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

• how the sugar modulates binding. Methods The inputs, simulation scripts, Galaxy workflows (a series of tools and dataset actions that run in sequence), and data for these simulations are available at https://github.com/chrisbarnettster/bjoc-paper-2020-sm. Simulation There is an increasing number of

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

• the dataset. D) Structural information tools 1. GlyMDB: Status: Available. Address: http://www.glycanstructure.org/glymdb/. Description: GlyMDB is a web-based database which links glycan microarray binding data from the CFG database to protein structures (PDB) [51]. A user can select a dataset from

• the CFG dataset available and set thresholds for binding versus nonbinding. The application can then show you motifs which make a significant binding contribution on the microarray. In addition it allows you to quickly search for PDB files with sequence identity matching to the protein sample put on

• CFG glycan array data; (B) screenshot of an example of Imperial College microarray data online portal. A demonstration of glycan array data visualization with GLAD. The dataset used is from Byrd-Leotis et al. [16], and is provided as a GLAD session file in the manuscript. The dataset contains data on

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

• statistical workflows. We used GlypNirO to analyse a published plasma glycoproteome dataset and identified changes in site-specific N- and O-glycosylation occupancy and structure associated with hepatocellular carcinoma as putative biomarkers of disease. Keywords: glycoproteomics; mass spectrometry; N

• Fisher) and Byonic (Protein Metrics), to extract occupancy and glycoform abundancy of all identified glycopeptides from LC–MS/MS datasets. We applied the workflow to a published dataset comparing the plasma glycoproteomes of liver cancer patients (heptatocellular carcinoma, HCC) and healthy controls [20

• provide a proof-of-concept use of GlypNirO, we performed an exploratory reanalysis of a previously published dataset [20] obtained from the ProteomeXchange Consortium via the MassIVE repository (PXD003369, MSV000079426). This study performed glycoproteomic LC–MS/MS analysis of whole plasma or plasma

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

• similar groups, making it easier to define peaks manually. Open-source software is then used to determine peak areas of the manually defined peaks. We successfully applied this semi-automated method to a dataset (containing 391 glycoprofiles) of monoclonal antibody biosimilars from a bioreactor

• . Here, we describe a computational solution for the identification and quantitation of glycans in a large glycomics CE dataset generated during process development of an anti-HER-2 antibody. The method is a semi-automated approach and improved accurate glycan assignments and quantitation compared to

• bioprocessing operation, a single set of tuned parameters failed to detect peaks and therefore quantitate them. On our dataset, the 32 Karat software needed tuning of parameters for multiple clusters of similar electropherograms; this job was laborious and thus motivated the implementation of our computational

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

• from Gibellula gamsii. In the current study, our efforts focused on phylogenetic analysis in order to identify the producers of pigmentosins 1 and 2 as well as glycoasperfuran (3), and gibellamines producers were also included in the dataset. Both phylogenetic data and HPLC-based metabolite profiles

Efficiency Eff_syn of complex syntheses as multicomponent reactions, its algorithm and calculations based on concrete criteria

• Heiner Eckert

Beilstein J. Org. Chem. 2019, 15, 1425–1433, doi:10.3762/bjoc.15.142

• efficiency is Effsyn = 2.9%, due to the high step number of 17 (real number of precursors). The same synthesis in linear architecture does not exist. A fictive comparison with the same dataset in a completely sequential reaction sequence results in a fictive yield of 2 yoa(fictive) = 0.192 (19%). The

Phylogenomic analyses and distribution of terpene synthases among Streptomyces

• Lara Martín-Sánchez,
• Kumar Saurabh Singh,
• Mariana Avalos,
• Gilles P. van Wezel,
• Jeroen S. Dickschat and
• Paolina Garbeva

Beilstein J. Org. Chem. 2019, 15, 1181–1193, doi:10.3762/bjoc.15.115

• generated using the protein dataset. Sequences were aligned with Mafft version 7.313 [55] using default parameters including --auto and --inputorder. All the alignments were trimmed for gaps and ambiguously aligned regions with BMGE – v 1.12 [56] using default parameters. For phylogenetic analyses, ProtTest

The effect of milling frequency on a mechanochemical organic reaction monitored by in situ Raman spectroscopy

• Patrick A. Julien,
• Ivani Malvestiti and
• Tomislav Friščić

Beilstein J. Org. Chem. 2017, 13, 2160–2168, doi:10.3762/bjoc.13.216

• starting materials and the product exhibit characteristic signals, and the PMMA spectrum is featureless (Figure 2). Fitting the dataset A principal challenge associated with in situ monitoring of a milling reaction is the variation of the amount of sample in the beam due to the motion of the milling

