Methodology for awakening the potential secondary metabolic capacity in actinomycetes

• Shun Saito and
• Midori A. Arai

Beilstein J. Org. Chem. 2024, 20, 753–766, doi:10.3762/bjoc.20.69

• Shun Saito Midori A. Arai Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan 10.3762/bjoc.20.69 Abstract Secondary metabolites produced by actinomycete strains undoubtedly have great potential for use in applied research areas such as

Radical chemistry in polymer science: an overview and recent advances

• Zixiao Wang,
• Feichen Cui,
• Yang Sui and
• Jiajun Yan

Beilstein J. Org. Chem. 2023, 19, 1580–1603, doi:10.3762/bjoc.19.116

• inextricably linked to organic chemistry. However, the two fields took divergent paths over the past century. Many emergent radical chemistries in the organic chemistry community has not yet found a place in the polymer science. We believe this gap will narrow with a broader use of chemical informatics tools

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

• ) [17][29][49][50][51][52] as well as PRediction Informatics for Secondary Metabolomes (PRISM) [18][53][54][55]. In addition to PKSs and NRPSs, both tools identify a high number of NP classes and families using pHMMs (antiSMASH 6: 876 pHMMs, PRISM 4: 1772 pHMMS). Apart from BGC detection by pHMMs

Molecular and macromolecular electrochemistry: synthesis, mechanism, and redox properties

• Shinsuke Inagi and
• Mahito Atobe

Beilstein J. Org. Chem. 2022, 18, 1505–1506, doi:10.3762/bjoc.18.158

• so on, it has a high affinity to informatics approaches, e.g., machine learning, which is expected to become an increasingly important tool in the future. Progress in the design of organic molecules and polymers and the understanding of the redox behavior of these compounds has led to the development

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

• Generation Natural Products Chemistry, Tokyo 135-0064, Japan National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan Japan Biological Informatics Consortium (JBIC), Tokyo 135-0064, Japan Okinawa Institute of Science and Technology Graduate University, Okinawa, 904-0495

Unsaturated fatty acids and a prenylated tryptophan derivative from a rare actinomycete of the genus Couchioplanes

• Shun Saito,
• Kanji Indo,
• Naoya Oku,
• Hisayuki Komaki,
• Masashi Kawasaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2939–2949, doi:10.3762/bjoc.17.203

• Shun Saito Kanji Indo Naoya Oku Hisayuki Komaki Masashi Kawasaki Yasuhiro Igarashi Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• analysis of the extensive structural data can be overwhelming. Rapid analysis of trajectory data, with tools available in the Galaxy platform, can be used to understand key features and compare differences that inform the preferential ligand structure that favors binding. We illustrate this informatics

• that enable diverse, multidisciplinary research. In this paper, we show how an informatics approach provides a high-level overview, thus enabling rapid observations of changes in molecular details pertinent to the system under investigation. We apply this approach to the binding of glycosylated

• forward previously that glycosylation alters the conformational equilibrium of the antigen. Conclusion We have shown how an informatics approach can be used to rapidly obtain key indicators of structural features for understanding the molecular level behavior of a system. We illustrated this informatics

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

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

• structural informatics tools. Keywords: data analysis; glycan binding; glycan microarray; glycomics; informatics; Introduction Glycans represent a major type of biomolecule in all living things, along with DNA, RNA, lipids and proteins [1]. In mammals, glycans commonly occur as post-translational

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

• complexity of glycan heterogeneity requires that downstream analysis often involves manual processing in addition to standard informatics workflows. Here, we developed and used GlypNirO, an automated bioinformatic workflow for label-free quantitative N- and O-glycoproteomics that focuses on improving

Opening up connectivity between documents, structures and bioactivity

• Christopher Southan

Beilstein J. Org. Chem. 2020, 16, 596–606, doi:10.3762/bjoc.16.54

• advantage of setting up a virtuous circle of reciprocal connectivity with PubMed where DARCP curated by GtoPdb has been submitted to PubChem. This is outlined in Figure 5. Anomalies in the system The wider informatics ecosystem exhibits a range of quirks related to DARCP and DC capture. These can complicate

Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0

• Bernd Strehmel,
• Christian Schmitz,
• Ceren Kütahya,
• Yulian Pang,
• Anke Drewitz and
• Heinz Mustroph

Beilstein J. Org. Chem. 2020, 16, 415–444, doi:10.3762/bjoc.16.40

Comparative cell biological study of in vitro antitumor and antimetastatic activity on melanoma cells of GnRH-III-containing conjugates modified with short-chain fatty acids

• Eszter Lajkó,
• Sarah Spring,
• Rózsa Hegedüs,
• Beáta Biri-Kovács,
• Sven Ingebrandt,
• Gábor Mező and
• László Kőhidai

Beilstein J. Org. Chem. 2018, 14, 2495–2509, doi:10.3762/bjoc.14.226

• Eszter Lajko Sarah Spring Rozsa Hegedus Beata Biri-Kovacs Sven Ingebrandt Gabor Mezo Laszlo Kohidai Department Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad tér 4., 1089 Budapest, Hungary Department of Informatics and Microsystem Technology, University of Applied Sciences

Natural and redesigned wasp venom peptides with selective antitumoral activity

• Marcelo D. T. Torres,
• Gislaine P. Andrade,
• Roseli H. Sato,
• Cibele N. Pedron,
• Tania M. Manieri,
• Giselle Cerchiaro,
• Anderson O. Ribeiro,
• Cesar de la Fuente-Nunez and
• Vani X. Oliveira Jr.

