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

• restriction sites and verified by DNA sequencing (Eurofins Genomics). pTip-QC1-hyg17 plasmid [10] was transformed into Rhodococcus jostii RHA1 [11]. Cultures were grown in Luria Bertani (LB) media supplemented with 34 µg mL−1 chloramphenicol at 30 °C while shaking at 200 rpm for 48 h reaching an OD600 of ≈1.4

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

• Island, Ou, Kumejima, Shimajiri District, Okinawa, Japan. Genomic DNA was prepared, and the 16S rRNA gene was amplified by PCR using the method of Inahashi and co-workers [23]. The sequencing analysis was performed by Eurofins Genomics. Similarity of 16S rRNA gene sequence was computed by using

Discovery of unguisin J, a new cyclic peptide from Aspergillus heteromorphus CBS 117.55, and phylogeny-based bioinformatic analysis of UngA NRPS domains

• Sharmila Neupane,
• Marcelo Rodrigues de Amorim and
• Elizabeth Skellam

Beilstein J. Org. Chem. 2024, 20, 321–330, doi:10.3762/bjoc.20.32

• ). Comparative genomics/Clinker analysis was performed using Cagecat [18][19]. A and C domains were identified via Scan Prosite [20] and fungiSMASH [21]. Sequence alignments (Figures S1 and S2, Supporting Information File 1) and phylogenetic trees were generated using GeneiousTM. Functional domain motifs were

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

• -TEV vector, and finally transformed in NEB5α strain to form the pET40b-TEV-CMA1-Nter and pET40b-TEV-CMA1-Cter plasmids. All plasmids and new vectors were verified by sequencing (Eurofins Genomics, Ebersberg, Germany). Primers were purchased from Eurofins Genomics (Ebersberg, Germany). E. coli BL21

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

• Friederike Biermann Sebastian L. Wenski Eric J. N. Helfrich Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany

• phylogenetic analyses or ML approaches. In many cases, these ML approaches are based on well-established strategies adopted from other disciplines (e.g., natural language processing or comparative genomics) that were adapted by the NP community [41]. In the following section, we will look at representative

• comparative genomics approach to identify non-canonical BGCs Another concept for the expansion of NP biosynthetic space is based on a Comparative Genomics Approach (CGA). This approach relies on the fact that many BGCs are introduced into microbial genomes via horizontal gene transfer (HGT). A genome can be

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

• Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China 10.3762/bjoc.18.173 Abstract An approach to aberrarone, an antimalarial diterpenoid natural product with tetracyclic skeleton is reported. Key to the stereoselective preparation of

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

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

• Genomics Workbench (Qiagen Bioinformatics) using default parameters or parameters specified as follows: bubble size, 100; automatic word size; minimum contig length, 600. A BUSCO analysis (Supporting Information File 1, Figure S3) was performed to validate the completeness of the transcriptome

Anthelmintic drug discovery: target identification, screening methods and the role of open science

• Frederick A. Partridge,
• Ruth Forman,
• Carole J. R. Bataille,
• Graham M. Wynne,
• Marina Nick,
• Angela J. Russell,
• Kathryn J. Else and
• David B. Sattelle

Beilstein J. Org. Chem. 2020, 16, 1203–1224, doi:10.3762/bjoc.16.105

• ]. At the time of writing, this database contains information on 142 species of parasites and other helminths, including genomes, comparative genomics data and RNAseq studies, along with a number of tools facilitating access to this data including a genome browser, BioMart (a tool for exporting tables

• of selected information) and a REST API, an interface for programmatic access to the database. But how can we get from genomic information to new drug targets? A recent comparative genomics study from a large international consortium of researchers has really helped with this question, by comparing

Opening up connectivity between documents, structures and bioactivity

• Christopher Southan

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

• between bioinformatics and cheminformatics points towards the root of the problems we currently face. Over more than three decades the links between sequence data and the literature have become a blazing success, first for molecular biology followed by genomics. This was driven mainly by the combination

Nanangenines: drimane sesquiterpenoids as the dominant metabolite cohort of a novel Australian fungus, Aspergillus nanangensis

• Heather J. Lacey,
• Cameron L. M. Gilchrist,
• Andrew Crombie,
• John A. Kalaitzis,
• Daniel Vuong,
• Peter J. Rutledge,
• Peter Turner,
• John I. Pitt,
• Ernest Lacey,
• Yit-Heng Chooi and
• Andrew M. Piggott

Beilstein J. Org. Chem. 2019, 15, 2631–2643, doi:10.3762/bjoc.15.256

• unidentified [42]. While we cannot conclusively determine each strain to be A. nanangensis, the ITS sequences of all three strains are identical and they clearly clade in section Jani (Figure S48 in Supporting Information File 1). A comparative genomics survey of all publicly available genomes on NCBI and the

