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

• scientists. The Privateer software is a validation and analysis tool that provides access to a number of metrics and links to external experimental resources, allowing users to evaluate structures using carbohydrate-specific methods. Here, we present the Privateer database, a free resource that aims to

• complement the growing glycan content of the PDB. Keywords: carbohydrates; database; N-glycans; N-glycosylation; polysaccharides; validation; website; Introduction Carbohydrate modelling is an important but often cumbersome stage in the macromolecular X-ray structure solution workflow. The accurate

• new resources, including services and databases [9][10][11][12][13], and standalone software [14][15][16][17][18]. Among these, the Privateer software package has been a key tool for glycoprotein and protein–carbohydrate complex validation: Privateer analyses the conformational plausibility of each

New variochelins from soil-isolated Variovorax sp. H002

• Jabal Rahmat Haedar,
• Aya Yoshimura and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2024, 20, 692–700, doi:10.3762/bjoc.20.63

• disruption plasmid, pGM160-ΔvarG. The cassette was sequenced for validation. The disruption plasmid was introduced into E coli S17-1 λpir by electroporation. Both Variovorax sp. H002 and E. coli S17-1 λpir were cultured overnight at 30 °C in 2xR2A and LB, respectively. The overnight cultures were washed with

• , Ser: serine, Pro: proline, Orn: ornithine). (b) Validation of var biosynthetic gene cluster. The plasmid constructed for the generation of the varG null-mutant strain (varG::cmR) using the cmR gene cassette (left), and HPLC-profile comparison of the Variovorax sp. H002 wild type strain and the varG

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A

• Michael O. Akintubosun and
• Melanie A. Higgins

Beilstein J. Org. Chem. 2024, 20, 589–596, doi:10.3762/bjoc.20.51

• annotations and in vivo studies [8]. However, validation by in vitro approaches or biochemical analysis of the individual enzymes is lacking. Here, we verify that Hyg17 is a myo-inositol dehydrogenase and show that it has a distinct substrate scope. In addition, we use sequence similarity networks to compare

Ligand effects, solvent cooperation, and large kinetic solvent deuterium isotope effects in gold(I)-catalyzed intramolecular alkene hydroamination

• Ruichen Lan,
• Brock Yager,
• Yoonsun Jee,
• Cynthia S. Day and
• Amanda C. Jones

Beilstein J. Org. Chem. 2024, 20, 479–496, doi:10.3762/bjoc.20.43

• ) protodeauration (Scheme 1), the depth of experimental mechanistic validation achieved for allenes and alkynes have not been reproduced with alkenes. In an important foundational study by Toste, the expected alkylgold intermediate from intramolecular alkene hydroamination was isolated, however, turnover

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

• ), which we contrasted with the established R-type lectin Ricinus communis agglutinin 1 (RCA1). We also report binding of specific glycosaminoglycan subtypes and a general enhancement of binding by sulfation. Further validation using agglutination, thermal shift assays, and surface plasmon resonance

• ]. Multiple iterations of anisotropic restrained maximum likelihood refinement using REFMAC 5.8 [38] and manual building using Coot [39] were performed. Hydrogen atoms were added in their riding positions during refinement and 5% of the observations were set aside for cross-validation analysis. Upon

• inspection of the electron density maps, carbohydrate moieties were introduced and checked using Privateer [40]. The final model was validated using the wwPDB validation server (https://validate-rcsb-1.wwpdb.org). Structure figures were made using PyMol 2.5.7 and ChimeraX 1.6 [31]. The parameters for CH−π

NMRium: Teaching nuclear magnetic resonance spectra interpretation in an online platform

• Luc Patiny,
• Hamed Musallam,
• Alejandro Bolaños,
• Michaël Zasso,
• Julien Wist,
• Metin Karayilan,
• Eva Ziegler,
• Johannes C. Liermann and
• Nils E. Schlörer

Beilstein J. Org. Chem. 2024, 20, 25–31, doi:10.3762/bjoc.20.4

• ; structure elucidation; Introduction For the validation of molecular structures, nuclear magnetic resonance (NMR) spectroscopy is an indispensable methodology in the daily routine of synthetic chemistry laboratories. Arguably, NMR experiments serve as the ‘eye of the synthetic chemist’ because they allow a

