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

• column with 100 mM tricine with 100 mM NaCl at pH 7.5 as the mobile phase. Protein size exclusion chromatography standards (BioRad) were used to determine molecular masses. Nitramine degradation assays LC–MS analysis was performed using an Agilent 1260 LC stack equipped with a Zorbax RX-C18 column (5 μm

• buffer is 100 mM tricine 100 mM NaCl buffer at pH 7.5. Dashed grey lines represent elution volumes of molecular mass standards. Theoretical molecular weights are as follows Vs NnlA: 21,869 Da; Mr NnlA: 20638 Da; Pd NnlA: 18,473 Da; Ms NnlA : 18,239 Da; and Ps NnlA: 19,042 Da. UV–vis absorption spectra of

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

• . (b) HPLC chromatograms comparing standards with metabolites extracted from S. clavuligerus cultured in YMS and XTM media. Biosynthesis of drimenol congeners. (a) The cav BGC. (b) Proposed biosynthetic pathway for drimenol congeners 2–4. (c) HPLC analysis of metabolites from genetically engineered

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

• standards (CD3OD: δH 3.31, δC 49.0). LC–MS experiments and ESI–TOF MS/MS analyses were performed with an amaZon SL-NPC (Bruker Daltonics) or LCMS-2020 (Shimadzu) spectrometer coupled with a Shimadzu HPLC system equipped with an LC-20AD intelligent pump. GC–MS experiments were performed with a Shimadzu

• filter, and then injected into an LC–MS system, Cosmosil 5C18-MS-II (2 mm ID × 100 mm, Nacalai Tesque) (oven 40 °C; flowrate 0.2 mL/min) using a gradient of MeCN/H2O (1:9 to 6:4) containing 0.1% formic acid for 45 minutes. The standards were processed in the same manner. Whole genome analysis of

• triplicate, according to the Clinical Laboratory Standards Institute testing standard, in 96-well plate microbroth dilution assays. Compounds were tested against Gram-negative bacteria (Escherichia coli JW5503, Bukholderia multivorans NBRC 102086 and Bukholderia plantarii NBRC 104884) and Gram-positive

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

• ) and broad-leaved signal grass (BRAPP). We used 1 and 5 as standards to assess the potential of the new lead structures. Both standards showed sufficient crop selectivity only at the lower application rate of 50 g/ha. [1,3]Thiazolo[4,5-b]pyridine 5 showed good control of all tested warm-season weeds

• (ALOMY_R, also known as slender foxtail or black twitch) and ryegrass (LOLSS_R). Remarkably, 2,3-dihydro[1,3]thiazolo[4,5-b]pyridine 7b turned out to be superior to market standards (i.e., 1 and 2 in wheat) in terms of overall efficacy and resistance breaking potential. Halogen-free target compound 7c also

• internal standards cinmethylin (1) and methiozolin (2) against selected resistant and nonresistant monocotyledon weeds in wheat at application rates of 200 and 50 g/ha in advanced greenhouse trials, e.g., LOLSS_R and ALOMY_R (replicates: 10 plants per pot). Preemergence efficacy of 2,3-dihydro[1,3]thiazolo

Comparison of glycosyl donors: a supramer approach

• Anna V. Orlova,
• Nelly N. Malysheva,
• Maria V. Panova,
• Nikita M. Podvalnyy,
• Michael G. Medvedev and
• Leonid O. Kononov

Beilstein J. Org. Chem. 2024, 20, 181–192, doi:10.3762/bjoc.20.18

• maintained with an accuracy of ±0.2 °C. After the instrument was warmed up for at least 1 h (as experience suggests, after this period the temperature within the instrument remains stable for at least 8–10 h of continuous work) the instrument readings were verified against the quartz standards (α = +21.267

• measurement of the quartz standards (to monitor the instrument stability). Each measurement at a particular concentration was repeated 10 times, then averaged and plotted against concentration. The standard deviations were calculated by using the Student’s distribution (95% probability) and did not exceed 1

GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data

• Thomas Barillot,
• Baptiste Schindler,
• Baptiste Moge,
• Elisa Fadda,
• Franck Lépine and
• Isabelle Compagnon

Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134

• each monosaccharide unit is measured, and subsequently identified by comparison with a library of reference spectra of synthetic monosaccharide standards. In the early days of MS–IR spectroscopy, ca. one hour was necessary to record the IR fingerprint of a single molecule and the identification was

• ultimately be included in the algorithm for an optimal coverage of complex carbohydrates. (a) Fingerprint of an unknown monosaccharide. (b) Labelled reference spectra of monosaccharide standards. Typical experimental MS–IR spectra of the four categories of monosaccharides included in the first dataset. Blue

Synthesis of ether lipids: natural compounds and analogues

• Marco Antônio G. B. Gomes,
• Alicia Bauduin,
• Chloé Le Roux,
• Romain Fouinneteau,
• Wilfried Berthe,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96

