Unprecedented visible light-initiated topochemical [2 + 2] cycloaddition in a functionalized bimane dye

• Metodej Dvoracek,
• Brendan Twamley,
• Mathias O. Senge and
• Mikhail A. Filatov

Beilstein J. Org. Chem. 2025, 21, 500–509, doi:10.3762/bjoc.21.37

• and is therefore not expected to undergo this topochemical reaction (Figure 6b). Examination of the reported structure of 9,10-dioxa-syn(carboethoxy,methyl)bimane in the CCDC database (BESGAH) [19][21], shows that it crystallizes in the monoclinic (P2(1)/c space group, unlike Me2B which crystallizes

Molecular diversity of the reactions of MBH carbonates of isatins and various nucleophiles

• Zi-Ying Xiao,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2025, 21, 286–295, doi:10.3762/bjoc.21.21

• 2390715), 7a (CCDC 2390716) and 8a (CCDC 2390717) have been deposited at the Cambridge Crystallographic Database Center. Supporting Information File 2: Experimental procedures, 1H, 13C NMR, and HRMS spectra for all new compounds. Funding This work was financially supported by the National Natural Science

Chemical glycobiology

• Elisa Fadda,
• Rachel Hevey,
• Benjamin Schumann and
• Ulrika Westerlind

Beilstein J. Org. Chem. 2025, 21, 8–9, doi:10.3762/bjoc.21.2

• methods that underlie modern glycobioinformatics approaches [15]. Validation of glycoprotein structure is an important aspect of contemporary structural biology, and Dialpuri et al. present the Privateer database to allow for facile quality control of such structures [16]. Finally, Barillot et al. bridge

Machine learning-guided strategies for reaction conditions design and optimization

• Lung-Yi Chen and
• Yi-Pei Li

Beilstein J. Org. Chem. 2024, 20, 2476–2492, doi:10.3762/bjoc.20.212

• the Open Reaction Database (ORD) [36], an open-source initiative to collect and standardize chemical synthesis data from various literature sources. The ORD allows chemists to upload reaction data associated with their publications, and aims to serve as a benchmark for ML development. However, the ORD

• . Therefore, a preprocessing step to standardize the labels and reduce redundancy is also essential. Gao et al. [18] developed a large-scale model for predicting reaction conditions, using a deep learning approach trained on the Reaxys database. Their model could sequentially predict the catalysts, solvents

Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers

• Andreas Wiest and
• Pavel Kielkowski

Beilstein J. Org. Chem. 2024, 20, 2323–2341, doi:10.3762/bjoc.20.199

• set up labile, open and closed searches and how we recalculated the published MS data for different linkers in this review can be downloaded from the publicly available database (PRIDE data set identifier PXD043402) [65]. Furthermore, the data processing can be adjusted and paralleled accordingly

Catalysing (organo-)catalysis: Trends in the application of machine learning to enantioselective organocatalysis

• Stefan P. Schmid,
• Leon Schlosser,
• Frank Glorius and
• Kjell Jorner

Beilstein J. Org. Chem. 2024, 20, 2280–2304, doi:10.3762/bjoc.20.196

• , Corminboeuf and co-workers reported OSCAR, a computational repository of 4,000 organocatalyst structures mined from the literature and Cambridge Structural Database (CSD) [31]. In addition, the authors utilised the combinatorial nature of organocatalysts to create data bases comprising more than 8,000 NHC

• literature-mined reaction database to train an XGBoost model. The turn-over frequency of a reaction was determined using a volcano plot based on reaction energies [135][136][137], where the latter were again predicted using an XGBoost model based on the literature-mined dataset. Using fragments derived from

• their OSCAR [31] database, the authors used the NaviCatGA genetic algorithm [118] to find the most general catalysts. The fitness function comprised multiple objectives, including the median of the enantioselectivity and activity across the generality probing set. The usage of a multi-objective

Natural resorcylic lactones derived from alternariol

• Joachim Podlech

Beilstein J. Org. Chem. 2024, 20, 2171–2207, doi:10.3762/bjoc.20.187

• comparison of NMR spectra [44]. Occasionally, natural products have been reported more than one time as new compounds and were given several names. Only the first given name should be used and further names are thus obsolete: Verrulactone D is erroneously given in the SciFinder database as synonym for

• the parent alternariol (1, 1099 publications given in the SciFinder database at 04/2024), 9-O-methylalternariol (2, 578 entries), altenuene (54, 320), altenusin (47, 130), dehydroaltenusin (74, 55), altertenuol (31, 45), and isoaltenuene (55, 24), where the most abundant Alternaria toxins are usually

