DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

• Yongdong Su,
• Maitsetseg Bayarjargal,
• Tracy K. Hale and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65

• provide either a zwitterionic phosphoramidate with N+ modification or a negatively charged phosphoramidate for Ts modification in the DNA sequence. The incorporation of these N+ and Ts modifications led to the formation of thermally stable parallel DNA triplexes, regardless of the number of modifications

• incorporated into the oligodeoxynucleotides (ONs). For both N+ and Ts-modified ONs, the antiparallel duplexes formed with complementary RNA were more stable than those formed with complementary DNA (except for ONs with modification in the middle of the sequence). Additionally, the incorporation of N

• responsible for the stabilisation of duplexes with N+ modification. N+ONs also demonstrated greater resistance to nuclease digestion by snake venom phosphodiesterase I than the corresponding Ts-ONs. Cell uptake studies showed that Ts-ONs can enter the nucleus of mouse fibroblast NIH3T3 cells without any

Simulating the enzymes of ganglioside biosynthesis with Glycologue

• Andrew G. McDonald and
• Gavin P. Davey

Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64

• modification of monosaccharides, for example through sulfation, acetylation or phosphorylation, which follow the same pattern as decoration. Glycologue structure identifiers order branches by linkage position, writing the branch with the lowest linkage first, reading from right to left. Modifiers are written

• will also influence the kinetics [48][51]. Future extensions to this work will consider the effects of acetylation of sialic acid residues, since this modification reduces the negative charge of the carbohydrate, thus altering binding affinity, while an increased incidence of 9-O-acetylated GD3 is

Effective microwave-assisted approach to 1,2,3-triazolobenzodiazepinones via tandem Ugi reaction/catalyst-free intramolecular azide–alkyne cycloaddition

• Maryna O. Mazur,
• Oleksii S. Zhelavskyi,
• Eugene M. Zviagin,
• Svitlana V. Shishkina,
• Vladimir I. Musatov,
• Maksim A. Kolosov,
• Elena H. Shvets,
• Anna Yu. Andryushchenko and
• Valentyn A. Chebanov

Beilstein J. Org. Chem. 2021, 17, 678–687, doi:10.3762/bjoc.17.57

• cycloaddition approach to the synthesis of 1,2,3-triazolobenzodiazepinones. Results and Discussion The development of the tandem Ugi/Click reaction approach for 1,2,3-triazolobenzodiazepinone synthesis can be logically divided into two principal parts: modification and performing synthesis of Ugi-reaction

Synthesis, structural characterization, and optical properties of benzo[f]naphtho[2,3-b]phosphoindoles

• Mio Matsumura,
• Takahiro Teramoto,
• Masato Kawakubo,
• Masatoshi Kawahata,
• Yuki Murata,
• Kentaro Yamaguchi,
• Masanobu Uchiyama and
• Shuji Yasuike

Beilstein J. Org. Chem. 2021, 17, 671–677, doi:10.3762/bjoc.17.56

• ] with n-butyllithium in dry THF at −78 °C and subsequently with dichlorophenylphosphine resulted in ring closure, affording the desired product containing 6-phenyl-6H-benzo[f]naphtho[2,3-b]phosphoindole (2) in 52% yield via the 3,3′-dilithio-2,2′-binaphthyl intermediate. The chemical modification of the

• approximately 50 nm longer than that of our oxide 3 [16]. The fluorescence wavelength, including the maximum emission (λem), and the quantum yield depend on the nature of the P-modification. Phosphine oxide 3, cation 5, and boron complex 6 emitted blue fluorescence in the visible-light region, with λem at 395

• Information File 1. Parent compound 2 and borane complex 6 showed reversible reduction peaks (Ered = −1.25 and −1.26 V, respectively). Due to the increased electron–acceptor character of the phosphorus center, P-modification compounds 4 and 5 show a more positive oxidation potential than parent 2 [26

[2 + 1] Cycloaddition reactions of fullerene C₆₀ based on diazo compounds

• Yuliya N. Biglova

Beilstein J. Org. Chem. 2021, 17, 630–670, doi:10.3762/bjoc.17.55

• universe), the discovery in 1985 of its new allotropic modification, fullerene, has resulted in an avalanche-like expansion of studies in this area [1]. The exceptional physicochemical properties of the fullerene family and, above all, its main representative, C60, predetermine the broad practical interest

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

• data indicate that GuNA[Me] could be a useful modification for therapeutic antisense oligonucleotides. Keywords: artificial nucleic acid; duplex-forming ability; oligonucleotide synthesis; Introduction The efficacy and safety of therapeutic oligonucleotides can be controlled by chemical modifications

