Molecular diversity of the base-promoted reaction of phenacylmalononitriles with dialkyl but-2-ynedioates

• Hui Zheng,
• Ying Han,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2022, 18, 991–998, doi:10.3762/bjoc.18.99

• (CCDC 2176736) have been deposited at the Cambridge Crystallographic Database Center (http://www.ccdc.cam.ac.uk). Supporting Information File 222: Characterization data and 1H NMR, 13C NMR, and HRMS spectra of the compounds. Funding This work was financially supported by National Natural Science

On Reuben G. Jones synthesis of 2-hydroxypyrazines

• Pierre Legrand and
• Yves L. Janin

Beilstein J. Org. Chem. 2022, 18, 935–943, doi:10.3762/bjoc.18.93

• also mentioned that this heterocycle appears to be under-represented in the DrugBank database (in comparison with pyridine-containing substances) plausibly because of a lesser “availability of pyrazine fragments in vendors”. For chemists, this statement could be translated as “fragments” far more

Copper-catalyzed multicomponent reactions for the efficient synthesis of diverse spirotetrahydrocarbazoles

• Shao-Cong Zhan,
• Ren-Jie Fang,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2022, 18, 796–808, doi:10.3762/bjoc.18.80

• conditionsa. Supporting Information The crystallographic data of the compounds 1f (CCDC 2109575), 2b (CCDC 2109576), 2g’ (CCDC 2109577), 3a (CCDC 2109578), 4e (CCDC 2109579) and 5b (CCDC 2109580) have been deposited at the Cambridge Crystallographic Database Center (http://www.ccdc.cam.ac.uk). Supporting

Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity

• Jamshid Amiri Moghaddam,
• Huijuan Guo,
• Karsten Willing,
• Thomas Wichard and
• Christine Beemelmanns

Beilstein J. Org. Chem. 2022, 18, 722–731, doi:10.3762/bjoc.18.72

• network with Ptases deposited in the Uniprot database (Figure 2 and Table S1 in Supporting Information File 1). A subsequent network analysis uncovered that the genomes of analyzed bacterial genera encoded only four (G1–G4) out of eight previously reported Ptase groups. The first group of Ptases (G1

• , Belgium). Bioinformatic analysis: Amino acid sequences of all described prenyltransferases were retrieved from the UniProtKB/Swiss-Prot database. Other Ptase amino acid sequences of marine Flavobacteria and Saccharomonopora strains were obtained using Blast searches against defined genome groups within

• the PATRIC database (3.6.12) [34]. The sequence clustering was generated by the CLANS (CLuster ANalysis of Sequences) program [35]. In brief, the relationships between sequences were assessed based on an all-against-all BLAST search and the E-values better (lower) than 1.0E−6 were used to connect each

Tri(n-butyl)phosphine-promoted domino reaction for the efficient construction of spiro[cyclohexane-1,3'-indolines] and spiro[indoline-3,2'-furan-3',3''-indolines]

• Hui Zheng,
• Ying Han,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2022, 18, 669–679, doi:10.3762/bjoc.18.68

• Characterization data and 1H NMR, 13C NMR, HRMS spectra of the compounds are available. The crystallographic data of the compounds 3l (CCDC 2166451), 3s (CCDC 2166452), 3f’ (CCDC 2173182), 5a (CCDC 2166453), 8a (CCDC 2166454) have been deposited at the Cambridge Crystallographic Database Center (http

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

• three different seawater-based media, and butanolic extracts of the fermented cultures were subjected to HPLC/DAD analysis, which detected several unknown metabolites not present in our in-house UV database, showing UV end-absorption in the culture extract of A11M seawater medium. Purification of these

GlycoBioinformatics

• Kiyoko F. Aoki-Kinoshita,
• Frédérique Lisacek,
• Niclas Karlsson,
• Daniel Kolarich and
• Nicolle H. Packer

Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184

• transcription factors using next-generation sequencing expression data of glycoenzymes in cancer cell lines. The latter paper uses knowledge from current open access glycomic databases to curate and validate glycan structures reported on proteins in the Protein Data Bank (PDB) database. Overall, the wide

