Synthesis of O⁶-alkylated preQ₁ derivatives

• Laurin Flemmich,
• Sarah Moreno and
• Ronald Micura

Beilstein J. Org. Chem. 2021, 17, 2295–2301, doi:10.3762/bjoc.17.147

• this end, robust synthetic routes towards O6-alkylated 7-aminomethyl-7-deazaguanines are urgently needed and reported here. Results and Discussion Biological and synthetic background Role of preQ1 in queuosine biosynthesis and gene regulation Queuine (Q base) is a derivative of guanine that is involved

Halides as versatile anions in asymmetric anion-binding organocatalysis

• Lukas Schifferer,
• Martin Stinglhamer,
• Kirandeep Kaur and
• Olga García Macheño

Beilstein J. Org. Chem. 2021, 17, 2270–2286, doi:10.3762/bjoc.17.145

• , the regulation of membrane potentials is one of such applications, in which the transport of chloride anions is facilitated by noncovalent hydrogen bonding interactions (Figure 1a) [6]. Noncovalent interactions are in fact one of the essential factors for the molecular recognition in enzymatic

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

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

• prenylation of fumigaclavine A leads to fumigaclavine C (19), the final product of fumigaclavine biosynthesis [159]. Biosynthesis of the intermediate festuclavine as well as fumigaclavines A–C is dependent on LaeA regulation [124]. Its numerous bioactive effects hold the potential for a pharmaceutical use

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

• previous studies are based on discrete glycogene promoter region analysis and reporter assays. These studies have established some notable TF–glycogene relationships, though they are limited to distinct cell types. Examples include the regulation of MGAT5 by ETS2 in NIH3T3 fibroblasts [6], control of the

• potential signaling pathways. This resulted in a relationship between cell signaling, TF activity regulation, and glycan structure changes (Supporting Information File 3, Tables S4 and S5). The data are presented as alluvial plots for the 29 cancer types (Supporting Information File 1). Here, the TFs were

• identified three large communities of TF–glycogene interactions. The largest community detected in this analysis had TFs enriched for RUNX3 signaling, IL-21 signaling, MECP2, and PTEN regulation. Overrepresentation glycosylation pathway analysis performed on the TFs in this community suggests that these TFs

A comprehensive review of flow chemistry techniques tailored to the flavours and fragrances industries

• Guido Gambacorta,
• James S. Sharley and
• Ian R. Baxendale

Beilstein J. Org. Chem. 2021, 17, 1181–1312, doi:10.3762/bjoc.17.90

• ., benzaldehydes) and low-molecular-weight enolate nucleophiles, therefore, temperature regulation is vital for selectivity. This requirement for strict temperature control makes aldol reactions highly suited to flow processing conditions. In 2008, Tanaka et al. [96] disclosed several examples of aldol reaction in

N-tert-Butanesulfinyl imines in the asymmetric synthesis of nitrogen-containing heterocycles

• Joseane A. Mendes,
• Paulo R. R. Costa,
• Miguel Yus,
• Francisco Foubelo and
• Camilla D. Buarque

Beilstein J. Org. Chem. 2021, 17, 1096–1140, doi:10.3762/bjoc.17.86

• , and regulation of the immune response. Starting from α-alkoxy aldimines ent-126, the utility of this methodology was also demonstrated in the synthesis of alkaloid (+)-cassine (130), isolated from the leaves and twigs of Cassia excelsa, displaying antimicrobial activity. Methylmagnesium bromide was

• compound (+)-L-733,060 (140), a potent neurokinin substance P receptor antagonist. This compound displays a wide variety of biological activities, including inhibition of neurogenic inflammation, blocking of pain transmission and regulation of immune response (Scheme 38). A stereoselective synthesis of ʟ

Synthesis of 10-O-aryl-substituted berberine derivatives by Chan–Evans–Lam coupling and investigation of their DNA-binding properties

• Peter Jonas Wickhorst,
• Mathilda Blachnik,
• Denisa Lagumdzija and
• Heiko Ihmels

Beilstein J. Org. Chem. 2021, 17, 991–1000, doi:10.3762/bjoc.17.81

• monitoring of the temperature-dependent Förster resonance energy transfer (FRET) between the dyes [46]. The particular oligonucleotide sequences were chosen because they are known to be involved in biologically relevant processes, namely in the transcription regulation of myc (FmycT) [47][48], kit (FkitT