• community working on the analysis of EL that require the preparation of standards for analytical purposes. The analysis and quantification of ether lipids is a very important field of research and development that was previously reviewed [47][48]. In this review, we focus on synthesis methodologies applied

Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements

• Robert N. Goldberg,
• Robert T. Giessmann,
• Peter J. Halling,
• Carsten Kettner and
• Hans V. Westerhoff

Beilstein J. Org. Chem. 2023, 19, 303–316, doi:10.3762/bjoc.19.26

• Robert N. Goldberg Robert T. Giessmann Peter J. Halling Carsten Kettner Hans V. Westerhoff Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, USA Institute for Globally Distributed Open Research and Education (IGDORE), Berlin

• general discussion of various aspects of these equilibrium measurements as well as STRENDA (Standards for Reporting Enzymology Data) recommendations regarding the measurements and the reporting of results. Keywords: enzyme-catalyzed reactions; equilibrium constant; standards; thermodynamics; Perspective

• 1. Introduction and motivation for recommendations The aim of the STRENDA (Standards for Reporting Enzymology Data) Commission [1] is to establish standards for reporting the results of measurements related to enzymology with the aim to improve the quality and the findability, accessibility

Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives

• Martin Kalník,
• Sergej Šesták,
• Juraj Kóňa,
• Maroš Bella and
• Monika Poláková

Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24

• standards. The enzymes screened included two Golgi types (GMIIb and AMAN-2) and two lysosomal types (LManII and JBMan) (Table 1). As for the Golgi-type mannosidases, AMAN-2 is a more relevant enzyme because its amino acid sequence and the 3D structure of its active site are almost identical to those of

Investigation of cationic ring-opening polymerization of 2-oxazolines in the “green” solvent dihydrolevoglucosenone

• Solomiia Borova and
• Robert Luxenhofer

Beilstein J. Org. Chem. 2023, 19, 217–230, doi:10.3762/bjoc.19.21

• K. HFIP was supplemented with 3 g/L potassium triflate, and the flow rate was adjusted to 0.50 mL/min. Calibration was performed using PEG standards with molar masses ranging from 0.1–1,000 kg/mol. Before every measurement, samples were filtered through 0.2 µm PTFE filters, Roth (Karlsruhe, Germany

• typically set from 1000 m/z to 7000 m/z. After parameter optimization, the instrument was calibrated with PEG standards depending on the m/z range of the individual sample. Samples were prepared with sinapinic acid (3,5-dimethoxy-4-hydroxycinnamic acid, SA) as matrices using the dried-droplet spotting

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

• based on tentative GC–MS assignments, often even without comparison to authentic standards, which results in a lot of information of questionable relevance. The large number of such papers published today makes it more and more difficult to find the relevant information in the literature. With this work

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

• (O)CH3 27.4 [49]/28.61; (iPrO)2P(O)H 4.2 [43]/4.54; PMe3 −62 [44]/−61.58 [50]). We have also included chemical shifts in more polar solvents (i.e., DMSO and methanol) when those were the only reported values. The chemical shifts of two commonly used reference standards for 31P NMR calculations

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

• advanced Marfey’s method [16][17][18] involving the complete hydrolysis of compound 1 followed by derivatization of the resultant amino acid residues with N-α-(2,4-dinitro-5-fluorophenyl)-ʟ-alanine amide (ʟ-FDAA). Similar derivatization reactions between ʟ-FDAA and authentic amino acid standards, followed

• promising antimicrobial properties in comparison to the laboratory standards ampicillin and amphotericin B. Compound 1 produced interesting biological activity against the Gram-negative bacteria Shigella sonnei, Shigella flexneri and the multidrug resistant Gram-positive Staphylococcus aureus with IC50 of

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

• available, and in fact only few papers describe corresponding synthetic methods [19][20][21][22]. It is well known that labelled compounds (such as those with 2H and 13C labels) can be used as internal standards for the quantitative measurements of the equal compound without label, e.g., straight from the

The stereochemical course of 2-methylisoborneol biosynthesis

• Binbin Gu,
• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 818–824, doi:10.3762/bjoc.18.82

• Supporting Information File 1). All compounds were identified from their EI mass spectra and retention indices in comparison to synthetic standards [29]. The substrate (R)-2-Me-LPP gave high yields of compound 1 (62% of total enzyme products in GC), besides 2-methylenebornane (10, 21%) and small amounts of 2

Sesquiterpenes from the soil-derived fungus Trichoderma citrinoviride PSU-SPSF346

• Wiriya Yaosanit,
• Vatcharin Rukachaisirikul,
• Souwalak Phongpaichit,
• Sita Preedanon and
• Jariya Sakayaroj

Beilstein J. Org. Chem. 2022, 18, 479–485, doi:10.3762/bjoc.18.50

• , 321.1309; found, 321.1320. Antimicrobial assay Antimicrobial activity was evaluated according to the Clinical and Laboratory Standards Institute [16]. Vancomycin was used as a positive control for S. aureus and methicillin-resistant S. aureus and exhibited MIC values of 0.25 and 1.0 μg/mL, respectively

