Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• (resistivity ≥ 18 MΩ cm) and filtered through a membrane filter (0.45 µm pore size). K-phosphate-buffer (22AG, a2): 25 mM K2HPO4, 70 mM KCl; pH 7.0; Na-cacodylate buffer (F21T, Fa2T, FmycT, FkitT, and FkrasT): 90 µM LiCl, 10 mM KCl, 10 mM Na(CH3)2AsO2 × 3H2O, pH 7.2–7.3. The K-phosphate buffer solutions and

• in K+-phosphate buffer) was used as a cosolvent. For the CD spectra, solutions of G4-DNA in K+-phosphate butter and the ligands in buffer/DMSO were recorded after an equilibration time of 30 min. For the thermal DNA denaturation analyses stock solutions of the ligand (20 µM) and the G4-DNA (50 µM) in

• ; cDNA = 200 μM) in K+-phosphate buffer (pH 7.0) with 10% v/v DMSO). The arrows indicate the development of the absorption or emission bands with increasing DNA concentration. Insets: Plots of Abs./Abs.0 and I/I0, respectively, versus cDNA/c3c. Inset B1: Picture of the emission color and intensity of

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• electrostatic and (C–H)···O− hydrogen bonds involving the acidic proton at the 2-position of the imidazolium moiety to bind to ATP and other phosphate analytes [46]. A number of cyclophanes and tweezers [53][54][55][56] have been reported possessing the following common structural features: a) the presence of

• of anthracene tagged imidazolium receptors responded to ATP through an amplified fluorescence quenching [60]. Based on these results, we wanted to develop similar self-assembled systems which would show a “turn-on” response in the presence of ATP or other phosphate analytes. The current design of

• issues of a sensor design is the selectivity for an analyte in comparison to other interfering analytes. Therefore, we carried out selectivity studies with the multivalent sensors for ATP over the other adenosine phosphates ADP and AMP, PPi and inorganic phosphate (Pi). We employed PBIm12 (75 µM) for

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes

• Lena Reinke,
• Julia Bartl,
• Marcus Koch and
• Stefan Kubik

Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219

• water/methanol 1:2 (v/v). These anions caused the bright red solutions of the nanoparticles to change their color because of nanoparticle aggregation followed by precipitation, whereas halides or oxoanions such as sulfate, nitrate, or carbonate produced no effect. The sensitivity of phosphate sensing

• preferred binding mode of zinc(II)–dipicolylamine complexes with phosphate anions which involves binding of the anion between two metal centers. This work thus provided information on how the behavior of mixed monolayer-protected gold nanoparticles is affected by multivalent interactions, at the same time

• . The extent of aggregation of AuNPs containing peripheral phosphate groups in the presence of an externally added low molecular weight bis(zinc(II)–DPA) complex could be controlled by diphosphate anions, which in turn allowed correlating the optical properties of the nanoparticle solution with 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

• represent known modifications (Table 3: MR1). For example, “A[2P]” represents a galactose with its second position modified by a phosphate. However, this specific modification may not always be known. Therefore, in addition to “ [] ” as exact modifications, we recommended using the “ $ ” sign to represent a

Anion exchange resins in phosphate form as versatile carriers for the reactions catalyzed by nucleoside phosphorylases

• Julia N. Artsemyeva,
• Ekaterina A. Remeeva,
• Tatiana N. Buravskaya,
• Irina D. Konstantinova,
• Roman S. Esipov,
• Anatoly I. Miroshnikov,
• Natalia M. Litvinko and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2020, 16, 2607–2622, doi:10.3762/bjoc.16.212

• Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 GSP-7, Moscow B-437, Russian Federation 10.3762/bjoc.16.212 Abstract In the present work, we suggested anion exchange resins in the phosphate form as a source of phosphate, one of the

• found that phosphorolysis of uridine, thymidine, and Ara-U in the presence of Dowex® 1X8 (phosphate; Dowex-nPi) proceeded smoothly in the presence of magnesium cations in water at 20–50 °C for 54–96 h giving rise to quantitative formation of the corresponding pyrimidine bases and PF-1Pis. The resulting