• ]. The modification of oligonucleotides with GuNA[H]-T improved the nuclease resistance, cell membrane permeability, and binding affinity toward complementary single-stranded DNAs (ssDNAs) and RNAs (ssRNAs). We also synthesized and evaluated a GuNA[H]-T analog bearing a methyl group in the guanidine

• spectra of ON2/ssRNA and ON2/ssDNA were found to be similar to those of the ON7/ssRNA and ON7/ssDNA duplexes, demonstrating that one modification with GuNA[Me] does not affect the whole duplex structures. Similar results were observed for ON4/ssRNA and ON4/ssDNA (Figure S15 in Supporting Information File

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

• to the action of chemical (acids, air, halogens, solvents) or physical agents (heat, light). For polymers, the properties involved are, for instance, tensile strength, colour or shape, the change of which is usually associated with a modification of the chemical composition (e.g., as a consequence of

Synthesis of N-perfluoroalkyl-3,4-disubstituted pyrroles by rhodium-catalyzed transannulation of N-fluoroalkyl-1,2,3-triazoles with terminal alkynes

• Olga Bakhanovich,
• Viktor Khutorianskyi,
• Vladimir Motornov and
• Petr Beier

Beilstein J. Org. Chem. 2021, 17, 504–510, doi:10.3762/bjoc.17.44

• , agrochemicals, and functional materials (polymers, dyes, films, etc.) (Figure 1) [1][2][3][4]. Numerous methods exist for pyrrole synthesis, including the classical and industrially important condensation approaches, such as the Hantzsch, Huisgen, and Paal–Knorr processes [5]. However, the direct modification

Deoxygenative C2-heteroarylation of quinoline N-oxides: facile access to α-triazolylquinolines

• Geetanjali S. Sontakke,
• Rahul K. Shukla and
• Chandra M. R. Volla

Beilstein J. Org. Chem. 2021, 17, 485–493, doi:10.3762/bjoc.17.42

• simplicity of the developed protocol. The current transformation was also found to be compatible for the late-stage modification of natural products. Keywords: amination; heteroarylation; quinoline N-oxides; regioselective; triazoles; Introduction Quinoline is a key heterocyclic moiety found in many

• transformation for late-stage modification of complex natural products was explored, and as shown in Scheme 4, the protocol was tested with various natural-product-derived triazoles. Novel C2-triazolyl products 4a–c were synthesized in good yield of 61–70% from triazoles derived from thymol, cholesterol and

• scaffolds. The late-stage modification of natural products is the salient feature of this current transformation. Experimental General procedure for the C2-selective synthesis of α-triazolylquinolines 3 To an oven-dried reaction tube equipped with a magnetic stirring bar were added quinoline N-oxide (1a, 29

Synthetic strategies of phosphonodepsipeptides

• Jiaxi Xu

Beilstein J. Org. Chem. 2021, 17, 461–484, doi:10.3762/bjoc.17.41

• ester 87 was then coupled with dibenzyl (S)-2-hydroxypentanedioate (88) using BOP as the activating agent to generate the γ-phosphonodepsidipeptide 89. After hydrazinolysis, acylation with arenecarbonyl chlorides or arenecarboxylic acids, and further modification, the γ-phosphonodepsidipeptide

• are derivatives of the new antimalarial drug fosmidomycin and inhibited the 1-deoxy-ᴅ-xylulose 5-phosphate reductoisomerase. The phosphonodepsipeptides 194 were synthesized as prodrugs with an increased activity after oral administration due to a chemical modification of the phosphonate moiety. For

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

• receptor (β2AR) [29]. In this work conjugation of the CF3 group to an aromatic ring was shown to give rise to substantially improved 19F NMR chemical shift sensitivities over the more traditional thiol-specific trifluoromethyl tags (Figure 3b) [28]. In addition to chemical modification, novel methodologies

• are being investigated that enable the enzymatic post-translational modification of non-nucleophilic residues, such as glutamate [31]. As recently demonstrated by Kojima and co-workers, recombinant protein transglutaminase (TGase) could be used to catalyse the chemical replacement of the γ

• combined with the aforementioned chemical approaches based on cysteine and lysine modification. It is worth noting that for small proteins and peptides the chemical incorporation of the desired fluorinated amino acids using SPPS protocols still remains the method of choice, as it enables the site-specific

