjoc.13.47

• were referenced to the solvent signal (δH(D) 2.50). ESITOFMS were recorded on a Bruker microTOF focus. Microorganism Streptomyces sp. strain TP-A0882 was isolated from a deep seawater collected in the Toyama Bay, Japan. The strain was identified as a member of the genus Streptomyces on the basis of

Posttranslational isoprenylation of tryptophan in bacteria

• Masahiro Okada,
• Tomotoshi Sugita and
• Ikuro Abe

Beilstein J. Org. Chem. 2017, 13, 338–346, doi:10.3762/bjoc.13.37

• found in peptide pheromones from a specific microorganism, as an essential modification for the pheromonal activity. Thus, it is conceivable that the posttranslational isoprenylation of tryptophan is actually widespread. Therefore, more research should be focused on the details and the diversity of the

A non-canonical peptide synthetase adenylates 3-methyl-2-oxovaleric acid for auriculamide biosynthesis

• Daniel Braga,
• Dirk Hoffmeister and
• Markus Nett

Beilstein J. Org. Chem. 2016, 12, 2766–2770, doi:10.3762/bjoc.12.274

• microorganism as a promising source of natural products. Genes for nonribosomal peptide synthetases (NRPSs) were found to be preponderant, either solely or organised in combination with polyketide synthase (PKS) genes, representing four and five clusters, respectively. Two PKS and three putative bacteriocin

Muraymycin nucleoside-peptide antibiotics: uridine-derived natural products as lead structures for the development of novel antibacterial agents

• Daniel Wiegmann,
• Stefan Koppermann,
• Marius Wirth,
• Giuliana Niro,
• Kristin Leyerer and
• Christian Ducho

Beilstein J. Org. Chem. 2016, 12, 769–795, doi:10.3762/bjoc.12.77

• in vitro activity of potential agents against certain bacteria is the determination of minimum inhibitory concentrations (MIC). MICs are defined as the lowest concentration at which a potential antimicrobial agent inhibits the visible growth of a microorganism [75]. They are easily determined and

• reflect several effects such as target interaction, cellular uptake and potential resistance mechanisms of the microorganism. MIC values are therefore widely used, also in studies on muraymycin analogues (e.g., [22][76][77][78]) and have been the basis of many structure–activity relationship studies (see

Selected synthetic strategies to cyclophanes

• Sambasivarao Kotha,
• Mukesh E. Shirbhate and
• Gopalkrushna T. Waghule

Beilstein J. Org. Chem. 2015, 11, 1274–1331, doi:10.3762/bjoc.11.142

• ]. Macrocidin A (19) and macrocidin B (20) [64] belong to a family of plant pathogens produced by Phoma macrostoma, a microorganism parasitic to Canadian thistle. Macrocidins contain a tetramic acid group in their skeleton and show selective herbicidal activity on broadleaf weeds but do not affect grasses

New depsidones and isoindolinones from the mangrove endophytic fungus Meyerozyma guilliermondii (HZ-Y₂) isolated from the South China Sea

• Senhua Chen,
• Zhaoming Liu,
• Yayue Liu,
• Yongjun Lu,
• Lei He and
• Zhigang She

Beilstein J. Org. Chem. 2015, 11, 1187–1193, doi:10.3762/bjoc.11.133

• Senhua Chen Zhaoming Liu Yayue Liu Yongjun Lu Lei He Zhigang She School of Chemistry and Chemical Engineering, Sun Yat-Sen University, 135 Xin gang West Road, Guangzhou 510275, China Guangdong Province Key Laboratory of Functional Molecules in Oceanic Microorganism, Bureau of Education, Sun Yat

Aspergiloid I, an unprecedented spirolactone norditerpenoid from the plant-derived endophytic fungus Aspergillus sp. YXf3

• Zhi Kai Guo,
• Rong Wang,
• Wei Huang,
• Xiao Nian Li,
• Rong Jiang,
• Ren Xiang Tan and
• Hui Ming Ge

Beilstein J. Org. Chem. 2014, 10, 2677–2682, doi:10.3762/bjoc.10.282

• ), a cleistanthane-type diterpenoid (aspergiloid C), and norcleistanthane-type diterpenoids (asergiloids A, B, and F–H), many of which were reported from this microorganism for the first time [7][8][9]. Interestingly, sphaeropsidins A and B were also discovered from both Aspergillus chevalieri and