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Search for "detection" in Full Text gives 526 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.

Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers

  • Andreas Wiest and
  • Pavel Kielkowski

Beilstein J. Org. Chem. 2024, 20, 2323–2341, doi:10.3762/bjoc.20.199

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  • provide unprecedented depth of proteome coverage and the possibility to detect desired modified peptides with high sensitivity. The chemical ‘linker’ connecting an active compound–protein conjugate with a detection tag is the critical component of all chemical proteomic workflows. In this review, we
  • source of information steering the site identifications and increasing the confidence in those identifications in MS-based chemical proteomics. In-gel chemical proteomics The detection of the probe–protein conjugate(s) is based on the enhanced signal stemming from the probe–protein conjugate above the
  • background from total protein present in the lysate. The detection can be done in several different ways. To obtain an overview of how many proteins are labeled in total and what is the intensity of the labeling, the probe–protein–tag conjugates are separated on sodium dodecyl sulfate polyacrylamide gel (SDS
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Published 12 Sep 2024

Computational toolbox for the analysis of protein–glycan interactions

  • Ferran Nieto-Fabregat,
  • Maria Pia Lenza,
  • Angela Marseglia,
  • Cristina Di Carluccio,
  • Antonio Molinaro,
  • Alba Silipo and
  • Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

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  • ]. Docking calculations can be conducted in two distinct ways: blind dockings, which explore the entire protein surface [112], and directed docking, typically employed when prior knowledge of the binding pocket exists and performed within a predefined box. Blind dockings are performed using cavity detection
  • programs and online servers, as follows: 1. CB-Dock2 [113]: Cavity-detection guided Blind Docking 2 (https://cadd.labshare.cn/cb-dock2/index.php) is an online protein–ligand docking program designed to perform blind docking at predicted sites instead of the entire surface of a protein. Thus CB-Dock
  • automatically recognises putative binding sites to determine their centre and size, with the aim to adjust the docking box to suit specific query ligands. Finally, molecular docking calculations are performed with Autodock Vina (see below). 2. Fpocket [114]: It is an open-source pocket detection package based
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Published 22 Aug 2024

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

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  • , 5:5, 6:4, 7:3, and 8:2, v/v). The third (4:6) and fourth fractions (5:5) contained the peaks of our target, which were combined (35 mg) and purified by ODS-HPLC (Cosmosil C18 AR-II, 10 × 250 mm, 4 mL/min, UV detection at 254 nm) eluted with 33% MeCN/0.1% HCO2H solution to yield 1 (1.2 mg, tR 10.1
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Published 13 Aug 2024

Discovery of antimicrobial peptides clostrisin and cellulosin from Clostridium: insights into their structures, co-localized biosynthetic gene clusters, and antibiotic activity

  • Moisés Alejandro Alejo Hernandez,
  • Katia Pamela Villavicencio Sánchez,
  • Rosendo Sánchez Morales,
  • Karla Georgina Hernández-Magro Gil,
  • David Silverio Moreno-Gutiérrez,
  • Eddie Guillermo Sanchez-Rueda,
  • Yanet Teresa-Cruz,
  • Brian Choi,
  • Armando Hernández Garcia,
  • Alba Romero-Rodríguez,
  • Oscar Juárez,
  • Siseth Martínez-Caballero,
  • Mario Figueroa and
  • Corina-Diana Ceapă

Beilstein J. Org. Chem. 2024, 20, 1800–1816, doi:10.3762/bjoc.20.159

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  • enzymes from the clostridial clade were downloaded from the BV-BRCPATRIC platform in FASTA format. Subsequently, the genomes were analyzed using AntiSMASH 6.0 [3] with the following parameters: Detection stringency: relaxed; additional features: all turned on, including BLAST with known sets, BLAST of
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Published 30 Jul 2024

Photoswitchable glycoligands targeting Pseudomonas aeruginosa LecA

  • Yu Fan,
  • Ahmed El Rhaz,
  • Stéphane Maisonneuve,
  • Emilie Gillon,
  • Maha Fatthalla,
  • Franck Le Bideau,
  • Guillaume Laurent,
  • Samir Messaoudi,
  • Anne Imberty and
  • Juan Xie

Beilstein J. Org. Chem. 2024, 20, 1486–1496, doi:10.3762/bjoc.20.132

Graphical Abstract
  • through alumina or molecular sieves-containing cartridges using a solvent purificator MBRAUN SPS-800. All the reactions with azobenzene-containing substrates were carried out in the dark. Reactions were monitored by TLC on Silica Gel 60F-254 plates with detection by UV (254 nm or 365 nm) or by spraying
  • with 10% H2SO4 in EtOH and heating about 30 s at 400–600 °C. Column chromatography purification was performed on CombiFlash® Rf+ and RediSep® RF or RF Gold normal phase silica columns (with UV detection at 254 and 350 nm for all azobenzene derivatives), or by flash column chromatography employing
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Published 03 Jul 2024