• structure) discouraged a thorough investigation of their biological activities, especially of their toxicities. The European Food Safety Authority (EFSA) stated that “at present (2011), the knowledge on the possible effects of Alternaria toxins on farm and companion animals as well as the database

O,S,Se-containing Biginelli products based on cyclic β-ketosulfone and their postfunctionalization

• Kateryna V. Dil and
• Vitalii A. Palchykov

Beilstein J. Org. Chem. 2024, 20, 2143–2151, doi:10.3762/bjoc.20.184

• ). This reaction is believed to be one of the most famous MCRs with >2000 papers published in the last 20 years (according to Scopus database). These MCRs allow the direct synthesis of known DHMP drugs such as monastrol, piperastrol, enastron, fluorastrol etc. (Scheme 1B) and dozens of highly bioactive

• products and publications as analyzed by Reaxys database. The search was performed using depicted substructures “on all atoms” (May 2024). Distribution of compounds 2a–r, 3–7 (log P (y)–MW (x)) through LLAMA software. The chemical structure of a representative compound 2m is shown. The general Biginelli

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• are reported [72][73][74]. Currently, different databases, which are described below, collect adiabatic energy maps facilitating the construction of glycan 3D models by enabling the selection only of permitted low energy conformations: 1. CSDB [75][76][77]: Carbohydrate Structure Database is a

• spectroscopic and other information on glycan and glycoconjugate structures of prokaryotic, plant and fungal origin. The retrospective literature analysis is the main source of structural data, which are then manually curated and approved. Besides structures, the database includes bibliography, abstracts

• , keywords, biological source data up to strains, methods used to elucidate structures, NMR signal assignment and other information (http://csdb.glycoscience.ru/database/). 2. Disac3DB: free annotated database that contains the 3D structural information of about 120 entries of disaccharides. For each

Hetero-polycyclic aromatic systems: A data-driven investigation of structure–property relationships

• Sabyasachi Chakraborty,
• Eduardo Mayo Yanes and
• Renana Gershoni-Poranne

Beilstein J. Org. Chem. 2024, 20, 1817–1830, doi:10.3762/bjoc.20.160

• on a range of electronic molecular properties of PASs. Keywords: computational chemistry; database; dataset; π-conjugated; polycyclic aromatic hydrocarbons; polycyclic aromatic systems; Introduction Polycyclic aromatic systems (PASs) – molecules made up of fused aromatic rings – are among the most

• PAS chemical space is with data-driven methods, which have proven in the last few years to be extremely successful at uncovering underlying structure–property relationships. To enable such exploration, we initiated the COMPAS Project (COMputational database of PASs), the first database dedicated to

• properties. We emphasize that there is still much more to be learned from this rich database, including the reciprocal effects of adjacent building blocks, the importance of multi-ring substructures, and the interplay of different building blocks. Combining different types of heterocycles has been found to

Discovery of antimicrobial peptides clostrisin and cellulosin from Clostridium: insights into their structures, co-localized biosynthetic gene clusters, and antibiotic activity

• Moisés Alejandro Alejo Hernandez,
• Katia Pamela Villavicencio Sánchez,
• Rosendo Sánchez Morales,
• Karla Georgina Hernández-Magro Gil,
• David Silverio Moreno-Gutiérrez,
• Eddie Guillermo Sanchez-Rueda,
• Yanet Teresa-Cruz,
• Brian Choi,
• Armando Hernández Garcia,
• Alba Romero-Rodríguez,
• Oscar Juárez,
• Siseth Martínez-Caballero,
• Mario Figueroa and
• Corina-Diana Ceapă

Beilstein J. Org. Chem. 2024, 20, 1800–1816, doi:10.3762/bjoc.20.159

• -BRC platform [40], utilizing the "Reference and representative genomes-Proteins-(faa)" database with a maximum of 100 results and a minimum E-value of 0.0001. All results from each analysis were retained for subsequent studies. The identified homologous LanM amino acid sequences, alongside the 28

• Supporting Information File 1). For the similarity network, a database was created containing 145 precursor peptides of lanthipeptides reported in the MIBiG [38], RiPPMiner [5], and UniProt [57] databases. This input was utilized in the EFI-EST [51] web platform, employing the "FASTA" analysis option with

