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

• aspects of glycan identification, quantification and visualisation, some of which will be further developed throughout this article. Biological molecules express their function throughout their three-dimensional structures. For this reason, structural biology places great emphasis on the three-dimensional

A proposed sustainability index for synthesis plans based on input provenance and output fate: application to academic and industrial synthesis plans for vanillin as a case study

• John Andraos

Beilstein J. Org. Chem. 2020, 16, 2346–2362, doi:10.3762/bjoc.16.196

• adequate for rapid identification of best and worst plans in a given set of synthesis plans, whereas, the more detailed poset pairwise dominance analysis is appropriate for obtaining a precise ranking of intermediate performing plans. Application of these ranking methods to 22 synthesis plans for vanillin

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

• positions. This enables identification of terminal residues (i.e. those with all backbone carbon positions without linkages except one). In addition, it uses a new algorithm termed minimum-redundance, maximum-relevance (mRMR) to perform the subtree mining, yielding more fine-tuned results. The authors have

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

• diseased states [8]. The current state-of-the art technology for the characterisation, identification, and quantification of the glycome or glycoproteome is liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) [9]. Popular and powerful glycoproteomic workflows typically involve standard

• packages have been developed for analysis of outputs from MS technology to automate the process of transformation of raw MS data into ion intensities and matching them with appropriate glycan and peptide sequence databases for glycopeptide identification (reviewed in [12][13][14][15][16]). However, there

• use a predefined list of analytes and masses to interrogate MS1 data, and I-GPA [20], GlycopeptideGraphMS [21], GlycoFragwork [22], and GlycReSoft [23], which integrate identification and abundance/intensity information for glycopeptides (a recent review is provided in [10]). Importantly, the

Muyocopronones A and B: azaphilones from the endophytic fungus Muyocopron laterale

• Ken-ichi Nakashima,
• Junko Tomida,
• Tomoe Tsuboi,
• Yoshiaki Kawamura and
• Makoto Inoue

Beilstein J. Org. Chem. 2020, 16, 2100–2107, doi:10.3762/bjoc.16.177

• Technologies). DNA sequencing was performed using an Applied Biosystems 3130 genetic analyzer. Silica gel AP-300 (Toyota Kako) was employed for column chromatography (CC). Silica gel 60 F254 and RP-18 F254S (both Merck) were used for TLC. Fungal material and identification Muyocopron laterale ECN279 was

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

• qualitatively curate large cohort CE-LIF glycomics data. For glycan identification, a previously reported method based on internal triple standards is used. For determining the glycan relative quantities our method uses a clustering algorithm to ‘divide and conquer’ highly heterogeneous electropherograms into

• 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

• antibody glycosylation accurately, high-throughput analysis of hundreds to thousands of profiles is required for the identification of critical process parameters that control the glycosylation CQAs [8]. For complete bioprocessing analysis, favorable glyco-analytical methods need to convey a qualitative

Syntheses of spliceostatins and thailanstatins: a review

• William A. Donaldson

Beilstein J. Org. Chem. 2020, 16, 1991–2006, doi:10.3762/bjoc.16.166

• human spliceosome, splicing factor 3b [6], which inhibits pre-mRNA splicing, and as such act as potent cytotoxic compounds. A review of the discovery, target identification, and biological applications of the compounds that exhibit these binding characteristics has been published [7]. These compounds

A complementary approach to conjugated N-acyliminium formation through photoredox-catalyzed intermolecular radical addition to allenamides and allencarbamates

• Olusesan K. Koleoso,
• Matthew Turner,
• Felix Plasser and
• Marc C. Kimber

Beilstein J. Org. Chem. 2020, 16, 1983–1990, doi:10.3762/bjoc.16.165

• very challenging and we can account for this instability by the identification of 14a in the 1H NMR spectrum of the crude reaction mixture. A comparable instability profile was observed in the formation of N-acyl-N’-aryl-N,N’-aminals derived from enamides [50]; however, to our knowledge, there are no