Efficient synthesis of polyfunctionalized carbazoles and pyrrolo[3,4-c]carbazoles via domino Diels–Alder reaction

• Ren-Jie Fang,
• Chen Yan,
• Jing Sun,
• Ying Han and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2021, 17, 2425–2432, doi:10.3762/bjoc.17.159

• (CCDC 2099074), 3b (CCDC 2099075), and 4g (CCDC 2099076) have been deposited at the Cambridge Crystallographic Database Centre (http://www.ccdc.cam.ac.uk). Representative bioactive carbazole derivatives. Single crystal structure of the isomer 3a. Single crystal structure of the isomer 3b. Single crystal

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

• colony of the UIAU-6B strain was purified by repeated subculture on pseudomonas agar base plates. The strain was identified by analysis of the molecular DNA sequencing of its 16S rDNA and the sequence obtained was compared with the Genbank database using the BLAST search of the National Center for

A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis

• Theodore Groth,
• Rudiyanto Gunawan and
• Sriram Neelamegham

Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119

• pathways is largely unknown. In this work, we performed data mining of TF–glycogene relationships from the Cistrome Cancer database (DB), which integrates chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA-Seq data to constitute regulatory relationships. In total, we observed 22,654 potentially

• include: i) data from the Gene Transcription Regulatory Database (GTRD) [40], which has analyzed publicly available ChIP-Seq data with multiple algorithms to systematically catalog TF–gene relationships across several organisms and cellular contexts; ii) the Regulatory Circuits DB [41], which relies on

Volatile emission and biosynthesis in endophytic fungi colonizing black poplar leaves

• Christin Walther,
• Pamela Baumann,
• Katrin Luck,
• Beate Rothe,
• Peter H. W. Biedermann,
• Jonathan Gershenzon,
• Tobias G. Köllner and
• Sybille B. Unsicker

Beilstein J. Org. Chem. 2021, 17, 1698–1711, doi:10.3762/bjoc.17.118

• , Weiterstadt, Germany). The obtained sequences were aligned using Geneious 6.0.5 [84] and compared to the NCBI sequence database [85] (Supporting Information File 1, Table S1). In case of isolates with multiple 99–100 % identity hits on several species within the same genus, we identified these only to the

• mature black poplar (Populus nigra) trees.a Volatiles emitted from endophytic fungi growing in culture on potato dextrose agar (PDA).a Supporting Information Supporting Information File 134: Sequences of isolated endophytic fungi and identification according to NCBI database, primer used in this study

Breaking paracyclophane: the unexpected formation of non-symmetric disubstituted nitro[2.2]metaparacyclophanes

• Suraj Patel,
• Tyson N. Dais,
• Paul G. Plieger and
• Gareth J. Rowlands

Beilstein J. Org. Chem. 2021, 17, 1518–1526, doi:10.3762/bjoc.17.109

• chemistry can produce any substitution pattern there are few unsymmetrical [2.2]metaparacyclophanes (3) and only one X-ray crystallographic structure found in the CCDC database, and this is a triple-layered cyclophane [44]. We have been interested in the formation of substituted [2.2]paracyclophanes for a

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

• , and the relative amounts of the significant features were displayed as a boxplot. The selected significant features were further searched in the raw HRMS profiles to identify those with the reliable isotopic pattern assigned to a metabolite. The m/z values were searched in the METLIN database, using a

Structural effects of meso-halogenation on porphyrins

• Keith J. Flanagan,
• Maximilian Paradiz Dominguez,
• Zoi Melissari,
• Hans-Georg Eckhardt,
• René M. Williams,
• Dáire Gibbons,
• Caroline Prior,
• Gemma M. Locke,
• Alina Meindl,
• Aoife A. Ryan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88

• the crystallographic structural characteristics of 13 mesox-halo-substituted porphyrins. Data obtained from the CSD crystal structure database accompanied by data obtained from our group are discussed [25]. Furthermore, any general structural motif that appears consistent among the mesox-halo

