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

• (100% water, 0.1% FA) and B (100% acetonitrile, 0.1% FA), with a linear gradient elution mode 10 to 65% CH3CN for 50 min and 65–100% CH3CN over 20 min at a flow rate of 1.0 mL/min and monitored by a diode array HPLC detector at 340 nm. The HPLC traces were aligned and visualized using data analysis as

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

Analogs of the carotane antibiotic fulvoferruginin from submerged cultures of a Thai Marasmius sp.

• Birthe Sandargo,
• Leon Kaysan,
• Rémy B. Teponno,
• Christian Richter,
• Benjarong Thongbai,
• Frank Surup and
• Marc Stadler

Beilstein J. Org. Chem. 2021, 17, 1385–1391, doi:10.3762/bjoc.17.97

• like hercynolactone. However, NMR data analysis disclosed that the position C-9 (δC 70.8) is hydroxylated. The ROESY spectrum indicates H-9 (δH 4.88) to be cofacial with H-5 and H-13. Thus, fulvoferruginin F could also be named 9-hydroxyhercynolactone [9]. Assessing the bioactivity of the

Antiviral therapy in shrimp through plant virus VLP containing VP28 dsRNA against WSSV

• Santiago Ramos-Carreño,
• Ivone Giffard-Mena,
• Jose N. Zamudio-Ocadiz,
• Alfredo Nuñez-Rivera,
• Ricardo Valencia-Yañez,
• Jaime Ruiz-Garcia,
• Maria Teresa Viana and
• Ruben D. Cadena-Nava

Beilstein J. Org. Chem. 2021, 17, 1360–1373, doi:10.3762/bjoc.17.95

• data analysis indicates that VLP-dsRNAvp28 by oral therapy reduces the mortality rate by reducing the WSSV infection. Mejía-Ruiz et al. [28] reported that antiviral protection provided by a single IM administration of dsRNAvp28 is short-lived, 10 to 20 days post-treatment (dpt), with 63% and 87

A new glance at the chemosphere of macroalgal–bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry

• Marine Vallet,
• Filip Kaftan,
• Veit Grabe,
• Fatemeh Ghaderiardakani,
• Simona Fenizia,
• Aleš Svatoš,
• Georg Pohnert and
• Thomas Wichard

Beilstein J. Org. Chem. 2021, 17, 1313–1322, doi:10.3762/bjoc.17.91

• statistical analysis were uploaded and are freely accessible in the Max Planck repository Edmond (https://dx.doi.org/10.17617/3.4v). Significant features analysis and metabolite identification Data analysis was conducted in MetaboAnalyst 4.0 [48] to perform univariate and multivariate statistical tests and

Multiswitchable photoacid–hydroxyflavylium–polyelectrolyte nano-assemblies

• Alexander Zika and
• Franziska Gröhn

Beilstein J. Org. Chem. 2021, 17, 166–185, doi:10.3762/bjoc.17.17

• experiment, one initial injection of 15 μL to saturate the titration cell wall was followed by 35 injections of 7.5 μL each. The time span between subsequent injections was 100 s. All experiments were conducted at 25 °C. Data analysis was performed with the modified model described and implemented in the

• MicroCal ITC data analysis software for Origin 7.0. Top: pelargonidin cation (Flavy) and network of chemical reactions; bottom: corresponding UV–vis spectra of the different states of Flavy. Characterization of Flavy: a) 1H NMR spectrum at pH 7.0 (form A) before and after irradiation; b) 13C NMR spectrum

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• painting. However, even though HDXMS is a very reproducible and straightforward method (albeit the experiment has to be carefully and properly performed), data analysis, even with recent software automation, is the major limitation as the interpretation requires a certain level of expertise. Biophysical

• ., the protein–protein interface. Limitations of this approach include the possibility of having no protease cleavage regions in the interface region and the size of the probes used [22]. These limitations can be overcome by using HDXMS. Even though HDX dates back to the 1950s [26], advances in data

• analysis software and automation in liquid chromatography–mass spectrometry over the past decade made HDXMS an increasingly attractive tool for biochemists. In HDXMS, changes in the mass associated with the isotopic exchange between amide hydrogen atoms and surrounding deuterated solvent are measured. The

Chemical constituents of Chaenomeles sinensis twigs and their biological activity