Beilstein J. Org. Chem. 2018, 14, 1693–1703, doi:10.3762/bjoc.14.144

• Group, MIT Synthetic Biology Center, Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard, The Center for Microbiome Informatics and Therapeutics

Biomimetic molecular design tools that learn, evolve, and adapt

• David A Winkler

Beilstein J. Org. Chem. 2017, 13, 1288–1302, doi:10.3762/bjoc.13.125

• , informatics methods attempt to use mathematical methods to identify the most relevant features in these data sets so that interpretation of experiments is easier, and predictions of outcomes in new experiments are more reliable (see for example Saeys et al. [27]). In our research we have adapted an elegant

Isosorbide and dimethyl carbonate: a green match

• Fabio Aricò and
• Pietro Tundo

Beilstein J. Org. Chem. 2016, 12, 2256–2266, doi:10.3762/bjoc.12.218

• Fabio Arico Pietro Tundo Department of Environmental Sciences, Informatics and Statistics, Ca’ Foscari University, Scientific Campus Via Torino 155 , 30170 Venezia Mestre, Italy 10.3762/bjoc.12.218 Abstract In this review the reactivity of the bio-based platform compounds D-sorbitol and

Regioselective 1,4-trifluoromethylation of α,β-unsaturated ketones via a S-(trifluoromethyl)diphenylsulfonium salts/copper system

• Satoshi Okusu,
• Yutaka Sugita,
• Etsuko Tokunaga and
• Norio Shibata

Beilstein J. Org. Chem. 2013, 9, 2189–2193, doi:10.3762/bjoc.9.257

• -mediated conjugate trifluoromethylation of α,β-unsaturated ketones 1 with 3a.a Supporting Information Supporting Information File 548: Experimental section. Acknowledgements This study was financially supported in part by the Platform for Drug Discovery, Informatics, and Structural Life Science from the

Exploring chemical diversity via a modular reaction pairing strategy

• Joanna K. Loh,
• Sun Young Yoon,
• Thiwanka B. Samarakoon,
• Alan Rolfe,
• Patrick Porubsky,
• Benjamin Neuenswander,
• Gerald H. Lushington and
• Paul R. Hanson

Beilstein J. Org. Chem. 2012, 8, 1293–1302, doi:10.3762/bjoc.8.147

• . Computational analyses were employed to explore and evaluate the chemical diversity of the library. Keywords: benzoxathiazocine 1,1-dioxides; chemical diversity; informatics; nucleophilic aromatic substitution (SNAr); sultams; Introduction The demand for functionally diverse chemical libraries has emerged, as

Similarity analysis, synthesis, and bioassay of antibacterial cyclic peptidomimetics

• Workalemahu M. Berhanu,
• Mohamed A. Ibrahim,
• Girinath G. Pillai,
• Alexander A. Oliferenko,
• Levan Khelashvili,
• Farukh Jabeen,
• Bushra Mirza,
• Farzana Latif Ansari,
• Ihsan ul-Haq,
• Said A. El-Feky and
• Alan R. Katritzky

Beilstein J. Org. Chem. 2012, 8, 1146–1160, doi:10.3762/bjoc.8.128

• structure, involving smaller rings and heteroatoms, as well as a limited conformational flexibility, makes it difficult to classify or compare such compounds by their ring sizes. Fortunately, chemical informatics provides formalized procedures for comparing chemical compounds based on composition and

Kinetic evaluation of the solvolysis of isobutyl chloro- and chlorothioformate esters

• Malcolm J. D’Souza,
• Matthew J. McAneny,
• Dennis N. Kevill,
• Jin Burm Kyong and
• Song Hee Choi

Beilstein J. Org. Chem. 2011, 7, 543–552, doi:10.3762/bjoc.7.62

• generated using the KnowItAll® Informatics System, ADME/Tox Edition, from BioRad Laboratories, Philadelphia, PA. Molecular structures of syn-isobutyl chloroformate (1), syn-isobutyl chlorothioformate (2), phenyl chloroformate (3), phenyl chlorodithioformate (4), and isopropyl chloroformate (5). The 3-D

(−)-Complanine, an inflammatory substance of marine fireworm: a synthetic study

• Kazuhiko Nakamura,
• Yu Tachikawa and
• Daisuke Uemura

Beilstein J. Org. Chem. 2009, 5, No. 12, doi:10.3762/bjoc.5.12

• Kazuhiko Nakamura Yu Tachikawa Daisuke Uemura Department of Biosciences and Informatics, Keio University 3-14-1 Hiyoshi Yokohama 223-8622, Japan Graduate School of Science, Nagoya University Furo-cho Chikusa Nagoya 464-8566, Japan 10.3762/bjoc.5.12 Abstract The synthesis of (−)-complanine, an