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Search for "validation" in Full Text gives 89 result(s) in Beilstein Journal of Organic Chemistry.
Navigating and expanding the roadmap of natural product genome mining tools
Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178
- -like structures and prioritized based on the taxonomic distribution of the cluster. decRiPPter was successfully used for the identification of a new lanthipeptide subfamily, providing experimental validation of the algorithm [65]. A more advanced form of supervised learning is deep learning (Figure 4
Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups
Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137
- binding positions (Figure 6a and b) that could lead to restricted ligand flexibility and hence the observed increase of emission. A more detailed experimental validation will be the focus of an experimental study in the near future. Three variants of 1 will be synthesized to gain a deeper insight into the
(Phenylamino)pyrimidine-1,2,3-triazole derivatives as analogs of imatinib: searching for novel compounds against chronic myeloid leukemia
Beilstein J. Org. Chem. 2021, 17, 2260–2269, doi:10.3762/bjoc.17.144
- for designing new series of substances with greater potency and less toxicity than IMT, with lesser effects for the patient. Molecular docking Validation of the molecular docking protocol was performed through redocking of the IMT complexed to the BCR-Abl-1 structure (PDB code: 3PYY) [37]. Thus, the
- structures of the compounds were constructed and optimized by the semi-empirical Recife Model 1 (RM1) method using the Spartan 14 program (Wavefunction, Inc.). Validation of the molecular docking protocol was performed through the redocking of IMT complexed with the BCR-Abl-1 structure (PDB code: 3PYY), free
Nomimicins B–D, new tetronate-class polyketides from a marine-derived actinomycete of the genus Actinomadura
Beilstein J. Org. Chem. 2021, 17, 2194–2202, doi:10.3762/bjoc.17.141
- the dominant tautomers in solution. This is the first validation to state that the keto carbonyl unit in the five-membered ring (C24 in Figure 5) and the acyl ketone connecting at C2 (C3 in Figure 5) are preferably enolized to form stable isomeric structures in spirotetronic acids. The molecular
A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis
Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119
- relationships, the starting point for experimental system-wide validation. Keywords: ChIP-Seq; glycoinformatics; glycosylation; TCGA transcription factor; Introduction The glycan signatures of cells and tissue are controlled by the expression pattern of 300–350 glycosylating-related genes that are together
- signaling pathways contribute to altered glycan structures in diseases such as diabetes and cancer. Thus, this work represents a rich starting point for wet-lab validation and glycoinformatics DB construction. Visualizing TF–glycogene interaction networks revealed communities of glycogenes in each cancer
- experimentally discovering the TFs regulating glycosylation. The findings would likely vary between cell types, and thus additional efforts are necessary before a wet-lab-validated framework emerges. Orthogonal datasets containing other ChIP-Seq and omics data may also enhance in silico validation. Some examples
Recent advances in palladium-catalysed asymmetric 1,4–additions of arylboronic acids to conjugated enones and chromones
Beilstein J. Org. Chem. 2021, 17, 1048–1085, doi:10.3762/bjoc.17.84
- included in the theoretical model. The experimental validation of the predicted results is therefore a challenge that has to be finished [68]. Conclusion In this review, we focused on palladium-catalysed asymmetric 1,4-addition reactions of arylboronic acids to conjugated enones and chromones. The
Novel library synthesis of 3,4-disubstituted pyridin-2(1H)-ones via cleavage of pyridine-2-oxy-7-azabenzotriazole ethers under ionic hydrogenation conditions at room temperature
Beilstein J. Org. Chem. 2021, 17, 156–165, doi:10.3762/bjoc.17.16
- ), DIPEA, DMF, 60 °C, 16 h, 44–71% 32a–h); d) TFA, rt, 30 min. for Boc protected amines (32b,c); e) Pd(OAc)2, TES, DCM/MeOH, rt, 16 h for Cbz protected amines. Selected results from conditions’ screening for pyridin-2-(1H)-one formation (7). Validation of library conditions.a Selected results from
Molecular basis for protein–protein interactions
Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1
- validation of PPIs can then be determined by using HDXMS together with cryoEM. The full thermodynamic profile can subsequently be determined using biophysical methods, yielding the full picture of a particular PPI. For instance, Cash et al. used cryo-EM complemented with HDXMS and enzymatic assays to fully
Pentannulation of N-heterocycles by a tandem gold-catalyzed [3,3]-rearrangement/Nazarov reaction of propargyl ester derivatives: a computational study on the crucial role of the nitrogen atom
Beilstein J. Org. Chem. 2020, 16, 3059–3068, doi:10.3762/bjoc.16.255
- temperature (Table 1, entry 6). However, none of these attempts were met with success, and indeed, a very sluggish reactivity was recorded in all these cases. Unfortunately, these results confirmed the negative predictions arising from the above calculations, but at the same time, they serve as a validation
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
- GlycopeptideGraphMS with MS/MS validation, whereas the Byonic-only search resulted in 35 compositions (Table S4, Supporting Information File 1). Of note, four glycan compositions (H2N3F1, H2N4F1, H5N3F1S1, H5N5F2S1) were not included in the N-glycan search list of Byonic, and hence not included for the calculation of
