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

• overall conformation of N-glycans comes to that of validated deposited structures [16]. The PDB-REDO [21] database is a separate resource, albeit linked to the PDB in that the entries that compound PDB-REDO are those original PDB crystallographic entries that included experimental data (i.e., reflection

Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria

• Kara A. Strickland,
• Brenda Martinez Rodriguez,
• Ashley A. Holland,
• Shelby Wagner,
• Michelle Luna-Alva,
• David E. Graham and
• Jonathan D. Caranto

Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75

• physiological function of NNG are discussed below. Results Screening of Vs NnlA homologs for NNG degradation activity To select Vs NnlA homologs to test for NNG degradation activity, we performed a BLAST search of the Vs NnlA amino acid sequence in the NCBI database. This search resulted in retrieval of 99

Advancements in hydrochlorination of alkenes

• Daniel S. Müller

Beilstein J. Org. Chem. 2024, 20, 787–814, doi:10.3762/bjoc.20.72

• ). Conveniently, these parameters are freely available on Mayr's database of reactivity parameters [28]. On the other hand, one can assess the stability of the in situ-generated cation. The greater its stability, the easier the protonation of the alkene will be, making it more reactive towards hydrochlorination

• of a single report concerning the catalytic asymmetric hydrochlorination of alkenes. Hence, this represents another important challenge for the future. Mayr’s nucleophilicity parameters for several alkenes. References for each compound can be consulted via the database. Hydride affinities relating to

Genome mining of labdane-related diterpenoids: Discovery of the two-enzyme pathway leading to (−)-sandaracopimaradiene in the fungus Arthrinium sacchari

• Fumito Sato,
• Terutaka Sonohara,
• Shunta Fujiki,
• Akihiro Sugawara,
• Yohei Morishita,
• Taro Ozaki and
• Teigo Asai

Beilstein J. Org. Chem. 2024, 20, 714–720, doi:10.3762/bjoc.20.65

• underexplored family of natural products. In the biosynthesis of fungal LRDs, bifunctional terpene cyclases (TCs) consisting of αβγ domains are generally used to synthesize the polycyclic skeletones of LRDs. Herein, we conducted genome mining of LRDs in our fungal genome database and identified a unique pair of

• Aspergillus oryzae and biochemical characterization of recombinant enzymes unveiled a fungal two-enzyme pathway to isopimaradiene, which is unprecedented for fungal LRDs. Results and Discussion To explore the fungal LRDs, we searched our in-house database by BLAST using known fungal bifunctional TCs such as

• public database, there are no similar BGCs with separate type TCs (Figure S5 in Supporting Information File 1). Heterologous expression of CiCPS-PS with AsGGS also gave 1 as a product (Figure 5A and Figure S2 in Supporting Information File 1), showing that CiCPS-PS retains the same activity as those of

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

• ), which has the invaluable advantage of being an alphanumeric code and which nowadays mostly dispenses use of Greek letters for annotating anomericity. Look – as an example – at entry G75903TQ in the relevant database GlyTouCan (glytoucan.org) [7] for the structure that we will herein baptize Na6-4(AF)F6

Chemical and biosynthetic potential of Penicillium shentong XL-F41

• Ran Zou,
• Xin Li,
• Xiaochen Chen,
• Yue-Wei Guo and
• Baofu Xu

Beilstein J. Org. Chem. 2024, 20, 597–606, doi:10.3762/bjoc.20.52

• database confirmed its identification as Penicillium sp. This strain is preserved at the Shandong Laboratory of Yantai Drug Discovery. Fermentation in shaking flasks For large-scale fermentations, fresh mycelia of Penicillium shentong XL-F41 were first cultivated in liquid potato dextrose broth at 28 °C

Recent developments in the engineered biosynthesis of fungal meroterpenoids

• Zhiyang Quan and
• Takayoshi Awakawa

Beilstein J. Org. Chem. 2024, 20, 578–588, doi:10.3762/bjoc.20.50

• resulting cation intermediate at C-4' to induce an acyl shift, forming the steroid-like structure of 7 with a 6-6-6-5 ring (Figure 2). Swapping terpenoid cyclases in heterologous expression systems A search of the genome database for Trt1-homolog CYCs revealed the enzyme AusL (41% identity with Trt1) in

