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Search for "protein" in Full Text gives 655 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
Synthesis of N-acetyl diazocine derivatives via cross-coupling reaction
Beilstein J. Org. Chem. 2025, 21, 490–499, doi:10.3762/bjoc.21.36
- accumulation in the environment after excretion [1][6][7]. These superior properties of diazocines have been exploited in several applications such as the control of protein folding by implementation as cross-linkers between protein side chains [8] or in peptide backbones [9], as photoswitchable
Synthesis of electrophile-tethered preQ1 analogs for covalent attachment to preQ1 RNA
Beilstein J. Org. Chem. 2025, 21, 483–489, doi:10.3762/bjoc.21.35
- transcription or translation of the mRNA and results in altered transcript and/or protein levels [5]. In recent years, there has been a growing interest in the modification of preQ1. preQ1 derivatives, preQ1 analogs and mimics of preQ1 have greatly expanded our understanding of preQ1-binding biomolecules, such
- preQ1 congeners into oligonucleotide strands at specific recognition sites. In addition, the potential of modified preQ1 for protein enzyme-independent RNA labeling has also been demonstrated [12][17]. In a recent study [4], sequence-specific RNA–small molecule crosslinking (Scheme 1B) was achieved in
- our research program to tailor non-covalent RNA–small molecule ligands to their covalent counterparts. While “covalent drugs” have become a leading principle in medicinal chemistry in the “protein world” [35][36] – approximately 30% of all FDA-approved drugs form a covalent bond with their target
Identification and removal of a cryptic impurity in pomalidomide-PEG based PROTAC
Beilstein J. Org. Chem. 2025, 21, 407–411, doi:10.3762/bjoc.21.28
- Bingnan Wang Yong Lu Chuo Chen Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA 10.3762/bjoc.21.28 Abstract Chemically induced dimerization is a powerful tool for studying protein function, wherein the IMiD (the “immunomodulatory
- drug”) class of PROTAC molecules with a PEG linker is frequently used to promote targeted protein degradation. The standard protocol for their synthesis involves nucleophilic aromatic substitution of 4-fluorothalidomide with a PEG-amine. We report herein the identification of a commonly ignored
- contamination. Keywords: glutarimide; IMiD; impurity; nucleophilic acyl substitution; PROTAC; Introduction Targeted protein degradation capitalizing on the concept of chemically induced dimerization has emerged as a new therapeutic approach recently [1]. In particular, the modularity of proteolysis targeting
Synthesis, characterization, antimicrobial, cytotoxic and carbonic anhydrase inhibition activities of multifunctional pyrazolo-1,2-benzothiazine acetamides
Beilstein J. Org. Chem. 2025, 21, 348–357, doi:10.3762/bjoc.21.25
- evolves [3]. Complex chemical scaffolds with more than one protein-engaging functionality in a single molecule are advantageous for selectivity. This concept of synergistic compounds and complex chemical interactions helps to boost biological activity and prolongs the emergence of resistance in pathogens
Antibiofilm and cytotoxic metabolites from the entomopathogenic fungus Samsoniella aurantia
Beilstein J. Org. Chem. 2025, 21, 327–339, doi:10.3762/bjoc.21.23
- Information File 1), it is likely that the activity of farinosones D (1) and A (2) does not interfere with the factors essential for fibronectin binding, particularly the fibronectin-binding proteins such as fibronectin binding protein (FnBPA and B) [18]. FnBPs are adhesions and are known to play a key role
Synthesis of disulfides and 3-sulfenylchromones from sodium sulfinates catalyzed by TBAI
Beilstein J. Org. Chem. 2025, 21, 253–261, doi:10.3762/bjoc.21.17
- groups in organic synthesis [1][2][3][4]. In chemistry and biology, disulfide bonds play crucial roles in protein folding and stabilization [5][6][7][8] and in the rubber industry, they are used to link different polymer chains [9][10]. The disulfide bond backbone is commonly used as a linker for
Chemical glycobiology
Beilstein J. Org. Chem. 2025, 21, 8–9, doi:10.3762/bjoc.21.2
- certainly by choice, but also by necessity. It is difficult to convey to non-glycoscientists how we still struggle with challenges that have been solved years or decades ago for proteins and nucleic acids. When molecular cloning and recombinant protein production became routine, these technologies were not
- in the glycosciences. A key aspect is the modelling of protein–glycan interactions. Marcisz et al. study the power of umbrella sampling in distinguishing the interactions between different glycosaminoglycans and their receptors [14]. Nieto-Fabregat et al. provide a detailed overview on computational
Synthesis of extended fluorinated tripeptides based on the tetrahydropyridazine scaffold
Beilstein J. Org. Chem. 2024, 20, 3174–3181, doi:10.3762/bjoc.20.262
