Cyclodextrin-based rotaxanes for polymer materials: challenge on simultaneous realization of inexpensive production and defined structures

• Yosuke Akae

Beilstein J. Org. Chem. 2024, 20, 3026–3049, doi:10.3762/bjoc.20.252

• molecule a good host molecule that interacts with guest molecules via hydrophobic interactions. To maximize the host–guest hydrophobic interaction, suitable guest molecules for CDs generally fit well with their cavity sizes. Put differently, α-CD fits well with a linear aliphatic chain, β-CD does with a

• substituted benzene ring, and γ-CD can host further bigger guest molecules, such as pyrene or two aliphatic chains, in one cavity. The ability of CD to form an inclusion complex structure is drastically affected by the cavity size or the modification strategy for the hydroxy groups on CD. To evaluate the

Tailored charge-neutral self-assembled L₂Zn₂ container for taming oxalate

• David Ocklenburg and
• David Van Craen

Beilstein J. Org. Chem. 2024, 20, 3007–3015, doi:10.3762/bjoc.20.250

• selectively over other dicarboxylates by maintaining the receptor stability. This study highlights the importance of a highly modular receptor design so that tailored hosts can be designed to tackle the recognition of challenging competitive analytes. Keywords: anion recognition; charge-neutral host

• this issue is to exchange the counteranions with less competitive ones, such as replacing tetrafluoroborate with tetrakis[3,5-bis(trifluoromethyl)phenyl]borate [64]. Alternatively, an emerging solution is the utilization of ligand–metal combinations that self-assemble into charge-neutral host systems

• be volatile to simplify complex purification. Second, the solubility of the neutral host complexes usually needs to be improved by the installation of solubility groups, which must be considered during ligand design. The biggest strength of metallocages and metallocontainers, whether they are

4,6-Diaryl-5,5-difluoro-1,3-dioxanes as chiral dopants for liquid crystal compositions

• Maurice Médebielle,
• Peer Kirsch,
• Jérémy Merad,
• Carolina von Essen,
• Clemens Kühn and
• Andreas Ruhl

Beilstein J. Org. Chem. 2024, 20, 2940–2945, doi:10.3762/bjoc.20.246

• appears, the more efficient is the induction of chirality in a nematic host. Additionally, the location of the chiral substructure within the dopant molecule seems to play a role. A more ‘central’ location within in the mesogenic core structure corresponds to a higher HTP of the resulting chiral compound

• -1,3-diphenyl-1,3-propanediol (rac-2). These enantiomers were then evaluated as chiral dopants using two commercially available liquid crystal host mixtures (Host 1 and Host 2 from Merck KGaA) (Scheme 2). Results and Discussion Racemic anti-2,2-difluoro-1,3-diol rac-2 was easily prepared through a

• two achiral nematic host mixtures (Host 1 and Host 2 from Merck) (Table 1). (R,R)-3 and (S,S)-3 with a more liquid crystal-like shape have higher HTP [16 µm−1 (Host 1), 38 µm−1 (Host 2)] than the dimethylacetal analogues (R,R)-4 and (S,S)-4 [8 µm−1 (Host 1), 15 µm−1 (Host 2)]. The difference between

Investigation of a bimetallic terbium(III)/copper(II) chemosensor for the detection of aqueous hydrogen sulfide

• Parvathy Mini,
• Michael R. Grace,
• Genevieve H. Dennison and
• Kellie L. Tuck

Beilstein J. Org. Chem. 2024, 20, 2818–2826, doi:10.3762/bjoc.20.237

• program, was used to determine the binding constant of Cu2+ ions to Tb.1 in both Tris-HCl buffer and HEPES buffer. The host–guest binding modes (1:1, 1:2 or 2:1) were evaluated using the luminescent data (λex = 250 nm, λem = 450–650 nm) from the respective titration experiments. In both cases the 1:1 host

• ), anion/sulfur compound (50 µM) and Na2S (15 µM), n = 3. Chemical structure and mode of action of [Tb(DPA-N3)3]3− for detection of H2S(g) [11]. Synthesis of Tb.1. Binding constant determination for the 1:1 host–guest interaction (Tb.1 + Cu2+ ions), determined using supramolecular.org [18]. Supporting

Deciphering the mechanism of γ-cyclodextrin’s hydrophobic cavity hydration: an integrated experimental and theoretical study