• grasp functionality would make it a preselected tool for the review process of chemistry publications. Future developments of NMRium include the processing of 2D NMR experiments, as well as a CASE- and prediction-supported assignment tool with an integrated validation function for assigned data [44

GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data

• Thomas Barillot,
• Baptiste Schindler,
• Baptiste Moge,
• Elisa Fadda,
• Franck Lépine and
• Isabelle Compagnon

Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134

• the present study. For this study, a first set of 33 labelled experimental spectra obtained as described previously [4] were collected for training and validation of the model. The standard instrumental conditions for recording MS–IR data consist in a laser-enabled mass spectrometer equipped with a 3D

• category of molecules. Finally, 70% of them were used for training of the models, and 30% were used for validation. The composition of the datasets used for training, validation and tests is summarized in Table 1. Model architecture In this study we opted for a fully connected feed-forward network based on

• the trained model. Results and Discussion Model classification accuracy Our GlAIcomics model shows a classification accuracy of 100% on the validation set and 99.98% on the test set (S.M : dataset 2 in Table 1). The 8000 synthetic spectra of set 2 were sorted by noise level, amplitude modulation

Secondary metabolites of Diaporthe cameroonensis, isolated from the Cameroonian medicinal plant Trema guineensis

• Bel Youssouf G. Mountessou,
• Élodie Gisèle M. Anoumedem,
• Blondelle M. Kemkuignou,
• Yasmina Marin-Felix,
• Frank Surup,
• Marc Stadler and
• Simeon F. Kouam

Beilstein J. Org. Chem. 2023, 19, 1555–1561, doi:10.3762/bjoc.19.112

• -1121341), the AvH Research Hub project CECANAPROF (3.4-CMR-Hub) and the International Foundation for Science (grant I1-F-6554-1). Author Contributions Conceptualization, S.F.K. and M.S.; methodology, B.Y.G.M., E.G.M.A. and Y.M.-F.; validation, S.F.K. and M.S.; collection of the plant material and

Strategies to access the [5-8] bicyclic core encountered in the sesquiterpene, diterpene and sesterterpene series

• Cécile Alleman,
• Charlène Gadais,
• Laurent Legentil and
• François-Hugues Porée

Beilstein J. Org. Chem. 2023, 19, 245–281, doi:10.3762/bjoc.19.23

• intermediate 53 could be obtained in only 8 steps and at a large scale. Validation of this strategy allowed the authors to extend this approach to the total synthesis of alterbrassicicene D (54) and 3(11)-epoxyhypoestenone (55). 1.1.2 Other chemical series possessing a [5-8] unit; 1.1.2.1 Early-stage

Preparation of β-cyclodextrin/polysaccharide foams using saponin

• Max Petitjean and
• José Ramón Isasi

Beilstein J. Org. Chem. 2023, 19, 78–88, doi:10.3762/bjoc.19.7

• . This one might be useful for quantification purposes, provided some validation can be obtained using other appropriate methodologies. A shift of the 1000 cm−1 C–O band towards higher wavenumbers (Supporting Information File 1, Figure S4) occurs for each matrix when going from 100:0 to 0:100 ratio of

Navigating and expanding the roadmap of natural product genome mining tools

• Friederike Biermann,
• Sebastian L. Wenski and
• Eric J. N. Helfrich

Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178

• -like structures and prioritized based on the taxonomic distribution of the cluster. decRiPPter was successfully used for the identification of a new lanthipeptide subfamily, providing experimental validation of the algorithm [65]. A more advanced form of supervised learning is deep learning (Figure 4

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• binding positions (Figure 6a and b) that could lead to restricted ligand flexibility and hence the observed increase of emission. A more detailed experimental validation will be the focus of an experimental study in the near future. Three variants of 1 will be synthesized to gain a deeper insight into the

(Phenylamino)pyrimidine-1,2,3-triazole derivatives as analogs of imatinib: searching for novel compounds against chronic myeloid leukemia

