Polymer and small molecule mechanochemistry: closer than ever

• José G. Hernández

Beilstein J. Org. Chem. 2022, 18, 1225–1235, doi:10.3762/bjoc.18.128

• time, two main experimental strategies to produce physical and chemical responses in a system when mechanical force is applied have been established. One of them, often called polymer mechanochemistry, relies on the use of polymers to transduce mechanical loads to mechanically sensitive probes

Scope of tetrazolo[1,5-a]quinoxalines in CuAAC reactions for the synthesis of triazoloquinoxalines, imidazoloquinoxalines, and rhenium complexes thereof

• Laura Holzhauer,
• Chloé Liagre,
• Olaf Fuhr,
• Nicole Jung and
• Stefan Bräse

Beilstein J. Org. Chem. 2022, 18, 1088–1099, doi:10.3762/bjoc.18.111

• diversity of metal complexes incorporating 1,2,3-triazoles as ligands have been reported [16][17][18]. Triazole ligands with N-heterocycles such as Pyta (4-(2-pyridyl)-1,2,3-triazole) and related structures were employed to obtain novel metal complexes as catalysts [19][20] and imaging probes [21], as well

• especially used as CO2 reduction catalysts [38][39][40] and noninvasive imaging probes [12][41]; examples for the application in organic light-emitting diodes [35] and as photoactive CO-releasing molecule [42][43] have been reported as well. For the complexation experiments, compounds with three different

Facile and diastereoselective arylation of the privileged 1,4-dihydroisoquinolin-3(2H)-one scaffold

• Dmitry Dar’in,
• Grigory Kantin,
• Alexander Bunev and
• Mikhail Krasavin

Beilstein J. Org. Chem. 2022, 18, 1070–1078, doi:10.3762/bjoc.18.109

• -DHIQ adducts synthesized in this work, they were deemed efficient probes for the perturbation of vital cellular targets. Screening of these compounds against lung carcinoma cancer cell lines confirmed high cytotoxicity of selected analogs, which validates this new chemotype for further investigation as

Synthesis, optical and electrochemical properties of (D–π)₂-type and (D–π)₂Ph-type fluorescent dyes

• Kosuke Takemura,
• Kazuki Ohira,
• Taiki Higashino,
• Keiichi Imato and
• Yousuke Ooyama

Beilstein J. Org. Chem. 2022, 18, 1047–1054, doi:10.3762/bjoc.18.106

• ][16][17][18][19][20][21][22], as well as fluorescent probes [23][24][25][26][27][28] for bioimaging and fluorescent sensors for specific target species [29][30][31][32]. Among many kinds of organic fluorescent dyes, much efforts have been made on the development of donor–π–acceptor (D–π–A)-type

New azodyrecins identified by a genome mining-directed reactivity-based screening

• Atina Rizkiya Choirunnisa,
• Kuga Arima,
• Yo Abe,
• Noritaka Kagaya,
• Kei Kudo,
• Hikaru Suenaga,
• Junko Hashimoto,
• Manabu Fujie,
• Noriyuki Satoh,
• Kazuo Shin-ya,
• Kenichi Matsuda and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2022, 18, 1017–1025, doi:10.3762/bjoc.18.102

• natural products, despite their notable biological activities. Reactivity-based screening is an emerging strategy in natural products discovery, in which chemical probes are used for the specific detection of the unique functionality of interest in crude metabolites [5][6]. The reactions usually

Syntheses of novel pyridine-based low-molecular-weight luminogens possessing aggregation-induced emission enhancement (AIEE) properties

• Masayori Hagimori,
• Tatsusada Yoshida,
• Yasuhisa Nishimura,
• Yukiko Ogawa and
• Keitaro Tanaka

Beilstein J. Org. Chem. 2022, 18, 580–587, doi:10.3762/bjoc.18.60

• have been reported [7][8][9][10]. Because the aggregated state of AIEE-based compounds is affected by the external environment, these compounds have found use in clinical applications as chemical sensors or fluorescent probes [7][8][9][10]. Pyridine is a nitrogen-containing heterocyclic compound found

Comparative study of thermally activated delayed fluorescent properties of donor–acceptor and donor–acceptor–donor architectures based on phenoxazine and dibenzo[a,j]phenazine

• Saika Izumi,
• Prasannamani Govindharaj,
• Anna Drewniak,
• Paola Zimmermann Crocomo,
• Satoshi Minakata,
• Leonardo Evaristo de Sousa,
• Piotr de Silva,
• Przemyslaw Data and
• Youhei Takeda

Beilstein J. Org. Chem. 2022, 18, 459–468, doi:10.3762/bjoc.18.48

• organic light-emitting diodes (OLEDs) by Adachi in 2012 [2], TADF-active compounds have emerged as emitters in high-performance organic light-emitting diodes (OLEDs) [3][4][5][6][7][8], biological probes [9], photocatalysis [10], and some others [11]. Specifically, TADF-active purely organic compounds