Mechanistic investigations of polyaza[7]helicene in photoredox and energy transfer catalysis

  • Johannes Rocker,
  • Till J. B. Zähringer,
  • Matthias Schmitz,
  • Till Opatz and
  • Christoph Kerzig

Beilstein J. Org. Chem. 2024, 20, 1236–1245, doi:10.3762/bjoc.20.106

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  • recorded with an LFP setup using 355 nm pulses (20 mJ) of ≈5 ns duration (see Supporting Information File 1 for experimental details). A delay of 250 ns was used between excitation and detection, which is sufficiently long to avoid the detection of the singlet-excited state (Figure 1B, black). Two broad TA
  • in equilibrium with the dimeric solvent radical anion in MeCN, it weakly absorbs in our detection window and this species is rather short-lived compared to the triplet as well as the radical cation [71]. The oscillator strengths for the electronic transitions of 3Aza-H (purple) and the radical cation
  • contribution of the radical cation to the TA signal at 640 nm is only minor, which allows us to estimate a triplet lifetime of ≈28 µs at this detection wavelength. Based on our observations, an isolated triplet spectrum can be obtained from the spectral difference between the black and the red spectrum in
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Published 28 May 2024
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  • modified cardboard box were utilized for detection of TLC spots. Melting points were determined in open capillary tubes using a Mel-Temp apparatus, and are uncorrected. Proton nuclear magnetic resonance (1H NMR) spectra and carbon nuclear magnetic resonance (13C NMR) spectra were recorded on either a
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Published 17 May 2024

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

Graphical Abstract
  • supernatant. There are two main types of molecular probes based on their detection methods: imaging and UV–vis (Figure 2A). An imaging probe contains a mass spectrometry (MS) tag, oftentimes a halogen with a distinct isotopic ratio such as chlorine or bromine. A UV–vis probe contains a UV-tag, such as an
  • natural products containing furan moieties, it was tested with crude cell supernatants. Experiments were first performed to determine the limit of detection of the cycloadduct in the cell extracts when run on a UPLC-MS (Figure S23 in Supporting Information File 1). Specifically, a cell supernatant from a
  • determine the limit of detection for both the starting material 14, as well as the cycloadduct product in the complete cell supernatant. The reactions were run at various concentrations of compound 14 ranging from 71 mM to 17 µM. Gratifyingly, the cycloadduct has 260-fold increase in sensitivity compared to
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Published 02 May 2024

Carbonylative synthesis and functionalization of indoles

  • Alex De Salvo,
  • Raffaella Mancuso and
  • Xiao-Feng Wu

Beilstein J. Org. Chem. 2024, 20, 973–1000, doi:10.3762/bjoc.20.87

Graphical Abstract
  • -arylindoles by reductive carbonylation of unfunctionalized nitroarenes in the presence of arylalkynes and Pd(phen)2(BF4)2 as catalyst has been demonstrated by Cenini's group. The reaction was regioselective, with no detection of 2-arylindole byproducts. No prefunctionalization of the ortho position of the
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Published 30 Apr 2024

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

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  • allows for release and subsequent detection of heme-ligated iron [47]. Protein concentration was determined using bicinchoninic acid protein quantification assay (Pierce). The oligomeric state was determined by processing the protein through Superdex 200 Increase 10/300 GL analytical size exclusion
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Published 17 Apr 2024

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

Graphical Abstract
  • positions of drimenol (Figure 3d). However, the remaining two P450 enzymes, CavE and CavG, appear to be non-functional either in the native S. clavuligerus or heterologous expression systems. Given the detection of two terpene cyclases (CavC and CavF) and the exclusive DMTs generated, we also speculated
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Published 16 Apr 2024

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

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  • . Sixteen of the abovementioned strains were randomly selected and cultured on five different media to obtain metabolic profile data according to culture temperature. This analysis resulted in the detection of newly isolated metabolites, metabolites exhibiting enhanced production, metabolites exhibiting
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Published 10 Apr 2024

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

Graphical Abstract
  • sample was subsequently subjected to another round of centrifugation using an ultrafiltration centrifugal tube, resulting in the detection of a signal for a thioester carbonyl group in the filtrate for both samples derived from (S)- and (R)-11 at δ = 203.35 ppm (Figure 1E). This observation supports
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Published 05 Apr 2024

Isolation and structure determination of a new analog of polycavernosides from marine Okeania sp. cyanobacterium

  • Kairi Umeda,
  • Naoaki Kurisawa,
  • Ghulam Jeelani,
  • Tomoyoshi Nozaki,
  • Kiyotake Suenaga and
  • Arihiro Iwasaki