A new analog of dihydroxybenzoic acid from Saccharopolyspora sp. KR21-0001

• Rattiya Janthanom,
• Yuta Kikuchi,
• Hiroki Kanto,
• Tomoyasu Hirose,
• Arisu Tahara,
• Takahiro Ishii,
• Arinthip Thamchaipenet and
• Yuki Inahashi

Beilstein J. Org. Chem. 2024, 20, 497–503, doi:10.3762/bjoc.20.44

• spectrum, did not match any compound in the Dictionary of Natural Products database (version 32.1). Fermentation, isolation, structural elucidation, and biological activity of 1 are described in the following. Results and Discussion Saccharopolyspora sp. KR21-0001 was isolated from soil in Ōha island

Identification of the p-coumaric acid biosynthetic gene cluster in Kutzneria albida: insights into the diazotization-dependent deamination pathway

• Seiji Kawai,
• Akito Yamada,
• Yohei Katsuyama and
• Yasuo Ohnishi

Beilstein J. Org. Chem. 2024, 20, 1–11, doi:10.3762/bjoc.20.1

• , Bunkyo-ku, Tokyo 113-8657, Japan 10.3762/bjoc.20.1 Abstract Recently, we identified the biosynthetic gene cluster of avenalumic acid (ava cluster) and revealed its entire biosynthetic pathway, resulting in the discovery of a diazotization-dependent deamination pathway. Genome database analysis revealed

• , presumably in an ATP-independent manner [9][10][11][12][13][14]. Moreover, the genome database analysis indicated that there are many orphan BGCs containing genes encoding the ANS pathway, which implies that the biosynthesis of many unknown natural products requires nitrous acid derived from the ANS pathway

• finally substituted for a hydride derived from NADPH by AvaA7. Interestingly, there are more than 100 BGCs that possess a set of ava gene homologs in the genome database, suggesting that these BGCs are responsible for the biosynthesis of avenalumic acid or its derivatives [13]. In this study, we focused

Construction of diazepine-containing spiroindolines via annulation reaction of α-halogenated N-acylhydrazones and isatin-derived MBH carbonates

• Xing Liu,
• Wenjing Shi,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2023, 19, 1923–1932, doi:10.3762/bjoc.19.143

• cm−1; HRMS–ESI TOF (m/z): [M + Na]+ calcd for C34H28ClN4O3SNa, 595.1774; found, 595.1765. The crystallographic data of compound 7a (CCDC 2280223) have been deposited at the Cambridge Crystallographic Database Centre. Single crystal structure of the spiro compound 7a. Representative [4 + 3

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

• spectroscopic fingerprints database. In MS–IR experiments, the IR data as well as the mass of the molecule are simultaneously acquired, therefore the mass could readily be used as a prefilter. More generally, all experimental data obtained in a glycomics workflow – such as MS/MS; HPLC; ion mobility; … – could

Functional characterisation of twelve terpene synthases from actinobacteria

• Anuj K. Chhalodia,
• Houchao Xu,
• Georges B. Tabekoueng,
• Binbin Gu,
• Kizerbo A. Taizoumbe,
• Lukas Lauterbach and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 1386–1398, doi:10.3762/bjoc.19.100

• ionisation (EI) mass spectrum suggested the structure of δ-cadinol (10) by comparison to a mass spectrum included in the NIST Standard Reference Database (Figure 3A and 3B). Only minor amounts of acyclic products were obtained from GPP (myrcene, ocimene, linalool) and GGPP (β-springene), while GFPP was not

Selective construction of dispiro[indoline-3,2'-quinoline-3',3''-indoline] and dispiro[indoline-3,2'-pyrrole-3',3''-indoline] via three-component reaction

• Ziying Xiao,
• Fengshun Xu,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2023, 19, 1234–1242, doi:10.3762/bjoc.19.91

• mechanism. Optimizing reaction conditions.a Synthesis of the dispirooxindoles 3a–m.a Synthesis of dispirooxindoles 4a–p.a Supporting Information The crystallographic data of compounds 3a (CCDC 2223538) and 4a (CCDC 2223539) have been deposited at the Cambridge Crystallographic Database Center (http

