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

• percentage of Cy5-positive cell detection and a higher MFI compared to the hCMEC/D3 barrier (Figure 2D and Supporting Information File 1, Figure S4). Collectively, these data suggest that the candidate LNPs, particularly LNP B9 G-3 T7, may increase uptake through tight junctions and prove useful in

• Nano ZS (Malvern Instruments, UK), having He–Ne 633 nm laser at an angle of detection of 90°, with an incubation time of 60 s. Samples were diluted 50-fold in Milli-Q water and placed into the disposable plastic cuvettes for measurement performed in triplicates (n ≥ 3) to obtain a mean value. NTA

• h later, the apical layer was removed, and the basolateral cells were washed, trypsinized, and resuspended in 1× PBS. Detection of Cy5 was measured by flow cytometry on a BD Accuri™ C6 device (Becton, Dickinson and Company, NJ), and the data was analyzed using FlowJo™ Version 10.7.1 (Becton

Microwave-assisted multicomponent reactions in heterocyclic chemistry and mechanistic aspects

• Shivani Gulati,
• Stephy Elza John and
• Nagula Shankaraiah

Beilstein J. Org. Chem. 2021, 17, 819–865, doi:10.3762/bjoc.17.71

• organic synthesis (2000–10), witnessed microwaves with optic fibre or IR pyrometers for temperature detection along with specific glass reaction vessels that can withstand pressure and temperature in the reaction generated especially by low boiling solvents. Microwave-assisted heating reduces reaction

Synthesis and physicochemical evaluation of fluorinated lipopeptide precursors of ligands for microbubble targeting

• Masayori Hagimori,
• Estefanía E. Mendoza-Ortega and
• Marie Pierre Krafft

Beilstein J. Org. Chem. 2021, 17, 511–518, doi:10.3762/bjoc.17.45

• blood circulation times by allowing them to evade immune detection. PEGs often play a key role in the design of the ligands as a spacer between the nanocarrier surface and the lipid. PEGs have, however, some shortcomings, such as a broad molecular weight distribution, large steric hindrance, and the

Identification of volatiles from six marine Celeribacter strains

• Anuj Kumar Chhalodia,
• Jan Rinkel,
• Dorota Konvalinkova,
• Jörn Petersen and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2021, 17, 420–430, doi:10.3762/bjoc.17.38

• (indole-2H5)tryptophan were performed, but none of these experiments resulted in a detectable incorporation of labeling. Conclusively, a non-biological origin of this part of the molecule seems likely, which may also explain why the detection of 41 in Celeribacter was not always reproducible. Notably, 2

1,2,3-Triazoles as leaving groups: S_NAr reactions of 2,6-bistriazolylpurines with O- and C-nucleophiles

• Dace Cīrule,
• Irina Novosjolova,
• Ērika Bizdēna and
• Māris Turks

Beilstein J. Org. Chem. 2021, 17, 410–419, doi:10.3762/bjoc.17.37

• Agilent Technologies 1200 Series chromatograph equipped with an Agilent XDB-C18 (4.6 × 50 mm, 1.8 µm) column was used. Eluent A: 0.1% TFA solution with 5% v/v MeCN added; eluent B – MeCN. Gradient: 10–95% B 5 min, 95% B 5 min, 95–10% B 2 min. Flow: 1 mL/min. Wavelength of detection was 260 nm. LC–MS was

Regioselective chemoenzymatic syntheses of ferulate conjugates as chromogenic substrates for feruloyl esterases

• Olga Gherbovet,
• Fernando Ferreira,
• Apolline Clément,
• Mélanie Ragon,
• Julien Durand,
• Sophie Bozonnet,
• Michael J. O'Donohue and
• Régis Fauré

Beilstein J. Org. Chem. 2021, 17, 325–333, doi:10.3762/bjoc.17.30

• , France 10.3762/bjoc.17.30 Abstract Generally, carbohydrate-active enzymes are studied using chromogenic substrates that provide quick and easy color-based detection of enzyme-mediated hydrolysis. For feruloyl esterases, commercially available chromogenic ferulate derivatives are both costly and limited

• lignocellulosic matrix. Moreover, Faes are useful tools to obtain commercially relevant ferulic acid, which represents up to 3 wt % of plant the cell wall dry weight [8]. So far, the detection and characterization of Faes has mainly relied on either the use of HPLC or on UV–visible spectrophotometry, using