• letter to the editor Kalckar reported for the first time that specific inosine nucleosidase from rat liver catalyzes the reversible reaction “inosine + phosphate ⇌ hypoxanthine + ribose-1-phosphate”: the equilibrium of this reaction in water at pH 6.5 is displaced to the nucleoside synthesis. Moreover

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

• formed between the charged head group of the encapsulated amino acid and one of the phosphate moieties attached to the tweezer’s central benzene ring [5]. Supramolecular tweezers have not only proven to be interesting tools to modulate protein–protein interactions [6][7], reverse amyloid fibril formation

• severely destabilized by the mutation, while the stability of the wild-type tetramer was not affected. The binding of several anionic supramolecular ligands to the model protein ubiquitin was compared using NMR by Crowley’s lab [82]. These ligands, including phosphate tweezers (CLR01), sulfonatocalix[4

• though a total of 6 basic residues are present [80]. Most of the identified patches bound by the tweezers contain two basic residues. QM/MM calculations [7] show that one of these residues is bound inside the tweezer cavity while the second residue can form a salt bridge with the second phosphate group

Recent developments in enantioselective photocatalysis

• Callum Prentice,
• James Morrisson,
• Andrew D. Smith and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2020, 16, 2363–2441, doi:10.3762/bjoc.16.197

• "Brønsted acid catalysis", yet interestingly their conjugate bases can also be used as efficient hydrogen bonding catalysts. Knowles et al. showed that a tricatalytic system using chiral phosphate 235 can mediate the deracemisation of cyclic urea rac-236 (Scheme 36) [97]. The proposed mechanism involves a

• decarboxylation. The excited photocatalyst is reductively quenched by 242• to give the imine intermediate 243. Indoles 241 and 243 are then brought together by the chiral phosphate catalyst 244 and the lithium counterion in a hydrogen-bonded complex 245 to give the desired enantioenriched products 246 in

• -centred radical. The previous example used a chiral cation to induce enantioselectivity, while Luo et al. used a chiral phosphate base 251 as a counterion to Mes-Acr+ (Scheme 40) [101]. With this combination, they successfully developed an enantioselective variant of Nicewicz’s hydroetherification

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• performed for the conjugate Dex-1b in water and in phosphate-buffered saline (PBS) solution (Figure 4A, see Experimental). Nonfunctionalized dextran showed very low scattering and poor autocorrelation functions as there is limited association among dextran chains and single chains have limited scattering

• (hydrodynamic diameter) of the nanoparticles in H2O was 198 ± 42 nm (Figure 4A, black). The measurements were performed also in phosphate-buffered saline (PBS) solution to evaluate a potential additional aggregation in cell medium. The aggregates were stable in solution and did not precipitate over time. The

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

• large cohort glycomic studies, where the comparison of glyco-profiles is important to clinical studies, cellular biology, and glycobiology in general. Experimental Materials Sodium phosphate (Merck) and glycine·HCl (Merck) were purchased from Merck. Tris-HCl and EX-CELL Advanced CHO Fed-batch medium

• , GE Healthcare, USA). The columns were equilibrated and washed via centrifugation (100g, 30 s) with 20 mM sodium phosphate (pH 7.0). The sample was loaded to each column (maximum volume of 600 µL) and incubated end-over-end for 10 min. The column was washed with 20 mM sodium phosphate (pH 7.0) via

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

• detected in the reaction even after 72 h in the presence of 1 equiv of potassium phosphate or carbonate with TEBAC (0.1 equiv, Table 1, entries 4 and 5). If potassium fluoride or cesium carbonate were used as a base, the initial phosphonate 6e was consumed in a few hours, but unidentified products were

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

• )pyrrole (GCP) cation 1 as a synthetic analogue of the guanidinium cations, somehow a “super-guanidinium” conceived to drive “arginine magic” [20][21] to the extreme (Figure 1) [23]. The power of the Schmuck cation to bind carboxylate and phosphate anions in competitive water has several origins [22