• Stiliyana Pereva,
• Stefan Dobrev,
• Tsveta Sarafska,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2024, 20, 2635–2643, doi:10.3762/bjoc.20.221

• Sciences, 1113 Sofia, Bulgaria, University of Chemical Technology and Metallurgy, 8 St. Kliment Ohridski Blvd, 1756 Sofia, Bulgaria 10.3762/bjoc.20.221 Abstract Cyclodextrins (CDs) are host systems with inherent capability for inclusion complex formation with various molecular entities, mostly hydrophobic

• substances. Host CDs are highly accommodative to water molecules as well and usually contain water in the native state. There is still an ongoing discussion on both the total number of water molecules and their preferred binding position inside the cavities of the CDs. To understand the hydration/dehydration

• residues, but α-CDs with 6 and γ-CDs with 8 glucopyranose units, respectively, have also been widely used as potent host structures encapsulating various substances of interest to science and industry. The shape of CDs is toroid-like with one opening (lower rim) wider than the other (upper rim). These

Cell-free protein synthesis with technical additives – expanding the parameter space of in vitro gene expression

• Tabea Bartsch,
• Stephan Lütz and
• Katrin Rosenthal

Beilstein J. Org. Chem. 2024, 20, 2242–2253, doi:10.3762/bjoc.20.192

• biocatalysts [1][2]. The open environment allows easy manipulation of the protein synthesis [3] and coupling to subsequent enzyme activity assays, e.g., for substrate screening [4][5]. The CFPS system is advantageous for proteins that are difficult to express in a viable host cell, e.g., due to toxic effects

Natural resorcylic lactones derived from alternariol

• Joachim Podlech

Beilstein J. Org. Chem. 2024, 20, 2171–2207, doi:10.3762/bjoc.20.187

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• interaction with host proteins [5][6]. Notably, the complexity of the glycome far surpasses that of the genome, transcriptome, and proteome, not only due to the structural and conformational diversity of glycans, whose synthesis is not template driven, but also due to their dynamic nature [5][6]. Although

• for humans, animals and plants, including drug design [14][15], vaccine development [15][16] and numerous other possibilities in the field of carbohydrate chemistry and biology. Notably, the regulation of the host immune response is often mediated by glycans, particularly through their recognition by

• class of GBP is represented by anti-carbohydrate antibodies, that are generally produced by the host organism for example against bacterial, fungal, and viral carbohydrates [35]. Given the wide variety of biological processes influenced by the protein–glycan interplay, an increasing attention has been

The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)

• Cristina Martini,
• Muhammad Idham Darussalam Mardjan and
• Andrea Basso

Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162

• a [1,5]-H shift [19], indazolo[3’,2’:2,3]imidazo[1,5-c]quinazolin-6(5H)-one 18 (Scheme 7) [20]. The favorable host–guest interaction between 14 and the reactants (demonstrated by 2D NMR and FTIR spectroscopy as well as by scanning electron micrography), combined with the acidity of the succinyl

Discovery of antimicrobial peptides clostrisin and cellulosin from Clostridium: insights into their structures, co-localized biosynthetic gene clusters, and antibiotic activity

• Moisés Alejandro Alejo Hernandez,
• Katia Pamela Villavicencio Sánchez,
• Rosendo Sánchez Morales,
• Karla Georgina Hernández-Magro Gil,
• David Silverio Moreno-Gutiérrez,
• Eddie Guillermo Sanchez-Rueda,
• Yanet Teresa-Cruz,
• Brian Choi,
• Armando Hernández Garcia,
• Alba Romero-Rodríguez,
• Oscar Juárez,
• Siseth Martínez-Caballero,
• Mario Figueroa and
• Corina-Diana Ceapă

Beilstein J. Org. Chem. 2024, 20, 1800–1816, doi:10.3762/bjoc.20.159

• -peptide accumulation did not impact the expression host. This assumption was made due to reports of auto-proteolysis for other lanthipeptides during production in this cell system. This leads us to believe that at least a few mature peptides might have been present. Despite this, the growth curves of the

• . These peptides were expressed in an E. coli host and produced in sufficient concentrations to perform bioactivity assays. The C39-associated domain was purified to facilitate the transformation from pre-peptide to the mature configuration. The mature clostrisin and cellulosin exhibited antimicrobial

Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty

• Weimao Zhong and
• Vinayak Agarwal

Beilstein J. Org. Chem. 2024, 20, 1635–1651, doi:10.3762/bjoc.20.146

• enzyme RagaA7 was produced in a Bacillus subtilis host and characterized to be a neoagarotetraose-producing GH-16 family endo-type β-agarase with a pH and temperature optima being 7.0 and 50 °C, respectively. Another thermostable neoagarotetraose-producing GH-16 endo-type β-agarase rAgaA was identified

• and cloned from deep-sea-derived Microbulbifer sp. JAMB-A94 with pH and temperature optima being 7.0 and 55 °C, respectively [26]. The recombinant enzyme was likewise produced using a B. subtilis host. The crystal structure of the catalytic domain was determined to show a β-jelly roll fold with

• –12 against Staphlyococcus aureus indicated that 7 and 12 were bacteriostatic, while 9 and 10 were bactericidal. Compound 9 was also active towards another two commensal Gram-positive bacteria Bacillus sp. and Planococcus sp. isolated from the host sponge. Compound 9 can be detected in situ in the

Benzylic C(sp³)–H fluorination

• Alexander P. Atkins,
• Alice C. Dean and
• Alastair J. J. Lennox

Beilstein J. Org. Chem. 2024, 20, 1527–1547, doi:10.3762/bjoc.20.137

• of a host of functional groups [68]. This approach can also be applied for nucleophilic fluorination of benzylic substrates. This occurs via sequential electron-transfer and proton-transfer steps, as outlined in Figure 35 [87]. Single-electron oxidation of benzylic substrate I at the anode generates

Photoswitchable glycoligands targeting Pseudomonas aeruginosa LecA

• Yu Fan,
• Ahmed El Rhaz,
• Stéphane Maisonneuve,
• Emilie Gillon,
• Maha Fatthalla,
• Franck Le Bideau,
• Guillaume Laurent,
• Samir Messaoudi,
• Anne Imberty and
• Juan Xie

Beilstein J. Org. Chem. 2024, 20, 1486–1496, doi:10.3762/bjoc.20.132

• bacterial infections occur by adhesion to host tissues through receptor–ligand interaction between bacterial carbohydrate-binding proteins (lectins) and oligosaccharides at the host cell surface. Pseudomonas aeruginosa (PA), a Gram-negative, opportunistic and ubiquitous environmental bacterium, is known as

• biosynthetic pathways of the bacterium [2][3]. The soluble lectins LecA and LecB produced by PA play a key role in the infection [4]. PA LecA is demonstrated to be crucial for biofilm formation and internalization, while the extracellular LecB plays a key role in bacterial adhesion to the host and biofilm

Bioinformatic prediction of the stereoselectivity of modular polyketide synthase: an update of the sequence motifs in ketoreductase domain

• Changjun Xiang,
• Shunyu Yao,
• Ruoyu Wang and
• Lihan Zhang

Beilstein J. Org. Chem. 2024, 20, 1476–1485, doi:10.3762/bjoc.20.131

• cannot be directly inferred from the final product structure, and we discuss these KRs separately based on their module types. The curated 1,762 KR sequences were grouped into different types based on their product structure and the taxonomy of their host strains (Figure 2a). Among the KR sequences we

• fingerprint motifs and deduced from product structure identified by chemical methods are shown on the right. (a) Classification and distribution of the collected KR sequences according to host taxonomy, module types, and stereoconfigurations of the product. Here, “EDH” and “ZDH” respectively denote the E

Synthesis of cyclic β-1,6-oligosaccharides from glucosamine monomers by electrochemical polyglycosylation

• Md Azadur Rahman,
• Hirofumi Endo,
• Takashi Yamamoto,
• Shoma Okushiba,
• Norihiko Sasaki and
• Toshiki Nokami

Beilstein J. Org. Chem. 2024, 20, 1421–1427, doi:10.3762/bjoc.20.124

• reactions. Therefore, electrochemical polymerizations can be utilized for selective synthesis. Cyclic oligosaccharides are an important class of host molecules, and some natural cyclic oligosaccharides are produced by enzymatic processes. However, the corresponding chemical syntheses are still primitive [6