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
- development, exchange, extension, and validation of glycosylation models and analysis tools. Here we bring explicit attention to the concerns we raise above, we provide a focused, text-based representation of reaction rules that have been introduced for the purpose of formalizing these communications. GlycoCT
- discussed or described. We hope to encourage that adoption through our LiCoRRICE examples. Increased FAIRness will facilitate the validation and distribution of developing glycoinformatics toolkits. Easy-to-use glycoinformatics toolkits, made possible by the fluency of interoperability across tools, are one
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer
Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204
- initiatives have stored results in publicly available databases, some of which can be accessed through API interfaces. In the present work, we will describe how the Privateer carbohydrate structure validation software has been extended to harness results from glycomics projects, and its use to greatly improve
- the validation of 3D glycoprotein structures. Keywords: electron cryomicroscopy; glycoinformatics; glycomics; Privateer; X-ray crystallography; Introduction Glycosylation-related processes are prevalent in life. The attachment of carbohydrates to macromolecules extends the capabilities of cells to
- -centric [15]. As a consequence, the glycan chains in glycoprotein models that have been elucidated before recent developments in carbohydrate validation and modelling software tend to contain a significant amount of errors: wrong carbohydrate nomenclature [13], biologically implausible glycosidic linkage
In silico rationalisation of selectivity and reactivity in Pd-catalysed C–H activation reactions
Beilstein J. Org. Chem. 2020, 16, 1465–1475, doi:10.3762/bjoc.16.122
- initial guess due to particularly bad initial geometry – discard the conformer/intermediate, (iv) decomposed intermediate (no Pd–C bond determined by interatomic distance analysis) – discard intermediate. Literature validation In order to test the developed algorithm, a representative literature data
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
- 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
- /pharmacological proof-of-concept for target validation. Whilst RNA interference and CRISPR methodologies are now being applied to parasites themselves [110][111][112], inevitably, large-scale functional genomic resources are mainly found in C. elegans. The C. elegans Gene Knockout Consortium has obtained putative
- cost. Another open source resource with immediate applicability to target identification and validation is the Open Worm Movement Database [115]. This is an open platform for analysing and sharing worm behavioural data, such as that obtained from worm tracking software. For example, the researcher can
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
- photoreactors. Bottom, from left to right: photoreactor OFF, ON, and ON through protective yellow filter. TLC–MS equipment: analysis of 5 reactions in 5 minutes. Pre-QC validation by 60 MHz benchtop NMR. One-day workflow for fragment-based library generation. QC: Quality control. MPLC: Medium-pressure liquid
Opening up connectivity between documents, structures and bioactivity
Beilstein J. Org. Chem. 2020, 16, 596–606, doi:10.3762/bjoc.16.54
- , structural homology, disease associations and genetic variation (e.g., for target validation). Those cases where the link is only compound-to-document can be referred to as D-C (or c2d). These have become available in a large excess over full DARCLP since they are technically easier to obtain and can be
Synthesis and herbicidal activities of aryloxyacetic acid derivatives as HPPD inhibitors
Beilstein J. Org. Chem. 2020, 16, 233–247, doi:10.3762/bjoc.16.25
- Supporting Information File 1. The chemical structures of all title compounds were confirmed by 1H and 13C NMR spectroscopic analyses and HRMS spectrometric analyses. X-ray diffraction Single crystals of compounds I18 and III4 were cultivated for structure validation. Compound I18 was recrystallized from a
An improved, scalable synthesis of Notum inhibitor LP-922056 using 1-chloro-1,2-benziodoxol-3-one as a superior electrophilic chlorinating agent
Beilstein J. Org. Chem. 2019, 15, 2790–2797, doi:10.3762/bjoc.15.271
- biology of Notum and build target validation to underpin new drug discovery programs. Results: An improved, scalable synthesis of 1 is reported. Key modifications include: (1) the introduction of the C7-cyclopropyl group was most effectively achieved with a Suzuki–Miyaura cross-coupling reaction with MIDA
- to 1 which contains functional groups sensitive to certain reagents employed (vide infra). An improved synthetic route should allow 1 to become more readily available as a chemical tool to explore the fundamental biology of Notum and build target validation to underpin new drug discovery programs for
Host–guest interactions between p-sulfonatocalix[4]arene and p-sulfonatothiacalix[4]arene and group IA, IIA and f-block metal cations: a DFT/SMD study
Beilstein J. Org. Chem. 2019, 15, 1321–1330, doi:10.3762/bjoc.15.131
- + Mn+ → [C[4]A–M](4−n)− and TC[4]A + Mn+ → [TC[4]A–M](4−n)−. Metal cationic radii (Å). Supporting Information Supporting Information File 144: Validation of the chosen computational level, additional structural data and thermodynamic parameters for the complex formation reactions.
