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

Pigmentosins from Gibellula sp. as antibiofilm agents and a new glycosylated asperfuran from Cordyceps javanica

• Soleiman E. Helaly,
• Wilawan Kuephadungphan,
• Patima Phainuphong,
• Mahmoud A. A. Ibrahim,
• Kanoksri Tasanathai,
• Suchada Mongkolsamrit,
• Janet Jennifer Luangsa-ard,
• Souwalak Phongpaichit,
• Vatcharin Rukachaisirikul and
• Marc Stadler

Beilstein J. Org. Chem. 2019, 15, 2968–2981, doi:10.3762/bjoc.15.293

• due to atropisomerism (Figure 2), although the TDDFT-ECD curve of (3S,3′S,6R)-1 showed a further small positive Cotton effect around 228 nm. Nevertheless, due to the high similarity of both curves, we believe that the calculated ECD data could not distinguish between (3R,3′R,6R)-1 and (3S,3′S,6R)-1

• and HSQC NMR data revealed a similarity to compound 1 (Table 1). In addition, the presence of resonances δC (in ppm) corresponding to two carbonyl carbon atoms at 172.4 (C-1/C-1′), two methyl carbon atoms at 20.8 (C-11′) and 24.1 (C-13′), respectively, two methoxy carbon atoms at 56.5 (C-7/C-7′), two

Two new aromatic polyketides from a sponge-derived Fusarium

• Mada Triandala Sibero,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Ocky K. Karna Radjasa,
• Agus Sabdono,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2019, 15, 2941–2947, doi:10.3762/bjoc.15.289

• . Results and Discussion A fungal strain was isolated from a sponge Xestospongia sp. collected in Karimunjawa National Park, Central Java, and identified as a member of Fusarium on the basis of sequence similarity of the internal transcribed spacer (ITS) domain to Fusarium oxysporum strains in the DNA

• ][30]. Strain KJMT.FP.4.3 was identified as Fusarium on the basis of the gene sequence analytical data of the ITS domain of partial 18S rRNA gene and 28S rRNA gene. Strain KJMT.FP.4.3 showed 99.7% similarity of ITS domain of partial 18S rRNA gene and 28S rRNA gene (555 nucleotides, GeneBank accession

• number MK393925.1) to Fusarium oxysporum strain NZZCDHL (549 nucleotides, GeneBank accession number KU939031.1) and 99.5% similarity of ITS domain of partial 18S rRNA gene and 28S rRNA gene to Fusarium oxysporum isolate DG-2 (548 nucleotides, GeneBank accession number MK429839.1). Fermentation Strain

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

• NRPSs), bacterial TCs show only little overall sequence similarity [1]. The lack of conservation in primary sequence has slowed down our understanding of terpene cyclization and, as a result, hampered the development of efficient genome mining platforms for the detection of bacterial terpene BGCs

• . antiSMASH [48] is the only open source web application that annotates bacterial terpene BGCs. As a result of the low conserved sequence similarity between TCs, terpene BGCs are missed more frequently by antiSMASH than other BGC classes [49]. In contrast to the well-characterized biosynthetic rules of

Emission and biosynthesis of volatile terpenoids from the plasmodial slime mold Physarum polycephalum

• Xinlu Chen,
• Tobias G. Köllner,
• Wangdan Xiong,
• Guo Wei and
• Feng Chen

Beilstein J. Org. Chem. 2019, 15, 2872–2880, doi:10.3762/bjoc.15.281

• similarities occurred between PpolyTPS1 and PpolyTPS4 (72%) and between PpolyTPS2 and PpolyTPS3 (64%). PpolyTPS1/4 and PpolyTPS2/3, however, showed only ≈30% sequence similarity to each other. Terpene synthases can be classified into class I and class II, based on the reaction mechanisms they catalyze. These

Palladium-catalyzed synthesis and nucleotide pyrophosphatase inhibition of benzo[4,5]furo[3,2-b]indoles

• Hoang Huy Do,
• Saif Ullah,
• Alexander Villinger,
• Joanna Lecka,
• Jean Sévigny,
• Peter Ehlers,
• Jamshed Iqbal and
• Peter Langer