The role of chemistry in the success of oligonucleotides as therapeutics

• Pawan Kumar and
• Tom Brown

Beilstein J. Org. Chem. 2022, 18, 197–199, doi:10.3762/bjoc.18.22

• oligonucleotide primers and probes for use in diagnostic testing kits for the detection of COVID-19 for tackling the pandemic. With this thematic issue, we express our sincere gratitude to all the scientists for their ground-breaking work to bring oligonucleotide therapeutics to the bedside. We also express our

Synthetic strategies toward 1,3-oxathiolane nucleoside analogues

• Umesh P. Aher,
• Dhananjai Srivastava,
• Girij P. Singh and
• Jayashree B. S

Beilstein J. Org. Chem. 2021, 17, 2680–2715, doi:10.3762/bjoc.17.182

• Academy of Higher Education, Manipal-576104, Karnataka, India 10.3762/bjoc.17.182 Abstract Sugar-modified nucleosides have gained considerable attention in the scientific community, either for use as molecular probes or as therapeutic agents. When the methylene group of the ribose ring is replaced with a

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

• are ideal probes to study polysaccharides at the molecular level and identify structure–property correlations. Access to synthetic polysaccharides facilitated the correlation of chemical structure with molecular conformations [5][6], intermolecular interactions [7][8], and biological response [9

Asymmetric organocatalyzed synthesis of coumarin derivatives

• Natália M. Moreira,
• Lorena S. R. Martelli and
• Arlene G. Corrêa

Beilstein J. Org. Chem. 2021, 17, 1952–1980, doi:10.3762/bjoc.17.128

• acetylcholinesterase inhibitors [11][12][13], being LSPN223 the most potent compound (Figure 2). Furthermore, coumarin derivatives have been used as fluorescent probes, laser dyes, fluorescent chemosensors, light absorbers for solar cells, optical brighteners, and organic light emitting diodes (OLEDs) [14][15]. From a

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

• /bjoc.17.116 Abstract Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA’s chemistry, optimization of structure and function, applications as probes

• binding is highly sequence specific as one Watson–Crick base pair mismatch can drop the melting temperature of the complex with PNA by 8–20 °C making PNA an excellent nucleic acid analogue for development of probes and diagnostics. This strong and selective binding has made PNA a key component of assays

• uracil with fluorine or trifluoromethyl improved PNA binding affinity for complementary DNA and RNA [127]. Moreover, fluorination increased the cellular uptake of PNAs [127]. Fluorinated uracil derivatives are also useful probes for studying different binding modes of PNA using 19F NMR [128]. PNA

Double-headed nucleosides: Synthesis and applications

• Vineet Verma,
• Jyotirmoy Maity,
• Vipin K. Maikhuri,
• Ritika Sharma,
• Himal K. Ganguly and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98

• was hybridized with a DNA target. The double-headed nucleoside 41 has potential in DNA invader probes as well as in RNA targeting and detection [23]. 1,3-Furanosyl double-headed nucleosides In this section, all double-headed nucleosides with furanosyl ring structures are collected. The first

Design, synthesis and photophysical properties of novel star-shaped truxene-based heterocycles utilizing ring-closing metathesis, Clauson–Kaas, Van Leusen and Ullmann-type reactions as key tools

• Shakeel Alvi and
• Rashid Ali

Beilstein J. Org. Chem. 2021, 17, 1374–1384, doi:10.3762/bjoc.17.96

• applications ranging from organic thin‐film transistors (OTFTs), organic light-emitting diodes (OLEDs), dye‐sensitized solar cells (DSSCs), fluorescent probes, organic photovoltaics (OPVs) to the high hole mobility semiconductors, blue light-emitting materials, nonlinear optical materials and so forth [5][6][7

Photoinduced post-modification of graphitic carbon nitride-embedded hydrogels: synthesis of 'hydrophobic hydrogels' and pore substructuring

• Cansu Esen and
• Baris Kumru

Beilstein J. Org. Chem. 2021, 17, 1323–1334, doi:10.3762/bjoc.17.92

• –fluorescein isothiocyanate and fluorescein isothiocyanate–dextran fluorescent probes were subjected to HGCM and HGCM-vTA samples with a comparatively shorter releasing experiment than the one performed for RhB dye (Supporting Information File 1, Figure S4a). The static experiment principally relies on

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• nuclease-resistant probes for studying RNA–protein interactions [70]. To better elucidate the structural features of 3'-NP DNA responsible for this enhanced selective binding and stability, the Egli group determined the crystal structure of the fully modified 3'-NP DNA duplex with the sequence 5'-d

Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides

• Roslyn M. Ray,
• Anders Højgaard Hansen,
• Maria Taskova,
• Bernhard Jandl,
• Jonas Hansen,
• Citra Soemardy,
• Kevin V. Morris and
• Kira Astakhova

Beilstein J. Org. Chem. 2021, 17, 891–907, doi:10.3762/bjoc.17.75

• aptamers present an additional potential route for LNP internalization and target cell specificity. In order to assess the ability of aptamers to drive LNP internalization, short complementary Cy5-DNA oligonucleotides specific for each aptamer were used as probes to detect LNP uptake in different cells. In