- ; Introduction The synthesis of molecules capable of mimicking the various secondary structures and key functions of proteins is a major challenge in medicinal chemistry, especially in the fields of protein–protein interactions [1][2]. Accordingly, the incorporation of heterocyclic amino acids into peptides
Multicomponent reactions driving the discovery and optimization of agents targeting central nervous system pathologies
Beilstein J. Org. Chem. 2024, 20, 3151–3173, doi:10.3762/bjoc.20.261
- antagonist of the N-methyl-ᴅ-aspartate (NMDA) receptor to regulate excessive glutamate stimulation [27]. The β-amyloid hypothesis for AD is based on the formation of senile plaques, which are formed after the accumulation of insoluble aggregates of β-amyloid protein, primarily Aβ-42, in the brain. The gene
- for amyloid precursor protein (APP), found on chromosome 21, undergoes a mutation that causes the production of Aβ-42 instead of Aβ-40. APP, a transmembrane protein, is typically cleaved by α-secretase and γ-secretase, which leads to the formation of soluble Aβ-40. However, when cleaved by β-secretase
- and γ-secretase, it produces Aβ-42. This form misfolds, leading to the formation of insoluble protein aggregates known as senile plaques, causing toxicity [28][29]. Oxidative stress occurs when there is an imbalance between prooxidants and antioxidants in the body, leading to damage in various
Chemical structure metagenomics of microbial natural products: surveying nonribosomal peptides and beyond
Beilstein J. Org. Chem. 2024, 20, 3050–3060, doi:10.3762/bjoc.20.253
- protein sequencing by Edman degradation used to be standard practice in studying proteins but nowadays is rarely performed [39]. This is because the rules of transcription and translation are understood well enough for the sequence of a protein (its primary structure) to be predicted based on the
- recognizes and activates a specific substrate BB. Notably, the BBs are in most cases amino acids, wherein a much broader variety are used in NRP biosynthesis than the 20 canonical amino acids used in protein biosynthesis [52]. The modules are usually arranged co-linearly to the BGC sequence, which makes
- ]. It is unlikely that a Syn-BNP is able to target a specific protein or pathway, unless it in fact recapitulated key structural feature(s) of a NRP. These observations are a testament to the feasibility of this approach. This approach has also been applied to focus on NRPs with particular physical
Recent advances in transition-metal-free arylation reactions involving hypervalent iodine salts
Beilstein J. Org. Chem. 2024, 20, 2891–2920, doi:10.3762/bjoc.20.243
- ) [91]. This method manifests the synthesis of stable thioether-linked synthetic conjugates 93 and 96 displaying its efficacy via the alteration of the affibody zEGFR and the histone protein H2A. The procedure involved synthesizing the diaryliodonium salt and appraising the proficiency of oxime ligation
- chemistry on the histone H2A protein. The protein was demonstrated as the T120C mutant via site-directed mutagenesis in Escherichia coli and decontaminated by HPLC. A notable reconciliation was changing the aqueous buffer from HEPES to phosphate owing to side-product generation during the arylation in HEPES
- protein conjugate was effectively done with various hydroxylamines with the assistance of the nucleophilic catalyst 5-methoxyanthranilic acid. The resultant histone protein conjugates were functionalized with TAMRA, biotin and the cell-penetrating peptide 'penetratin' through oxime ligation, achieving
N-Glycosides of indigo, indirubin, and isoindigo: blue, red, and yellow sugars and their cancerostatic activity
Beilstein J. Org. Chem. 2024, 20, 2840–2869, doi:10.3762/bjoc.20.240
- , and Parkinson's disease, cardiovascular diseases, inflammation, AIDS and others have their origin in context with the activities of protein kinases, such as glycogen synthase kinase-3 (GSK-3β) and cyclin-dependent kinases (CDK’s). The phosphorylation of the amino acid moieties of several enzymes is
- controlled by such protein kinases. Therefore, the investigation of the influence of drugs on protein kinases plays an important role in current medicinal chemistry. Indigo naturalis is a traditional drug, derived from indigo plants, which has been used in China for centuries and also more recently against
- entirely cancelled by antioxidative pretreatment and cancer cell viability and proliferation were fully regenerated. Complete activation of cascades of caspases-3, -4, -6, -7, -8, and -9, loss of mitochondrial membrane potential, activation of proapoptotic PKCδ (protein kinase C delta), and inhibition of
Synthesis and antimycotic activity of new derivatives of imidazo[1,2-a]pyrimidines
Beilstein J. Org. Chem. 2024, 20, 2806–2817, doi:10.3762/bjoc.20.236