• . Equation 3 provides the best values of x that minimize the difference between A * x and E. The described linear least-squares fitting procedure was applied to every spectrum in the in situ dataset and, following Equation 1 and Equation 2, enabled us to evaluate the relative spectral contribution of each

Aggregation behaviour of a single-chain, phenylene-modified bolalipid and its miscibility with classical phospholipids

• Simon Drescher,
• Vasil M. Garamus,
• Christopher J. Garvey,
• Annette Meister and
• Alfred Blume

Beilstein J. Org. Chem. 2017, 13, 995–1007, doi:10.3762/bjoc.13.99

• , UK) with accuracy ± 0.1 °C. Twenty consecutive frames (each 0.05 s) comprising the measurement of the solvent (phosphate buffer pH 7.4) and sample were performed. In order to verify that no artefacts as a result of radiation damage occurred, all scattering curves of a recorded dataset were compared

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

• of these potentials is the Boltzmann distribution. The frequency of occurrence of atom pairs is converted into a potential using Boltzmann’s distribution of states. Since these potentials use target–ligand complex data already available, they are highly dependent on the dataset used to create them

Conformational equilibrium in supramolecular chemistry: Dibutyltriuret case

• Karina Mroczyńska,
• Małgorzata Kaczorowska,
• Erkki Kolehmainen,
• Ireneusz Grubecki,
• Marek Pietrzak and
• Borys Ośmiałowski

Beilstein J. Org. Chem. 2015, 11, 2105–2116, doi:10.3762/bjoc.11.227

• smallest residuals starting from ca. 0.8 [G]:[H] ratio till infinite guest concentration. Due to the sigmoidal behavior of all titration curves the fitting is not possible for the beginning of the dataset. Also it is not possible to divide these data into two separate sets as before [9] because no saddle

Consequences of the electronic tuning of latent ruthenium-based olefin metathesis catalysts on their reactivity

• Karolina Żukowska,
• Eva Pump,
• Aleksandra E. Pazio,
• Krzysztof Woźniak,
• Luigi Cavallo and
• Christian Slugovc

Beilstein J. Org. Chem. 2015, 11, 1458–1468, doi:10.3762/bjoc.11.158

• similar (Figure 3). Bond lengths and angles of 5a, 14 and 15 are very similar, so their different tendencies to form the corresponding cis-complexes could not be rationalized based on this dataset. The only feature worth mentioning is a slightly decreased Ru(1)-C(22) bond length in compound 15 compared to

Azobenzene-based inhibitors of human carbonic anhydrase II

• Leander Simon Runtsch,
• David Michael Barber,
• Peter Mayer,
• Michael Groll,
• Dirk Trauner and
• Johannes Broichhagen

Beilstein J. Org. Chem. 2015, 11, 1129–1135, doi:10.3762/bjoc.11.127

• purification, crystallization and binding data analysis. P.M. collected X-ray datasets of 1a–i and solved the structures. M.G. collected hCAII X-ray dataset and solved the structure. J.B., D.M.B and D.T. wrote the manuscript with input from all authors.

Synthesis, characterization and luminescence studies of gold(I)–NHC amide complexes

• Adrián Gómez-Suárez,
• David J. Nelson,
• David G. Thompson,
• David B. Cordes,
• Duncan Graham,
• Alexandra M. Z. Slawin and
• Steven P. Nolan

Beilstein J. Org. Chem. 2013, 9, 2216–2223, doi:10.3762/bjoc.9.260

• yellow. The excitation and emission maxima were then determined. These measurements were conducted on more concentrated (ca. 4 mmol/L) CH2Cl2 solutions, compared to those used for UV–vis spectroscopy. In each case, the relevant maxima could be identified. An example dataset is presented in Figure 3

Studies on the photodegradation of red, green and blue phosphorescent OLED emitters

• Susanna Schmidbauer,
• Andreas Hohenleutner and
• Burkhard König

Beilstein J. Org. Chem. 2013, 9, 2088–2096, doi:10.3762/bjoc.9.245

• showed a similar degradation behavior. This is in good agreement with observations of the solvent dependency for the other emitters. Under inert conditions, no reliable dataset could be obtained. Expected degradation products like species formed by fluorine cleavage, which were reported previously for

Temperature measurements with two different IR sensors in a continuous-flow microwave heated system

• Jonas Rydfjord,
• Fredrik Svensson,
• Magnus Fagrell,
• Jonas Sävmarker,
• Måns Thulin and
• Mats Larhed

