Search results
Search for "identification" in Full Text gives 436 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
The fluorescence of a mercury probe based on osthol
Beilstein J. Org. Chem. 2021, 17, 22–27, doi:10.3762/bjoc.17.3
- be used for the quantitative detection and monitoring of mercury ions in the environment. Results and Discussion OST fluorescence probe for Hg2+ identification Selectivity of the fluorescent OST probe to metal ions The specificity of a probe for metal ions is the key factor to evaluate the
Molecular basis for protein–protein interactions
Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1
- can only be fully exploited via interactions, either in the form of PPIs or with other metabolites and biomolecules, such as nucleic acids. Thus, the identification of the molecular binding partners that proteins interact with is an interesting avenue to facilitate the discovery of the protein
- 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
- fundamental in proteomics, and the identification of PPIs has the potential to confer new drug targets for diseases, such as cancer. As a result, research involving PPIs is imperative for our biological knowledge and future aspects in medicine. Different methodologies employed to study PPIs. The protein used
Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification
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
- digest from affinity-purified immunoglobulins G and A was analyzed on a nano-reversed-phase liquid chromatography–tandem mass spectrometry platform with a high-resolution mass analyzer and higher-energy collisional dissociation fragmentation. Initial glycopeptide identification based on MS/MS data was
- aided by the Byonic software. Additional MS1-based glycopeptide identification relying on accurate mass and retention time differences using GlycopeptideGraphMS considerably expanded the set of confidently annotated glycopeptides. For glycopeptide quantification, the performance of LaCyTools was
Controlled decomposition of SF6 by electrochemical reduction
Beilstein J. Org. Chem. 2020, 16, 2948–2953, doi:10.3762/bjoc.16.244
- also monitored by 19F NMR (Figure 5). After 3 hours experience, unidentified side-products were detected by NMR. Identification of these fleeting species as well as their potential reactivity are under current investigation in our laboratory. The left part of Figure 5 clearly demonstrates the total
On the mass spectrometric fragmentations of the bacterial sesterterpenes sestermobaraenes A–C
Beilstein J. Org. Chem. 2020, 16, 2807–2819, doi:10.3762/bjoc.16.231
- allows to identify interesting candidate genes coding for terpene synthases for further studies by genome mining. A major difficulty in the GC–MS-based identification of terpenes is associated with the high similarity of the mass spectra of structurally related terpenes. For this reason, the unambiguous
- identification of terpenes requires either the direct comparison to an authentic standard, or, since such a standard is not always available, a very good match of the measured mass spectrum to a library spectrum and of the measured retention index to literature data. Mass spectrometric fragmentations proceed
Synthesis of purines and adenines containing the hexafluoroisopropyl group
Beilstein J. Org. Chem. 2020, 16, 2739–2748, doi:10.3762/bjoc.16.224
- rotamers in hand, an Eyring plot was generated, and the enthalpy and entropy of activation were derived (Table 2). The structural identification of the major and minor rotamers was not attempted by NMR, but in silico investigations of 3a supported the intuitive notion that the rotamer of lower energy was
Nocarimidazoles C and D, antimicrobial alkanoylimidazoles from a coral-derived actinomycete Kocuria sp.: application of 1JC,H coupling constants for the unequivocal determination of substituted imidazoles and stereochemical diversity of anteisoalkyl chains in microbial metabolites
Beilstein J. Org. Chem. 2020, 16, 2719–2727, doi:10.3762/bjoc.16.222
- of the genus Kocuria, isolated from a stony coral Mycedium sp., led to the identification of two new alkanoylimidazoles, nocarimidazoles C (1) and D (2) as well as three known congeners, nocarimidazoles A (3) and B (4) and bulbimidazole A (5). Structure analysis of 1 and 2 by NMR and MS revealed that
- alkanoylimidazoles, nocarimidazoles C (1) and D (2), along with the identification of three known related compounds, nocarimidazoles A (3) and B (4) as well as bulbimidazole A (5). We also discuss the stereochemical diversity of the anteisoalkanoyl group in these compounds. Results and Discussion Strain T35-5 was
A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)
Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215
- representations. We believe the utility of these wild-cards extends beyond biosynthesis modeling (Table 9) and may be useful in the description of glycan-chemosynthetic procedures, lectin identification of glycan motifs, and any other purpose where a group of glycans (rather than an individual glycan) is being
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer
Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204
- used to counteract the need for complementary analytic techniques. One of the examples of this is tandem mass spectrometry, where the glycan fragmentation is controlled to obtain the identification of the glycosylation sites and a complete description of the glycan structure compositions, including