- fingerprints (IFP) between the docking ligands and the protein shows that, similar to the reference ligand voriconazole, the compounds interact with the protein through hydrophobic interactions with hydrophobic residues of the protein and the formation of coordination bonds with the haem iron (Table 3). At the
- ) Superposition of docked compounds 4a–e and 5e in a CYP51 ACb. aThe amino acid residues of the protein are colored green, compound 4e is colored gold and the haem is colored grey. The heterocyclic nitrogen of compound 5e appears to be orientated towards iron and is located 2.8 Å away from it, which may indicate
- –protein interactions for voriconazole and compounds selected during docking.a Supporting Information Supporting Information File 14: General reaction procedures, compound characterization data, copies of NMR and mass spectra for all new products. Acknowledgements The research results were partially
Synthesis of fluoroalkenes and fluoroenynes via cross-coupling reactions using novel multihalogenated vinyl ethers
Beilstein J. Org. Chem. 2024, 20, 2691–2703, doi:10.3762/bjoc.20.226
- fact, several inhibitors of the β-site amyloyd β A4 precursor protein cleaving enzyme (BACE1), which is involved in the production of β-amyloid, and fluoroalkene analogs of dipeptidyl peptidase-4 inhibitors have previously been reported [2][3]. These inhibitors possess higher drug efficacies than their
Applications of microscopy and small angle scattering techniques for the characterisation of supramolecular gels
Beilstein J. Org. Chem. 2024, 20, 2608–2634, doi:10.3762/bjoc.20.220
Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers
Beilstein J. Org. Chem. 2024, 20, 2323–2341, doi:10.3762/bjoc.20.199
- provide unprecedented depth of proteome coverage and the possibility to detect desired modified peptides with high sensitivity. The chemical ‘linker’ connecting an active compound–protein conjugate with a detection tag is the critical component of all chemical proteomic workflows. In this review, we
- disease [2][3]. In parallel, mass spectrometry (MS) has been crucial in many areas centered around the characterization of NPs [4]. First to annotate their often complex structures using diverse fragmentation techniques [4]. Nowadays, MS is applied for the identification of NPs’ cellular protein targets
- the desired protein coverage and robustness. Still, the critical part of the process starts with the careful design of a NP analogue and selection of the proper biological system, which may include animal models, 3D tissue-organoids, or 2D cell culture. Depending on the project aim, which typically
Cell-free protein synthesis with technical additives – expanding the parameter space of in vitro gene expression
Beilstein J. Org. Chem. 2024, 20, 2242–2253, doi:10.3762/bjoc.20.192
- established itself as a successful tool in organic synthesis. A particularly fast technique for screening enzymes is the in vitro expression or cell-free protein synthesis (CFPS). The system is based on the transcription and translation machinery of an extract-donating organism to which substrates such as
- nucleotides and amino acids, as well as energy molecules, salts, buffer, etc., are added. After successful protein synthesis, further substrates can be added for an enzyme activity assay. Although mimicking of cell-like conditions is an approach for optimization, the physical and chemical properties of CFPS
- tested additives. Keywords: cell-free protein synthesis; cGAS; Escherichia coli cell-free extract; sfGFP; TX-TL; Introduction In addition to other applications such as biomanufacturing or biosensing, cell-free protein synthesis (CFPS) of enzymes has established itself as a tool for rapid screening of
Natural resorcylic lactones derived from alternariol
Beilstein J. Org. Chem. 2024, 20, 2171–2207, doi:10.3762/bjoc.20.187
- isolated. Nevertheless, alternariol sulfates were isolated from Alternaria sp. and alternariol-9-O-sulfate (14) turned out to be active against 23 protein kinases with IC50 values ranging from 0.22 to 8.4 µg/mL and to be cytotoxic against L5178Y cells (EC50: 4.5 µg/mL) [147]. The sulfated 9-O
- ] and Alternaria sp. [28][47][154] (Figure 8). It showed antioxidant activity with an IC50 value of 42.8 μM [153], inhibited about 90% of iNOS (inducible nitric oxide synthase) expression when applied at 20 μM, decreased the protein expression levels of pro-inflammatory cytokines (tumor necrosis factor
- -α, interleukin-6, and monocyte chemotactic protein 1), and reduced the production of NO as low as 10 μM in LPS-induced RAW264.7 cells [154]. Biosynthetic metabolization of alternariol and its 9-O-methyl ether is predominantly started with a hydroxylation in 4-position (c.f., chapter on biosynthesis
O,S,Se-containing Biginelli products based on cyclic β-ketosulfone and their postfunctionalization
Beilstein J. Org. Chem. 2024, 20, 2143–2151, doi:10.3762/bjoc.20.184