• -substituted porphyrins In the CSD database, there are a few other notable examples which whilst they are interesting, they do not constitute a significant library to support a complete discussion (compounds 20–24, Figure 21) [37][38][39]. Other examples do exist in the CSD, such as strapped systems [40], but

Direct synthesis of anomeric tetrazolyl iminosugars from sugar-derived lactams

• Michał M. Więcław and
• Bartłomiej Furman

Beilstein J. Org. Chem. 2021, 17, 115–123, doi:10.3762/bjoc.17.12

• groups are omitted for clarity. Full crystallographic data available in Supporting Information File 2 and Supporting Information File 3, and in Cambridge Crystallographic Database under CCDC-2001373 and CCDC-2001372 numbers, respectively. Proposed structures of compounds 5a and 2-epi-5a with 1H-1H

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

• complexes, with most of the complexes being homooligomeric complexes [58]. In fact, an analysis done in the BRENDA enzyme database [59] shows that there are more homooligomeric complexes than expected [60]. PPIs in homooligomeric complexes are usually difficult to predict using computational measures

• for illustration is the heterodimer of human NAD-dependent isocitrate dehydrogenase (Protein Database (PDB): 6KDF) [10]. Figure adapted from Carter et al. [11]. Mechanisms of homooligomeric complex formations. a) Domain swapping of RNase A (PDB: 1A2W) [73]. The swapped regions are shown in red. b

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

• its glycopeptide coverage. Those glycans were only present in low abundance on the glycopeptides, and often no MS/MS spectrum was present (Figure 3). However, it highlights the importance of a complete glycan composition list for a database-based identification of glycopeptides, something that is less

• database including 71,591 protein sequences (20,205 from Swiss-Prot and 51,386 from TrEMBL). The C-terminal cleavage of lysine and arginine and a maximum of two missed cleavages was allowed. A tolerance of 10 ppm was applied for the precursors and 20 ppm for fragment ions. A carbamidomethylation was set as

• a fixed modification for cysteine residues. Methionine oxidation was enabled as a variable modification. The search for N- and O-glycopeptides was separately performed. For this purpose, either the database “N-glycan 309 mammalian no sodium” (Supporting Information File 7) or “O-glycan 78 mammalian

Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities

• Heiko T. Kiesewalter,
• Carlos N. Lozano-Andrade,
• Mikael L. Strube and
• Ákos T. Kovács

Beilstein J. Org. Chem. 2020, 16, 2983–2998, doi:10.3762/bjoc.16.248

• reads were assigned to the respective samples with an average of 12,083 reads per sample (range: 751 to 34,802; Table S3, Supporting Information File 1). The 16S rRNA reference sequences with a 99% identity criterion obtained from the SILVA database release 132 were trimmed to the V3-V4 region, bound by

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

• specification of Linear Code to reaction rules, we aim to minimize inconsistent symbology thereby making glycan database queries easier. With a clear guide for generating reaction rule descriptions, glycan synthesis models will be more interoperable and reproducible thereby moving glycoinformatics closer to

• in database queries. Both GlycoCT and WURCS produce unambiguous representations and are thereby invaluable for many applications, ranging from systems biology analyses [17] to an international glycan structure repository [26][27][28][29]. GlycoCT and WURCS provide a high degree of unambiguous detail

• -glycan database called UniCorn, based upon a Perl implementation of reactions on glycans represented in Linear Code [37]. Though Linear Code is computer-parsable, there is still substantial work necessary to implement that parsing because there is no standard representation for handling the wide variety

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

• distributed together with Privateer. If the existence of a glycan in the database is confirmed, then the software can attempt to find records about the sequence on other, more specialised databases (currently only GlyConnect) to obtain information such as the source organism, the type of glycosylation and the

• structures. Importantly, the majority of the glycan chains that do have a unique GlyTouCan accession ID assigned (except for single residues linked to protein backbones), have also been successfully matched on the GlyConnect database (Table 2). Results Examples of use As observed in previous studies

