Monitoring carbohydrate 3D structure quality with the Privateer database

• Jordan S. Dialpuri,
• Haroldas Bagdonas,
• Lucy C. Schofield,
• Phuong Thao Pham,
• Lou Holland and
• Jon Agirre

Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83

• Protein Data Bank (PDB), from the initial works of Lütteke, Frank and von der Lieth [6][7], who identified numerous issues affecting nomenclature and linkages (estimated to affect 30% of the structures at the time), to the reports of surprising – or indeed glyco-chemically impossible – linkages in a

• sugar model [3], checks that structures match the nomenclature used for deposition in the PDB [14], compares glycan compositions to known structures as reported by glycomics (e.g., GlyConnect [19]) and glyco-informatics (e.g., GlyTouCan [20]) databases and repositories [15], and checks how close the

• nomenclature for glycan SVG, and an array of sugar entries. The validation data calculated by Privateer for each sugar entry is shown in Table 2, and that for each linkage is shown in Table 3. Visualising a validation report While the database is available on GitHub for programmatic access, viewing a

Introduction of a human- and keyboard-friendly N-glycan nomenclature

• Friedrich Altmann,
• Johannes Helm,
• Martin Pabst and
• Johannes Stadlmann

Beilstein J. Org. Chem. 2024, 20, 607–620, doi:10.3762/bjoc.20.53

• greatly facilitate keyboard-based mining for glycan substructures in glycan repositories. Keywords: N-glycans; nomenclature; structural features; Introduction Virtually any article on protein glycosylation starts with imposing assurances about the biological significance of the various structures. This

• and ask yourself, how one could label an Eppendorf vial with the most condensed approved version of the IUPAC code (Figure 1). The graphical depictions are far more illustrative. On top, the “Symbol Nomenclature for Glycans” (SNFG) format, which was pioneered by the Consortium of Functional Glycomics

• “proglycan” nomenclature, an acronym derived from our then nom de guerre “protein-glycosylation analysis” group. By the way, glycan analysis also funneled in activities in the area of allergy diagnosis, where the term MUXF3 enjoys widespread use [38][39][40]. Finally, our work on the isomer-specific analysis

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

• broadly binding lectin. However, we noticed that the commonality of these two epitopes is hidden in the IUPAC-condensed nomenclature: Both substructures exhibited a bulky substituent on C2 of galactose, either a fucosyl (Fucα1-2Gal) or N-acetyl (GalNAc) moiety (Figure 2d). We thus conclude that CMA1 is

• * cells. Characterizing the binding specificity of CMA1. (a, b) Lectin produced in mammalian cells was analyzed on the NCFG array (a) and the ICL array (b). Representative structures bound by CMA1 are shown via the “Symbol Nomenclature For Glycans” (SNFG), drawn with GlycoDraw [23]. Everything except the

Linker, loading, and reaction scale influence automated glycan assembly

• Marlene C. S. Dal Colle,
• Manuel G. Ricardo,
• Nives Hribernik,
• José Danglad-Flores,
• Peter H. Seeberger and
• Martina Delbianco

Beilstein J. Org. Chem. 2023, 19, 1015–1020, doi:10.3762/bjoc.19.77

• showed the presence of capped linker (*), capped dimer (†), and Lev-containing dimer (‡). The monosaccharides are represented following the symbol nomenclature for glycans (SNFG). Supporting Information Supporting Information File 120: Experimental procedures and characterization data. Funding We thank

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

• . Thus, attention must be paid to the identification of the substances, specification of the reaction(s), the conditions of reaction, the definition of the equilibrium constant(s) and standard states, the use of standard nomenclature, symbols, and units, and uncertainties. This document contains a

• -colon-separated), PDF, or Excel format. 3.3. Standard nomenclature, symbols, and units Results for all property values should be reported by using internationally accepted names for quantities and symbols and SI units [10][18]. 3.4. Specification of the reaction One must specify the reaction that has

Identification and determination of the absolute configuration of amorph-4-en-10β-ol, a cadinol-type sesquiterpene from the scent glands of the African reed frog Hyperolius cinnamomeoventris

• Angelique Ladwig,
• Markus Kroll and
• Stefan Schulz

Beilstein J. Org. Chem. 2023, 19, 167–175, doi:10.3762/bjoc.19.16

• -octahydronaphthalen-1-ol) (R-14) or, according to the nomenclature used initially [17][18], (10R,1S,6R,7R,10R)-amorph-4-ene-10β-ol (see Figure S3 in Supporting Information File 1 for a comparison of compound numbering). To the best of our knowledge, this is the first determination of the absolute configuration of

Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants

• Karan Malhotra and
• Jakob Franke

Beilstein J. Org. Chem. 2022, 18, 1289–1310, doi:10.3762/bjoc.18.135

• CYPs involved in tailoring of triterpenoids and steroids in plants. We will first introduce the nomenclature and mechanistic properties of these enzymes, before we describe the phylogenetic distribution of triterpenoid-modifying CYPs and summarise their reaction space. Lastly, we will highlight

• addition, readers might also be interested in other excellent reviews or resources providing a more general overview over plant CYPs or CYPs from other plant pathways [6][8][9][10][11][12][13]. Review Nomenclature Considering the enormous numbers of genes encoding cytochrome P450 monooxygenases in plants

• , a universal naming system is crucial to group related CYPs and to facilitate functional predictions. Hence, CYPs from all kingdoms are systematically named according to their amino acid identity by the cytochrome P450 nomenclature committee (David Nelson: dnelson@uthsc.edu). CYPs are grouped into

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

DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

• Yongdong Su,
• Maitsetseg Bayarjargal,
• Tracy K. Hale and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65

• was confirmed by electrospray ionization mass spectrometry (ESIMS) in the negative mode (Table 1). For clarity, we introduced the following nomenclature of the ONs synthesised. The prefix 5ʼ- or 3ʼ- with either N+ or Ts- means that the first phosphate at the 5ʼ- or 3ʼ-end was modified; m-N+ or m-Ts

Simulating the enzymes of ganglioside biosynthesis with Glycologue

• Andrew G. McDonald and
• Gavin P. Davey

Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64

• produced by the actions of the 10 enzymes included in the model. The different ganglioside nomenclature systems in common use are compared and a systematic variant of the widely used Svennerholm nomenclature is described. Knockouts of specific enzyme activities are used to simulate congenital defects in

• ganglioside biosynthesis, and altered ganglioside status in cancer, and the effects on network structure are predicted. The simulator is available at the Glycologue website, https://glycologue.org/. Keywords: gangliosides; Glycologue; glycosyltransferases; neuropathy; Svennerholm nomenclature; Introduction

• before sugars units, and multiple modifiers on the same monosaccharide are again ordered by linkage position, from lowest to highest, reading right to left. Nomenclature of gangliosides Gangliosides are commonly labelled according to the abbreviated Svennerholm [20] nomenclature, or else by the expanded

Synthesis, crystal structures and properties of carbazole-based [6]helicenes fused with an azine ring

• Daria I. Tonkoglazova,
• Anna V. Gulevskaya,
• Konstantin A. Chistyakov and
• Olga I. Askalepova

Beilstein J. Org. Chem. 2021, 17, 11–21, doi:10.3762/bjoc.17.2

• . Sonogashira coupling of compounds 7 with p-tolylacetylene. Acid-induced isomerization of compounds 9 into carbazole-based [6]helicenes 10. Comparison of X-ray data of the carbazole-based [6]helicenes (atomic numbering does not correspond to IUPAC nomenclature). Photophysical properties of carbazole-based [6

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

• Benjamin P. Kellman,
• Yujie Zhang,
• Emma Logomasini,
• Eric Meinhardt,
• Karla P. Godinez-Macias,
• Austin W. T. Chiang,
• James T. Sorrentino,
• Chenguang Liang,
• Bokan Bao,
• Yusen Zhou,
• Sachiko Akase,
• Isami Sogabe,
• Thukaa Kouka,
• Elizabeth A. Winzeler,
• Iain B. H. Wilson,
• Matthew P. Campbell,
• Sriram Neelamegham,
• Frederick J. Krambeck,
• Kiyoko F. Aoki-Kinoshita and
• Nathan E. Lewis

Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215

• representations are not designed to be human-readable or included in the main text of a manuscript confining many design details to the supplement of a publication. As systems glycobiology develops, there is a need to develop a standard nomenclature for unambiguous and readable reaction rules to facilitate

• illustrations, Linear Code described a simplified version of IUPAC nomenclature [31]. Specifically, Linear Code is a syntax for representing glycoconjugates and their associated molecules in a simple linear fashion. While keeping the linkage and branch information, Linear Code removes the hyphens between