Synthesis of monophosphorylated lipid A precursors using 2-naphthylmethyl ether as a protecting group

• Jundi Xue,
• Ziyi Han,
• Gen Li,
• Khalisha A. Emmanuel,
• Cynthia L. McManus,
• Qiang Sui,
• Dongmian Ge,
• Qi Gao and
• Li Cai

Beilstein J. Org. Chem. 2020, 16, 1955–1962, doi:10.3762/bjoc.16.162

• ][8][9]. Various lipid A derivatives have since been synthesized to dissociate endotoxic effects from beneficial immunomodulatory activities. Lipid X, 2-N;3-O-di[(R)-3-hydroxytetradecanoyl]-ᴅ-glucosamine-1-phosphate, is the naturally occurring early monosaccharide precursor of lipid A biosynthesis

• showed that synthetic lipid X could be contaminated with small amounts of disaccharide-1-phosphate containing four (R)-3-hydroxytetradecanoic acids at the 2,2’ and 3,3’ positions (structure 2, Figure 1). This disaccharide precursor 2 was identified as the main immunostimulatory side product [12][13

• )-ᴅ-glucosamine disaccharide 1-phosphate) (Figure 1). The synthesis of such precursors is particularly important as it will facilitate the aforementioned goal of harnessing the immunostimulatory effects of lipid A through development of a clear understanding of the structure–activity relationship

Selective preparation of tetrasubstituted fluoroalkenes by fluorine-directed oxetane ring-opening reactions

• Clément Q. Fontenelle,
• Thibault Thierry,
• Romain Laporte,
• Emmanuel Pfund and
• Thierry Lequeux

Beilstein J. Org. Chem. 2020, 16, 1936–1946, doi:10.3762/bjoc.16.160

• antiviral agents, respectively (Figure 1) [5][6]. The field of acyclonucleotides (ACN) has been explored less, however, the introduction of fluorine atoms showed remarkable effects. The most representative examples are phosphate analogues such as the nucleoside phosphorylase inhibitor III and acyclic

• VIII was observed due to the difficulty of phosphorylation of the substrate by kinases [16]. The first kinase phosphorylation step is generally rate limiting, and the prior introduction of a phosphate or phosphonate function can circumvent this problem. The preparation of diols VIII was realized by

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• -acetylglucosaminyltransferase I (GnT-I) reaction transition state [11]. Previously, we have designed 2-thiohexofuranoside skeletons bearing a phosphate group in position 1 by molecular modeling as potential transition state inhibitors of human glycosyltransferase I (GnT-I) [12], the bisubstrate enzyme requiring a metal co

• originally suggested by molecular modeling having the 1-O-phosphate group stabilized by anomeric sulfones on the ᴅ-fructofuranose and ᴅ-tagatofuranose skeleton (1–3, Figure 1). Similarities in the TS structures of GnT-I and GlfT2 prompted us to examine these molecules against GlfT2, a possible target for the

• -up of lipid-linked galactan precursors. The crude enzymes used in the assay allow for in situ synthesis of the acceptor for galactan polymerization, decaprenyl-P-P-GlcNAc-Rha (GL2), from endogenous decaprenyl phosphate and sugar nucleotides UDP-GlcNAc and TDP-Rha supplied in the reaction mixture

One-pot synthesis of oxazolidinones and five-membered cyclic carbonates from epoxides and chlorosulfonyl isocyanate: theoretical evidence for an asynchronous concerted pathway

• Esra Demir,
• Ozlem Sari,
• Yasin Çetinkaya,
• Ufuk Atmaca,
• Safiye Sağ Erdem and
• Murat Çelik

Beilstein J. Org. Chem. 2020, 16, 1805–1819, doi:10.3762/bjoc.16.148

• . Linezolid (3) is the first oxazolidinone drug approved in 2000 by the Food and Drug Administration (FDA) for the treatment of multidrug resistant Gram-positive bacterial infections (Scheme 1) [10]. Cytoxazone is a microbial metabolite exhibiting potent cytokine-modulating activity. Tedizolid phosphate

Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies

• Giovanni Picca,
• Markus Probst,
• Simon M. Langenegger,
• Oleg Khorev,
• Peter Bütikofer,
• Anant K. Menon and
• Robert Häner

Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145

• . Reports of using phosphoramidite chemistry for the preparation of carbohydrates via the anomeric position are relatively rare [18][19][20][21][22][23]. Alternatively, the H-phosphonate approach has been used to convert carbohydrates into phosphate-linked derivatives at the anomeric center [24][25][26][27

• headgroup and simultaneously introduced the linking phosphate group. Furthermore, we demonstrate a novel, reliable, and efficient way to synthesize the carbohydrate phosphoramidite with a defined configuration at the anomeric position, a strategy that gives access to future molecular probes containing pure

One-pot synthesis of isosorbide from cellulose or lignocellulosic biomass: a challenge?

• Isaline Bonnin,
• Raphaël Mereau,
• Thierry Tassaing and
• Karine De Oliveira Vigier

Beilstein J. Org. Chem. 2020, 16, 1713–1721, doi:10.3762/bjoc.16.143

• isosorbide. The hydrolysis of cellulose to glucose, the first step, is reported using acid catalysts such as H3PO4, H2SO4 and HCl as well as heterogeneous catalysts tungstolitic acid (H4SiW12O40), niobium phosphate, Amberlyst-70 and Dowex-H [1][12]. For the second step (hydrogenation of glucose to sorbitol

• to sorbitol. Several homogeneous catalysts were used such as mineral acids, boron phosphate and heteropolyacids (Scheme 2). Palkovits et al. studied the combination of supported noble metal catalysts based on Pt, Pd and Ru with dilute mineral acids such as phosphoric or sulfuric acid for the

• showed that the acidity is important in the conversion of lignocellulosic biomass to isosorbide and that the acid can react with the metal-supported catalyst. Another study was devoted to the use of boron phosphate for the conversion of cellulose into liquid hydrocarbon C1–C6 over Ru/C [23]. A mixture of

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

• . The mobile phase was a mixture of water (0.1 % NH4FA, pH 3.2) and acetonitrile. The injection volume was 5 µL. The following gradient was used with a flow rate of 150 µL/min (Table 2). ITC measurements For determination of binding constants ITC was measured in phosphate buffered solutions (pH 7.4, 100

• chromatograms of a reference library for all possible tripeptide dimers ([M + H]+ ions). a) HPLC–MS chromatograms of the dimers (CFC)2 and templates YY and FF. b) Amplification of the peak areas. ITC of YY (30 mM) to a(CFC)2 (1.5 mM) in phosphate buffer (pH 7.4, 100 mM). Continuously varied NMR measurements of

• ). Measured by ITC in phosphate buffer (pH 7.4, 100 mM). Data fitted with a 1:1 model. Solvent gradients for HPLC. Supporting Information Supporting Information File 338: Synthesis, additional data, and NMR spectra. Acknowledgements We would like to thank Dr. Kevin Eckey, Jens Fangmeyer and Prof. Dr. Uwe

Photocatalyzed syntheses of phenanthrenes and their aza-analogues. A review

• Alessandra Del Tito,
• Havall Othman Abdulla,
• Davide Ravelli,
• Stefano Protti and
• Maurizio Fagnoni

Beilstein J. Org. Chem. 2020, 16, 1476–1488, doi:10.3762/bjoc.16.123

• phosphate base (50 mol %). Thus, the latter played a key role in the PCET event which triggered the activation of the N–H bond in 18.1a–d and led to the N-centered radicals 18.2·a–d. Ensuing cyclization onto the pendant aromatic group, followed by rearomatization enabled by molecular oxygen, gave the

Activated carbon as catalyst support: precursors, preparation, modification and characterization