• Luiz Claudio Ferreira Pimentel,
• Lucas Villas Boas Hoelz,
• Henayle Fernandes Canzian,
• Frederico Silva Castelo Branco,
• Andressa Paula de Oliveira,
• Vinicius Rangel Campos,
• Floriano Paes Silva Júnior,
• Rafael Ferreira Dantas,
• Jackson Antônio Lamounier Camargos Resende,
• Anna Claudia Cunha,
• Nubia Boechat and
• Mônica Macedo Bastos

Beilstein J. Org. Chem. 2021, 17, 2260–2269, doi:10.3762/bjoc.17.144

• for designing new series of substances with greater potency and less toxicity than IMT, with lesser effects for the patient. Molecular docking Validation of the molecular docking protocol was performed through redocking of the IMT complexed to the BCR-Abl-1 structure (PDB code: 3PYY) [37]. Thus, the

• structures of the compounds were constructed and optimized by the semi-empirical Recife Model 1 (RM1) method using the Spartan 14 program (Wavefunction, Inc.). Validation of the molecular docking protocol was performed through the redocking of IMT complexed with the BCR-Abl-1 structure (PDB code: 3PYY), free

Nomimicins B–D, new tetronate-class polyketides from a marine-derived actinomycete of the genus Actinomadura

• Zhiwei Zhang,
• Tao Zhou,
• Taehui Yang,
• Keisuke Fukaya,
• Enjuro Harunari,
• Shun Saito,
• Katsuhisa Yamada,
• Chiaki Imada,
• Daisuke Urabe and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2194–2202, doi:10.3762/bjoc.17.141

• the dominant tautomers in solution. This is the first validation to state that the keto carbonyl unit in the five-membered ring (C24 in Figure 5) and the acyl ketone connecting at C2 (C3 in Figure 5) are preferably enolized to form stable isomeric structures in spirotetronic acids. The molecular

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

• relationships, the starting point for experimental system-wide validation. Keywords: ChIP-Seq; glycoinformatics; glycosylation; TCGA transcription factor; Introduction The glycan signatures of cells and tissue are controlled by the expression pattern of 300–350 glycosylating-related genes that are together

• signaling pathways contribute to altered glycan structures in diseases such as diabetes and cancer. Thus, this work represents a rich starting point for wet-lab validation and glycoinformatics DB construction. Visualizing TF–glycogene interaction networks revealed communities of glycogenes in each cancer

• experimentally discovering the TFs regulating glycosylation. The findings would likely vary between cell types, and thus additional efforts are necessary before a wet-lab-validated framework emerges. Orthogonal datasets containing other ChIP-Seq and omics data may also enhance in silico validation. Some examples

Recent advances in palladium-catalysed asymmetric 1,4–additions of arylboronic acids to conjugated enones and chromones

• Jan Bartáček,
• Jan Svoboda,
• Martin Kocúrik,
• Jaroslav Pochobradský,
• Alexander Čegan,
• Miloš Sedlák and
• Jiří Váňa

Beilstein J. Org. Chem. 2021, 17, 1048–1085, doi:10.3762/bjoc.17.84

• included in the theoretical model. The experimental validation of the predicted results is therefore a challenge that has to be finished [68]. Conclusion In this review, we focused on palladium-catalysed asymmetric 1,4-addition reactions of arylboronic acids to conjugated enones and chromones. The

Novel library synthesis of 3,4-disubstituted pyridin-2(1H)-ones via cleavage of pyridine-2-oxy-7-azabenzotriazole ethers under ionic hydrogenation conditions at room temperature

• Romain Pierre,
• Anne Brethon,
• Sylvain A. Jacques,
• Aurélie Blond,
• Sandrine Chambon,
• Sandrine Talano,
• Catherine Raffin,
• Branislav Musicki,
• Claire Bouix-Peter,
• Loic Tomas,
• Gilles Ouvry,
• Rémy Morgentin,
• Laurent F. Hennequin and
• Craig S. Harris