• Joon Min Cha,
• Dong Hyun Kim,
• Lalita Subedi,
• Zahra Khan,
• Sang Un Choi,
• Sun Yeou Kim and
• Chung Sub Kim

Beilstein J. Org. Chem. 2020, 16, 3078–3085, doi:10.3762/bjoc.16.257

• together with 11 known phytochemicals through chromatographic methods. The chemical structure of the new isolate 1 was determined by conventional 1D and 2D NMR data analysis, ECD experiment, hydrolysis followed by a modified Mosher’s method, and LC–MS analysis. The characterized compounds’ biological

• a new megastigmane-type norsesquiterpenoid glycoside 1 along with 11 known compounds (2–12, Figure 1). The structure of the new compound 1 was established on the basis of spectroscopic and spectrometric data analysis, and chiral derivatization coupled with NMR or LC–MS experiments. All isolated

• . sinensis twigs and their structures were characterized by intensive 1D and 2D NMR data analysis, ECD experiment, modified Mosher’s method, and LC–MS analysis. The 12 phytochemicals were evaluated for their anticancer, antineuroinflammatory, and neurotrophic effects and the active compounds 8–11 could be

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification

• Steffen Lippold,
• Arnoud H. de Ru,
• Jan Nouta,
• Peter A. van Veelen,
• Magnus Palmblad,
• Manfred Wuhrer and
• Noortje de Haan

Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253

• complex, reflecting the high structural diversity of peptide and glycan portions. The use of glycopeptide-centered glycoproteomics by mass spectrometry is rapidly evolving in many research areas, leading to a demand in reliable data analysis tools. In recent years, several bioinformatic tools were

• automated processing of several IgA glycopeptides. Finally, this study presents a semiautomated workflow for reliable glycoproteomic data analysis by the combination of software packages for MS/MS- and MS1-based glycopeptide identification as well as the integration of analyte quality control and

• high complexity of glycosylation itself, data analysis is further complicated by interfering background signals from biological matrices and isomeric and near-isobaric ambiguities resulting from combinations of monosaccharides, adducts, amino acids, and amino acid modifications [10][11]. Efforts have

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• approach by investigating the in-silico binding of a peptide and glycopeptide epitope of the glycoprotein Mucin 1 (MUC1) binding with the antibody AR20.5. To study the binding, we performed molecular dynamics simulations using OpenMM and then used the Galaxy platform for data analysis. The same analysis

• of the analyses was carried out using Galaxy, the popular open web-based platform for bioinformatics and computational data analysis, which enables the creation of repeatable analysis pipelines (workflows). There are several well-known molecular dynamics analysis packages (MDAnalysis [37], Bio3D [38

Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• experimental methods for studying binding. We highlight the importance of this knowledge before moving on to the data analysis. We then highlight a number of tools for the analysis of glycan microarray data such as data repositories, data visualization and manual analysis tools, automated analysis tools and

• structural informatics tools. Keywords: data analysis; glycan binding; glycan microarray; glycomics; informatics; Introduction Glycans represent a major type of biomolecule in all living things, along with DNA, RNA, lipids and proteins [1]. In mammals, glycans commonly occur as post-translational

• microarray experiment. Such a centralized database would greatly help the glycoscience community and help develop newer software for glycan microarray data analysis. B) Data visualization/manual data analysis 1. GLAD: Status: Available. Address: https://glycotoolkit.com/GLAD/. Description: Traditionally

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• ). Origin 7.0 software, supplied by the manufacturer, was used for data analysis. During the titration of ct-DNA, d: poly(rA)–poly(rU), poly(dAdT)–poly(dAdT), and poly(dGdC)–poly(dGdC) with the compound 4, one aliquot of 2 μL and 27 aliquots of 10 μL of 4 (c = 1.0 × 10−4 M) were injected from rotating

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• automated software pipeline which integrates the complementary outputs of Byonic and Proteome Discoverer to allow high-throughput automated quantitative glycoproteomic data analysis. The output of GlypNirO is clearly structured, allowing manual interrogation, and is also appropriate for input into diverse

• robustness and throughput. Our workflow uses a collection of scripts built on an in-house sequence string handling library and the scientific Python data handling package pandas [24], and integrates outputs of two commonly used software packages in glycoproteomic MS data analysis, Proteome Discoverer (Thermo

• quantitative glycoproteomic data analysis. GlypNirO takes Byonic and Proteome Discover output files, and user-defined sample information and processing parameters, performs a series of automated data integration and computational steps, and provides informative and intuitive output files with site or peptide

Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations

• Ian Walsh,
• Matthew S. F. Choo,
• Sim Lyn Chiin,
• Amelia Mak,
• Shi Jie Tay,
• Pauline M. Rudd,
• Yang Yuansheng,
• Andre Choo,
• Ho Ying Swan and
• Terry Nguyen-Khuong

Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176

• optimization study. The key advantage of this computational approach is that all runs can be analyzed simultaneously with high accuracy in glycan identification and quantitation and there is no theoretical limit to the scale of this method. Keywords: capillary electrophoresis; clustering; data analysis

• different parameter settings for each electropherogram (or groups of similar electropherograms) requiring substantial human intervention to check correctness of the automated picked peaks and tuning parameters. This level of human manual data analysis is impractical when dealing with thousands of samples

• approach. The main reason quantitation was complicated by automated data analysis methods, whether using 32 Karat software [17] or HappyTools quantitation functions, was because of Gaussian peak approximation [16]. Using 32 Karat with a single set of default parameters there were difficulties with

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• automated HT format with image-based information. To summarize briefly what has been outlined previously in more detail [56], HCS requires automated high-speed microscopy, including robotic liquid handlers and plate washers, automated data analysis tools, and large data storage systems for the terabits of

Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0

• Bernd Strehmel,
• Christian Schmitz,
• Ceren Kütahya,
• Yulian Pang,
• Anke Drewitz and
• Heinz Mustroph

Beilstein J. Org. Chem. 2020, 16, 415–444, doi:10.3762/bjoc.16.40

• application [66]. Data collection [67] in combination with self-leaning software related to artificial intelligence (A.I.) drives their use in applications with more efficiency in large workflows. Such tools can recognize failures in industrial processes just by collection of data in a big database where data

• analysis of global production may solve issues related to the materials. Review Synthesis of cyanines absorbing in the NIR Cyanines comprising the patterns I–V (Scheme 1) have received much importance as NIR absorbers applied in different technologies [1][8][9][11][12][13][14][15][16][17][18][19][20][32

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

• Panagiotis S. Gritzapis,
• Panayiotis C. Varras,
• Nikolaos-Panagiotis Andreou,
• Katerina R. Katsani,
• Konstantinos Dafnopoulos,
• George Psomas,
• Zisis V. Peitsinis,
• Alexandros E. Koumbis and
• Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

• energies, Δ0[Τ1 − S0] for 11 and 12. All numerical values in kcal/mol, in aqueous solution. Supporting Information The Supporting Information features 1) general procedures for the synthesis of all compounds and data analysis; 2) 1H NMR and 13C NMR of amidoxime, ethanone oxime and aldoxime carbamates; 3

Ultrafast processes triggered by one- and two-photon excitation of a photochromic and luminescent hydrazone

• Alessandro Iagatti,
• Baihao Shao,
• Alberto Credi,
• Barbara Ventura,
• Ivan Aprahamian and
• Mariangela Di Donato

Beilstein J. Org. Chem. 2019, 15, 2438–2446, doi:10.3762/bjoc.15.236

• fitting method using Felix data analysis from Horiba Scientific Ltd. Transient absorption spectroscopy The apparatus used for the transient absorption spectroscopy (TAS) measurements is based on a Ti:sapphire regenerative amplifier (BMI Alpha 1000) system pumped by a Ti:sapphire oscillator (Spectra

Friedel–Crafts approach to the one-pot synthesis of methoxy-substituted thioxanthylium salts

• Kenta Tanaka,
• Yuta Tanaka,
• Mami Kishimoto,
• Yujiro Hoshino and
• Kiyoshi Honda

Beilstein J. Org. Chem. 2019, 15, 2105–2112, doi:10.3762/bjoc.15.208

• = 464 nm) showed a large red shift compared to thioxanthylium salt 4b (λmax = 383 nm), which has no methoxy groups (Figure 4 and Figure 5). Finally, we measured the cyclic voltammograms (CV) of thioxanthylium salts 3b and 4b (Figure 6). The CV data analysis implies that the reduction potential of 3b (E

Analysis of sesquiterpene hydrocarbons in grape berry exocarp (Vitis vinifera L.) using in vivo-labeling and comprehensive two-dimensional gas chromatography–mass spectrometry (GC×GC–MS)