• Melanie Iwanow,
• Tobias Gärtner,
• Volker Sieber and
• Burkhard König

Beilstein J. Org. Chem. 2020, 16, 1188–1202, doi:10.3762/bjoc.16.104

• structures in the carbon source [6]. Diamadopoulos and co-workers observed also the production of smaller surface areas by H3PO4 activation of bagasse and rice husk due to a reaction of the activating reagent with the carbon precursor. Thereby, phosphate esters or polymerization byproducts are formed, which

• forming phosphate esters or polymerization byproducts that bind on the solid carbon matrix [30]. Boehm titrations: Boehm titrations are used for the determination of acidic or basic surface oxygen functional groups of solid materials. The acidic character is caused by carboxyl groups (R–COOH), lactones (R

Fluorinated phenylalanines: synthesis and pharmaceutical applications

• Laila F. Awad and
• Mohammed Salah Ayoup

Beilstein J. Org. Chem. 2020, 16, 1022–1050, doi:10.3762/bjoc.16.91

• able to increase the secretion of insulin by the pancreas that modulates blood sugar level when it is high. Sitagliptin was granted FDA approval in October, 2006 [116]. Retagliptin phosphate: Retagliptin phosphate (184) is under investigation as a DPP-4 inhibitor for treating type-2 diabetes. It is an

Reaction of indoles with aromatic fluoromethyl ketones: an efficient synthesis of trifluoromethyl(indolyl)phenylmethanols using K₂CO₃/n-Bu₄PBr in water

• Thanigaimalai Pillaiyar,
• Masoud Sedaghati and
• Gregor Schnakenburg

Beilstein J. Org. Chem. 2020, 16, 778–790, doi:10.3762/bjoc.16.71

• was reduced to 91% (Table 1, entry 7) and 81% (Table 1, entry 9), respectively, while it was increased to 97% (Table 1, entry 8) in the presence of K2CO3. The reaction in the presence of tripotassium phosphate base (Table 1, entry 10; 89%), dipotassium phosphate base (Table 1, entry 11; 70%) or sodium

Recent advances in Cu-catalyzed C(sp³)–Si and C(sp³)–B bond formation

• Balaram S. Takale,
• Ruchita R. Thakore,
• Elham Etemadi-Davan and
• Bruce H. Lipshutz

Beilstein J. Org. Chem. 2020, 16, 691–737, doi:10.3762/bjoc.16.67

• reagent (7), to successfully convert benzyl phosphate 6 to benzylic silanes 8. Curiously, the reaction proceeded even in the absence of a ligand, albeit with lower yield (25%; Scheme 3). However, only one example was reported and a more general method for the preparation of alkylsilanes was developed by

Recent advances in photocatalyzed reactions using well-defined copper(I) complexes

• Mingbing Zhong,
• Xavier Pannecoucke,
• Philippe Jubault and
• Thomas Poisson

Beilstein J. Org. Chem. 2020, 16, 451–481, doi:10.3762/bjoc.16.42

• hydrogen phosphate ((R)-BNDHP) under similar reaction conditions and using the same copper catalyst provided the δ-functionalization of the alcohol (Scheme 28). This reaction manifold was applied to a large variety of N-alkoxyphthalimide derivatives using glycine ester derivatives and was also extended to

Oligomeric ricinoleic acid preparation promoted by an efficient and recoverable Brønsted acidic ionic liquid

• Fei You,
• Xing He,
• Song Gao,
• Hong-Ru Li and
• Liang-Nian He

Beilstein J. Org. Chem. 2020, 16, 351–361, doi:10.3762/bjoc.16.34

• sustainable synthesis protocol is urgently needed to make the product really green. In this work, an environment-friendly Brønsted acidic ionic liquid (IL) 1-butanesulfonic acid diazabicyclo[5.4.0]undec-7-ene dihydrogen phosphate ([HSO3-BDBU]H2PO4) was developed as the efficient catalyst for the production of

• that the cation also affected the catalytic activity of the IL. Taking the decrease of acid value as catalytic activity index, the ionic liquid 1-butanesulfonic acid triethylamine dihydrogen phosphate ([HSO3-BNEt3]H2PO4) performed best among the tested ionic liquids in this study (Table 1, entry 8