• Linear Code adaptations to represent reaction rules, we have seen increasing diversity in the syntax, including branch constraints, duplicate monosaccharides omission, logical operators, etc. Here we critically review reaction rule nomenclature. In doing so, we seek to promote the development of a

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• and protein interactions [12]. Unfortunately, significant challenges have affected the determination of glycoprotein structures for decades and have had a detrimental impact on the quality and reliability of the produced models. Anomalies have been reported regarding carbohydrate nomenclature [13

• -centric [15]. As a consequence, the glycan chains in glycoprotein models that have been elucidated before recent developments in carbohydrate validation and modelling software tend to contain a significant amount of errors: wrong carbohydrate nomenclature [13], biologically implausible glycosidic linkage

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• glycobiologists or any researcher looking for a ready to use, simple program for the sketching or building of glycans. Keywords: bioinformatics; carbohydrate; glycan; glycobiology; nomenclature; oligosaccharide; polysaccharide; representation; structure; Introduction Glycoscience is a rapidly surfacing and

• structures replacing monosaccharides. The description of carbohydrate structures using standard symbolic nomenclature enables easy understanding and communication within the scientific community. Research groups working on carbohydrates have developed schematic depictions with symbols [3] and expansions with

• greyscale colouring as the so-called Oxford nomenclature (UOXF) [4][5], and even fully coloured schemes later on. Among these, some of the proposed representation forms have been accepted and implemented by several groups and initiatives, namely the Consortium for Functional Glycomics (CFG) [6]. Whereas the

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

• interactive to show the glycan structure provided the glycans are labeled using the CFG linear nomenclature system. This makes it particularly useful for manual data analysis. The plots and structures produced can directly be saved as SVG vector graphic files which can be used by most illustration software to

• which the motifs need to be defined using MotifSpeak language which is an extension of the CFG linear nomenclature. The software is freely available for noncommercial uses, and needs to be installed in order to run. It has extensive documentation in the manual on how to perform different analysis either

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• ultimately understand more clearly the relationships between sequence and structure in complex carbohydrates. Representative structures of the plant N-glycans studied in this work with corresponding nomenclature. The letters f, x, and g indicate the presence of Fuc, Xyl and β(1-3) Gal, respectively, and ng

• the absence of β(1-3) Gal. LeA stands for Lewis A antigen. The N-glycans structures are shown with the (1-3) and (1-6) arms on the left and on the right, respectively. The monosaccharides colouring follows the SFNG nomenclature. The plants N-glycan characteristic linkages are indicated in the legend

• structures are shown with the (1-3) and (1-6) arms on the left and on the right, respectively. The monosaccharides colouring follows the SFNG nomenclature. The structure rendering was done with VMD (https://www.ks.uiuc.edu/Research/vmd/) and the graphical statistical analysis with RStudio (https

Synthesis of new dihydroberberine and tetrahydroberberine analogues and evaluation of their antiproliferative activity on NCI-H1975 cells

• Giacomo Mari,
• Lucia De Crescentini,
• Serena Benedetti,
• Francesco Palma,
• Stefania Santeusanio and
• Fabio Mantellini

Beilstein J. Org. Chem. 2020, 16, 1606–1616, doi:10.3762/bjoc.16.133

• elemental analysis. Mass spectra were recorded in the ESI and EI modes. The nomenclature was generated using ACD/IUPAC Name (version 3.50, 5 Apr. 1998), Advanced Chemistry Development Inc., Toronto, ON (Canada). General procedure for the synthesis of hydrazono-dihydroberberines (DHBERs) 2a–n. To a solution

Opening up connectivity between documents, structures and bioactivity

• Christopher Southan

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

• to the Open Parser for Systematic IUPAC Nomenclature (OPSIN) tool [7]. Here again, both the automatic and manual procedures are error prone. Locally-stored SAR data from an Excel sheet or an ELN can be used to populate draft manuscripts (and with lower error rates) but the irony is conversion to PDF

Light-controllable dithienylethene-modified cyclic peptides: photoswitching the in vivo toxicity in zebrafish embryos

• Sergii Afonin,
• Oleg Babii,
• Aline Reuter,
• Volker Middel,
• Masanari Takamiya,
• Uwe Strähle,
• Igor V. Komarov and
• Anne S. Ulrich