• might not necessarily be experts in structural glycobiology. The fact that these glycans could not be matched to standard database entries should be enough to raise the question with depositors, and at the very least write a caveat on a deposited entry where glycans could not be correctly identified

Conformational preferences of fluorine-containing agrochemicals and their implications for lipophilicity prediction

• Daniela Rodrigues Silva,
• Joyce K. Daré and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2020, 16, 2469–2476, doi:10.3762/bjoc.16.200

• the most likely conformations to correlate with experimental log P, one can assess the dependence of log P with molecular conformation. Accordingly, a consistent set of fluorine-containing agrochemicals (Figure 4) with experimentally available log P data was selected from a single database [24], which

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

• interface for generating carbohydrate structures to query the database included in GlyCosmos: GlyTouCan [34]. GlyCosmos is a web portal that integrates resources linking glycosciences with life sciences. Besides elements such as “SugarDrawer” and GlyTouCan (carbohydrate database), the platform GlyCosmos

• can be further used to search the GlyTouCan [34] database to explore the literature details related to the input structure. GlycoGlyph is an efficient tool for sketching or building glycans with a highly usable interface that can significantly help researchers to improve the uniformity in glycan

• notations for the University of Oxford (UOXF) format. The input complies with various linear sequence and text formats. They include GlycoCT, GLYcan structural Data Exchange using Connection Tables (GLYDE-II), Bacterial Carbohydrate Structures DataBase (BCSDB) [41], carbohydrate sequence markup language

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

• version published in June 2016 can be found at: https://www.beilstein-institut.de/download/1458/mirage_glycan_array_guidelines_version_1.0__22_june_2016.pdf. Tools for glycan microarray data A) Repositories of glycan microarray data 1. CFG Database: Status: Available. Address: http

• ://www.functionalglycomics.org/glycomics/publicdata/primaryscreen.jsp. Description: The Consortium for Functional Glycomics (CFG) database of glycan array data (Figure 3A) is one of the largest archival resources for glycan microarray data. The CFG was founded in 2001 and was funded for about 10 years, during which time the

• main website and database were created [33]. The microarray work was then taken over by the National Center for Functional Glycomics (NCFG) which was established in 2013. The CFG database has over 3000 experimental results files with 2 major types of arrays, the mammalian glycan printed array (noted as

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

• DDA files (n = 12) downloaded from a previously published dataset [20] obtained from the ProteomeXchange Consortium via the MassIVE repository (PXD003369, MSV000079426). Two searches were conducted on each file, one N-linked and one O-linked. A human protein database was used (UniProt UP000005640

• peptide. For N-linked searches (N-X-S/T) a database of 164 N-glycans was used (Supporting Information File 1, Table S41) and for the O-linked searches (at any S/T) a database of 49 O-glycans (Supporting Information File 1, Table S42) was used. All glycan modifications were set as “Rare 1” allowing each

• included, parsed from the online UniProtKB database using an inhouse Python library. Statistical analyses Significant differences in glycoform abundances between healthy and diseased samples were evaluated using an unpaired two-tailed t-test without corrections for multiple comparisons. Missing values were

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

• based on a triple standard GU calculation [10][11] and database matching whilst the quantitation used HappyTools calibration and area calculation [14]. The GU calculation involved standardizing the migration time of the peaks by generating a ‘virtual’ glucose unit (GU) ladder calculated using the

• bracketing standards in the electropherograms, the variation of GU values for glycan peaks generally were within a very small range (Figure 1A and 1B) allowing for consistent database matching against a GU CE database (APTS fluorescent labelled) [10]. HappyTools was used to calibrate the migration times of

• label). The UPLC-MS approach was used to characterize a commercial Anti-HER-2 reference standard (Section 4.3.4 from mentors) using the UNIFI software and GU/mass database (RFMS labelled) provided by Waters Corp [18]. Figure 5A shows that 14 glycans were identified in 13 UPLC peaks using UPLC-MS