Two new lanostanoid glycosides isolated from a Kenyan polypore Fomitopsis carnea

• Winnie Chemutai Sum,
• Sherif S. Ebada,
• Didsanutda Gonkhom,
• Cony Decock,
• Rémy Bertrand Teponno,
• Josphat Clement Matasyoh and
• Marc Stadler

Beilstein J. Org. Chem. 2023, 19, 1161–1169, doi:10.3762/bjoc.19.84

• into the SARs of lanostanoid triterpenoids and expands the database of their bioactive compounds for subsequent studies. Conclusion The genus Fomitopsis remains to be a prolific source of several metabolites with health-promoting effects. We provide a new evidence of lanostanoid glycosides 1 and 2 from

Cyclodextrins as building blocks for new materials

• Miriana Kfoury and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2023, 19, 889–891, doi:10.3762/bjoc.19.66

• . CDs are the most studied supramolecular hosts. They provide the most extensive database on molecular recognition in the literature, with more than 100,000 publications [2]. CDs owe their success not only to the unique molecular structure [3], which allows them to act as host compounds, but also to

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

• .). In addition to the total concentration of ATP in all of its bound or liganded forms, one should report the unambiguous identifier of the substance that was actually used in the study. The identifiers can be a CAS number, a PubChem CID, ChEBI ID, or any database entry (e.g., adenosine 5′-triphosphate

Germacrene B – a central intermediate in sesquiterpene biosynthesis

• Houchao Xu and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 186–203, doi:10.3762/bjoc.19.18

• comparison of the measured to a database retention index may at least in terms of the relative configuration be a correct structural assignment [105]. Taken together, the confusing situation for 50 in the literature demonstrates impressively, how inaccurate data reporting can lead to unclear structural

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

• and I of 12 and 14, not present in the NIST 17 database will be made publically available in computer readable format through the open access mass spectra data base MACE [28]. Conclusion In this work, we have characterized compound A to be (10R,1S,6R,7R,10R)-amorph-4-ene-10β-ol or (1R,4R,4aR,8aS)-4

Inclusion complexes of the steroid hormones 17β-estradiol and progesterone with β- and γ-cyclodextrin hosts: syntheses, X-ray structures, thermal analyses and API solubility enhancements

• Alexios I. Vicatos,
• Zakiena Hoossen and
• Mino R. Caira

Beilstein J. Org. Chem. 2022, 18, 1749–1762, doi:10.3762/bjoc.18.184

• products and those of known isostructural CD inclusion complexes retrieved from the Cambridge Structural Database (CSD) [40]. Figure 2 and Figure 3 show representative examples of peak-matching for isostructural complexes [41] and the respective PXRD patterns of β-CD·BES and γ-CD·BES are also available

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

• bioinformatically [39]. State-of-the-art genome mining tools are ideally suited for the detection of assembly line-like pathways. The focus on these pathways led to a strong bias in training sets: In the MIBiG database of characterized BGCs nearly 80% of all deposited NP BGCs are PKS, NRPS, or terpene BGCs (April

• 2022) [20]. As the largest database of characterized BGCs, MIBiG is frequently used as a training data set for the development of genome mining algorithms. The imbalanced representation of NP BGCs in the database, however, might introduce a bias when it comes to the training of novel algorithms

• Pfam domains (protein domains annotated in the protein family database) instead of individual genes. pHMMs are calculated using training sets of known BGCs and non-BGC sequences. Here, two states “BGC” and “non-BGC” are distinguished depending on the Pfam domain frequency in the training data set and

Synthetic study toward the diterpenoid aberrarone

• Liang Shi,
• Zhiyu Gao,
• Yiqing Li,
• Yuanhao Dai,
• Yu Liu,
• Lili Shi and
• Hong-Dong Hao

Beilstein J. Org. Chem. 2022, 18, 1625–1628, doi:10.3762/bjoc.18.173

• The crystallographic data of compound 10 (CCDC 2204711) has been deposited at the Cambridge Crystallographic Database Center (http://www.ccdc.cam.ac.uk). Supporting Information File 306: Characterization data and 1H NMR, 13C NMR, and HRMS spectra of the compounds. Funding We are grateful for

