Discovery and biosynthesis of bacterial drimane-type sesquiterpenoids from Streptomyces clavuligerus

• Dongxu Zhang,
• Wenyu Du,
• Xingming Pan,
• Xiaoxu Lin,
• Fang-Ru Li,
• Qingling Wang,
• Qian Yang,
• Hui-Min Xu and
• Liao-Bin Dong

Beilstein J. Org. Chem. 2024, 20, 815–822, doi:10.3762/bjoc.20.73

• subfamilies within the sesquiterpenoids. Our discovery significantly broadens the scope for future exploration of bacterial DMTs. Discovery and identification of a DMS in the cav BGC in S. clavuligerus To explore the BGC responsible for DMTs production in S. clavuligerus, we performed bioinformatics research

Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization

• Senze Qiao,
• Zhongyu Cheng and
• Fuzhuo Li

Beilstein J. Org. Chem. 2024, 20, 721–733, doi:10.3762/bjoc.20.66

• -acetylcysteamine. Via bioinformatics analysis, Parkinson and co-workers most recently reported the characterization of Ulm16, the PBP-TE predicted to cyclize ulleungymycin. Compared with previously studied PBP-TEs, Ulm16 showed much higher efficiency and broader substrate scope, producing a variety of ullemgymycin

• stability, etc. Emerging research methods on bioinformatics, computational modeling, deep learning, protein engineering, and high-throughput screening will accelerate the pace of enzyme discovery to provide a broader platform of tools for employing chemoenzymatic strategies [64][87][88][89]. More

New variochelins from soil-isolated Variovorax sp. H002

• Jabal Rahmat Haedar,
• Aya Yoshimura and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2024, 20, 692–700, doi:10.3762/bjoc.20.63

• )-ʟ-alaninamide) derivatives [5]. In addition, a combination of NOESY and bioinformatics analyses proposed all three stereocenters of 4-amino-7-guanidino-3-hydroxy-2-methylheptanoic acid as S configured [5]. The stereochemistry of these moieties in 3–5 are discussed in the next section, regarding the

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

• applications. Despite the extensive catalog of secondary metabolites discovered, the pace of new findings has decelerated. However, the advent of bioinformatics analysis tools has reinvigorated the search for fungal secondary metabolites. The estimated number of non-redundant clusters in Penicillium is around

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

• cross-coupling between two aromatic rings [43]. In the future, further developments in bioinformatics, structural biology, and AI techniques will enable the design of biosynthetic enzymes and pathways to produce desired bioactive compounds, although understanding the chemistry catalyzed by individual

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

• , MeOH); UV (photodiode array, MeCN/H2O) λmax = 219 and 279 nm; HRESIMS m/z: [M + H]+ calcd for C41H57N8O7+, 773.4345; found, 773.4338, [M + Na]+ calcd for C41H56N8O7Na+, 795.4164; found, 795.4162. For the 1H and 13C NMR spectroscopic data, see Table 1. Bioinformatics The A. heteromorphus CBS 117.55

Characterization of a new fusicoccane-type diterpene synthase and an associated P450 enzyme

• Jia-Hua Huang,
• Jian-Ming Lv,
• Liang-Yan Xiao,
• Qian Xu,
• Fu-Long Lin,
• Gao-Qian Wang,
• Guo-Dong Chen,
• Sheng-Ying Qin,
• Dan Hu and
• Hao Gao

Beilstein J. Org. Chem. 2022, 18, 1396–1402, doi:10.3762/bjoc.18.144

• corresponding products. Bioinformatics analysis of the tad cluster. A) Phylogenetic tree of TadA and representative fungal DTSs. B) Putative functions of the tad cluster. HPLC–MS analysis of mycelial extracts from A. oryzae NSAR1 transformants. A) The HPLC profiles monitored at 208 nm. B) The HPLC profiles

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

Isolation and biosynthesis of daturamycins from Streptomyces sp. KIB-H1544

• Yin Chen,
• Jinqiu Ren,
• Ruimin Yang,
• Jie Li,
• Sheng-Xiong Huang and
• Yijun Yan

Beilstein J. Org. Chem. 2022, 18, 1009–1016, doi:10.3762/bjoc.18.101

• daturamycin C, were isolated and identified. The new diarylcyclopentenones possess a rare class of a tricyclic 6/5/6 system. Based on the bioinformatics analysis, the daturamycins biosynthetic gene cluster has been identified and confirmed by the inactivation of the structural gene datA. The following

Anti-inflammatory aromadendrane- and cadinane-type sesquiterpenoids from the South China Sea sponge Acanthella cavernosa

• Shou-Mao Shen,
• Qing Yang,
• Yi Zang,
• Jia Li,
• Xueting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 916–925, doi:10.3762/bjoc.18.91

• yet been discovered. Phenolic sesquiterpenoids, for instance, illudacetalic acid and illudinine from Omphalotus olearius, were also discovered. Based on bioinformatics analysis, their aromatic rings were proposed to be constructed by putative P450 enzymes or oxidoreductase [33]. The Huang group

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

• Kiyoko F. Aoki-Kinoshita Frederique Lisacek Niclas Karlsson Daniel Kolarich Nicolle H. Packer Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji-shi, Tokyo, Japan University of Geneva and Swiss Institute of Bioinformatics, CUI - 7, route de Drize, 1211 Geneva