• ] and (ii) spontaneous oxidation and subsequent dimerization forming the insoluble blue 5-bromo-4-chloro-substituted indigo dye [15]. In an alternative demonstration, 1a was also used for colony level detection of FAE using yeast cells (Yarrowia lipolytica [30]) that actually coexpressed AnFaeA and

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

• estrogen receptor (ER) co-activator peptides and enabled the sensitive detection of their protein–peptide interaction inhibition by the ER antagonist tamoxifen [20]. Significantly, different secondary structure conformational preferences were also found among the diastereomers of perfluoro-tert

• the aforementioned issues, Virta and co-workers have explored the application of trifluoromethyl analogues of guanosine, cytidine and uridine based in 2’-O-[(4-trifluoromethyltriazol-1-yl)methyl] reporter groups as 19F NMR probes for the detection of RNA secondary structures (Figure 14). As shown by

• , but only one could be detected (SF5-catechol) despite the 19F NMR analysis showing the presence of multiple fluorometabolites. Detection and biosynthesis of natural organofluorine compounds As naturally-occurring organofluorine compounds are so rare, it is possible to easily detect them in a crude

1,2,3-Triazoles as leaving groups in S_NAr–Arbuzov reactions: synthesis of C6-phosphonated purine derivatives

• Kārlis-Ēriks Kriķis,
• Irina Novosjolova,
• Anatoly Mishnev and
• Māris Turks

Beilstein J. Org. Chem. 2021, 17, 193–202, doi:10.3762/bjoc.17.19

• an Agilent Technologies 1200 Series system equipped with an XBridge C18 column, 4.6 × 150 mm, particle size 3.5 μm, with a flow rate of 1 mL/min, using eluent A–0.1% TFA/H2O with 5 vol % MeCN and eluent B–MeCN as the mobile phase. The wavelength of detection was 260 nm. Gradient: 30–95% B 5 min, 95

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

• selectivity for Hg2+. The fluorescence intensity of OST showed a good linear correlation with the Hg2+ concentration (6.0 × 10−5 to 24.0 × 10−5 mol∙L−1, R2 = 0.9954), and the detection limit of the probe was 5.04 × 10−8 mol∙L−1, which can be used for the determination of Hg2+ traces. Keywords: fluorescence

• irreversible nerve damage. Therefore, it is very important to develop a highly sensitive and selective method for mercury detection. At present, the detection of mercury mainly includes atomic absorption and atomic emission spectrometry [4], inductively coupled plasma mass spectrometry [5][6], and capillary

• electrophoresis [7]. However, the application of these analytical methods in mercury detection is limited due to the complex sample pretreatment procedures, expensive instruments, and other factors [8][9]. Fluorescent-probe instruments have been widely used due to the advantages of the simple operation, low cost

Synthesis, crystal structures and properties of carbazole-based [6]helicenes fused with an azine ring

• Daria I. Tonkoglazova,
• Anna V. Gulevskaya,
• Konstantin A. Chistyakov and
• Olga I. Askalepova

Beilstein J. Org. Chem. 2021, 17, 11–21, doi:10.3762/bjoc.17.2

• -detection (see Supporting Information File 1, Figures S38–S40). X-ray molecular structures The structures of the title compounds 10a–c were further explored by a single-crystal X-ray diffraction analysis (Figure 1, see also Supporting Information File 1, Figures S35–S37 and Table S1) and compared with that

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

• developed to facilitate and improve both the identification and quantification of glycopeptides. Here, a selection of these tools was combined and evaluated with the aim of establishing a robust glycopeptide detection and quantification workflow targeting enriched glycoproteins. For this purpose, a tryptic

• ]. Advances in MS technologies tremendously enhanced the detection and informative fragmentation of glycopeptides in the past years [9]. The large amount of highly complex data acquired using these technologies shifted the major bottleneck in glycopeptide analysis to the data processing steps. Next to the

• coverage was maximized by combining all measurements. For the MS1-based assignment, the variation between replicates was found in the minor glycan species, which were on the borderline of the limit of detection. Further, the stochastic nature of MS/MS selection is a known factor, which may cause

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

• , and Paenibacillus. The remaining most abundant genera in the mock communities were below the detection limit. The comparison of the abundance ratios between the control communities and B. subtilis WT-treated communities revealed that Lysinibacillus and Viridibacillus were significantly decreased 9.4

