A new glance at the chemosphere of macroalgal–bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry

• Marine Vallet,
• Filip Kaftan,
• Veit Grabe,
• Fatemeh Ghaderiardakani,
• Simona Fenizia,
• Aleš Svatoš,
• Georg Pohnert and
• Thomas Wichard

Beilstein J. Org. Chem. 2021, 17, 1313–1322, doi:10.3762/bjoc.17.91

• similarity with standards. Using combined imaging mass spectrometry and confocal laser scanning microscopy, we then linked the chemical and microscopic observations that characterise the symbiotic association (cLSM). Results and Discussion Comparative metabolomics using AP-SMALDI-HRMS identifies metabolites

• class (Figure 1c). Among the statistically significant features in all datasets (Table S1, Supporting Information File 1), six metabolites were identified, which were annotated using spectral similarity with analytical standards. For example, the features m/z 104.1064 and m/z 143.0815 were selected

• chemical formula based on exact mass. We also used spectral similarity matching of data acquired from analytical standards. Choline was identified from the molecular peak m/z 104.1064 for [M]+ (calculated m/z as 104.1069 ± 4.8 ppm for C5H14NO) in the profiles of axenic U. mutabilis (Figure 2a). This small

Metal-free glycosylation with glycosyl fluorides in liquid SO₂

• Krista Gulbe,
• Jevgeņija Lugiņina,
• Edijs Jansons,
• Artis Kinens and
• Māris Turks

Beilstein J. Org. Chem. 2021, 17, 964–976, doi:10.3762/bjoc.17.78

• community we have demonstrated an application of saturated solutions of SO2 in conventional solvents that do not require a specific equipment, but can be performed in widely available glass pressure tubes (Table 5). In this context it has technically a similarity with ammonia solutions in organic solvents

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• '-stereoisomer of FANA, FRNA also demonstrates improved binding to RNA, relative to DNA [185]. Circular dichroism spectra of FANA/RNA and ANA/RNA duplexes show similarity to that of DNA/RNA [178][183]. Both ANA and FANA demonstrate good stability to nucleases [183][186]. Hybrid duplexes of ANA and FANA with

Amino- and polyaminophthalazin-1(2H)-ones: synthesis, coordination properties, and biological activity

• Zbigniew Malinowski,
• Emilia Fornal,
• Agata Sumara,
• Renata Kontek,
• Karol Bukowski,
• Beata Pasternak,
• Dariusz Sroczyński,
• Joachim Kusz,
• Magdalena Małecka and
• Monika Nowak

Beilstein J. Org. Chem. 2021, 17, 558–568, doi:10.3762/bjoc.17.50

• ]. All selected compounds (Figure 3) contain some specific structural elements (e.g., an ethylenediamine moiety, similarity to bipyridyl or even to isocyclam skeleton) allowing them to act as ligands and form complexes. In our tests, we hoped that putting in the 4-position of the skeleton a substituent

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

• their high similarity (Figure 12D). The variants containing Pro and R-Flp did not show a clearly defined pucker, whereas the variant with S-Flp was found in a single C4-endo-pucker conformation. Overall, the crystal structures illustrate that the pucker preference observed in small molecules (Figure 6

Multiswitchable photoacid–hydroxyflavylium–polyelectrolyte nano-assemblies

• Alexander Zika and
• Franziska Gröhn

Beilstein J. Org. Chem. 2021, 17, 166–185, doi:10.3762/bjoc.17.17

• again. Cycle II shows similarity to cycle I. For both cycles, the largest size range that is covered when going through all switching steps – that is from RH ≈ 150 nm to RH ≈ 350 nm for cycle I and to RH ≈ 300 nm for cycle II – is realized for the loading ratio l = 0.9, which represents the model case

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

• Information File 1), which were in line with the literature (Table S6, Supporting Information File 1) [17][18]. Skyline and LaCyTools showed the highest similarity in the relative quantification results (Figure S20, Supporting Information File 2). Both tools had a median relative standard deviation (RSD) of 4

Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities

• Heiko T. Kiesewalter,
• Carlos N. Lozano-Andrade,
• Mikael L. Strube and
• Ákos T. Kovács

Beilstein J. Org. Chem. 2020, 16, 2983–2998, doi:10.3762/bjoc.16.248

• not see differences between the mock communities. Therefore, we determined the beta diversity only for the treated and untreated mock communities cocultivated for 48 h. The analysis underlined a high similarity in the composition of the mock communities treated with B subtilis strains (Figure 4B

• similarity to the untreated control communities. In contrast, the communities supplemented with NRP-producing B. subtilis strains clustered together and indicated a lower dissimilarity to each other than to the control communities. Notably, the communities treated with the srfAC mutant had a higher

• highest similarity to the untreated communities, suggesting that the supplementation of the NRP-producing B. subtilis strains affected the communities. The vectors of Acinetobacter ASVs had a direction either to NRP-treated or NRP-untreated communities, indicating that the NRPs influenced species within

Ultrasound-assisted Strecker synthesis of novel 2-(hetero)aryl-2-(arylamino)acetonitrile derivatives

• Emese Gal,
• Luiza Gaina,
• Hermina Petkes,
• Alexandra Pop,
• Castelia Cristea,
• Gabriel Barta,
• Dan Cristian Vodnar and
• Luminiţa Silaghi-Dumitrescu

Beilstein J. Org. Chem. 2020, 16, 2929–2936, doi:10.3762/bjoc.16.242

• -recognized Ames test to screen the mutagenic potential for three selected C-substituted α-aminoacetonitriles comprising different hetero(aromatic) units: phenothiazinyl (2c), ferrocenyl (2i), and phenyl (2l), respectively. The similarity of the tested aminoacetonitrile series was set aside by the N

On the mass spectrometric fragmentations of the bacterial sesterterpenes sestermobaraenes A–C

• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2020, 16, 2807–2819, doi:10.3762/bjoc.16.231

• allows to identify interesting candidate genes coding for terpene synthases for further studies by genome mining. A major difficulty in the GC–MS-based identification of terpenes is associated with the high similarity of the mass spectra of structurally related terpenes. For this reason, the unambiguous

Nocarimidazoles C and D, antimicrobial alkanoylimidazoles from a coral-derived actinomycete Kocuria sp.: application of ¹J_C,H coupling constants for the unequivocal determination of substituted imidazoles and stereochemical diversity of anteisoalkyl chains in microbial metabolites

• Md. Rokon Ul Karim,
• Enjuro Harunari,
• Amit Raj Sharma,
• Naoya Oku,
• Kazuaki Akasaka,
• Daisuke Urabe,
• Mada Triandala Sibero and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 2719–2727, doi:10.3762/bjoc.16.222

• basis of 100.0% similarity in the 16S rRNA gene sequence (1381 nucleotides; DDBJ accession number LC556325) to Kocuria palustris DSM 11925T (accession number Y16263). Fermentation In a similar manner as described in [22], the strain T35-5 was maintained on Marine Agar 2216 (Difco). A loopful of the

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

• Benjamin P. Kellman,
• Yujie Zhang,
• Emma Logomasini,
• Eric Meinhardt,
• Karla P. Godinez-Macias,
• Austin W. T. Chiang,
• James T. Sorrentino,
• Chenguang Liang,
• Bokan Bao,
• Yusen Zhou,
• Sachiko Akase,
• Isami Sogabe,
• Thukaa Kouka,
• Elizabeth A. Winzeler,
• Iain B. H. Wilson,
• Matthew P. Campbell,
• Sriram Neelamegham,
• Frederick J. Krambeck,
• Kiyoko F. Aoki-Kinoshita and
• Nathan E. Lewis

Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215

• demonstrating non-trivial functional-group (Table 5) relations between monosaccharides (Figure 2). We used RDKit, an open-source cheminformatics toolkit, to identify chiral centers and further determine stereochemical equivalence classes. Monosaccharides were clustered with an 80% stereo-similarity threshold