Understanding the unexpected effect of frequency on the kinetics of a covalent reaction under ball-milling conditions
Beilstein J. Org. Chem. 2019, 15, 1226–1235, doi:10.3762/bjoc.15.120
- developing a fundamental understanding of these solid-state processes. The validation of reaction kinetic models has been a powerful approach for investigating fundamental processes in chemistry and physics. This has led to significant advancement in the understanding of molecular and submolecular phenomena
Unexpected polymorphism during a catalyzed mechanochemical Knoevenagel condensation
Beilstein J. Org. Chem. 2019, 15, 1141–1148, doi:10.3762/bjoc.15.110
- data using cross validation with 20 randomly selected segments. MCR iterations were initialized with the constraints of "non-negative spectra" and "non-negative concentrations", and sensitivity to pure compounds was set to 100. The maximum number of iterations was set at 250. Mass spectrometry: Mass
New terpenoids from the fermentation broth of the edible mushroom Cyclocybe aegerita
Beilstein J. Org. Chem. 2019, 15, 1000–1007, doi:10.3762/bjoc.15.98
- spectrometry and NMR spectroscopy. The relative configurations of 2–4 were assigned by ROESY correlations, and 3JH,H coupling constants in the case of 4. Applying quantitative PCR for gene expression validation, we linked the production of bovistol and its derivatives to the respective biosynthesis gene
Design and synthesis of multivalent α-1,2-trimannose-linked bioerodible microparticles for applications in immune response studies of Leishmania major infection
Beilstein J. Org. Chem. 2019, 15, 623–632, doi:10.3762/bjoc.15.58
- intracellular monitoring and validation of T cell antigen presentation. This new probe would also be linked to the surface of a polyanhydride copolymer microparticle based on 1,6-bis(p-carboxyphenoxy)hexane (CPH) and sebacic anhydride (SA) to allow for enhanced internalization and uptake of the immunogenic
- pathogen (1 μm in diameter) and provide a multivalent display of the synthetic α-1,2-trimannose similar to the Leishmania promastigote cell-wall glycans. Furthermore, a tethered fluorophore would allow for immunofluorescence assays, intracellular trafficking, and validation of T cell-mediated antigen
Synthesis of the polyketide section of seragamide A and related cyclodepsipeptides via Negishi cross coupling
Beilstein J. Org. Chem. 2019, 15, 577–583, doi:10.3762/bjoc.15.53
- A (1, Scheme 1) [1][2], is an ideal situation for the validation of the chemoselectivity and efficiency of photoaffinity labelling. Recently, it has been determined by cryo-electron microscopy how jasplakinolide A (1) binds to F-actin and alters the actin skeleton in vivo, resulting in pronounced
Aqueous olefin metathesis: recent developments and applications
Beilstein J. Org. Chem. 2019, 15, 445–468, doi:10.3762/bjoc.15.39
- reactions can be integrated in the toolbox of chemical proteomics. Recently, following a similar strategy, Lu et al. reported on-DNA RCM and CM, an application potentially useful to generate DNA-encoded libraries for hit identification and target validation [90]. Substrates appended to oligonucleotides
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