• indicated a significantly lower (P ≤ 0.01) abundance (0.03%) compared to the control communities. Notably, in two of the WT-treated community replicates, Viridibacillus was below the detection level. Nevertheless, the abundance of this genus in the sfp-treated communities (0.26%) was statistically not

• back to different growth rates among the present species. A substantial shift in the community compositions was observed between in vivo and in vitro communities since the majority of the genera present in the in vitro communities was below the detection limit in the soil sample. However, during the 12

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

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

• labeled with environmentally sensitive/FRET fluorophores have allowed direct detection/monitoring of biomolecules in aqueous media and in live cells. In this review, key peptide-based approaches for different biological applications are presented. Keywords: fluorescent probe; fluorophores; molecular

• for biomolecule detection [27][28]. Being intrinsically modular, peptide scaffolds also allow the attachment of multiple fluorophores simultaneously [29]. It provides the opportunity of developing ratiometric fluorescent sensors from the interaction between multiple fluorophores (Figure 1B

• to perform FRET in vitro and in vivo, particularly in living cells [30]. FRET-based peptide probes are heavily used for ratiometric fluorescence detection of biomolecules. Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs) are considerably used for targeting nucleic acids [31

Controlled decomposition of SF₆ by electrochemical reduction

• Sébastien Bouvet,
• Bruce Pégot,
• Stéphane Sengmany,
• Erwan Le Gall,
• Eric Léonel,
• Anne-Marie Goncalves and
• Emmanuel Magnier

Beilstein J. Org. Chem. 2020, 16, 2948–2953, doi:10.3762/bjoc.16.244

• , CNRS, ICMPE, UMR 7182, 2 rue Henri Dunant, 94320 Thiais, France 10.3762/bjoc.16.244 Abstract The electroreduction of SF6 is shown at ambient temperature in acetonitrile using an array of platinum microelectrodes to improve the electrical detection. Its half reduction potential occurs at −2.17 V vs Fc

• . All potentials were measured against a pseudo silver reference electrode (SRE). The addition of ferrocene in the electrolyte gives access to an internal reference [33]. In order to improve the current detection level of SF6, platinum disk electrodes were used as working electrode (Pt

• counter electrode. Electrochemical measurements were covered by a wide range of a potentiostat for more effective current detection. A potentiostat–galvanostat such as Princeton Applied Research Model 263 was monitored by its front panel and analogue-to-digital conversion was provided by «Powerlab». A

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

• reversibility was achieved by the addition of the rhodium porphyrin 19 that reversed the system reviving the state SelfSORT-I. Since both self-sorted states exhibited a distinct fluorescence due to the changes at the zinc porphyrin sites, luminescence was used for the selective detection of DABCO in a mixture

3-Acetoxy-fatty acid isoprenyl esters from androconia of the ithomiine butterfly Ithomia salapia

• Florian Mann,
• Daiane Szczerbowski,
• Lisa de Silva,
• Melanie McClure,
• Marianne Elias and
• Stefan Schulz

Beilstein J. Org. Chem. 2020, 16, 2776–2787, doi:10.3762/bjoc.16.228

• vicinity of the male wings, although the evaporation rate might be increased by erection of the androconia hairpencils (Figure 1). Alternatively, direct or close contact might be needed for detection, probably taking place during contact of the female antennae with the male wings. What this potential

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

• presence of positive surface charges on the multivalent aggregates led to ATP binding which was accompanied by a significant increase in the excimeric emission intensity. This provided a convenient way of monitoring ATP binding in a “turn-on” mode and an efficient detection of ATP was achieved in aqueous

• buffer and also in buffer containing 150 mM NaCl at physiological pH value. Furthermore, the multivalent aggregates demonstrated a significant selectivity in ATP detection over ADP, AMP and pyrophosphate. Keywords: amphiphile; ATP; excimer; multivalency; self-assembly; Introduction Supramolecular anion

• years, anion responsive materials [5][6] have also emerged as an interesting class of stimuli-responsive materials. Among the different varieties of anionic species, the selective and sensitive detection of bio-anions is particularly important due to their involvement in various biological functions

Nocarimidazoles C and D, antimicrobial alkanoylimidazoles from a coral-derived actinomycete Kocuria sp.: application of ¹J_C,H coupling constants for the unequivocal determination of substituted imidazoles and stereochemical diversity of anteisoalkyl chains in microbial metabolites