The preparation and properties of 1,1-difluorocyclopropane derivatives

• Kymbat S. Adekenova,
• Peter B. Wyatt and
• Sergazy M. Adekenov

Beilstein J. Org. Chem. 2021, 17, 245–272, doi:10.3762/bjoc.17.25

• addition, another modification was made in order to increase the speed of the reaction of sodium halodifluoroacetate and alkenes. This was achieved by the use of microwave irradiation in THF solution, which allowed the reactions to be completed within 5 minutes [31]. An application of this method 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

• Minzan Zuo Krishnasamy Velmurugan Kaiya Wang Xueqi Tian Xiao-Yu Hu College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China 10.3762/bjoc.17.15 Abstract Due to the unique characteristics of macrocycles (e.g., the ease of modification

Direct synthesis of anomeric tetrazolyl iminosugars from sugar-derived lactams

• Michał M. Więcław and
• Bartłomiej Furman

Beilstein J. Org. Chem. 2021, 17, 115–123, doi:10.3762/bjoc.17.12

• review articles have been written about this topic, enclosing most of the advances made to date [3][4][5]. A fascinating subset of these transformations encompass the reduction of amides to imines, with direct subsequent functionalization. One of the methodologies for such a modification was developed by

• employment of these methods for modification of lactams is a challenge in its own right – there are hardly any examples of such transformations available in the literature [23]. Our group was the first to surmount this challenge by means of Schwartz’s reagent-mediated reductive functionalization. Since then

• , we have performed a number of different functionalizations of such cyclic systems with various complexity, and with a particular focus on the modification of sugar-derived lactams. As summarized in Scheme 1, this includes simple nucleophile addition to in situ-generated imines [23], the consecutive

Supramolecular polymers with reversed viscosity/temperature profile for application in motor oils

• Jan-Erik Ostwaldt,
• Christoph Hirschhäuser,
• Stefan K. Maier,
• Carsten Schmuck and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2021, 17, 105–114, doi:10.3762/bjoc.17.11

• specific viscosity decreases significantly upon increasing the temperature (the same was also observed in toluene solution, see Supporting Information File 1, chapter 6.3.2). Thus, the modification of the linking unit by insertion of one amino acid (to give compound 3) has a detrimental effect on the RVT

Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders

• David Straßburger,
• Svenja Herziger,
• Katharina Huth,
• Moritz Urschbach,
• Rainer Haag and
• Pol Besenius

Beilstein J. Org. Chem. 2021, 17, 97–104, doi:10.3762/bjoc.17.10

• the effect of sulfate modification on the self-assembly properties of the dendritic peptide amphiphiles were performed using circular dichroism (CD) spectroscopy and electron transmission microscopy (TEM) as well as cryogenic TEM. Finally, the binding affinity of the sulfated supramolecular polymers

Control over size, shape, and photonics of self-assembled organic nanocrystals

• Chen Shahar,
• Yaron Tidhar,
• Yunmin Jung,
• Haim Weissman,
• Sidney R. Cohen,
• Ronit Bitton,
• Iddo Pinkas,
• Gilad Haran and
• Boris Rybtchinski

Beilstein J. Org. Chem. 2021, 17, 42–51, doi:10.3762/bjoc.17.5

• monolayer surface so that it does not allow facile bulk fabrication and restricts control over the crystal morphology [22][23]. Crystalline nanobelts assembled from perylene and perylene diimide (PDI) derivatives were reported, but their size and shape could not be controlled [24][25]. Modification of the

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

• compared to Skyline, and GlycopeptideGraphMS. All quantification packages resulted in comparable glycosylation profiles but featured differences in terms of robustness and data quality control. Partial cysteine oxidation was identified as an unexpectedly abundant peptide modification and impaired the

• features, such as the linkage position and anomeric configuration, make protein glycosylation a highly complex posttranslational modification (PTM). Glycoproteomics has become important for many life science disciplines, in particular for biomedical and biopharmaceutical research [3][4][5]. Glycopeptide

• glycopeptide clusters of interest, Cys oxidation (+15.9949 Da) was assigned as an unexpected modification in all Cys-containing glycopeptides (five out of 11) at a high relative abundance (65.4–77.2%) and confirmed upon manual inspection of the MS/MS data (Figures S13 and S16–S18, Supporting Information File 2

Regioselective synthesis of heterocyclic N-sulfonyl amidines from heteroaromatic thioamides and sulfonyl azides

• Vladimir Ilkin,
• Vera Berseneva,
• Tetyana Beryozkina,
• Tatiana Glukhareva,
• Lidia Dianova,
• Wim Dehaen,
• Eugenia Seliverstova and
• Vasiliy Bakulev