Diameter-selective extraction of single-walled carbon nanotubes by interlocking with Cu-tethered square nanobrackets

• Guoqing Cheng and
• Naoki Komatsu

Beilstein J. Org. Chem. 2024, 20, 1298–1307, doi:10.3762/bjoc.20.113

• Guoqing Cheng Naoki Komatsu Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan 10.3762/bjoc.20.113 Abstract We have been working with carbon nanotube separation through host–guest chemistry. Herein, a new macrocyclic host molecule, Cu-tethered

• host–guest chemistry has advantages in terms of the rational design of the host molecules to target specific structures and the thorough removal of the dispersants, host molecules in our case, to recover pristine carbon nanotubes (CNTs) after separation. Moreover, the association constants of the

• complexation between host molecules and SWNTs are strongly related to the molecular structures, making it possible to tune the binding affinity [8]. The host molecules we employed so far for CNT separation through molecular recognition have been developed as “nanotweezers” [9], “nanocalipers” [10] and

Spin and charge interactions between nanographene host and ferrocene

• Akira Suzuki,
• Yuya Miyake,
• Ryoga Shibata and
• Kazuyuki Takai

Beilstein J. Org. Chem. 2024, 20, 1011–1019, doi:10.3762/bjoc.20.89

• -magnetic guest molecule to activated carbon fibers (ACFs) as a nanographene-based host having localized spins originating from zigzag edges of graphene. The introduction of the guest molecule was confirmed by FTIR for ACFs-FeCp2 introduced at 55 (150) °C (FeCp2-ACFs-55(150)). The appearance of satellite

• Fe2p peaks and the increase in shake-up peak intensity of the C1s in the XPS spectrum proved the emergence of charge-transfer host–guest interaction in FeCp2-ACFs-150, supported by the red-shift of the G-band in the Raman spectrum. The six-times enhancement in the spin concentration in FeCp2-ACFs-150

• compared with ACFs indicates the spin magnetism of the non-magnetic guest FeCp2+ molecule induced by a charge-transfer host–guest interaction in the nanographene host. The larger ESR linewidth than that expected from the dipolar interaction estimated by the localized spin concentration suggests the

Enhancing structural diversity of terpenoids by multisubstrate terpene synthases

• Min Li and
• Hui Tao

Beilstein J. Org. Chem. 2024, 20, 959–972, doi:10.3762/bjoc.20.86

• selective sesqui-TSs failed to transform 104–112. After further modification with cytochrome P450 CYP720B1 in the yeast host, 28 noncanonical terpenoids were generated, 10 of them are shown in Figure 8c (113–122) [58]. Notably, the widespread biosynthesis of C16 terpenoids was reported in a recent study in

Monitoring carbohydrate 3D structure quality with the Privateer database

• Jordan S. Dialpuri,
• Haroldas Bagdonas,
• Lucy C. Schofield,
• Phuong Thao Pham,
• Lou Holland and
• Jon Agirre

Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83

• a whole host of other interesting pieces of information. In an analogous way to looking at glycosylation over time, the type and validity of carbohydrates in the PDB can also be observed over time. The statistics page available alongside the Privateer Web App contains up-to-date plots of validation

Confirmation of the stereochemistry of spiroviolene

• Yao Kong,
• Yuanning Liu,
• Kaibiao Wang,
• Tao Wang,
• Chen Wang,
• Ben Ai,
• Hongli Jia,
• Guohui Pan,
• Min Yin and
• Zhengren Xu

Beilstein J. Org. Chem. 2024, 20, 852–858, doi:10.3762/bjoc.20.77

• alteration of stereochemical assignment of spiroviolene would have consequences for a different mechanistic proposal. We herein report the production of spiroviolene (1) in a heterologous host by taking advantage of an artificial isopentenol utilization pathway [21][22][23][24][25][26], and confirm its

Synthesis and characterization of water-soluble C₆₀–peptide conjugates

• Yue Ma,
• Lorenzo Persi and
• Yoko Yamakoshi

Beilstein J. Org. Chem. 2024, 20, 777–786, doi:10.3762/bjoc.20.71

• either 1) covalent functionalization of the fullerene surface with polar moieties or 2) complexation with water-soluble host molecules or polymers. Related to the former approach, the Nakamura group [11], Wudl group [12], and Hirsch group [13] reported initial work in the early 1990s on water-soluble C60