• , Queensland 4222, Australia Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia 10.3762/bjoc.17.184 Keywords: bioinformatics; glycobioinformatics; glycoinformatics; In order to introduce this thematic issue “GlycoBioinformatics” [1] in the Beilstein Journal of Organic

• Chemistry, it would be appropriate to define what we actually mean by this term. This is important not only for newcomers to the field but also in order for researchers that have used or developed “glycobioinformatics” to place their work into a wider context of this diverse field. The term “bioinformatics

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

• 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

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. Keywords: bioinformatics; cysteine oxidation; glycoproteomics; immunoglobulins; mass spectrometry; Introduction Protein glycosylation mainly occurs in the form of N- and O-glycosylation. N-Glycans are attached to Asn within an amino acid consensus sequence (Asn-Xxx-Ser/Thr, Xxx ≠ Pro) and O

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

• ]. Originally built to support bioinformatics, Galaxy now supports a much more expansive community including proteomics [2], metabolomics [3], cheminformatics [4], glycoinformatics [5], and chemistry [6]. Of value to these communities are the broad range of tools and ways to connect tools (workflows) in Galaxy

• of the analyses was carried out using Galaxy, the popular open web-based platform for bioinformatics and computational data analysis, which enables the creation of repeatable analysis pipelines (workflows). There are several well-known molecular dynamics analysis packages (MDAnalysis [37], Bio3D [38

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

• 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

• , and thus already laying a foundation for the generation of unique WURCS notations and providing a straightforward access to bioinformatics databases that are integrated in the GlyTouCan project. Methods The algorithm used to generate the WURCS notation in Privateer is based on the description

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

• glycobiologists or any researcher looking for a ready to use, simple program for the sketching or building of glycans. Keywords: bioinformatics; carbohydrate; glycan; glycobiology; nomenclature; oligosaccharide; polysaccharide; representation; structure; Introduction Glycoscience is a rapidly surfacing and

A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA

• Ekaterina A. Bryushkova,
• Erik R. Gandalipov and
• Julia V. Nuzhina

Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100

•  1, Table S1 and Figure S1). Based on the results of the bioinformatics analysis, an RNA sequence of 60 nucleotides (nt) was selected as a target (Table S2, 60-AR_RNA). This sequence was located in the conserved exon 1, position 1–2140 nt. The specificity of 60-AR_RNA for the human androgen receptor

A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium

• Shun Saito,
• Kota Atsumi,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Naoya Oku,
• Md. Rokon Ul Karim,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97

• bioinformatics and culture collections are available. Experimental General experimental procedures Optical rotations were measured using a JASCO DIP-3000 polarimeter. The UV spectra were recorded on a Hitachi U-3210 spectrophotometer. The IR spectra were measured on a PerkinElmer Spectrum 100. NMR spectra were

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

Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering

• Eric J. N. Helfrich,
• Geng-Min Lin,
• Christopher A. Voigt and
• Jon Clardy

Beilstein J. Org. Chem. 2019, 15, 2889–2906, doi:10.3762/bjoc.15.283

• number of bacterial genome sequences available and the development of advanced bioinformatics tools, more type II/I diterpene TC tandems are likely to be discovered. By applying the same combinatorial concept, it is expected that the diterpene chemical space can be significantly expanded. Cytochrome

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

• bacteria, fungi, mammalian cells and plants. Bioinformatics analysis, including comparative analysis with other acyl drimenol-producing Aspergilli, led to the identification of a putative nanangenine biosynthetic gene cluster that corresponds to the proposed biosynthetic pathway for nanangenines. Keywords

Genome mining in Trichoderma viride J1-030: discovery and identification of novel sesquiterpene synthase and its products

• Xiang Sun,
• You-Sheng Cai,
• Yujie Yuan,
• Guangkai Bian,
• Ziling Ye,
• Zixin Deng and
• Tiangang Liu

Beilstein J. Org. Chem. 2019, 15, 2052–2058, doi:10.3762/bjoc.15.202

• prediction of the potential terpene synthases in J1-030 genome, gene Tvi09626 was selected and the following bioinformatics analysis of the function of this unidentified terpene synthase was performed. A protein blast search against the NCBI database was performed with Tvi09626, revealing sequence identities

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

• bioinformatics as well as spectroscopy. First, we analyzed whether the isolated natural product possesses a D- or L-configured thiazoline ring. Previous studies had revealed that the D-thiazoline ring in pyochelin is due to an unusual methyltransferase-like epimerization domain in the biosynthesis protein PchE

• yersiniabactin biosynthesis (Table S2, Supporting Information File 1), which led us to infer that the absolute configuration at C-19 is S. It was hence possible to predict the configuration of all stereocenters in 1 except C-15 by bioinformatics. To conclude the stereochemical analysis, we resorted to the NOESY

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

• clusters. Keywords: bioinformatics; gene cluster analysis; natural products; secondary metabolites; structure elucidation; terpenes; Introduction The basidiomycete Agrocybe aegerita (synonym: A. cylindracea) was traditionally accommodated in the genus Agrocybe (family Bolbitiaceae) until a recent