Beilstein J. Org. Chem. 2019, 15, 2830–2839, doi:10.3762/bjoc.15.276

• 52% in case of ENPP3, amino acids sequence similarity with template, mouse ENPP1. The RMSD for ENPP1 was 0.613 Å and 1.349 Å for ENPP3, over 816 and 811 residues in comparison to the template, respectively. The Ramachandran plot represented promising stereochemical properties as above 98% amino acids

Design, synthesis and investigation of water-soluble hemi-indigo photoswitches for bioapplications

• Daria V. Berdnikova

Beilstein J. Org. Chem. 2019, 15, 2822–2829, doi:10.3762/bjoc.15.275

• (thio)indigo, the energy maximum in the ground state corresponds to the 90° rotation about the central double bond resulting in formation of a state with biradical-like character that is polarized along the molecule’s long axis [22]. The close structural similarity allows to expect a similar character

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

• terpene synthase family, showing similarity to haloacid dehalogenase (HAD)-like hydrolases [21]. Thus, we suspected that a related enzyme may be involved in the biosynthesis of the nanangenines, and used the amino acid sequence of AstC to probe the A. nanangensis genome. We also hypothesised that the acyl

1,5-Phosphonium betaines from N-triflylpropiolamides, triphenylphosphane, and active methylene compounds

• Vito A. Fiore,
• Chiara Freisler and
• Gerhard Maas

Beilstein J. Org. Chem. 2019, 15, 2603–2611, doi:10.3762/bjoc.15.253

• an intramolecular P···O coordination in the Z-isomers (vide supra), the chemical shift values by themselves (compare: δP = 18.7 ppm for (E)-Ph3P+–CH=CHMe Br− [31]) and the similarity of the chemical shifts for E/Z pairs indicate a tetracovalent rather than a pentacovalent phosphorus atom [28

Synthesis of novel sulfide-based cyclic peptidomimetic analogues to solonamides

• José Brango-Vanegas,
• Luan A. Martinho,
• Lucinda J. Bessa,
• Andreanne G. Vasconcelos,
• Alexandra Plácido,
• Alex L. Pereira,
• José R. S. A. Leite and
• Angelo H. L. Machado

Beilstein J. Org. Chem. 2019, 15, 2544–2551, doi:10.3762/bjoc.15.247

• , some observations can be made: (1) 9e is the only one among all the analogues derived from the acetaldehyde adduct that, regardless of the configuration of the stereogenic centres, has the same amino acid residue sequence found in solonamides; (2) despite the close similarity on the amino acid residue

Experimental and computational electrochemistry of quinazolinespirohexadienone molecular switches – differential electrochromic vs photochromic behavior

• Eric W. Webb,
• Jonathan P. Moerdyk,
• Kyndra B. Sluiter,
• Benjamin J. Pollock,
• Amy L. Speelman,
• Eugene J. Lynch,
• William F. Polik and
• Jason G. Gillmore

Beilstein J. Org. Chem. 2019, 15, 2473–2485, doi:10.3762/bjoc.15.240

• analysis of quinazolinespirohexadienone (QSHD) 3b (Figure 3) was qualitatively similar to the parent PSHDs 1a,b as expected based on structural similarity and computationally calculated molecular orbital diagrams (Figure 6 and Supporting Information File 1). Surprisingly, the Eored of the electrochemically

Ultrafast processes triggered by one- and two-photon excitation of a photochromic and luminescent hydrazone

• Alessandro Iagatti,
• Baihao Shao,
• Alberto Credi,
• Barbara Ventura,
• Ivan Aprahamian and
• Mariangela Di Donato

Beilstein J. Org. Chem. 2019, 15, 2438–2446, doi:10.3762/bjoc.15.236

• similarity of the successive evolution and of the transient spectra detected in the two cases indicates that a similar reactivity is induced upon one-photon and two-photon excitation, further confirming the two-photon photoswitching ability of hydrazone 1 already inferred by previous measurements [29]. Using