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

• and local models to guide the design of synthetic processes. Global models exploit the information from comprehensive databases to suggest general reaction conditions for new reactions, while local models fine-tune the specific parameters for a given reaction family to improve yield and selectivity

• calculations in generating data for ML applications will grow increasingly critical. At present, employing theoretical calculations systematically to construct accurate, large-scale databases of reaction conditions remains highly challenging for complex reaction systems, leading to a primary reliance on

• experimental data for building ML models. Overview of data sources for chemical reaction modeling Table 1 summarizes some of the commonly used chemical reaction databases and their characteristics. These databases differ in the types and sources of reactions they contain [33], as well as in the formats used

Photoredox-catalyzed intramolecular nucleophilic amidation of alkenes with β-lactams

• Valentina Giraldi,
• Giandomenico Magagnano,
• Daria Giacomini,
• Pier Giorgio Cozzi and
• Andrea Gualandi

Beilstein J. Org. Chem. 2024, 20, 2461–2468, doi:10.3762/bjoc.20.210

• lactams. Notably, all reported structures have alkyl or aryl substituents in position 3 of the clavam ring. Conversely, clavams substituted with alkyl chains at the 2-position, to the best of our knowledge, have not been previously reported and are absent from common organic compound databases. To explore

Cell-free protein synthesis with technical additives – expanding the parameter space of in vitro gene expression

• Tabea Bartsch,
• Stephan Lütz and
• Katrin Rosenthal

Beilstein J. Org. Chem. 2024, 20, 2242–2253, doi:10.3762/bjoc.20.192

• were taken from the databases Chemistry WebBook by the National Institute of Standards and Technology (NIST) (https://webbook.nist.gov/) at 1 bar and 25 °C, PubChem by the National Center for Biotechnology and Information (https://pubchem.ncbi.nlm.nih.gov/), and GESTIS-Stoffdatenbank by Institut für

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

• of interest is not present in the aforementioned databases, the Schrodinger Suite of programs through the Maestro graphical interface can be exploited to generate the maps by using the MM3 force field [66]. The Schrodinger platform (https://www.schrodinger.com/) offers several services for molecular

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

• biosynthetic enzymes hold promise as novel entities with untapped bioactive potential. Expression and purification of the CloA1 precursor peptide, CloA2 precursor peptide, and C39 peptidase domain We could not access the producing microorganisms, so the gene sequences reported in public databases (Supporting

• 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

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

• compared the GBB chemical space with common chemical databases (ChEMBL [42], PubChem [43], and ZINC15 [44]), as well as our stock screening compound collection [45]. Due to the enormous size of the databases, pairwise Tanimoto analysis was performed at the extended Bemis–Murcko scaffold level. First

• , extended Bemis–Murcko scaffolds were generated by cutting off the side chains of the molecules and retaining ring systems and linkers between them. After removal of duplicates, Tanimoto similarity coefficients were calculated for each pair of the molecules in the compared databases (T = 1 and 0 for similar

• 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

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

• 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

• sugar model [3], checks that structures match the nomenclature used for deposition in the PDB [14], compares glycan compositions to known structures as reported by glycomics (e.g., GlyConnect [19]) and glyco-informatics (e.g., GlyTouCan [20]) databases and repositories [15], and checks how close the

• validation report entry in plaintext can be difficult, time-consuming and would certainly be a poor experience for the end user. To improve the utility of this database, we have provided a visualisation of the information contained within the validation report for both PDB and PDB-REDO databases, which is

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

• have previously identified several Vs NnlA homologs in sequence databases [20], however, the NNG degradation activities of these homologs have not been tested. Doing so will differentiate between these two hypotheses by testing if NnlA homologs with NNG degradation activity are highly conserved or if

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

• suggests that such an endeavor could well be of practical importance. Developed to be a human and keyboard-friendly alternative to machine codes, the proglycan code nevertheless qualifies as a valuable component of glycan databases. A simple text search can retrieve all N-glycan structures with a

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

• member of characterized melon lectins, namely the Cucumis melo agglutinin (CMA1), an R-type lectin derived from melon. Prior to our study, CMA1 was only a predicted protein from genomic sequencing, with moderate certainty scores on lectin-specific databases. Our comprehensive analysis using glycan array

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

• of NMR data. While initially intended for small molecules data repositories and databases [34][35], NMRium provides unique functionalities that make it particularly well-suited for educational application. Teaching the interpretation of NMR spectra Nowadays, the interpretation of NMR experiments is

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

• molecules" (that is, previously referenced in databases) is expected to be significant compared to unknown ones, it is important to make sure that the model is discriminative and we want to maximize the precision of the model at this task. Indeed, the large amount of positive results would make it difficult

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

• used to search in NP databases for identical or related compounds [18][19]. While the BGC-centric approach might be more accurate, it is limited by the number of characterized BGCs in publicly available databases. Since significantly more NPs than NP BGCs are characterized, the search space of known

• ][44][45][46]. The advantage of such reference alignment methods that are based on sequence homology is their high confidence. The performance of these tools can be rapidly improved via the addition of new reference databases, which was contributing to their success at the beginning of the genome

• associated NP [56][57][58]. In silico dereplication to eliminate BGCs associated with known NPs is one of the major functions of genome mining to avoid the time-consuming and costly re-isolation of known NPs. For instance, the antiSMASH platform compares putative BGCs with reference databases to detect BGCs

Efficient production of clerodane and ent-kaurane diterpenes through truncated artificial pathways in Escherichia coli