• structures of 4 and 9 have one. The cyclohexane rings of all molecules have chair conformations, the cyclohexene rings of all molecules have half-chair conformations, and the furan rings of all molecules have flattened envelope conformations. See Supporting Information File 1 for detailed methods. Genomics

A toolbox of molecular photoswitches to modulate the CXCR3 chemokine receptor with light

• Xavier Gómez-Santacana,
• Sabrina M. de Munnik,
• Tamara A. M. Mocking,
• Niels J. Hauwert,
• Shanliang Sun,
• Prashanna Vijayachandran,
• Iwan J. P. de Esch,
• Henry F. Vischer,
• Maikel Wijtmans and
• Rob Leurs

Beilstein J. Org. Chem. 2019, 15, 2509–2523, doi:10.3762/bjoc.15.244

• Universiteit Amsterdam, 1081 HZ, Amsterdam, The Netherlands present address: Institute of Functional Genomics, Université de Montpellier, Unité 5302 CNRS and Unité U1191, INSERM, 34090 Montpellier, France 10.3762/bjoc.15.244 Abstract We report a detailed structure–activity relationship for the scaffold of

Genomics-inspired discovery of massiliachelin, an agrochelin epimer from Massilia sp. NR 4-1

• Jan Diettrich,
• Hirokazu Kage and
• Markus Nett

Beilstein J. Org. Chem. 2019, 15, 1298–1303, doi:10.3762/bjoc.15.128

• product, which was named massiliachelin, corresponds to the assembly line encoded by the identified siderophore locus. Keywords: agrochelin; genome mining; Massilia; massiliachelin; siderophore; stereochemistry; Introduction In recent years, chemical investigations as well as genomics led to the

New terpenoids from the fermentation broth of the edible mushroom Cyclocybe aegerita

• Frank Surup,
• Florian Hennicke,
• Nadine Sella,
• Maria Stroot,
• Steffen Bernecker,
• Sebastian Pfütze,
• Marc Stadler and
• Martin Rühl

Beilstein J. Org. Chem. 2019, 15, 1000–1007, doi:10.3762/bjoc.15.98

• Site Hannover-Braunschweig, Inhoffenstraße 7, 38124 Braunschweig, Germany Junior Research Group Genetics and Genomics of Fungi, Senckenberg Gesellschaft für Naturforschung, Georg-Voigt-Str. 14–16, 60325 Frankfurt am Main, Germany Institute of Food Chemistry and Food Biotechnology, Justus Liebig

Repurposing the anticancer drug cisplatin with the aim of developing novel Pseudomonas aeruginosa infection control agents

• Mingjun Yuan,
• Song Lin Chua,
• Yang Liu,
• Daniela I. Drautz-Moses,
• Joey Kuok Hoong Yam,
• Thet Tun Aung,
• Roger W. Beuerman,
• May Margarette Santillan Salido,
• Stephan C. Schuster,
• Choon-Hong Tan,
• Michael Givskov,
• Liang Yang and
• Thomas E. Nielsen

Beilstein J. Org. Chem. 2018, 14, 3059–3069, doi:10.3762/bjoc.14.284

• PAO1 reference genome using the CLC genomics Workbench 8.0 (CLC Bio-Qiagen, Aarhus, Denmark). The differentially expressed genes were identified by performing a negative binomial test using the DESeq [18] package of R/Bioconductor [19], using the cut off of fold-change larger than 2 and a BH (Benjamini

Volatiles from three genome sequenced fungi from the genus Aspergillus

• Jeroen S. Dickschat,
• Ersin Celik and
• Nelson L. Brock

Beilstein J. Org. Chem. 2018, 14, 900–910, doi:10.3762/bjoc.14.77

• from cantaloupe a structural revision to the Z stereoisomer is proposed. Ethyl (Z)-hept-4-enoate also occurs in Aspergillus clavatus and was identified by synthesis of an authentic standard. Keywords: Aspergillus; GC–MS; genomics; terpenes; volatiles; Introduction Ascomycete fungi are a highly

A practical and efficient approach to imidazo[1,2-a]pyridine-fused isoquinolines through the post-GBB transformation strategy

• Taofeng Shao,
• Zhiming Gong,
• Tianyi Su,
• Wei Hao and
• Chao Che

Beilstein J. Org. Chem. 2017, 13, 817–824, doi:10.3762/bjoc.13.82

• Taofeng Shao Zhiming Gong Tianyi Su Wei Hao Chao Che Laboratory of Chemical Genomics, Engineering Laboratory for Chiral Drug Synthesis, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China 10.3762/bjoc.13.82 Abstract Diversity-oriented

Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides

• Franziska Hemmerling and
• Frank Hahn

Beilstein J. Org. Chem. 2016, 12, 1512–1550, doi:10.3762/bjoc.12.148

• heterocyclic compounds are produced by a range of actinomycetes and a deeper understanding of their biosynthesis was for a long time hampered by the inability to identify their biosynthetic genes. Those were finally discovered by a comparative genomics approach in which the clusters of thiolactomycin (165

One-pot synthesis of tetracyclic fused imidazo[1,2-a]pyridines via a three-component reaction

• Bo Yang,
• Chuanye Tao,
• Taofeng Shao,
• Jianxian Gong and
• Chao Che

Beilstein J. Org. Chem. 2016, 12, 1487–1492, doi:10.3762/bjoc.12.145

• Bo Yang Chuanye Tao Taofeng Shao Jianxian Gong Chao Che Laboratory of Chemical Genomics, Engineering Laboratory for Chiral Drug Synthesis, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China 10.3762/bjoc.12.145 Abstract A novel three

Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides

• Andrew W. Truman

Beilstein J. Org. Chem. 2016, 12, 1250–1268, doi:10.3762/bjoc.12.120

• and characterisation of RiPP post-translational modifications in recent years [5][14]. Much of this has been led by genomics, which has informed both the study of established molecules whose biosynthetic origins were previously unknown (e.g., thiostrepton [72]) and the discovery of new pathways via

Automated solid-phase peptide synthesis to obtain therapeutic peptides

• Veronika Mäde,
• Sylvia Els-Heindl and
• Annette G. Beck-Sickinger

Beilstein J. Org. Chem. 2014, 10, 1197–1212, doi:10.3762/bjoc.10.118

• osteoporosis, cardiovascular diseases and inflammation can be treated by peptide-based drugs [4][5]. Within the last decades, the fast development of omics technologies such as genomics, proteomics and transcriptomics led to the identification of a great number of target peptides or proteins [6]. This trend

Biosynthesis of rare hexoses using microorganisms and related enzymes

• Zijie Li,
• Yahui Gao,
• Hideki Nakanishi,
• Xiaodong Gao and
• Li Cai

Beilstein J. Org. Chem. 2013, 9, 2434–2445, doi:10.3762/bjoc.9.281

• -gulose, L-galactose, L-fucose, allitol, D-talitol, and L-sorbitol. New systems and robust catalysts resulting from advancements in genomics and bioengineering are also discussed. Keywords: biosynthesis; enzyme; hexose; microorganism; rare sugars; Introduction Rare sugars are referred to as

• these monosaccharides [7]. Recently, inspired by the “Izumoring” tree, microbial and enzymatic transformations have become a very powerful tool for the synthesis of rare sugars owing to the advancements in genomics and an increasing availability of new and robust biocatalysts. Microbial transformation

• may lead to low to moderate yields and difficulties in product purification. Advancements in genomics and bioengineering can potentially solve this problem by improving the properties (activity, thermostability, or substrate-binding affinity) of existing enzymes or discovering new systems and robust

Activation of cryptic metabolite production through gene disruption: Dimethyl furan-2,4-dicarboxylate produced by Streptomyces sahachiroi

• Dinesh Simkhada,
• Huitu Zhang,
• Shogo Mori,
• Howard Williams and
• Coran M. H. Watanabe

Beilstein J. Org. Chem. 2013, 9, 1768–1773, doi:10.3762/bjoc.9.205

• ; Streptomyces; Findings It has become increasingly apparent that microbial diversity in nature far exceeds that reflected in laboratory strain collections. The advent of microbial genomics and the availability of published genome sequences suggest, that as much as 90% of the chemical potential of these

Synthesis and physicochemical characterization of novel phenotypic probes targeting the nuclear factor-kappa B signaling pathway

• Paul M. Hershberger,
• Satyamaheshwar Peddibhotla,
• E. Hampton Sessions,
• Daniela B. Divlianska,
• Ricardo G. Correa,
• Anthony B. Pinkerton,
• John C. Reed and
• Gregory P. Roth

Beilstein J. Org. Chem. 2013, 9, 900–907, doi:10.3762/bjoc.9.103

• Paul M. Hershberger Satyamaheshwar Peddibhotla E. Hampton Sessions Daniela B. Divlianska Ricardo G. Correa Anthony B. Pinkerton John C. Reed Gregory P. Roth Conrad Prebys Center for Chemical Genomics, Sanford-Burnham Medical Research Institute at Lake Nona, 6400 Sanger Road Orlando, FL 32827, USA

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

• rapid advances in the fields of genomics and proteomics during the “post-genome era” have resulted in an increase in potential therapeutic targets for which there are no known small-molecule modulators [1]. The lack of adequate screening technologies, as well as screening collections of molecules, has