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

• solvent protons (DMSO-d6: δH 2.50; CDCl3/CD3OD: δH 7.27) and carbons (DMSO-d6: δC 39.5; CDCl3/CD3OD: δC 77.0) as internal standards. HR–ESITOFMS spectra were measured on a Bruker compact qTOF mass spectrometer. Negative ion mode MS/MS experiments were operated on the same instrument under a multiple

Efficient synthesis of ethyl 2-(oxazolin-2-yl)alkanoates via ethoxycarbonylketene-induced electrophilic ring expansion of aziridines

• Yelong Lei and
• Jiaxi Xu

Beilstein J. Org. Chem. 2022, 18, 70–76, doi:10.3762/bjoc.18.6

• were conducted on a CEM discovery SP microwave reactor. The plates were visualized under UV light, as well as other TLC stains. 1H, 13C, and 31P NMR spectra were recorded on a Bruker 400 MHz spectrometer in CDCl3 with solvent peaks as internal standards, for 31P NMR, 85% H3PO4 as an external standard

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

• 13C NMR data, and high-resolution ESIMS data were presented. While an S-configuration was assigned for phialomustin B based on its positive specific rotation ([α]D25 +55.5, c 1.5, CHCl3) in comparison with those of synthetic standards [26], opposite negative signs in CHCl3 and MeOH ([α]D27 –12, c

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

• procedures. 1H NMR spectra were obtained using a Bruker AVANCE AV 400 spectrometer at a frequency of 400 MHz, respectively in CDCl3, CD3OD or D2O. Chemical shifts are reported in parts per million (ppm) and coupling constants in Hertz (Hz). The residual solvent peaks were used as internal standards. 1H NMR

Cryogels: recent applications in 3D-bioprinting, injectable cryogels, drug delivery, and wound healing

• Luke O. Jones,
• Leah Williams,
• Tasmin Boam,
• Martin Kalmet,
• Chidubem Oguike and
• Fiona L. Hatton

Beilstein J. Org. Chem. 2021, 17, 2553–2569, doi:10.3762/bjoc.17.171

• systems, progress can be made in achieving stable print structures for the ultra-high standards set by the human body. 5.2. Injectable cryogels Implantable biomaterials are proposed as a viable solution when dealing with issues relating to either the delivery or recruitment of cells. Currently the methods

Exfoliated black phosphorous-mediated CuAAC chemistry for organic and macromolecular synthesis under white LED and near-IR irradiation

• Azra Kocaarslan,
• Zafer Eroglu,
• Önder Metin and
• Yusuf Yagci

Beilstein J. Org. Chem. 2021, 17, 2477–2487, doi:10.3762/bjoc.17.164

• detector was calibrated with polystyrene standards having narrow molecular-weight distributions. The data were analyzed using Eco-SEC analysis software. A Hitachi HT7700 (TEM) with EXALENS (120 kV) working at a high-resolution (HR) mode was used to obtain transmission electron microscopy (TEM) images, high

Isolation and characterization of new phenolic siderophores with antimicrobial properties from Pseudomonas sp. UIAU-6B

• Emmanuel T. Oluwabusola,
• Olusoji O. Adebisi,
• Fernando Reyes,
• Kojo S. Acquah,
• Mercedes De La Cruz,
• Larry L. Mweetwa,
• Joy E. Rajakulendran,
• Digby F. Warner,
• Deng Hai,
• Rainer Ebel and
• Marcel Jaspars

Beilstein J. Org. Chem. 2021, 17, 2390–2398, doi:10.3762/bjoc.17.156

• compounds 1–5 was assigned as ʟ, based on the derivatization with Marfey’s reagent of compound 2 and 4 hydrolysates, which represented the two distinctive structural scaffolds and chemical shifts followed by HPLC analysis of the derivatized amino acid residuals in the hydrolysate and threonine standards

• shown in Figure S47 (Supporting Information File 1). Retention times (min) for the derivatized (ʟ-FDAA) threonine standards and for the observed peaks in the HPLC trace of each ʟ-FDAA-derivatized hydrolysis product under the reported conditions were as follows: retention times of standards: ʟ-Thr: 19.62

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

• Spectrum 100, respectively. All NMR experiments were performed on a Bruker AVANCE 500 spectrometer in CD3OD using the residual solvent proton (δΗ 3.31) and carbon (δC 49.2) signals as internal standards. HRESITOFMS were recorded on a Bruker micrOTOF focus mass spectrometer. An Agilent HP1200 system

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

• ][260]. The automated solid-phase approach required only two BBs with the amino group protected either with the N-TCA 79 or with the N-Cbz group 80 (Scheme 12). Compounds 81–85 served as standards to explore the conformational space of COS with different PA. NMR analysis and MD simulations revealed the