Beilstein J. Org. Chem. 2020, 16, 39–49, doi:10.3762/bjoc.16.6

• -closed photoforms. The compound numbers are shown next to the data points. The in vitro data is from [30]. Values for the parent peptide 1 are marked black, and a white filling highlights the initial prototype 2. Color codes for the remaining peptides are the same as in Figure 3. Nomenclature, sequences

Synthetic terpenoids in the world of fragrances: Iso E Super^® is the showcase

• Alexey Stepanyuk and
• Andreas Kirschning

Beilstein J. Org. Chem. 2019, 15, 2590–2602, doi:10.3762/bjoc.15.252

• the amount of Iso E Super® (33) in a commercial perfume [25][26]. This trend culminated in Schön´s creation of Molecule 01 in the year 2005, a perfume that contains nothing else than Iso E Super® (33). Orb_ital from Nomenclature (75% Iso E Super®) followed in the year 2015. This fragrance collection

Perspective isomorphs – a new classification of molecular structures based on artistic and chemical concepts

• Jannis Neumann,
• Ansgar Schnurr and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2019, 15, 2319–2326, doi:10.3762/bjoc.15.224

• equivalent from one standpoint in a specific orientation. We termed such a group of such molecules perspective isomorphs. The general concept is outlined together with a nomenclature system. Furthermore, this concept has been visualized by artistic representations of molecules. The concept of perspective

• isomorphs and its discussions herein will extend current models and stimulate the discourse about the nature of atoms and molecules and especially their models. Keywords: art and science; nomenclature; perspective; representation in chemistry; structure; Introduction Up to now, epistemological concepts of

• , however, be placed into a different PI class, when viewed from a different angle. This way, they are perspective isomorphe with 4-fluorobiphenyl or benzoic acid. Nomenclature/coding of perspective isomorphs In order to make the concept of perspective isomorphs practicable and unmistakably understandable

An overview of the cycloaddition chemistry of fulvenes and emerging applications

• Ellen Swan,
• Kirsten Platts and
• Anton Blencowe

Beilstein J. Org. Chem. 2019, 15, 2113–2132, doi:10.3762/bjoc.15.209

• this review will lead to increased interest in these fields, and others yet to be investigated. General structure of fulvenes, named according to the number of carbon atoms in their ring. Whilst fulvenes have been numbered using several different systems, Chemical Abstracts nomenclature is used

Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

• Silvie Rimpelová,
• Michal Jurášek,
• Lucie Peterková,
• Jiří Bejček,
• Vojtěch Spiwok,
• Miloš Majdl,
• Michal Jirásko,
• Miloš Buděšínský,
• Juraj Harmatha,
• Eva Kmoníčková,
• Pavel Drašar and
• Tomáš Ruml

Beilstein J. Org. Chem. 2019, 15, 1933–1944, doi:10.3762/bjoc.15.189

• ; TNF-α, tumor necrosis factor alpha; SCE, supercritical CO2 extraction; SL, sesquiterpene lactones. Comment on nomenclature This article uses semitrivial terpene nomenclature and hence the numbering of compounds atoms may differ from these obtained by using IUPAC names. The structure of the

Nanopatterns of arylene–alkynylene squares on graphite: self-sorting and intercalation

• Tristan J. Keller,
• Joshua Bahr,
• Kristin Gratzfeld,
• Nina Schönfelder,
• Marcin A. Majewski,
• Marcin Stępień,
• Sigurd Höger and
• Stefan-S. Jester

Beilstein J. Org. Chem. 2019, 15, 1848–1855, doi:10.3762/bjoc.15.180

• oriented relative to the HOPG main axis directions with γ(a,d1) = γ(b,d2) = (7 ± 2)°. The backbones are oriented with γ(c,d1) = (30 ± 4)° relative to the HOPG main axis direction d1. An additional nomenclature describes the orientation of the intermolecularly interdigitating OC16H33 (and OC10H21) side

New terpenoids from the fermentation broth of the edible mushroom Cyclocybe aegerita

• Frank Surup,
• Florian Hennicke,
• Nadine Sella,
• Maria Stroot,
• Steffen Bernecker,
• Sebastian Pfütze,
• Marc Stadler and
• Martin Rühl

Beilstein J. Org. Chem. 2019, 15, 1000–1007, doi:10.3762/bjoc.15.98

• the leading peer-reviewed taxonomic journals, and the authors did not follow good scientific practice for typification when proposing these taxonomic changes. However, they subsequently published their entries in Index Fungorum, making them valid according to the current nomenclature rules, and the