• symbols refer to previously characterized LanM sequences from the MIBiG database. The phylogenetic tree was built by concatenating 1000 shared clostridial genes (left) between the studied genomes, and the lanthipeptide class II synthetase clusters from the selected BGCs of this taxonomic clade are

pKalculator: A pK_a predictor for C–H bonds

• Rasmus M. Borup,
• Nicolai Ree and
• Jan H. Jensen

Beilstein J. Org. Chem. 2024, 20, 1614–1622, doi:10.3762/bjoc.20.144

• compile a dataset of 732 experimental pKa values in DMSO from two different sources, Bordwell [7] and iBonD [4]. The Bordwell dataset contains experimental C–H pKa values in DMSO from 419 molecules. For the iBonD database, we select experimental C–H pKa values in DMSO for 313 molecules. As the iBonD

• database only contains an image of each molecule, we employ the “Deep Learning for Chemical Image Recognition” software (DECIMER v. 2.0), developed by Rajan and co-workers [8][9][10]. While DECIMER converts molecular images into SMILES, manual intervention is required to ensure the SMILES string correctly

• the following reasons: (i) calculation errors concerning the expected minimum pKa site, (ii) discrepancies between literature structures and database structures, (iii) mislabeled experimental pKa values, or (iv) extrapolated pKa values. Notably, the extrapolated pKa values correspond to compounds

Generation of multimillion chemical space based on the parallel Groebke–Blackburn–Bienaymé reaction

• Evgen V. Govor,
• Vasyl Naumchyk,
• Ihor Nestorak,
• Dmytro S. Radchenko,
• Dmytro Dudenko,
• Yurii S. Moroz,
• Olexiy D. Kachkovsky and
• Oleksandr O. Grygorenko

Beilstein J. Org. Chem. 2024, 20, 1604–1613, doi:10.3762/bjoc.20.143

• showed biological activity according to the ChEMBL database. Keywords: fused rings; heterocycles; imidazoles; isonitrile; multicomponent reactions; Introduction Multicomponent reactions are widely recognized as a powerful source of biologically active compounds, in particular, for drug discovery

• and very dissimilar molecules, respectively). Average pairwise values for each molecule from the database of comparison are depicted in Figure 6. The mean values for all the databases were in the range of 0.44–0.45, which shows that despite there are some representatives that are similar to already

• the relatively high computational costs of this method, we randomly selected 50,000 compounds to represent each database. The dimension reduction algorithm uses molecular features as the starting inputs to generate a few coordinates (in this case, t-SNE1 and t-SNE2) reflecting the probability of the

Bioinformatic prediction of the stereoselectivity of modular polyketide synthase: an update of the sequence motifs in ketoreductase domain

• Changjun Xiang,
• Shunyu Yao,
• Ruoyu Wang and
• Lihan Zhang

Beilstein J. Org. Chem. 2024, 20, 1476–1485, doi:10.3762/bjoc.20.131

• , deepening our understanding of the stereocontrol of PKSs. Results and Discussion Preparation of KR sequence dataset We first curated the amino acid sequences of KR domains from characterized bacterial cis-AT PKSs recorded in MIBiG database [20] and by manual literature review. In total, 1,762 KRs whose

• Huang, Shengling Xie, Zhihan Zhang, Shanchong Chen, Cui Yang, Fanzhong Zhang, for KR sequence retrieval from public database. Funding This research was supported by the “Pioneer” and “Leading Goose” R&D Program of Zhejiang (2023SDXHDX0007) and National Natural Science Foundation of China General Program

Predicting bond dissociation energies of cyclic hypervalent halogen reagents using DFT calculations and graph attention network model

• Yingbo Shao,
• Zhiyuan Ren,
• Zhihui Han,
• Li Chen,
• Yao Li and
• Xiao-Song Xue

Beilstein J. Org. Chem. 2024, 20, 1444–1452, doi:10.3762/bjoc.20.127

• iodine [61][62][63][64][65][66][67][68][69][70][71][72][73][74][75][76] and the computational database of organic species by Paton and co-workers [77], geometry optimizations and single point energy calculations for homolytic BDEs are both performed using M06-2X/def2-TZVPP [78][79][80] in the gas phase

Rapid construction of tricyclic tetrahydrocyclopenta[4,5]pyrrolo[2,3-b]pyridine via isocyanide-based multicomponent reaction

• Xiu-Yu Chen,
• Ying Han,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2024, 20, 1436–1443, doi:10.3762/bjoc.20.126

• 2346135) and 6g (CCDC 2346136) have been deposited at the Cambridge Crystallographic Database Center (http://www.ccdc.cam.ac.uk). Supporting Information File 24: Characterization data and 1H NMR, 13C NMR, and HRMS spectra of compounds. Funding This work was financially supported by the National Natural

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