Using UHPLC–MS profiling for the discovery of new sponge-derived metabolites and anthelmintic screening of the NatureBank bromotyrosine library

• Sasha Hayes,
• Aya C. Taki,
• Kah Yean Lum,
• Joseph J. Byrne,
• Merrick G. Ekins,
• Robin B. Gasser and
• Rohan A. Davis

Beilstein J. Org. Chem. 2022, 18, 1544–1552, doi:10.3762/bjoc.18.164

• identify samples containing abundant or potentially new natural products. A sample from the Australian marine sponge Ianthella basta was chosen for large-scale isolation work after analysis of the UHPLC–MS data and the MarinLit database [1] suggested the presence of a new alkaloid. Herein, we describe the

• chromatograms). One extract derived from the marine sponge Ianthella basta showed five UV active peaks (P1–5) at 254 nm in the UHPLC–MS chromatogram (Figure 1) with P1–3 and P5 displaying quasi-molecular ion clusters in the positive MS mode. Subsequent dereplication, literature and MarinLit database [1] mining

• with the HMBC data for both exchangeable signals at δH 7.36 and 11.84, and methylene moiety (δH 3.35, δC 39.4) to the sp2 signals (δC 151.9 and 163.3) allowed a N-oxime substructure to be assigned (see Figure 3). MarinLit database mining using this fragment readily identified that compound 1 belonged

Characterization of a new fusicoccane-type diterpene synthase and an associated P450 enzyme

• Jia-Hua Huang,
• Jian-Ming Lv,
• Liang-Yan Xiao,
• Qian Xu,
• Fu-Long Lin,
• Gao-Qian Wang,
• Guo-Dong Chen,
• Sheng-Ying Qin,
• Dan Hu and
• Hao Gao

Beilstein J. Org. Chem. 2022, 18, 1396–1402, doi:10.3762/bjoc.18.144

• and Discussion Identification of a new fusicoccane-type DTS and an associated P450 enzyme We used MgMS, a previously identified FC-type DTS in our group [20], as a query to perform local BLAST search against our in-house fungal genome database, and then found a candidate enzyme TadA from T. wortmannii

On drug discovery against infectious diseases and academic medicinal chemistry contributions

• Yves L. Janin

Beilstein J. Org. Chem. 2022, 18, 1355–1378, doi:10.3762/bjoc.18.141

• is providing a very large database of predicted protein structures, being one of the latest achievements in the domain [5]. – The development of organic chemistry tools enabling a faster synthesis of compounds and, more important, a faster purification/identification (i.e., DNA-tracked synthesis

• , a subsequent virtual hit expansion/ligand-based screening starting with the isoquinoline-bearing inhibitors such as 6 and using the Ukrainian REAL database which contains 1.37 billion of compounds, actually failed to go beyond this chemical motif [83]. In any case, what would have been the results

New azodyrecins identified by a genome mining-directed reactivity-based screening

• Atina Rizkiya Choirunnisa,
• Kuga Arima,
• Yo Abe,
• Noritaka Kagaya,
• Kei Kudo,
• Hikaru Suenaga,
• Junko Hashimoto,
• Manabu Fujie,
• Noriyuki Satoh,
• Kazuo Shin-ya,
• Kenichi Matsuda and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2022, 18, 1017–1025, doi:10.3762/bjoc.18.102

• insights into the distribution and diversity of the biosynthetic gene clusters of aliphatic azoxy natural products, we searched for a pair of VlmA and VlmH, two key enzymes in the azoxy bond formation, encoded in close genetic loci in the reference genome of 3,146 actinobacteria in the NCBI database. A

• stepwise HMM-based search using models for “VlmA'' (PF09924: LPG_synthase_C) and the amino acid sequence of VlmH identified 179 pairs of VlmA/VlmH, indicating that approximately 5.7% of the actinobacteria present in the NCBI Refseq database are potential producers of aliphatic azoxy natural products. The

• in the Refseq database. Nodes are colored according to the host organism’s order. Enzymes with known biosynthetic products are colored red. N2H4-detecting colorimetric assay. Proposed biosynthetic pathway of azodyrecin. 1H (500 MHz) and 13C (125 MHz) NMR data for azodyrecin D (7), azodyrecin E (8