• , effective transport systems for brain drug delivery are highly warranted. Herein, we find that the LNP platform can be applied as a vehicle to circumvent the BBB and effectively deliver oligonucleotide probes to antigen-expressing cell lines. For HIV-1 there is currently a need for more effective delivery

Synthetic strategies of phosphonodepsipeptides

• Jiaxi Xu

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

• derivatives 85 were obtained. The phosphonate moiety in these analogues represented an important new lead in the development of folylpolyglutamate synthetase inhibitors (Scheme 14) [29]. γ-Phosphonodepsipeptides were also designed and synthesized as potent inhibitors and active site probes of γ-glutamyl

• the γ-phosphonodepsitripeptide 95 as an inhibitor of γ-gutamyl transpeptidase. Synthesis of phosphonodepsipeptides as inhibitors and probes of γ-glutamyl transpeptidase. Synthesis of phosphonyl depsipeptides 108 via DCC-mediated condensation and oxidation. Synthesis of phosphonodepsipeptides 111 with

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

• containing fluorine have been particularly well characterized for their use as spectroscopic probes, mainly in 19F NMR applications [12][13][14][15]. It is typical that the incorporation of fluorine into certain molecular fragments changes the local polarity as well as the electronic and conformational

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

• fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein–protein interactions, protein–ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate

• biosynthesis and biodegradation of fluorinated organic compounds is also described. Keywords: biotransformation; chemical biology; fluorine; 19F NMR; probes; protein structure; Introduction Although fluorine is abundant in the environment, it is not a nutrient nor is it a feature of biochemistry for most

• that can be used as 19F NMR reporters. Aromatic amino acids have been preferentially used as 19F NMR probes both in binding and in conformational studies owing to their ready availability. However, more recently fluoro-aliphatic, and in particular perfluoro-aliphatic amino acids, have become

The fluorescence of a mercury probe based on osthol

• Guangyan Luo,
• Zhishu Zeng,
• Lin Zhang,
• Zhu Tao and
• Qianjun Zhang

Beilstein J. Org. Chem. 2021, 17, 22–27, doi:10.3762/bjoc.17.3

• , and high sensitivity [10][11][12]. In recent years, many fluorescent molecular probes have been reported. Because Hg2+ has a very strong quenching effect on fluorescence, most of the fluorescent molecular Hg2+ probes are of the fluorescence-quenching type and are easily interfered with by other

• quenching processes [13][14][15][16][17]. Fluorescence-enhanced probes have received wide attention because of their enhanced fluorescence signal, which can better exclude the influence of instrument noise and other factors, reduce measurement errors, and thus have a higher sensitivity. Osthol (OST) is a

• performance of fluorescent probes. As shown in Figure 1A, the selectivity of OST to common metal ions is monitored by the fluorescence spectrum (λex = 325 nm). OST exhibits a weak fluorescence intensity at λex = 406 nm. When adding different metal ions (Hg2+, Ca2+, Na+, Mg2+, Al3+, Cd2+, Cu2+, Pb2+, Ni2+, Co2

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

• ., the protein–protein interface. Limitations of this approach include the possibility of having no protease cleavage regions in the interface region and the size of the probes used [22]. These limitations can be overcome by using HDXMS. Even though HDX dates back to the 1950s [26], advances in data

• protein–ligand interactions and conformational changes within a protein complex. In addition to this, HDXMS has the advantage of using a low concentration of proteins (in the high-nM or low-µM range) and providing higher-resolution data on the solvent accessibility, compared to probes used in protein

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• fluorescence techniques have attracted immense interest. Synthetic peptide-based fluorescent probes are advantageous over protein-based sensors, since they are synthetically accessible, more stable, and can be easily modified in a site-specific manner for selective biological applications. Peptide receptors

• organic fluorophore (reporter) with a specific peptide sequence is the common approach for designing peptide-based fluorescent probes [16]. Fluorophores on peptidic arms perform as reporter during the interaction with biomolecules [17][18]. The interaction with biomolecules will alter the fluorescence

• intensities of absorption or emission at two wavelengths minimizes the error from the physical or chemical fluctuations in the sample. Conventional peptide probes based on environment-sensitive fluorophores [20][21][22], fluorescence resonance energy transfer (FRET) pairs [13] and pyrene excimer/monomer [23

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

• . Accordingly, the field has developed to a stage that allows custom-design of RNA probes and tools for specific application. For example, investigations of RNA structures by NMR, EPR, or fluorescence spectroscopy require labeling of the RNA molecules with specific reporter groups [2][4][7][8][9][10]. Likewise

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

• labeled bacteria during cell division (Figure 2B). Another research direction in our group, which also involves the development of unconventional fluorescent probes, is the information protection at the molecular level [4][5][6]. In such studies [4][5][6], the emission patterns generated by the probes are

• security systems that can generate (pseudo) random fluorescence patterns [4][5][6]. Originally, the pattern-generating probes (or ID-probes [24]) were designed to detect multiple different analytes and their combinations [24][25][26]. In a later stage, we showed that the unique emission fingerprints