• conjugated N-acyliminium intermediate; (b) the calculated HOMO [54] for allenamide 15; (c) the identification of intermediate 14a by direct sample loop and flow injection HRESIMS analysis. Supporting Information Supporting Information File 366: Experimental details, analytical (1H NMR, 13C NMR) and ESIMS

Synthesis of 3(2)-phosphonylated thiazolo[3,2-a]oxopyrimidines

• Ksenia I. Kaskevich,
• Anastasia A. Babushkina,
• Vladislav V. Gurzhiy,
• Dmitrij M. Egorov,
• Nataly I. Svintsitskaya and
• Albina V. Dogadina

Beilstein J. Org. Chem. 2020, 16, 1947–1954, doi:10.3762/bjoc.16.161

• cyclization through the N3 atom of the starting 2-thiouracil [14][15][16][17][18][19][20][21][22][23][24]. The formation of 7-oxopyrimidines by cyclization through the N1 atom has been noted only in a few reports [29][30][31][32]. However, reliable data for the identification of the 5- and 7-oxo isomers are

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• summary of the efforts towards identification of GlfT1 and GlfT2 inhibitors revealed that most compounds were reported to have effects on these enzymes at low mM concentrations (up to 8 mM) [6]. These molecules were designed as substrate mimics or transition state analogs and their IC50 values, ranging

Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies

• Giovanni Picca,
• Markus Probst,
• Simon M. Langenegger,
• Oleg Khorev,
• Peter Bütikofer,
• Anant K. Menon and
• Robert Häner

Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145

• candidates (identification by mass spectrometry), and the other probe, MPC-2, consists of a fluorescent label to test candidates for scramblase activity in reconstitution-based assays. The molecular probes were prepared via phosphoramidite chemistry, which allowed the incorporation of the carbohydrate

• Financial support by the Swiss National Science Foundation (SNSF) is gratefully acknowledged: This research was funded by the Sinergia Project: Molecular identification of lipid transporters for protein glycosylation, Grant CRSII5_170923.

Antibacterial scalarane from Doriprismatica stellata nudibranchs (Gastropoda, Nudibranchia), egg ribbons, and their dietary sponge Spongia cf. agaricina (Demospongiae, Dictyoceratida)

• Cora Hertzer,
• Stefan Kehraus,
• Nils Böhringer,
• Fontje Kaligis,
• Robert Bara,
• Dirk Erpenbeck,
• Gert Wörheide,
• Till F. Schäberle,
• Heike Wägele and
• Gabriele M. König

Beilstein J. Org. Chem. 2020, 16, 1596–1605, doi:10.3762/bjoc.16.132

• Voogd, Steve C. de Cook, and Muhammad Abdul Wahab for discussions regarding the sponge identification. The organisms are listed in the collection event list of the Reference Collection of Sam Ratulangi University, Manado, Indonesia (SRU2015/01 SRU2016/02). Collection permits for all collected samples

4-Hydroxy-3-methyl-2(1H)-quinolone, originally discovered from a Brassicaceae plant, produced by a soil bacterium of the genus Burkholderia sp.: determination of a preferred tautomer and antioxidant activity

• Dandan Li,
• Naoya Oku,
• Yukiko Shinozaki,
• Yoichi Kurokawa and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1489–1494, doi:10.3762/bjoc.16.124

• compounds and a synthetic preparation of 1, allowed its first full NMR characterization and identification of 2-quinolone but not 2-quinolinol (2) as the preferred tautomer for this heterocyclic system. While the metal-chelating activity was negligible, compound 1 at 10 μM, a concentration lower than that

Oxime radicals: generation, properties and application in organic synthesis

• Igor B. Krylov,
• Stanislav A. Paveliev,
• Alexander S. Budnikov and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2020, 16, 1234–1276, doi:10.3762/bjoc.16.107

• makes EPR spectroscopy a convenient method for the identification of iminoxyl radicals, and for many of them, EPR is the only observation method due to low stability, and therefore low concentration in investigated systems. For the most stable iminoxyl radicals, sufficiently concentrated solutions were

Anthelmintic drug discovery: target identification, screening methods and the role of open science