Synthesis and properties of oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing adenine, guanine, or 5-methylcytosine nucleobases

• Naohiro Horie,
• Takao Yamaguchi,
• Shinji Kumagai and
• Satoshi Obika

Beilstein J. Org. Chem. 2021, 17, 622–629, doi:10.3762/bjoc.17.54

• (ASOs) modified with 2',4'-bridged nucleic acid/locked nucleic acid (2',4'-BNA/LNA; Figure 1) are now widely used for gene regulation in vitro and in vivo because 2',4'-BNA/LNA greatly increases the affinity toward the target RNAs, thus enhancing the efficacy of the modified ASOs [1][2][3][4][5][6

Valorisation of plastic waste via metal-catalysed depolymerisation

• Francesca Liguori,
• Carmen Moreno-Marrodán and
• Pierluigi Barbaro

Beilstein J. Org. Chem. 2021, 17, 589–621, doi:10.3762/bjoc.17.53

• water and has a melting point of 250 °C and a glass transition temperature Tg of 76 °C [162][163]. It was suggested that under certain circumstances, PET may leach phthalates [164], which are known for potentially adverse health effects and subject to ECHA regulation restrictions [165][166]. Coupled

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

• thermodynamic stabilization of proteins [29][30][31]. The regulation of the proline content in proteins is an evolutionary strategy for environmental adaptation in extremophilic organisms. Proline is of a higher abundance in the proteomes of thermophilic organisms (organisms living at a high temperature) and of

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

• kinetic information for complex systems can be obtained by 19F NMR. Another rapidly expanding and particularly challenging area of research where 19F NMR has found new applications is in the field of intrinsically disordered proteins (IDPs). IDPs play a key role in cell signalling and regulation processes

• important role in key biological processes such as gene expression and regulation [94][95], telomere length maintenance [96][97][98], transcription and DNA replication [99][100]. Investigation of the specific G-quadruplex structures associated with these biological events is therefore essential to

Insight into functionalized-macrocycles-guided supramolecular photocatalysis

• Minzan Zuo,
• Krishnasamy Velmurugan,
• Kaiya Wang,
• Xueqi Tian and
• Xiao-Yu Hu

Beilstein J. Org. Chem. 2021, 17, 139–155, doi:10.3762/bjoc.17.15

• cavity and strong bonding ability with various guests, macrocycles function as a tool to promote the specific conversion of substrates. On the one hand, the close inclusion of substrates by macrocycles can realize the intervention in, and regulation of the reaction, and thereby developing a new type of

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• functionality and the corresponding pathways. Important roles of PPIs include hormone reception [2], protease inhibition [3], antibody–antigen complexes [4], gene regulation [5], and large biomolecular assemblies [6]. PPI identification and prediction are important for targeting anticancer strategies [7

• because the methods normally neglect self-interactions. The advantages of homooligomeric complexes over monomer proteins include an increase in the diversity of the functions [61], allosteric regulation [62], protection against denaturation [63], and the oligomers being able to form without increasing the

• conserved than in non-isologous interfaces [66]. Furthermore, homooligomeric complexes have more disorder regions than heterooligomeric complexes, and thereby an increasing allosteric regulation [67]. Jayashree et al. [68] analysed datasets of 45 transient protein–protein complex structures and analysed the

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

• demonstrated that the production of these NRPs varies among coisolated B. subtilis environmental strains due to missing core genes or potentially altered gene regulation, highlighting the existing natural diversity of SM production in this species [51]. In this study, we focus on soil-derived semisynthetic

Fluorine effect in nucleophilic fluorination at C4 of 1,6-anhydro-2,3-dideoxy-2,3-difluoro-β-D-hexopyranose

• Danny Lainé,
• Vincent Denavit,
• Olivier Lessard,
• Laurie Carrier,
• Charles-Émile Fecteau,
• Paul A. Johnson and
• Denis Giguère

Beilstein J. Org. Chem. 2020, 16, 2880–2887, doi:10.3762/bjoc.16.237

• ; polyfluorinated carbohydrates; polyfluoroalditol analogues; Introduction The biological significance of carbohydrates includes, but are not limited to, immune regulation, infection, and cancer metastasis. Research in the field of molecular biology allowed the discovery of glycomimetics to study various