- glycan databases. Significantly, the GlyTouCan project aims to create a public repository of known glycan sequences by assigning them unique identification tags. Each identification tag describes a glycan sequence in the WURCS notation, and this allows to link specific glycans to other databases, such as
- and the conformations can be elucidated; middle: A medium resolution example where the identification starts to become difficult; right: A low-resolution example for which all prior knowledge must be used. Despite coming from different glycoprotein structures, the glycan has the same composition, and
Computational tools for drawing, building and displaying carbohydrates: a visual guide
Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199
- aspects of glycan identification, quantification and visualisation, some of which will be further developed throughout this article. Biological molecules express their function throughout their three-dimensional structures. For this reason, structural biology places great emphasis on the three-dimensional
A proposed sustainability index for synthesis plans based on input provenance and output fate: application to academic and industrial synthesis plans for vanillin as a case study
Beilstein J. Org. Chem. 2020, 16, 2346–2362, doi:10.3762/bjoc.16.196
- adequate for rapid identification of best and worst plans in a given set of synthesis plans, whereas, the more detailed poset pairwise dominance analysis is appropriate for obtaining a precise ranking of intermediate performing plans. Application of these ranking methods to 22 synthesis plans for vanillin
Tools for generating and analyzing glycan microarray data
Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187
- positions. This enables identification of terminal residues (i.e. those with all backbone carbon positions without linkages except one). In addition, it uses a new algorithm termed minimum-redundance, maximum-relevance (mRMR) to perform the subtree mining, yielding more fine-tuned results. The authors have
GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis
Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180
- diseased states [8]. The current state-of-the art technology for the characterisation, identification, and quantification of the glycome or glycoproteome is liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) [9]. Popular and powerful glycoproteomic workflows typically involve standard
- packages have been developed for analysis of outputs from MS technology to automate the process of transformation of raw MS data into ion intensities and matching them with appropriate glycan and peptide sequence databases for glycopeptide identification (reviewed in [12][13][14][15][16]). However, there
- use a predefined list of analytes and masses to interrogate MS1 data, and I-GPA [20], GlycopeptideGraphMS [21], GlycoFragwork [22], and GlycReSoft [23], which integrate identification and abundance/intensity information for glycopeptides (a recent review is provided in [10]). Importantly, the
Muyocopronones A and B: azaphilones from the endophytic fungus Muyocopron laterale
Beilstein J. Org. Chem. 2020, 16, 2100–2107, doi:10.3762/bjoc.16.177
- Technologies). DNA sequencing was performed using an Applied Biosystems 3130 genetic analyzer. Silica gel AP-300 (Toyota Kako) was employed for column chromatography (CC). Silica gel 60 F254 and RP-18 F254S (both Merck) were used for TLC. Fungal material and identification Muyocopron laterale ECN279 was
Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations
Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176
- qualitatively curate large cohort CE-LIF glycomics data. For glycan identification, a previously reported method based on internal triple standards is used. For determining the glycan relative quantities our method uses a clustering algorithm to ‘divide and conquer’ highly heterogeneous electropherograms into
- optimization study. The key advantage of this computational approach is that all runs can be analyzed simultaneously with high accuracy in glycan identification and quantitation and there is no theoretical limit to the scale of this method. Keywords: capillary electrophoresis; clustering; data analysis
- antibody glycosylation accurately, high-throughput analysis of hundreds to thousands of profiles is required for the identification of critical process parameters that control the glycosylation CQAs [8]. For complete bioprocessing analysis, favorable glyco-analytical methods need to convey a qualitative
Syntheses of spliceostatins and thailanstatins: a review
Beilstein J. Org. Chem. 2020, 16, 1991–2006, doi:10.3762/bjoc.16.166
- human spliceosome, splicing factor 3b [6], which inhibits pre-mRNA splicing, and as such act as potent cytotoxic compounds. A review of the discovery, target identification, and biological applications of the compounds that exhibit these binding characteristics has been published [7]. These compounds
A complementary approach to conjugated N-acyliminium formation through photoredox-catalyzed intermolecular radical addition to allenamides and allencarbamates
Beilstein J. Org. Chem. 2020, 16, 1983–1990, doi:10.3762/bjoc.16.165