• Frederick A. Partridge,
• Ruth Forman,
• Carole J. R. Bataille,
• Graham M. Wynne,
• Marina Nick,
• Angela J. Russell,
• Kathryn J. Else and
• David B. Sattelle

Beilstein J. Org. Chem. 2020, 16, 1203–1224, doi:10.3762/bjoc.16.105

• collaboration and the sharing of data and resources between organisations. In this review we discuss how open science has been applied to anthelmintic drug discovery. Open resources, including genomic information from many parasites, are enabling the identification of targets for new antiparasitic agents

• validation of drug targets and the identification of new candidate molecular targets. So how can a free-living worm contribute to our understanding of parasitic nematodes and the development of anthelmintic drugs? A key advantage is the ease of culture of C. elegans. Large numbers can be generated rapidly

• both the target parasite and the genetic model organism, but the precise target remains unclear, then C. elegans genetics can offer a route to target identification that would be difficult by any other route. The C. elegans community: historically an open science model Research into C. elegans was

Accelerating fragment-based library generation by coupling high-performance photoreactors with benchtop analysis

• Quentin Lefebvre,
• Christophe Salomé and
• Thomas C. Fessard

Beilstein J. Org. Chem. 2020, 16, 982–988, doi:10.3762/bjoc.16.87

• halides to get an insight into the specific reactivity of these building blocks. The workflow combined a powerful photoreactor with precise and reproducible conditions control with benchtop analytical tools such as TLC–MS and low-field NMR. This enabled the identification of privileged spirocyclic

Fabclavine diversity in Xenorhabdus bacteria

• Sebastian L. Wenski,
• Harun Cimen,
• Natalie Berghaus,
• Sebastian W. Fuchs,
• Selcuk Hazir and
• Helge B. Bode

Beilstein J. Org. Chem. 2020, 16, 956–965, doi:10.3762/bjoc.16.84

• unknown derivatives were identified and confirmed by MALDI–MS and MALDI–MS2 experiments in combination with an optimized sample preparation. This led to a total number of 22 novel fabclavine derivatives in eight strains, increasing the overall number of fabclavines to 32. Together with the identification

• of fabclavines as major antibiotics in several entomopathogenic strains, our work lays the foundation for the rapid fabclavine identification and dereplication as the basis for future work of this widespread and bioactive SM class. Keywords: antibiotic; fabclavine; NRPS-PKS hybrid; secondary

• modification step (Figure S1, Supporting Information File 1) [25]. Identification of new fabclavine derivatives To analyze the identified fcl BGCs, mutant strains were generated with a chemically inducible promoter in front of fclC or corresponding homologues (Figure 2). The inducible promoter was integrated

Six-fold C–H borylation of hexa-peri-hexabenzocoronene

• Mai Nagase,
• Kenta Kato,
• Akiko Yagi,
• Yasutomo Segawa and
• Kenichiro Itami

Beilstein J. Org. Chem. 2020, 16, 391–397, doi:10.3762/bjoc.16.37

• –Ishiyama borylation step is possibly increased by further conditions screening. The thus-obtained 1 was identical to the product from the C–H borylation of HBC according to 1H NMR spectroscopy, and the 13C NMR and HRMS by MALDI–TOF MS results also supported the identification. The hexaborylated HBC 1 was

Absolute configurations of talaromycones A and B, α-diversonolic ester, and aspergillusone B from endophytic Talaromyces sp. ECN211

• Ken-ichi Nakashima,
• Junko Tomida,
• Takao Hirai,
• Yoshiaki Kawamura and
• Makoto Inoue

Beilstein J. Org. Chem. 2020, 16, 290–296, doi:10.3762/bjoc.16.28

• leaves of Selaginella tamariscana (Selaginellaceae) were cultivated in Tajimi City, Gifu, Japan. The methods of isolation and identification of endophytic fungi were performed in a similar manner as described previously [8]. Based on the DNA sequencing of ITS of rDNA and the D1/D2 domain of 26S rDNA

Synthesis, liquid crystalline behaviour and structure–property relationships of 1,3-bis(5-substituted-1,3,4-oxadiazol-2-yl)benzenes

