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

• late Willy von der Lieth, pioneers of carbohydrate structure validation, whose research informed some of the methods showcased in the Privateer database. Funding Jordan Dialpuri is funded by the Biotechnology and Biological Sciences Research Council (BBSRC; grant No. BB/T0072221). Haroldas Bagdonas 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

• products. Experimental General reagents and protocols Isopropyl β-ᴅ-1-thiogalactopyranoside (IPTG) and 5-aminolevulinic acid (5-ALA) were purchased from Gold Biotechnology. NNG was purchased from AAblocks. 2-NAE was purchased from Toronto Research Chemicals. General buffers and media components were

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

• Friedrich Altmann Johannes Helm Martin Pabst Johannes Stadlmann Department of Chemistry, BOKU University, Vienna, Austria Department of Biotechnology, Delft University of Technology, Delft, The Netherlands 10.3762/bjoc.20.53 Abstract In the beginning was the word. But there were no words for N

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

• buffers (Tris-HCl, HEPES, CHES and CAPS) from pH 7.5 to 11. Different inositol substrates, including myo-inositol, scyllo-inositol, muco-inositol, epi-inositol, ᴅ-chiro-inositol, ʟ-chiro-inositol, and ᴅ-glucose were tested. Inositol substrates were purchased from TCI Chemicals or Santa Cruz Biotechnology

Pseudallenes A and B, new sulfur-containing ovalicin sesquiterpenoid derivatives with antimicrobial activity from the deep-sea cold seep sediment-derived fungus Pseudallescheria boydii CS-793

• Zhen Ying,
• Xiao-Ming Li,
• Sui-Qun Yang,
• Hong-Lei Li,
• Xin Li,
• Bin-Gui Wang and
• Ling-Hong Meng

Beilstein J. Org. Chem. 2024, 20, 470–478, doi:10.3762/bjoc.20.42

• Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Wenhai Road 1, Qingdao 266237, China 10.3762/bjoc.20.42 Abstract Pseudallenes A and B (1 and 2), the new and rare examples of

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

• Seiji Kawai Akito Yamada Yohei Katsuyama Yasuo Ohnishi Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan Collaborative Research Institute for Innovative Microbiology, The University of Tokyo

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• Mateusz Marcisz Sebastian Anila Margrethe Gaardlos Martin Zacharias Sergey A. Samsonov Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland Physics Department, Technical University

Synthetic approach to 2-alkyl-4-quinolones and 2-alkyl-4-quinolone-3-carboxamides based on common β-keto amide precursors

• Yordanka Mollova-Sapundzhieva,
• Plamen Angelov,
• Danail Georgiev and
• Pavel Yanev

Beilstein J. Org. Chem. 2023, 19, 1804–1810, doi:10.3762/bjoc.19.132

• experimental details and analytical data. Supporting Information File 26: Processed NMR spectra. Acknowledgements We are grateful to Prof. Tsanko Gechev and the Center of Plant Systems Biology and Biotechnology, Plovdiv, for providing access to their Waters Acquity - Synapt XS UPLC - mass spectrometry system

Synthesis of imidazo[1,2-a]pyridine-containing peptidomimetics by tandem of Groebke–Blackburn–Bienaymé and Ugi reactions

• Oleksandr V. Kolomiiets,
• Alexander V. Tsygankov,
• Maryna N. Kornet,
• Aleksander A. Brazhko,
• Vladimir I. Musatov and
• Valentyn A. Chebanov

Beilstein J. Org. Chem. 2023, 19, 727–735, doi:10.3762/bjoc.19.53

• , 61072, Kharkiv, Ukraine Faculty of Chemistry, V. N. Karazin Kharkiv National University, Svobody sq., 4, 61022, Kharkiv, Ukraine National Technical University "Kharkiv Polytechnic Institute", Kyrpychova st., 2, Kharkiv, 61002, Ukraine Laboratory of Biotechnology of Physiologically Active Substances

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Croatia Laboratory for Protein Biochemistry and Molecular Modelling, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia Laboratory for Molecular Plant Biology and

• Biotechnology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia 10.3762/bjoc.19.40 Abstract Two novel conjugate molecules were designed: pyrene and phenanthridine-amino acid units with a different linker length between the aromatic fragments. Molecular

Continuous flow synthesis of 6-monoamino-6-monodeoxy-β-cyclodextrin

• János Máté Orosz,
• Dóra Ujj,
• Petr Kasal,
• Gábor Benkovics and
• Erika Bálint

Beilstein J. Org. Chem. 2023, 19, 294–302, doi:10.3762/bjoc.19.25

• Janos Mate Orosz Dora Ujj Petr Kasal Gabor Benkovics Erika Balint Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary Department of Organic Chemistry, Faculty