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

• structure can further be used as a query for the search in glycan databases; using match percentage (Similarity) or by the number of components matched (Matched) criteria. Four predefined score matrices are available, named: N-glycans, O-glycans, Sphingolipids and Link_similarity. The “Link_similarity

Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations

• Ian Walsh,
• Matthew S. F. Choo,
• Sim Lyn Chiin,
• Amelia Mak,
• Shi Jie Tay,
• Pauline M. Rudd,
• Yang Yuansheng,
• Andre Choo,
• Ho Ying Swan and
• Terry Nguyen-Khuong

Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176

• ., the Anti-HER-2 peaks). The pairwise similarity between any two electropherograms was calculated using Euclidean distance metric. The clustering algorithm is presented in Supporting Information File 1, Figure S3. After clustering, each cluster contained N electropherograms and each peak's central

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• in Figure 4 and Table 2, the addition of all studied compounds resulted in very strong stabilisation effects on both, poly(dA-dT)2 and poly(A)-poly(U). This similarity of stabilisation of ds-DNA and ds-RNA supports the presence of an intercalative binding mode because DNA groove binders are usually

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• generally decreases with the size [18], this similarity is particularly impressive, considering that the COC carrying a 52 kDa protein is compared to a small undecapeptide. The compatibility of the assay with other fusion proteins and more adverse conditions, such as transient transfection, has never been

Three new O-isocrotonyl-3-hydroxybutyric acid congeners produced by a sea anemone-derived marine bacterium of the genus Vibrio

• Dandan Li,
• Enjuro Harunari,
• Tao Zhou,
• Naoya Oku and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1869–1874, doi:10.3762/bjoc.16.154

• completed the structure of 4 as O-isocrotonyl-3-hydroxybutyric acid (Figure 2). A close similarity of the NMR data for 1–3 (Table 1 and Table 2) allowed the same sequence of structure analysis. The compounds 1 and 2 were found to have extra C1 and C2 extensions on the butyric acid units, while in 3, an

• SI9 was isolated from its outer tissue specimen according to the method described previously [19] and identified as a member of the genus Vibrio on the basis of an 98.6% similarity in the 16S rRNA gene sequence (1458 nucleotides; DDBJ accession number LC498627) to Vibrio nereis DSM 19584T (accession

Rearrangement of o-(pivaloylaminomethyl)benzaldehydes: an experimental and computational study

• Csilla Hargitai,
• Györgyi Koványi-Lax,
• Tamás Nagy,
• Péter Ábrányi-Balogh,
• András Dancsó,
• Gábor Tóth,
• Judit Halász,
• Angéla Pandur,
• Gyula Simig and
• Balázs Volk

Beilstein J. Org. Chem. 2020, 16, 1636–1648, doi:10.3762/bjoc.16.136

• interconversion of these conformers is slow in the NMR time-scale. Although the NMR spectra have been measured in CDCl3, we are convinced that the conformations observed in CDCl3 are in good accordance with the ones computed considering the implicit solvent effect of DCM. Based on the structural similarity, the

A dynamic combinatorial library for biomimetic recognition of dipeptides in water

• Florian Klepel and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2020, 16, 1588–1595, doi:10.3762/bjoc.16.131

• compounds could not be achieved due to the high complexity of the library and the structural similarity of its members. Hence ESI-TOF mass spectrometry data can be interpreted qualitatively but not quantitatively. A full reference sample is shown in Figure 1. Each chromatogram represents a single

• our initial assumption that dynamic peptides, due to their similarity towards enzymes, can bind a broad scope of biomolecules. ITC measurements suggest that the cyclic tripeptide dimers a(CFC)2 and p(CFC)2 are stronger binders for the aromatic dipeptides FF and YY (K ≈ 229–702 M−1), then for the non

4-Hydroxy-3-methyl-2(1H)-quinolone, originally discovered from a Brassicaceae plant, produced by a soil bacterium of the genus Burkholderia sp.: determination of a preferred tautomer and antioxidant activity