Beilstein J. Org. Chem. 2024, 20, 645–652, doi:10.3762/bjoc.20.57

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  • AFCS [Ø 11 × 300 mm; flow rate 5 mL/min; detection at 254 nm; solvent gradient condition, hexane/EtOAc 28:72 → 7:93] to give a fraction that contained compound 1 (17.5 mg, tR = 32.0 min). The fraction that contained 1 was further purified by HPLC [Cosmosil 5C18-MS-II (Ø 20 mm × 250 mm); solvent MeOH
  • /H2O 85:15; flow rate 5 mL/min; detection UV 215 nm] to give a fraction that contained 1 (8.6 mg, last collected fraction). The fraction that contained 1 was further separated by HPLC [Cosmosil Cholester (Ø 20 mm × 250 mm); solvent MeCN/H2O 75:25; flow rate 5 mL/min; detection UV 254 nm] to give a
  • fraction that contained 1 (0.6 mg, tR = 32.8 min). The fraction that contained 1 was further separated by HPLC [Cosmosil 5PE-MS (Ø 20 mm × 250 mm); solvent MeOH/H2O 85:15; flow rate 5 mL/min; detection UV 270 nm] to give 1 (0.5 mg, tR = 37.3 min). Polycavernoside E (1): colorless oil; [α]D26 −19 (c 0.04
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Published 21 Mar 2024

Possible bi-stable structures of pyrenebutanoic acid-linked protein molecules adsorbed on graphene: theoretical study

  • Yasuhiro Oishi,
  • Motoharu Kitatani and
  • Koichi Kusakabe

Beilstein J. Org. Chem. 2024, 20, 570–577, doi:10.3762/bjoc.20.49

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  • , and derive the sufficient conditions for the adiabatic potential energy surface to have an activation barrier. The reaction pathway having an activation barrier has an advantage in the detection of adsorbed molecules using elastic wave measurements. We explore the conditions under which this advantage
  • modelled in single-layer graphene or in multilayer graphene. Graphene has been considered as an ideal material for the platform of biosensors [13][14][15][16][17][18][19][20][21][22][23], benefiting from its excellent properties such as large detection area and high thermal conductivity [14][24][25
  • planer conformation I at the detection stage, we may dry the sensor system by controlling the external gas pressure. Here, we mention another merit that a pyrene derivative has for another type of biosensor. In immobilizing proteins on graphene, a pyrene derivative has another merit: non-covalent
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Published 11 Mar 2024

Switchable molecular tweezers: design and applications

  • Pablo Msellem,
  • Maksym Dekthiarenko,
  • Nihal Hadj Seyd and
  • Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

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  • electron-rich coordinating guests. Detection by fluorescence was implemented using competition experiments with dimethylaminostyrylpyridine (DMASP). Intercalated DMASP is not emissive, but its displacement by a guest releases its free fluorescent form, which can be detected. The group of Nabeshima reported
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Published 01 Mar 2024

Pseudallenes A and B, new sulfur-containing ovalicin sesquiterpenoid derivatives with antimicrobial activity from the deep-sea cold seep sediment-derived fungus Pseudallescheria boydii CS-793

  • Zhen Ying,
  • Xiao-Ming Li,
  • Sui-Qun Yang,
  • Hong-Lei Li,
  • Xin Li,
  • Bin-Gui Wang and
  • Ling-Hong Meng

Beilstein J. Org. Chem. 2024, 20, 470–478, doi:10.3762/bjoc.20.42

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  • . Optical density at 600 nm was read by a multi-detection microplate reader (Infinite M1000 Pro, Tecan). The human pathogenic bacteria and aquatic pathogenic strains were offered by the Institute of Oceanology, Chinese Academy of Sciences. Chemical structures of compounds 1–5 isolated from P. boydii CS-793
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Published 28 Feb 2024

Spatial arrangements of cyclodextrin host–guest complexes in solution studied by 13C NMR and molecular modelling

  • Konstantin Lebedinskiy,
  • Ivan Barvík,
  • Zdeněk Tošner,
  • Ivana Císařová,
  • Jindřich Jindřich and
  • Radim Hrdina

Beilstein J. Org. Chem. 2024, 20, 331–335, doi:10.3762/bjoc.20.33

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  • delivery [2][3][4], in analytical and preparative chemistry for compound separation [5] and in materials science for small molecule detection [6][7]. Association (binding) constants between the host and guest molecules [8][9][10] are typically measured by 1H NMR titration [11][12] or isothermal titration
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Published 20 Feb 2024

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

  • Jon Lundstrøm,
  • Emilie Gillon,
  • Valérie Chazalet,
  • Nicole Kerekes,
  • Antonio Di Maio,
  • Ten Feizi,
  • Yan Liu,
  • Annabelle Varrot and
  • Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