Nostochopcerol, a new antibacterial monoacylglycerol from the edible cyanobacterium Nostochopsis lobatus

• Naoya Oku,
• Saki Hayashi,
• Yuji Yamaguchi,
• Hiroyuki Takenaka and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2023, 19, 133–138, doi:10.3762/bjoc.19.13

• Naoya Oku Saki Hayashi Yuji Yamaguchi Hiroyuki Takenaka Yasuhiro Igarashi Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan MAC Gifu Research Institute, MicroAlgae Corporation, 4-15 Akebono, Gifu 500-8148

Synthesis of C6-modified mannose 1-phosphates and evaluation of derived sugar nucleotides against GDP-mannose dehydrogenase

• Sanaz Ahmadipour,
• Alice J. C. Wahart,
• Jonathan P. Dolan,
• Laura Beswick,
• Chris S. Hawes,
• Robert A. Field and
• Gavin J. Miller

Beilstein J. Org. Chem. 2022, 18, 1379–1384, doi:10.3762/bjoc.18.142

• Sanaz Ahmadipour Alice J. C. Wahart Jonathan P. Dolan Laura Beswick Chris S. Hawes Robert A. Field Gavin J. Miller Department of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK Lennard-Jones Laboratory, School of Chemical

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

• Neda Rafieiolhosseini Matthias Killa Thorben Neumann Niklas Totsch Jean-Noel Grad Alexander Hoing Thies Dirksmeyer Jochen Niemeyer Christian Ottmann Shirley K. Knauer Michael Giese Jens Voskuhl Daniel Hoffmann Bioinformatics and Computational Biophysics, Center for Medical Biotechnology (ZMB

• Department of Molecular Biology II, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513

Ferrocenoyl-adenines: substituent effects on regioselective acylation

• Mateja Toma,
• Gabrijel Zubčić,
• Jasmina Lapić,
• Senka Djaković,
• Davor Šakić and
• Valerije Vrček

Beilstein J. Org. Chem. 2022, 18, 1270–1277, doi:10.3762/bjoc.18.133

• Mateja Toma Gabrijel Zubcic Jasmina Lapic Senka Djakovic Davor Sakic Valerije Vrcek Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia 10.3762

Synthesis of protected precursors of chitin oligosaccharides by electrochemical polyglycosylation of thioglycosides

• Md Azadur Rahman,
• Kana Kuroda,
• Hirofumi Endo,
• Norihiko Sasaki,
• Tomoaki Hamada,
• Hiraku Sakai and
• Toshiki Nokami

Beilstein J. Org. Chem. 2022, 18, 1133–1139, doi:10.3762/bjoc.18.117

• Md Azadur Rahman Kana Kuroda Hirofumi Endo Norihiko Sasaki Tomoaki Hamada Hiraku Sakai Toshiki Nokami Department of Chemistry and Biotechnology, Tottori University, 4-101 Koyamacho-minami, Tottori City, 680-8552 Tottori, Japan Center for Research on Green Sustainable Chemistry, Faculty of

A Streptomyces P450 enzyme dimerizes isoflavones from plants

• Run-Zhou Liu,
• Shanchong Chen and
• Lihan Zhang

Beilstein J. Org. Chem. 2022, 18, 1107–1115, doi:10.3762/bjoc.18.113

• activity was assayed using a Total Antioxidant Capacity Assay Kit with ABTS method (Beyotime Biotechnology). Briefly, the fresh ABTS working solution was prepared by mixing ABTS stock solution with oxidant solution for an overnight reaction, and then this mixture was diluted 50 times by 80% ethanol. To

Understanding the competing pathways leading to hydropyrene and isoelisabethatriene

• Shani Zev,
• Marion Ringel,
• Ronja Driller,
• Bernhard Loll,
• Thomas Brück and
• Dan T. Major

Beilstein J. Org. Chem. 2022, 18, 972–978, doi:10.3762/bjoc.18.97

• Shani Zev Marion Ringel Ronja Driller Bernhard Loll Thomas Bruck Dan T. Major Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University

• , increasing the IE products at the expense of the HP products is an important biotechnology mission for sustainable supply of the latter. In order to modulate the IE and HP enzyme pathways accordingly, it is important to understand the factors determining both synthetic routes. In the current work, we focus

• the field of Synthetic Biotechnology at TUM. This work was supported by a grant from the Israel Science Foundation (Grant 1683/18) (DTM) and by a grant from the German-Israeli Foundation for Scientific Research and Development (Grant I-85-302.14-2018) (DTM, TB, BL).