Methodology for awakening the potential secondary metabolic capacity in actinomycetes

• Shun Saito and
• Midori A. Arai

Beilstein J. Org. Chem. 2024, 20, 753–766, doi:10.3762/bjoc.20.69

• -acyltransferase polyketide synthase biosynthetic gene cluster sdl (80 kb) from Streptomyces sp. B59 was cloned and transferred into a heterologous host, Streptomyces albus J1074, resulting in the production of a class of polycyclic macrolide shuangdaolides A (1), B, and D and dumulmycin (2) [29]. Furthermore

• , genome mining of the marine actinomycete Streptomyces seoulensis A01 enabled the identification of a giant type I polyketide synthase gene cluster (asm) [30]. Heterologous expression of the cryptic asm cluster using a bacterial artificial chromosome vector in a heterologous host led to the production of

• HSMs from Streptomyces sp. CA40. Palmu et al. discovered gaudimycins by heterologous expression of the biosynthetic gene clusters pga or cab, which were silent in the producing strain Streptomyces sp. PGA64 or Streptomyces sp. H021 relative to another host, Streptomyces lividans TK24 [73]. Resistomycin

Genome mining of labdane-related diterpenoids: Discovery of the two-enzyme pathway leading to (−)-sandaracopimaradiene in the fungus Arthrinium sacchari

• Fumito Sato,
• Terutaka Sonohara,
• Shunta Fujiki,
• Akihiro Sugawara,
• Yohei Morishita,
• Taro Ozaki and
• Teigo Asai

Beilstein J. Org. Chem. 2024, 20, 714–720, doi:10.3762/bjoc.20.65

• and AsCPS as described below. First, we examined the heterologous expression of AsPS and AsCPS in the heterologous host Aspergillus oryzae NSAR1. These two genes along with AsGGS were amplified and integrated into the pUARA2 vector, yielding the plasmid pUARA2-AsGGS/AsCPS/AsPS (Table S1 in Supporting

• Supporting Information File 1). We also examined the expression of several oxidoreductases in the flanking region in the same host strain, but the possible products other than 1 were not clearly observed (data not shown). Further characterization of oxidative modifications is in progress and will be reported

• peaks were not related to diterpenoids and were likely derived from the host strain. B) Chemical structure of (−)-sandaracopimaradiene (1)). GC–MS analysis of the enzymatic reactions. A) Extracted ion chromatograms (EICs) at m/z 272 of the extracts from the reaction mixture of AsPS and AsCPS; AsPS and

Production of non-natural 5-methylorsellinate-derived meroterpenoids in Aspergillus oryzae

• Jia Tang,
• Yixiang Zhang and
• Yudai Matsuda

Beilstein J. Org. Chem. 2024, 20, 638–644, doi:10.3762/bjoc.20.56

• four enzymes in the Aspergillus oryzae NSARU1 strain [19]. Consequently, the A. oryzae transformant yielded two metabolites 1 and 2, which were absent in the host strain (Figure 2B, traces i and ii). Although we were unable to isolate compounds 1 and 2 because of their instability, high-resolution mass

• keto–enol tautomerization to form 8 (Figure S2, Supporting Information File 1). Incubation of 7 with the host A. oryzae strain indeed resulted in the formation of 8 (Figure S3, Supporting Information File 1), confirming that InsA7 is not involved in the enoylreduction. Our findings revealed that four

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

• will be discussed as examples of engineering biosynthetic pathways and key enzymes involved in fungal meroterpenoid biosynthesis. Furthermore, a construction of the artificial biosynthetic pathway composed of the fungal meroterpenoids pathway and the pathway from other species, in fungal host

•  2). In 2012, the biosynthesis of terretonin, a meroterpenoid derived from compound 5 and produced by the filamentous fungus Aspergillus terreus, was investigated [8][9] using the heterologous expression host Aspergillus oryzae strain NSAR1, a filamentous fungus developed by multiple mutations of

• , the combinatorial biosynthesis of diterpene pyrones, derived from a pyrone skeleton and a C20 terpenoid skeleton, has been achieved by combining multiple biosynthetic pathways in a fungal heterologous expression host [16]. First, subA (PKS), subC (PT), subD (GGPP synthase), subE (FMO), and subB (CYC