- very challenging and we can account for this instability by the identification of 14a in the 1H NMR spectrum of the crude reaction mixture. A comparable instability profile was observed in the formation of N-acyl-N’-aryl-N,N’-aminals derived from enamides [50]; however, to our knowledge, there are no
- conjugated N-acyliminium intermediate; (b) the calculated HOMO [54] for allenamide 15; (c) the identification of intermediate 14a by direct sample loop and flow injection HRESIMS analysis. Supporting Information Supporting Information File 366: Experimental details, analytical (1H NMR, 13C NMR) and ESIMS
Synthesis of 3(2)-phosphonylated thiazolo[3,2-a]oxopyrimidines
Beilstein J. Org. Chem. 2020, 16, 1947–1954, doi:10.3762/bjoc.16.161
- cyclization through the N3 atom of the starting 2-thiouracil [14][15][16][17][18][19][20][21][22][23][24]. The formation of 7-oxopyrimidines by cyclization through the N1 atom has been noted only in a few reports [29][30][31][32]. However, reliable data for the identification of the 5- and 7-oxo isomers are
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
Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152
- summary of the efforts towards identification of GlfT1 and GlfT2 inhibitors revealed that most compounds were reported to have effects on these enzymes at low mM concentrations (up to 8 mM) [6]. These molecules were designed as substrate mimics or transition state analogs and their IC50 values, ranging
Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies
Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145
- candidates (identification by mass spectrometry), and the other probe, MPC-2, consists of a fluorescent label to test candidates for scramblase activity in reconstitution-based assays. The molecular probes were prepared via phosphoramidite chemistry, which allowed the incorporation of the carbohydrate
- Financial support by the Swiss National Science Foundation (SNSF) is gratefully acknowledged: This research was funded by the Sinergia Project: Molecular identification of lipid transporters for protein glycosylation, Grant CRSII5_170923.
Antibacterial scalarane from Doriprismatica stellata nudibranchs (Gastropoda, Nudibranchia), egg ribbons, and their dietary sponge Spongia cf. agaricina (Demospongiae, Dictyoceratida)
Beilstein J. Org. Chem. 2020, 16, 1596–1605, doi:10.3762/bjoc.16.132
- Voogd, Steve C. de Cook, and Muhammad Abdul Wahab for discussions regarding the sponge identification. The organisms are listed in the collection event list of the Reference Collection of Sam Ratulangi University, Manado, Indonesia (SRU2015/01 SRU2016/02). Collection permits for all collected samples
4-Hydroxy-3-methyl-2(1H)-quinolone, originally discovered from a Brassicaceae plant, produced by a soil bacterium of the genus Burkholderia sp.: determination of a preferred tautomer and antioxidant activity
Beilstein J. Org. Chem. 2020, 16, 1489–1494, doi:10.3762/bjoc.16.124
- compounds and a synthetic preparation of 1, allowed its first full NMR characterization and identification of 2-quinolone but not 2-quinolinol (2) as the preferred tautomer for this heterocyclic system. While the metal-chelating activity was negligible, compound 1 at 10 μM, a concentration lower than that
Oxime radicals: generation, properties and application in organic synthesis
Beilstein J. Org. Chem. 2020, 16, 1234–1276, doi:10.3762/bjoc.16.107
- makes EPR spectroscopy a convenient method for the identification of iminoxyl radicals, and for many of them, EPR is the only observation method due to low stability, and therefore low concentration in investigated systems. For the most stable iminoxyl radicals, sufficiently concentrated solutions were
Anthelmintic drug discovery: target identification, screening methods and the role of open science
Beilstein J. Org. Chem. 2020, 16, 1203–1224, doi:10.3762/bjoc.16.105
- collaboration and the sharing of data and resources between organisations. In this review we discuss how open science has been applied to anthelmintic drug discovery. Open resources, including genomic information from many parasites, are enabling the identification of targets for new antiparasitic agents
- validation of drug targets and the identification of new candidate molecular targets. So how can a free-living worm contribute to our understanding of parasitic nematodes and the development of anthelmintic drugs? A key advantage is the ease of culture of C. elegans. Large numbers can be generated rapidly
- both the target parasite and the genetic model organism, but the precise target remains unclear, then C. elegans genetics can offer a route to target identification that would be difficult by any other route. The C. elegans community: historically an open science model Research into C. elegans was
Accelerating fragment-based library generation by coupling high-performance photoreactors with benchtop analysis
Beilstein J. Org. Chem. 2020, 16, 982–988, doi:10.3762/bjoc.16.87
- halides to get an insight into the specific reactivity of these building blocks. The workflow combined a powerful photoreactor with precise and reproducible conditions control with benchtop analytical tools such as TLC–MS and low-field NMR. This enabled the identification of privileged spirocyclic
Other Beilstein-Institut Open Science Activities