Electroreductive coupling of 2-acylbenzoates with α,β-unsaturated carbonyl compounds: density functional theory study on product selectivity

• Naoki Kise and
• Toshihiko Sakurai

Beilstein J. Org. Chem. 2022, 18, 956–962, doi:10.3762/bjoc.18.95

• Naoki Kise Toshihiko Sakurai Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101, Koyama-cho Minami, Tottori 680-8552, Japan 10.3762/bjoc.18.95 Abstract The electroreductive coupling of 2-acylbenzoates with acrylonitrile in the presence of TMSCl

Synthesis and HDAC inhibitory activity of pyrimidine-based hydroxamic acids

• Virginija Jakubkiene,
• Gabrielius Ernis Valiulis,
• Markus Schweipert,
• Asta Zubriene,
• Daumantas Matulis,
• Franz-Josef Meyer-Almes and
• Sigitas Tumkevicius

Beilstein J. Org. Chem. 2022, 18, 837–844, doi:10.3762/bjoc.18.84

• Engineering and Biotechnology, University of Applied Sciences, Stephanstr. 7, 64295 Darmstadt, Germany Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257 Vilnius, Lithuania 10.3762/bjoc.18.84 Abstract Histone deacetylases

Cholyl 1,3,4-oxadiazole hybrid compounds: design, synthesis and antimicrobial assessment

• Anas J. Rasras,
• Mohamed El-Naggar,
• Nesreen A. Safwat and
• Raed A. Al-Qawasmeh

Beilstein J. Org. Chem. 2022, 18, 631–638, doi:10.3762/bjoc.18.63

• 27272, Sharjah, United Arab Emirates The Regional Center for Mycology and Biotechnology, Al-Azhar University, Nasr City, Cairo, 11371, Egypt Department of Chemistry, The University of Jordan, Amman 11942, Jordan 10.3762/bjoc.18.63 Abstract A new chemical library based on the hybridization of cholic

Sesquiterpenes from the soil-derived fungus Trichoderma citrinoviride PSU-SPSF346

• Wiriya Yaosanit,
• Vatcharin Rukachaisirikul,
• Souwalak Phongpaichit,
• Sita Preedanon and
• Jariya Sakayaroj

Beilstein J. Org. Chem. 2022, 18, 479–485, doi:10.3762/bjoc.18.50

• for Genetic Engineering and Biotechnology (BIOTEC), Thailand. The fungus SPSF346 was identified based on its morphological and molecular characteristics. The molecular analysis of the internal transcribed spacers (ITS) (GenBank accession number MH997885) and partial large subunit (LSU) (GenBank

• support. Finally, National Center for Genetic Engineering and Biotechnology (BIOTEC) is acknowledged for evaluation of cytotoxic activity. Funding This work was supported by the NSTDA Chair Professor grant (the Fourth Grant) of the Crown Property Bureau.

Anomeric 1,2,3-triazole-linked sialic acid derivatives show selective inhibition towards a bacterial neuraminidase over a trypanosome trans-sialidase

• Peterson de Andrade,
• Sanaz Ahmadipour and
• Robert A. Field

Beilstein J. Org. Chem. 2022, 18, 208–216, doi:10.3762/bjoc.18.24

• Peterson de Andrade Sanaz Ahmadipour Robert A. Field Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK Iceni Glycoscience Ltd, Norwich Research Park NR4 7GJ, UK 10.3762/bjoc.18.24 Abstract Sialic acid is the

• Biotechnology and Biological Sciences Research Council (BBSRC) as part of UK Research and Innovation. This work was also supported by Innovate UK grant 76242: Sugars, Enzymes And Diagnostics (SEAD).

Asymmetric organocatalytic Michael addition of cyclopentane-1,2-dione to alkylidene oxindole

• Estelle Silm,
• Ivar Järving and
• Tõnis Kanger

Beilstein J. Org. Chem. 2022, 18, 167–173, doi:10.3762/bjoc.18.18

• Estelle Silm Ivar Jarving Tonis Kanger Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia 10.3762/bjoc.18.18 Abstract An asymmetric Michael reaction between cyclopentane-1,2-dione and alkylidene oxindole was studied in the

Tenacibactins K–M, cytotoxic siderophores from a coral-associated gliding bacterium of the genus Tenacibaculum

• Yasuhiro Igarashi,
• Yiwei Ge,
• Tao Zhou,
• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku and
• Agus Trianto

Beilstein J. Org. Chem. 2022, 18, 110–119, doi:10.3762/bjoc.18.12

• Yasuhiro Igarashi Yiwei Ge Tao Zhou Amit Raj Sharma Enjuro Harunari Naoya Oku Agus Trianto Biotechnology Research Center, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan Faculty of Fisheries and Marine Sciences, Diponegoro University, Tembalang Campus, St. Prof. Soedarto SH., Semarang