• Md. Rokon Ul Karim,
• Enjuro Harunari,
• Amit Raj Sharma,
• Naoya Oku,
• Kazuaki Akasaka,
• Daisuke Urabe,
• Mada Triandala Sibero and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 2719–2727, doi:10.3762/bjoc.16.222

• purification was achieved by preparative HPLC (Cosmosil AR-II, Nacalai Tesque Inc., 10 × 250 mm, 4 mL/min, UV detection at 254 nm) with an isocratic elution of MeCN/0.1% HCO2H (42:58) to afford nocarimidazole C (1, 2.4 mg, tR 8.45 min), nocarimidazole D (2, 3.2 mg, tR 14.9 min), nocarimidazole A (3, 3.8 mg, tR

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

• /bjoc.16.219 Abstract Gold nanoparticles covered with a mixture of ligands of which one type contains solubilizing triethylene glycol residues and the other peripheral zinc(II)–dipicolylamine (DPA) complexes allowed the optical detection of hydrogenphosphate, diphosphate, and triphosphate anions in

• )–dipicolylamine complexes beyond 25% had a negative impact on the limit of detection and the optical response. Transmission electron microscopy provided evidence that the changes of the nanoparticle properties observed in the presence of the phosphates were due to a nanoparticle crosslinking, consistent with the

• conformational reorganization of the linker connecting the chromophore with the surface. The likely most frequently used strategy of analyte detection relies on the color change of AuNP solutions resulting from analyte-induced nanoparticle crosslinking. Depending on whether soluble or insoluble aggregates are

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• formed to another carbohydrate unit. Crucially, the linkage detection in Privateer does not rely at all on metadata present in the structure file. Instead, linkages are identified based on the perceived chemistry of the input model: which atoms are close enough – but not too close – to be plausibly

• , glycoprotein models deposited in the PDB feature flaws ranging from minor irregularities to gross modelling errors [14][17][41][64]. The automated validation of minor irregularities was already possible with automated tools such as pdb-care [37], CARP [65], and Privateer [24]. However, the automated detection

• of gross modelling errors is currently a challenge due to the lack of publicly available tools. Our newly developed computational bridge between structural biology and glycomics databases makes the detection of gross modelling errors easier, as demonstrated by the following examples. Example 1 – 2H6O

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

• . If a signal broadens beyond detection and thus disappears from the spectrum, be it due to aggregation or intermediate exchange kinetics, it is also impossible to trace its trajectory and determine the chemical shift perturbation. In the case of a bifunctional GCP ligand binding to survivin [46], the

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• information, coupled with the emergence of new platforms and technologies, has benefitted glycoscience to the point of enabling the detection and high-resolution determination and representation of complex glycans [1]. Increasing numbers of carbohydrate sequences have accumulated throughout extensive work in

Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties

• Anka Utama Putra,
• Deniz Çakmaz,
• Nurgül Seferoğlu,
• Alberto Barsella and
• Zeynel Seferoğlu

Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189

• excitation leads to a red-shifted emission which is viable for the detection of various substrates in biological tissues and samples [28][29][30]. Recently, there was an increasingly growing interest in studies regarding push-pull organic molecules comprising of the dicyanomethylene group as a strong

• light indicated that the dye was deprotonated. Indeed, the addition of only 5 equiv of TFA regenerated the light yellow color of the solution indicative for the reversed protonation of 12. All dyes, except 8, showed this reversibility. Furthermore, the limits of detection (LOD) and quantification (LOQ

Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• utilizes a different mechanism of binding the ligands to the surface. Choosing an appropriate surface often depends on the type of glycoconjugates to be printed, as well as the GBP and detection wavelengths used. For example, a nitrocellulose surface has an intrinsic high background when scanned at 488 nm

• wavelength, thus making the surface incompatible with detection reagents which rely on this wavelength. While it is possible to use nitrocellulose slides at 488 nm wavelength with lower detector sensitivity (PMT setting) and lower scan power (laser power), it might be more advisable to check other

• placed on slide (≈70 μL), and a coverslip is placed on top to spread the sample evenly across the array surface of the slide and helps to prevent evaporation during the assay. Detailed protocols for either method of microarray experiment and that cover different types of samples and detection methods are

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• assumed to not quantitatively affect detection. These results were concatenated into the final output file, where columns are the different samples and rows are the different peptide and glycoforms that have been analysed. The protein name of each glycosylated protein detected in the analysis was also