• Fang-Ru Li,
• Xiaoxu Lin,
• Qian Yang,
• Ning-Hua Tan and
• Liao-Bin Dong

Beilstein J. Org. Chem. 2022, 18, 881–888, doi:10.3762/bjoc.18.89

• , as well as two possible producers (Streptomyces sp. San01 and Kitasatospora sp. CB02891) after a survey of the existing genome sequence databases, however, we discovered a strain, Kitasatosporia griseola DSM 43859, without a genome sequence disclosed, from the strain library of CGMCC. Using the

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

• tightly connected to mainstream bioinformatics. For example, databases and tools from genomics can be used for gaining information about genes encoding for glycosyltransferases, glycosidases, and glycan-binding proteins (lectins), and search engines initially designed for the detection of

• development and evolution of dedicated databases that store glyco-related quality information. With glycobioinformatics still being in its infancy, these requirements are continuing to evolve. The editors of this thematic issue represent both bioinformatics developers as well as users who have the conviction

• be detected when comparing similar glycomes by this method. The articles by Groth et al. [12] and by Bagdonas et al. [13] illustrate how glycoinformation can be harvested and integrated from available -omics databases, with the former paper identifying putative cell signaling molecules and

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

• methanolic extract from a small-scale culture of Pseudomonas sp. UIAU-6B in modified SGG medium indicated the presence of some interesting peaks with molecular ions which gave no hits when they were searched in natural product databases (Antibase). At the same time, the 1H NMR fingerprints suggested the

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

• , but enhancers present several kilobases away from the transcription state site (TSS) are neglected; and iii) most of these reported TF–glycogene relationships only have partial support in established bioinformatics databases (DBs, see Supporting Information File 1). Thus, these are limited hypothesis

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

• volatiles were identified by comparing their mass spectra with those of authentic standards or reference spectra from databases (Wiley, Version 8, National Institute of Standards and Technology (NIST, Version 11)) using GCMS SOLUTION v.4.20 (Shimadzu). In addition, non-isothermal Kovats retention indices

Breakdown of 3-(allylsulfonio)propanoates in bacteria from the Roseobacter group yields garlic oil constituents

• Anuj Kumar Chhalodia and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2021, 17, 569–580, doi:10.3762/bjoc.17.51

• suggests that the deallylation of AllMSP by the DmdA variants in these organisms may be less efficient than was observed for P. inhibens. Besides these sulfur compounds, only O. indolifex, but not the other two strains, released another compound, 27, whose mass spectrum was not included in our databases

Regioselective chemoenzymatic syntheses of ferulate conjugates as chromogenic substrates for feruloyl esterases

• Olga Gherbovet,
• Fernando Ferreira,
• Apolline Clément,
• Mélanie Ragon,
• Julien Durand,
• Sophie Bozonnet,
• Michael J. O'Donohue and
• Régis Fauré

Beilstein J. Org. Chem. 2021, 17, 325–333, doi:10.3762/bjoc.17.30

• enzyme-encoding sequences, filling up databases with a wealth of information. However, while resolving an early step in the discovery pipeline, these techniques progressively create a new bottleneck regarding enzyme characterization. Therefore, there is a pressing need to extend the enzymologist’s

Supramolecular polymers with reversed viscosity/temperature profile for application in motor oils

• Jan-Erik Ostwaldt,
• Christoph Hirschhäuser,
• Stefan K. Maier,
• Carsten Schmuck and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2021, 17, 105–114, doi:10.3762/bjoc.17.11

• viscosities of 40 °C and 100 °C are used to calculate the VI, using databases like viscosity index calculators of Evonik [32]. While the VI of Nynas NS8 was increased by 100% (VI 47 to 94) using compound 2, compound 4 was able to increase its VI by 89% (VI 47 to 89). In contrast to that, the VI of Nexbase

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

• quantification. Importantly, LaCyTools requires RT clusters to be defined in which MS1 spectra can be summed and further processed, which is facilitated by the GlycopeptideGraphMS output. The analyte list may be extended by including glycan compositions (e.g., from the literature or databases such as GlyConnect

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

• knowledge are bioinformatics databases that have been curated through the deposition of experimental data. Bioinformatics databases contain detailed descriptions of the glycan compositions and m/z values of specific glycans, and therefore aiding the process of glycan annotation [47]. Such bioinformatics

• databases can usually be interrogated using textual or graphical notations that describe the glycan sequence. However, due to the glycan complexity and the incremental nature of the different glycomics projects, numerous notations have been developed over the years – e.g., CarbBank [48] utilized CCSD [48

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

• several computer applications using a standardised notation. The earliest glycan editors allowed manual drawing similar to ChemDraw or used input files with glycan sequence KCF (KEGG Chemical Function) [9] in text format for similarity search against other structures deposited in the databases. Later

• glycoscience research, we have identified the tools and databases that are freely available on the internet and are regularly updated and improved [1]. The variety and complexity of glycan structures make their interpretation challenging. Consequently, in the past few years, several sketching, building and

• computational tools was inspected for general features related to sketching, representing and model building, all of which could be further used as input for translation into other formats, search from glycan databases or complex calculations such as molecular simulations. Several tools feature an interactive

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

• data collection databases for all commodity material resources, and so this significant limitation prevents estimation of time analyses pertaining to how long a given resource may exist under a so-called “sustainability condition”. For first generation chemical feedstocks arising from fossil fuels, the

• necessarily requires reliable databases that constantly track data annually. Such tracking is not always in industry’s best interest to disclose such information publicly for economic and political reasons. For example, providing inaccurate or incomplete information to governments and investors can leverage

• -derived materials. In any event, the task of tracing starting materials, catalysts, and reaction solvent syntheses is very tedious, especially for time-pressed chemists who wish to practice green chemistry. However, such a task can be significantly alleviated if synthesis databases of first, second, and