• Philipp P. Könen and
• Matthias Wüst

Beilstein J. Org. Chem. 2019, 15, 1945–1961, doi:10.3762/bjoc.15.190

• ) mode at −70 eV. The ion source temperature was 250 °C and the detector voltage was set to −2236.8 V. Ions in the mass range 35–250 amu were acquired at a rate of 100 spectra s−1. All samples were analyzed in triplicate. Data analysis Data processing was performed using the software ChromSpace (Markes

Unexpected polymorphism during a catalyzed mechanochemical Knoevenagel condensation

• Sebastian Haferkamp,
• Andrea Paul,
• Adam A. L. Michalchuk and
• Franziska Emmerling

Beilstein J. Org. Chem. 2019, 15, 1141–1148, doi:10.3762/bjoc.15.110

• monitoring multi-phase reactions during ball milling. Keywords: ball milling; C–C coupling; in situ; mechanochemistry; multivariate data analysis; Introduction Mechanochemistry offers a wide array of applications. It is used widely for synthesis of inorganic, metal-organic, and organic molecules and

• diffraction data. Results of multivariate data analysis of Raman spectra for 30 Hz milling experiments. Principal component analysis (PCA) of Raman data, showing (a) scores, and (b) loadings for (black) PC1 and (blue) PC2. (a) PC1 scores show a decrease in spectral component of 1a in the first minutes – cf

• be observed. Catalyzed mechanochemical Knoevenagel condensation of fluorobenzaldehydes and malonodinitrile. The milling process is symbolized by the three balls, proposed by Hanusa et al. [20]. Supporting Information Supporting Information File 508: XRPD data and multivariate data analysis.

Hoveyda–Grubbs catalysts with an N→Ru coordinate bond in a six-membered ring. Synthesis of stable, industrially scalable, highly efficient ruthenium metathesis catalysts and 2-vinylbenzylamine ligands as their precursors

• Kirill B. Polyanskii,
• Kseniia A. Alekseeva,
• Pavel V. Raspertov,
• Pavel A. Kumandin,
• Eugeniya V. Nikitina,
• Atash V. Gurbanov and
• Fedor I. Zubkov

Beilstein J. Org. Chem. 2019, 15, 769–779, doi:10.3762/bjoc.15.73

• preparation of the “chloroform adduct” (9) [51][52][53][54][55]. Even though these approaches provide good yields they have some drawbacks such as the use of expensive reagents, difficulties in the purification process, and data analysis. Here we propose an alternative reliable procedure for the synthesis of

Repurposing the anticancer drug cisplatin with the aim of developing novel Pseudomonas aeruginosa infection control agents

• Mingjun Yuan,
• Song Lin Chua,
• Yang Liu,
• Daniela I. Drautz-Moses,
• Joey Kuok Hoong Yam,
• Thet Tun Aung,
• Roger W. Beuerman,
• May Margarette Santillan Salido,
• Stephan C. Schuster,
• Choon-Hong Tan,
• Michael Givskov,
• Liang Yang and
• Thomas E. Nielsen

Beilstein J. Org. Chem. 2018, 14, 3059–3069, doi:10.3762/bjoc.14.284

• vigorous protocol was used for a second round of DNase treatment (Ambion). The 16S, 23S and 5S rRNA was removed using the Ribo-Zero Magnetic Kit (Bacteria) (Epicentre). RNA sequencing and data analysis Gene expression analysis was conducted via Illumina RNA sequencing (RNA-Seq technology). RNA-Seq was

Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae

• Bimal Koirala,
• Robert A. Hillman,
• Erin K. Tiwold,
• Michael A. Bertucci and
• Yftah Tal-Gan

Beilstein J. Org. Chem. 2018, 14, 1769–1777, doi:10.3762/bjoc.14.151

• reported as percent activation, which is the ratio between the Miller units of the analog and of the positive control. For calculation of Miller units, please see data analysis below. Analogs that exhibited high activity in the initial screening (see Figures S1 and S2, Supporting Information File 1) were

Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies

• Elias Christoforides,
• Andreas Papaioannou and
• Kostas Bethanis

Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69

• data analysis. The CLYCAM_06 force field [46] was applied to the atoms of β-CD, whereas GAFF parameters and AM1BCC charges were applied to the guest molecule using ANTECHAMBER [47]. The explicit solvent model TIP3P was used for water forming a periodic, octahedral box of at least 10 Å between the box