• Dandan Li,
• Naoya Oku,
• Yukiko Shinozaki,
• Yoichi Kurokawa and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1489–1494, doi:10.3762/bjoc.16.124

• . Though not alkylated, the close structural similarity to 3 suggests that 1 is also a member of the 2-alkyl-4-quinolone class signaling molecules/antibiotics known from Pseudomonas aeruginosa and some Burkholderia species [26][27]. Quinolones of this class are classified into two lineages, those with or

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

• widely used as an indicator of the taxonomic position of prokaryotes. It was believed that a high similarity of the 16S rRNA gene sequence implied the closeness or even the identity in other sets of genes including secondary metabolite biosynthetic genes. However, our recent analysis of Streptomyces

• experimental 1H and 13C NMR data of 1 presented a higher chemical shift similarity to those for 1b and thereby the (S)-configuration was suggested for C-2. Indeed, the DP4+ analysis [25] gave 100% probability for structure 1b and 0.0% probability for structure 1a (Table S2, Supporting Information File 2). This

• (Biological Resource Center, National Institute of Technology and Evaluation, Chiba, Japan). The strain was identified as a member of the genus Pseudosporangium on the basis of 99.7% similarity in the 16S rRNA gene sequence (1428 nucleotides; GenBank accession number LC512747) to Pseudosporangium ferrugineum

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

• Panagiotis S. Gritzapis,
• Panayiotis C. Varras,
• Nikolaos-Panagiotis Andreou,
• Katerina R. Katsani,
• Konstantinos Dafnopoulos,
• George Psomas,
• Zisis V. Peitsinis,
• Alexandros E. Koumbis and
• Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

• sulfonylethanone oxime derivatives were less reactive than the PNP one [10]. Due to the similarity in DNA photocleavage by p-pyridine amidoxime, ethanome oxime and aldoxime carbamoyl derivatives, mechanistic studies were performed for two active compounds from the series of amidoximes and aldoximes, 12 and 26

Two antibacterial and PPARα/γ-agonistic unsaturated keto fatty acids from a coral-associated actinomycete of the genus Micrococcus

• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku,
• Nobuyasu Matsuura,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 297–304, doi:10.3762/bjoc.16.29

• emerged on the plates, which were transferred onto a new agar medium to obtain pure isolates. One of these isolates, coded as C5-9, was identified as a member of the genus Micrococcus on the basis of 99.9% similarity in the 16S rRNA gene sequence (1395 nucleotides; DNA Data Bank of Japan/DDBJ accession

Absolute configurations of talaromycones A and B, α-diversonolic ester, and aspergillusone B from endophytic Talaromyces sp. ECN211

• Ken-ichi Nakashima,
• Junko Tomida,
• Takao Hirai,
• Yoshiaki Kawamura and
• Makoto Inoue

Beilstein J. Org. Chem. 2020, 16, 290–296, doi:10.3762/bjoc.16.28

• (Figure S1, Supporting Information File 1), the isolate was found to belong to the genus Talaromyces. Talaromyces sp. ECN211 exhibited 26S rDNA similarity (95.3%) to T. trachyspermus Bhopal (KX66827). The sequence data for Talaromyces sp. ECN211 have been deposited at the DNA Data Bank of Japan (DDBJ

Potent hemithioindigo-based antimitotics photocontrol the microtubule cytoskeleton in cellulo

• Alexander Sailer,
• Franziska Ermer,
• Yvonne Kraus,
• Rebekkah Bingham,
• Ferdinand H. Lutter,
• Julia Ahlfeld and
• Oliver Thorn-Seshold

Beilstein J. Org. Chem. 2020, 16, 125–134, doi:10.3762/bjoc.16.14

• colchicine. It is not the case that colchicine (or any other small-molecule inhibitor) represents an ideal structure that colchicine domain inhibitors (CDIs) should reproduce. Thus, our design focus was to introduce reversible photoresponse to a CDI rather than developing compounds with high similarity to