Beilstein J. Org. Chem. 2021, 17, 156–165, doi:10.3762/bjoc.17.16

• ), DIPEA, DMF, 60 °C, 16 h, 44–71% 32a–h); d) TFA, rt, 30 min. for Boc protected amines (32b,c); e) Pd(OAc)2, TES, DCM/MeOH, rt, 16 h for Cbz protected amines. Selected results from conditions’ screening for pyridin-2-(1H)-one formation (7). Validation of library conditions.a Selected results from

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

• validation of PPIs can then be determined by using HDXMS together with cryoEM. The full thermodynamic profile can subsequently be determined using biophysical methods, yielding the full picture of a particular PPI. For instance, Cash et al. used cryo-EM complemented with HDXMS and enzymatic assays to fully

Pentannulation of N-heterocycles by a tandem gold-catalyzed [3,3]-rearrangement/Nazarov reaction of propargyl ester derivatives: a computational study on the crucial role of the nitrogen atom

• Giovanna Zanella,
• Martina Petrović,
• Dina Scarpi,
• Ernesto G. Occhiato and
• Enrique Gómez-Bengoa

Beilstein J. Org. Chem. 2020, 16, 3059–3068, doi:10.3762/bjoc.16.255

• temperature (Table 1, entry 6). However, none of these attempts were met with success, and indeed, a very sluggish reactivity was recorded in all these cases. Unfortunately, these results confirmed the negative predictions arising from the above calculations, but at the same time, they serve as a validation

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

• GlycopeptideGraphMS with MS/MS validation, whereas the Byonic-only search resulted in 35 compositions (Table S4, Supporting Information File 1). Of note, four glycan compositions (H2N3F1, H2N4F1, H5N3F1S1, H5N5F2S1) were not included in the N-glycan search list of Byonic, and hence not included for the calculation of

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

• development, exchange, extension, and validation of glycosylation models and analysis tools. Here we bring explicit attention to the concerns we raise above, we provide a focused, text-based representation of reaction rules that have been introduced for the purpose of formalizing these communications. GlycoCT

• discussed or described. We hope to encourage that adoption through our LiCoRRICE examples. Increased FAIRness will facilitate the validation and distribution of developing glycoinformatics toolkits. Easy-to-use glycoinformatics toolkits, made possible by the fluency of interoperability across tools, are one

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

• initiatives have stored results in publicly available databases, some of which can be accessed through API interfaces. In the present work, we will describe how the Privateer carbohydrate structure validation software has been extended to harness results from glycomics projects, and its use to greatly improve

• the validation of 3D glycoprotein structures. Keywords: electron cryomicroscopy; glycoinformatics; glycomics; Privateer; X-ray crystallography; Introduction Glycosylation-related processes are prevalent in life. The attachment of carbohydrates to macromolecules extends the capabilities of cells to

• -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

In silico rationalisation of selectivity and reactivity in Pd-catalysed C–H activation reactions

• Liwei Cao,
• Mikhail Kabeshov,
• Steven V. Ley and
• Alexei A. Lapkin

Beilstein J. Org. Chem. 2020, 16, 1465–1475, doi:10.3762/bjoc.16.122

• initial guess due to particularly bad initial geometry – discard the conformer/intermediate, (iv) decomposed intermediate (no Pd–C bond determined by interatomic distance analysis) – discard intermediate. Literature validation In order to test the developed algorithm, a representative literature data

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

• 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

• /pharmacological proof-of-concept for target validation. Whilst RNA interference and CRISPR methodologies are now being applied to parasites themselves [110][111][112], inevitably, large-scale functional genomic resources are mainly found in C. elegans. The C. elegans Gene Knockout Consortium has obtained putative

• cost. Another open source resource with immediate applicability to target identification and validation is the Open Worm Movement Database [115]. This is an open platform for analysing and sharing worm behavioural data, such as that obtained from worm tracking software. For example, the researcher can

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

• photoreactors. Bottom, from left to right: photoreactor OFF, ON, and ON through protective yellow filter. TLC–MS equipment: analysis of 5 reactions in 5 minutes. Pre-QC validation by 60 MHz benchtop NMR. One-day workflow for fragment-based library generation. QC: Quality control. MPLC: Medium-pressure liquid