Beilstein J. Org. Chem. 2020, 16, 2937–2947, doi:10.3762/bjoc.16.243

• amidines 3t–aa in good yields (Scheme 3). Thus, a library of N-sulfonyl amidines bearing differently substituted 1,2,3-triazoles was successfully prepared. Among them are compounds bearing an NH-unsubstituted 1,2,3-triazole ring which gives extra possibilities for the modification of the molecules by the

Synthesis of imidazo[1,5-a]pyridines via cyclocondensation of 2-(aminomethyl)pyridines with electrophilically activated nitroalkanes

• Dmitrii A. Aksenov,
• Nikolai A. Arutiunov,
• Vladimir V. Maliuga,
• Alexander V. Aksenov and
• Michael Rubin

Beilstein J. Org. Chem. 2020, 16, 2903–2910, doi:10.3762/bjoc.16.239

• approach, however, seems less attractive as it requires an additional step for the proper modification of the starting material. An alternative, more appealing method would capitalize on the in situ generation of a less sterically hindered, and therefore more reactive electrophilic nitronate. As we have

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

• , assays that implement separation steps require RNA molecules conjugated to an affinity tag such as biotin, or any other functionality for functional selection [11][12]. Very importantly, terminal modification/functionalization is not always suitable to a specific aim. Thus, in addition to building blocks

• , molecular entities to RNA molecules may disturb functionality, and thus requires careful definition of the conjugation site. As mentioned above, in addition to 5’- and 3’-terminal conjugation, often internal modification of RNA molecules is required. Thus, in order to avoid changes to the RNA sequence

• Supporting Information File 1). The presence of the modified ribonucleotide in the synthesized sequence was confirmed by MALDI–TOF MS (Figure S1, Supporting Information File 1). Conclusion Oligonucleotides carrying a specific modification or functional entity at a pre-defined position are in high demand for

Encrypting messages with artificial bacterial receptors

• Pragati Kishore Prasad,
• Naama Lahav-Mankovski,
• Leila Motiei and
• David Margulies

Beilstein J. Org. Chem. 2020, 16, 2749–2756, doi:10.3762/bjoc.16.225

• information protection at the molecular level. Keywords: artificial receptors; cell surface modification; fluorescent probes; molecular cryptography; Introduction In living cells, information is processed and transferred via a series of recognition and signaling events, which normally begin by the binding

Synthesis of purines and adenines containing the hexafluoroisopropyl group

• Viacheslav Petrov,
• Rebecca J. Dooley,
• Alexander A. Marchione,
• Elizabeth L. Diaz,
• Brittany S. Clem and
• William Marshall

Beilstein J. Org. Chem. 2020, 16, 2739–2748, doi:10.3762/bjoc.16.224

• this method to the modification of biologically active imidazoles, such as adenine and purine derivatives. The results of this study are reported in this article. Results and Discussion Despite the presence of two electron-withdrawing nitrogen atoms in the aromatic ring, purine (2) was found to react

Vicinal difluorination as a C=C surrogate: an analog of piperine with enhanced solubility, photostability, and acetylcholinesterase inhibitory activity

• Yuvixza Lizarme-Salas,
• Alexandra Daryl Ariawan,
• Ranjala Ratnayake,
• Hendrik Luesch,
• Angela Finch and
• Luke Hunter

Beilstein J. Org. Chem. 2020, 16, 2663–2670, doi:10.3762/bjoc.16.216

• (BACE-1). The inhibition of AChE was measured using a modification of a previously described colorimetric assay (Figure 4a) [33]. It quickly became apparent that the limited solubility of piperine (1) in 50 mM Tris-HCl buffer, even in the presence of methanol as a co-solvent, was a major problem in this

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

• rules (SRS), modification rules (MR), branch rules (BR), repetition rules (RR), glycoconjugate rules (GR), and uncertainty rules (UR). The saccharide unit (SU) refers to a structure with four elements: anomericity, position number, modifications, and monosaccharide (MS). Stereospecificity and ring

• be written as AbG if the reducing end glucose is closed and AbGo if the glucose is open; the open "o" takes the place of the linkage in this context. If the glucose is phosphorylated, this structure would be written AbG[P]o. Modification rules specify a modification of a MS at certain positions (MR1

• ). MS + “ [ ” + modification + “ ] ” is used to denote the modification. For example, “G[2S]” describes sulfation on the second carbon of a ᴅ-glucopyranose. The anomericity is expressed to the right of the modification (i.e., “G[2S]a”). Multiple modifications to the same MS are ordered based on the