Peptide stapling by late-stage Suzuki–Miyaura cross-coupling

• Hendrik Gruß,
• Rebecca C. Feiner,
• Ridhiwan Mseya,
• David C. Schröder,
• Michał Jewgiński,
• Kristian M. Müller,
• Rafał Latajka,
• Antoine Marion and
• Norbert Sewald

Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1

• additional ethylene unit in the linker suggested a conformation with the highest similarity to the linear reference peptide P6 (see Supporting Information File 1), thus representing a good compromise between rigidity and preservation of the target secondary structure. Serine in i-position and glutamic acid

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

• Couchioplanes on the basis of 98.2% similarity in the 16S rRNA gene sequence (1418 nucleotides; DDBJ accession number LC512746) to Couchioplanes caeruleus strain DSM 44103T (accession number NR_026295.1). Fermentation Strain RD010705, grown on half-strength ISP medium 2 consisting of yeast extract 0.2%, malt

The PIFA-initiated oxidative cyclization of 2-(3-butenyl)quinazolin-4(3H)-ones – an efficient approach to 1-(hydroxymethyl)-2,3-dihydropyrrolo[1,2-a]quinazolin-5(1H)-ones

• Alla I. Vaskevych,
• Nataliia O. Savinchuk,
• Ruslan I. Vaskevych,
• Eduard B. Rusanov,
• Oleksandr O. Grygorenko and
• Mykhailo V. Vovk

Beilstein J. Org. Chem. 2021, 17, 2787–2794, doi:10.3762/bjoc.17.189

• ][2][3][4]. In its essence, the NPL score for any molecule estimates its similarity to natural products vs synthetic molecules; it is based on the occurrence frequencies of the corresponding molecular fragments in the two series mentioned above. Zero value of the score is characteristic for the

Synthetic strategies toward 1,3-oxathiolane nucleoside analogues

• Umesh P. Aher,
• Dhananjai Srivastava,
• Girij P. Singh and
• Jayashree B. S

Beilstein J. Org. Chem. 2021, 17, 2680–2715, doi:10.3762/bjoc.17.182

• higher antiviral activity and lower toxicity of the unnatural ʟ-(−)-enantiomer over the ᴅ-(−)-enantiomer. The enantiomers of natural nucleosides are known to have a greater biological activity since they possess structural and configurational similarity to naturally occurring counterparts. In turn, for

α-Ketol and α-iminol rearrangements in synthetic organic and biosynthetic reactions

• Scott Benz and
• Andrew S. Murkin

Beilstein J. Org. Chem. 2021, 17, 2570–2584, doi:10.3762/bjoc.17.172

• biologically. Prekinamycin (76) and isoprekinamycin (77) are diazo compounds isolated from Streptomyces murayamensis that differ in their ring system, with the former containing a fused 6-6-5-6 skeleton and the latter containing a 6-5-6-6 skeleton. Due to their similarity and common source, it had been

• similarity in reaction, 1-deoxy-ᴅ-xylulose-5-phosphate reductoisomerase (DXR) instead uses a retro-aldol/aldol sequence to accomplish its rearrangement of 68 to 69. c) The secondary metabolite aurachin C (71) is oxidized by the FAD-dependent monooxygenase AuaG to epoxide 72, which upon deprotonation by an

Nomimicins B–D, new tetronate-class polyketides from a marine-derived actinomycete of the genus Actinomadura

• Zhiwei Zhang,
• Tao Zhou,
• Taehui Yang,
• Keisuke Fukaya,
• Enjuro Harunari,
• Shun Saito,
• Katsuhisa Yamada,
• Chiaki Imada,
• Daisuke Urabe and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2194–2202, doi:10.3762/bjoc.17.141

• HRESITOFMS analysis ([M + Na]+ m/z 551.2612, Δ −0.3 mmu). Structural analogy between 1 and 4 was suggested by the global similarity of the UV and NMR spectra between the compounds. In the 13C NMR spectrum, four nonprotonated carbons assignable to the tetronic acid moiety were detected at δC 108.2, 170.4

• remaining four sp2 carbon atoms, C1, C2, C3, and C24, although only limited HMBC correlations H22/C24 and H25/C3 were available, a spirotetronate structure was assembled. This was in consideration of the high similarity of the 13C NMR chemical shifts of these carbon atoms to those for the corresponding

• (Table S1, Supporting Information File 1) and 3JHH coupling constants [15]. The absolute configuration of 1 was deduced to be the same as 4 in consideration of the overall similarity of the electronic circular dichroism (ECD) spectra of 1 and 4 (Figure 4). This proposition was evidenced by the density

Natural products in the predatory defence of the filamentous fungal pathogen Aspergillus fumigatus

• Jana M. Boysen,
• Nauman Saeed and
• Falk Hillmann

Beilstein J. Org. Chem. 2021, 17, 1814–1827, doi:10.3762/bjoc.17.124

• have been widely used for the identification of virulence attributes of pathogenic fungi, including Aspergillus spp., for their similarity with human phagocytic cells [32]. Nevertheless, the precise identity of amoeboid, nematode and arthropod predators that target filamentous fungi in their

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

• aristolochene synthase (pdb 20A6) as query and the de novo assembly as template revealed two genes with high similarity to other fungal TPS genes. The genes were designated CxTPS1 and CxTPS2. For functional characterization, the complete open reading frames of CxTPS1 and CxTPS2 were amplified from cDNA, cloned

• between calculated retention index and literature data were within ±5 points. Identified volatiles with a similarity hit above 90% and that were present in five out of seven replicates were included in this study, whereas VOCs which were also collected by blanks were removed from the final dataset. A

Icilio Guareschi and his amazing “1897 reaction”

• Gian Cesare Tron,
• Alberto Minassi,
• Giovanni Sorba,
• Mara Fausone and
• Giovanni Appendino

Beilstein J. Org. Chem. 2021, 17, 1335–1351, doi:10.3762/bjoc.17.93

• Guareschi” [42]. Triacetonamine bears a certain similarity to tropinone (9), the heterocyclic core of tropane alkaloids, and the one-pot preparation from acetone and ammonia reminds of, and anticipates by two decades, the Robinson synthesis of tropinone and the Willstätter synthesis of the corresponding 2

Photoinduced post-modification of graphitic carbon nitride-embedded hydrogels: synthesis of 'hydrophobic hydrogels' and pore substructuring

• Cansu Esen and
• Baris Kumru

Beilstein J. Org. Chem. 2021, 17, 1323–1334, doi:10.3762/bjoc.17.92

• similarity to natural tissues, meaning that they are stable networks with high water content [1][2][3]. The simplest synthesis of hydrogels can be conducted in an aqueous solution of a water-soluble monomer and crosslinker (bi- or more functional) in the presence of an initiator (generally radical initiation

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