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

• Jennifer Frommer and
• Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

• entities in our ribozyme design projects [21][22]. Strikingly, the C8-position of a specific adenosine in the loop region of the flavine mononucleotide (FMN) aptamer is a highly favorable position for covalent attachment of FMN to study regulation of an FMN dependent hairpin aptazyme in response to RNA

Using multiple self-sorting for switching functions in discrete multicomponent systems

• Amit Ghosh and
• Michael Schmittel

Beilstein J. Org. Chem. 2020, 16, 2831–2853, doi:10.3762/bjoc.16.233

• + + [Cu2(40)2]2+ + 2 × [Cu(42)]+ (= SelfSORT-II). With SelfSORT-I containing the heterocycle 42, a known organocatalyst, and SelfSORT-II holding the potential click catalyst [Cu(42)]+, it was speculated that both networked states could be catalytically active thus allowing the ON/OFF regulation of a dual

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

• . Krambeck Kiyoko F. Aoki-Kinoshita Nathan E. Lewis See end of main text. 10.3762/bjoc.16.215 Abstract Systems glycobiology aims to provide models and analysis tools that account for the biosynthesis, regulation, and interactions with glycoconjugates. To facilitate these methods, there is a need for a

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• and arginines occur as posttranslational modifications in proteins and are particularly important in histones, where they contribute to the regulation of chromatin structure and thus gene expression. The calixarenes can successfully bind to methylated histone tails and thus inhibit the binding of

Conformational preferences of fluorine-containing agrochemicals and their implications for lipophilicity prediction

• Daniela Rodrigues Silva,
• Joyce K. Daré and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2020, 16, 2469–2476, doi:10.3762/bjoc.16.200

• other variables, recent events have shown signs of recovery [1]. Currently, the agrochemical industry focuses on introducing new efficient and more environmentally friendly products, that attend the new regulation requirements, for replacing those agrochemicals that were banned due to either their

Convenient access to pyrrolidin-3-ylphosphonic acids and tetrahydro-2H-pyran-3-ylphosphonates with multiple contiguous stereocenters from nonracemic adducts of a Ni(II)-catalyzed Michael reaction

• Alexander N. Reznikov,
• Dmitry S. Nikerov,
• Anastasiya E. Sibiryakova,
• Victor B. Rybakov,
• Evgeniy V. Golovin and
• Yuri N. Klimochkin

Beilstein J. Org. Chem. 2020, 16, 2073–2079, doi:10.3762/bjoc.16.174

• to the possibility of creating enantiomerically pure compounds with several stereocenters through the directed regulation of diastereoselectivity in subsequent transformations, which can be realized as stepwise or cascade processes. Due to this reason, the Michael reaction was successfully used over

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

• neurons; the regulation and functioning of these processes is still not satisfactorily understood [1][2][3][4]. The MT cytoskeleton is a finely tuned complex system that is highly conserved through evolution. Direct genetic modifications of tubulin that affect its functions risk causing a diversity of

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

• component analysis [140], qPCR/proteomics [141], and iterative grid search [142] to troubleshoot and guide the tuning of the promoter strengths and copy numbers of each module/enzyme (Figure 11b). Toxicity of biosynthetic intermediates, endogenous regulation, and stability of genetic constructs are the main

• the novel 1-deoxy-ᴅ-xylulose 5-phosphate pathway (nDXP) [145] and the isopentenol utilization pathway (IUP) [146], that bypass (part of) the natural MVA or MEP pathway were designed to circumvent this complex endogenous interaction and regulation (Figure 11a). Lastly, integration of pathways into the

Photoreversible stretching of a BAPTA chelator marshalling Ca²⁺-binding in aqueous media

• Aurélien Ducrot,
• Arnaud Tron,
• Robin Bofinger,
• Ingrid Sanz Beguer,
• Jean-Luc Pozzo and
• Nathan D. McClenaghan

Beilstein J. Org. Chem. 2019, 15, 2801–2811, doi:10.3762/bjoc.15.273

• concentrations potentially allows greater control over certain biological functions. In order to permit remote regulation of Ca2+, a selective BAPTA-type synthetic receptor / host was integrated with a photoswitchable azobenzene motif, which upon photoirradiation would enhance (or diminish) the capacity to bind

• a water-soluble molecule which has a high affinity and selectivity for calcium, allowing binding of physiological levels of calcium, whose binding can be switched reversibly as efficiently as possible both in terms of affinity and quantum yield. In principle this would offer real-time regulation of