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  • lipid-linked glycans. Then the detecting solution composed of anti-polyHistidine (Sigma-Aldrich, Merck, SAB4200620) and biotin anti-mouse IgG (Sigma-Aldrich, Merck, B7264) antibodies (10 µg/mL, precomplexed in a ratio of 1:1) was overlaid onto the arrays for 1 h. The final detection was with a 30 min
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Published 19 Feb 2024

Photochromic derivatives of indigo: historical overview of development, challenges and applications

  • Gökhan Kaplan,
  • Zeynel Seferoğlu and
  • Daria V. Berdnikova

Beilstein J. Org. Chem. 2024, 20, 228–242, doi:10.3762/bjoc.20.23

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  • soft materials. A possibility to apply photochromic mono-arylated indigo derivatives as water sensors with high sensitivity was demonstrated by Dube and co-workers in 2018 [66]. The detection principle relied on a remarkable acceleration (up to 300 times) of the thermal Z–E relaxation of compound 20b
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Published 07 Feb 2024

Synthesis of the 3’-O-sulfated TF antigen with a TEG-N3 linker for glycodendrimersomes preparation to study lectin binding

  • Mark Reihill,
  • Hanyue Ma,
  • Dennis Bengtsson and
  • Stefan Oscarson

Beilstein J. Org. Chem. 2024, 20, 173–180, doi:10.3762/bjoc.20.17

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  • solution: 25 g ammonium molybdate tetrahydrate, 0.5 g Ce(SO4)2, 50 mL H2SO4, 450 mL EtOH). Chromatography Silica gel flash chromatography was carried out using Davisil® LC60A (40–63 μm) silica gel or with automated flash chromatography systems, Buchi Reveleris® X2 (UV 200–500 nm and ELSD detection
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Published 30 Jan 2024

Charge carrier transport in perylene-based and pyrene-based columnar liquid crystals

  • Alessandro L. Alves,
  • Simone V. Bernardino,
  • Carlos H. Stadtlober,
  • Edivandro Girotto,
  • Giliandro Farias,
  • Rodney M. do Nascimento,
  • Sergio F. Curcio,
  • Thiago Cazati,
  • Marta E. R. Dotto,
  • Juliana Eccher,
  • Leonardo N. Furini,
  • Hugo Gallardo,
  • Harald Bock and
  • Ivan H. Bechtold

Beilstein J. Org. Chem. 2023, 19, 1755–1765, doi:10.3762/bjoc.19.128

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  • photon counting [39] with a FluoTime 200 (PicoQuant). Excitation was provided using a 401 nm pulsed diode laser with repetition rates varying from 5.0 to 20 MHz. Fluorescence was collected perpendicular to excitation and passed through a polarizer set at the magic angle. The detection system consisted of
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Published 16 Nov 2023

Quinoxaline derivatives as attractive electron-transporting materials

  • Zeeshan Abid,
  • Liaqat Ali,
  • Sughra Gulzar,
  • Faiza Wahad,
  • Raja Shahid Ashraf and
  • Christian B. Nielsen

Beilstein J. Org. Chem. 2023, 19, 1694–1712, doi:10.3762/bjoc.19.124

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  • -derived ETMs across various fields, including all-PSCs, OSCs, DSSCs, OFETs, and OLEDs. Their unique properties, coupled with ongoing research, open up new avenues for their utilization in various fields. Qx derivatives have demonstrated promise in the development of gas sensors for detection
  • enhanced sensitivity, selectivity, and accuracy in biomarker detection, physiological parameter monitoring, and disease diagnosis. Furthermore, their efficient charge transport properties make them valuable in improving energy storage and conversion systems, including batteries and supercapacitors. The
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Published 09 Nov 2023

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

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  • detection of various analytes. Although several intriguing applications of crowned porphyrins have been elaborated, the potential of macrocycles encompassing pyrrole and crown ether motifs in a single macrocyclic framework is yet to be revealed. One can anticipate that an interesting system will be created
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Published 27 Oct 2023

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

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  • filtered and analyzed by HPLC without dilution. HPLC separation was performed on a 150 × 4.6 mm i.d. CAPCELL PAK C18 UG120 column (Osaka Soda) at 35 °C with isocratic elution using 20% CH3CN in 50 mM H3PO4 for 30 min and subsequent column washing with 90% CH3CN at a flow rate 0.8 mL/min. Detection at 250
  • detected, i.e., below the detection limit]. 1H and 13C NMR data for the aglycone moieties of 1–4.a 1H and 13C NMR data for the sugar moieties of 1, 2, and 4.a Supporting Information Supporting Information File 3: 1D and 2D NMR data for compounds 1–4. Supporting Information File 4: Calculated energies and
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Published 19 Oct 2023
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