Beilstein J. Org. Chem. 2013, 9, 2079–2087, doi:10.3762/bjoc.9.244

• ]: Acetonitrile, THF, toluene). In total the full dataset with all measurements contains 173 data points for IR sensor 1 and 172 for IR sensor 2. Data evaluation The data collected were analyzed with regards to the influence of set temperature, flow rate and solvent to be able to distinguish between the two types

• of IR sensors and find the best way to correlate the “real” internal temperature of the reactor to the reading from the IR sensor in order to be able to apply a calibration to the IR sensor reading. We opted for linear multiple regression models using the full dataset, with all the measured data

• points. We also constructed several models with subsets of the data based on high, medium or low solvent absorption and one model where THF and toluene where excluded. Results Characterization of IR sensors Examining the whole dataset for IR sensor 1 the average absolute error was 10.9 °C (Table 1). The

Diastereoselective synthesis of nitroso acetals from (S,E)-γ-aminated nitroalkenes via multicomponent [4 + 2]/[3 + 2] cycloadditions promoted by LiCl or LiClO₄

• Leandro Lara de Carvalho,
• Robert Alan Burrow and
• Vera Lúcia Patrocinio Pereira

Beilstein J. Org. Chem. 2013, 9, 838–845, doi:10.3762/bjoc.9.96

• solutions. Supporting Information Supporting Information File 95: Experimental section and characterization for 6a, 7b,b’, 9c,c’, 10a’, 11b, 12b,b’, 13c,c’ and 14c. Available edited spectra of IR, 1H NMR, 13C NMR, 2D COSY, HSQC and 2D NOESY. Supporting Information File 96: Dataset of X-ray crystallography

Regioselective synthesis of 7,8-dihydroimidazo[5,1-c][1,2,4]triazine-3,6(2H,4H)-dione derivatives: A new drug-like heterocyclic scaffold

• Nikolay T. Tzvetkov,
• Harald Euler and
• Christa E. Müller

Beilstein J. Org. Chem. 2012, 8, 1584–1593, doi:10.3762/bjoc.8.181

• . Acknowledgements A. Reiner, S. Terhart-Krabbe, M. Schneider and H. Passgang are gratefully acknowledged for skillful technical assistance. Dr. G. Schnakenburg and C. Rödde, Department for X-ray Single Crystal Structure Solution, Institute for Inorganic Chemistry, are acknowledged for collecting the dataset of

Similarity analysis, synthesis, and bioassay of antibacterial cyclic peptidomimetics

• Workalemahu M. Berhanu,
• Mohamed A. Ibrahim,
• Girinath G. Pillai,
• Alexander A. Oliferenko,
• Levan Khelashvili,
• Farukh Jabeen,
• Bushra Mirza,
• Farzana Latif Ansari,
• Ihsan ul-Haq,
• Said A. El-Feky and
• Alan R. Katritzky

Beilstein J. Org. Chem. 2012, 8, 1146–1160, doi:10.3762/bjoc.8.128

• dataset of existing analogues. As abundant data can be found in the literature for Staphylococcus aureus, this was chosen as a reference for antibacterial activity. SciFinder Scholar was used to retrieve the structures of 33 cyclic peptides with reported antibacterial activity (Table 1). The minimum

• growth inhibition constant (MIC) was used as the measure of antibacterial activity, and the data collected were converted where necessary to μg/mL. Three structures newly synthesized in our lab were also added to the general dataset (Table 1). All these structures were drawn with the Marvin Beans Suite

An easily accessible sulfated saccharide mimetic inhibits in vitro human tumor cell adhesion and angiogenesis of vascular endothelial cells

• Grazia Marano,
• Claas Gronewold,
• Martin Frank,
• Anette Merling,
• Christian Kliem,
• Sandra Sauer,
• Manfred Wiessler,
• Eva Frei and
• Reinhard Schwartz-Albiez

Beilstein J. Org. Chem. 2012, 8, 787–803, doi:10.3762/bjoc.8.89

• entire dataset, and to organize the results in such a way that areas on the protein surface exhibiting a strong binding affinity could be easily visualized by using standard display programs. In order to refine the docked structure of GSF a molecular dynamics (MD) simulation of the complex was performed

Planar-bilayer activities of linear oligoester bolaamphiphiles

• Jonathan K. W. Chui,
• Thomas M. Fyles and
• Horace Luong

Beilstein J. Org. Chem. 2011, 7, 1562–1569, doi:10.3762/bjoc.7.184

• encoded on the activity grid of each record. A single experiment consists of several records from a single day. Experiments were conducted over a period of time, with varying conditions of electrolyte, sequence of applied potentials, etc. The entire dataset of activity grids for a given compound was then