• Afef Mabrouki,
• Malek Fouzai,
• Armand Soldera,
• Abdelkader Kriaa and
• Ahmed Hedhli

Beilstein J. Org. Chem. 2020, 16, 149–158, doi:10.3762/bjoc.16.17

• realized in cooling and heating cycles for compounds 2b, 4a and 4b (Figure 2). POM technique has illustrated smectic phases for all compounds. Identification of the phase textures was accomplished by comparing with those reported in literature [24]. The texture of 2b (Figure 2a) seems to be a variant of

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

• results for bioassays, as well as species identification of the pigmentosin and glycoasperfuran producers. Acknowledgements This work was supported by the TRF through the Royal Golden Jubilee Ph.D. program (grant no. PHD/0163/2556 to WK); Alexander von Humboldt Foundation (Georg-Forster Grant to SEH

Two new aromatic polyketides from a sponge-derived Fusarium

• Mada Triandala Sibero,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Ocky K. Karna Radjasa,
• Agus Sabdono,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2019, 15, 2941–2947, doi:10.3762/bjoc.15.289

• summary, our chemical analysis of a sponge-derived fungus of the genus Fusarium led to the identification of two new and three known aromatic polyketides (1 and 2, and 3–5, respectively) and two sesquiterpenes (6 and 7). Although secondary metabolites of Fusarium were extensively studied in the past [26

Automated glycan assembly of arabinomannan oligosaccharides from Mycobacterium tuberculosis

• Alonso Pardo-Vargas,
• Priya Bharate,
• Martina Delbianco and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2019, 15, 2936–2940, doi:10.3762/bjoc.15.288

• ]. Identification of novel anti-TB agents that specifically target AMs with high sensitivity are required. Pure AM oligosaccharides may help to identify new lead compounds for the development of diagnostics. Since the isolation of pure oligosaccharides from MTB strains in sufficient quantities is challenging, the

Emission and biosynthesis of volatile terpenoids from the plasmodial slime mold Physarum polycephalum

• Xinlu Chen,
• Tobias G. Köllner,
• Wangdan Xiong,
• Guo Wei and
• Feng Chen

Beilstein J. Org. Chem. 2019, 15, 2872–2880, doi:10.3762/bjoc.15.281

• and gene expression patterns, the products of most DdTPSs were released as volatiles from D. discoideum at the multicellular developmental stage [14][15]. TPS genes previously were known to exist only in bacteria, fungi, and plants [13][17][18]. The identification of TPS genes in dictyostelid social

• . At the 18th day after the transfer, essentially the same profile of volatiles was detected (Figure 1A). Four terpene synthase genes were identified in P. polycephalum With the identification of terpenes from the headspace of P. polycephalum (Figure 1), the next question was how they are synthesized

• for one hour, the SPME fiber was withdrawn and then inserted into the injector port of a Shimadzu 17A gas chromatograph coupled to a Shimadzu QP5050A quadrupole mass selective detector for volatile identification and identification. Separation was performed on a Restek Rxi-5Sil MS column (30 m × 0.25

An improved, scalable synthesis of Notum inhibitor LP-922056 using 1-chloro-1,2-benziodoxol-3-one as a superior electrophilic chlorinating agent

• Nicky J. Willis,
• Elliott D. Bayle,
• George Papageorgiou,
• David Steadman,
• Benjamin N. Atkinson,
• William Mahy and
• Paul V. Fish

Beilstein J. Org. Chem. 2019, 15, 2790–2797, doi:10.3762/bjoc.15.271

• penetration is an essential requirement of the compound but would be an ideal peripherally restricted control. These data will contribute to the understanding of drug levels of 1 to overlay with appropriate in vivo efficacy endpoints, i.e., the PK-PD relationship. The identification of a suitable analogue of

• tool by capping off the acid as an amide. Although significant Notum inhibition activity could be achieved, none of these amides demonstrated the required combination of metabolic stability along with cell permeability without evidence of P-gp mediated efflux. The identification of a suitable analogue