- Supporting Information File 1). Next, we paid attention to testing the conditions we developed for the synthesis of the SO2-containing analogue 2r of potent anticancer drug enastron in gram scale (Scheme 3). Enastron is a novel dihydropyrimidine-based mitotic kinesin spindle protein KSP/Eg5 inhibitor [36
Computational toolbox for the analysis of protein–glycan interactions
Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180
- Ferran Nieto-Fabregat Maria Pia Lenza Angela Marseglia Cristina Di Carluccio Antonio Molinaro Alba Silipo Roberta Marchetti Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy 10.3762/bjoc.20.180 Abstract Protein–glycan interactions play pivotal roles in
- , both in free state and in complex with proteins, also with reference to the principles, methodologies, and applications of all-atom molecular dynamics simulations. Herein, we focused on the programs that are generally employed for preparing protein and glycan input files to execute molecular dynamics
- simulations and analyse the corresponding results. The presented computational toolbox represents a valuable resource for researchers studying protein–glycan interactions and incorporates advanced computational methods for building, visualising and predicting protein/glycan structures, modelling protein
Regioselective alkylation of a versatile indazole: Electrophile scope and mechanistic insights from density functional theory calculations
Beilstein J. Org. Chem. 2024, 20, 1940–1954, doi:10.3762/bjoc.20.170
- the treatment of paroxysmal nocturnal hemoglobinuria, and CPI-637 (2), an inhibitor of both cyclic-AMP response element binding protein (CBP) and adenoviral E1A binding protein [14][15][16]. The N2-substituted indazole analogs pazopanib (3), an FDA-approved tyrosine kinase inhibitor used for the
Solvent-dependent chemoselective synthesis of different isoquinolinones mediated by the hypervalent iodine(III) reagent PISA
Beilstein J. Org. Chem. 2024, 20, 1914–1921, doi:10.3762/bjoc.20.167
- ); isoquinolinone; solvent-dependence; Introduction Isoquinolinone is an important heterocyclic structure found in many natural products and biologically active compounds, including pharmaceuticals [1]. For instance, lycoricidine, found in the medicinal plant Lycoris radiata, may inhibit the MCPyV LT protein
2-Heteroarylethylamines in medicinal chemistry: a review of 2-phenethylamine satellite chemical space
Beilstein J. Org. Chem. 2024, 20, 1880–1893, doi:10.3762/bjoc.20.163
- requirements for access to γ-aminobutyric receptor type B (GABAB) [18]. Amino acids 10–12 were demonstrated [19][20][21] to act as substrates of GABAB (Scheme 3), key metabotropic receptors from the G-protein-coupled receptor superfamily responsible for CNS inhibitory synapses [22]. The authors concluded that
- solute carrier protein which is used as strategic target for blood–brain-barrier drug delivery. In general, the authors found the compounds less potent than the natural substrate ʟ-tryptophan, with exception of derivative 112 (Scheme 17). Tetrazoles: Taking advantage of using tetrazoles not as a phenyl
- -ring bioisostere, but as carboxylic acid one, Schwarz et al. [79] developed tetrazole-based pregabalin bioisosteres 113–118 (Scheme 18). The target protein α2-δ is involved in neurotransmitters release reduction, as a model of anxiety and neuropathic pain. In general, submicromolar affinities were
The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)
Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162
- work described below, KTGS was applied to multicomponent reactions in limited cases [25]. Van der Veken et al. selected as template the protein urokinase plasminogen activator, a serine protease targeted in oncology and inhibited by imidazopyridines [26]. The main challenges of this project were the
- protein in a manner comparable to the binding mode of known imidazopyridine inhibitors. Second, the possibility that reactants could covalently modify the enzyme was ruled out by analysis of the relevant literature. Finally, appropriate building blocks displaying additional functionalities capable of
- combination of reactants was studied, but a major hurdle was found to be the imine formation step in aqueous media. Consequently, imines were first prepared as metastable adducts (with benzotriazole or p-TSA as stabilizers) and then tested with isocyanides in the presence of the template protein, involving
Discovery of antimicrobial peptides clostrisin and cellulosin from Clostridium: insights into their structures, co-localized biosynthetic gene clusters, and antibiotic activity
Beilstein J. Org. Chem. 2024, 20, 1800–1816, doi:10.3762/bjoc.20.159
- catalyze the formation of Dha-Cys or Dhb-Cys [21]. Moreover, lanPt encodes a membrane protein with two ABC transporter domains and a C39 peptidase domain. The protein cleaves the leader peptide to generate mature lanthipeptides and exports them to the extracellular environment [22]. The diversity of
- the Clostridium genus encountered 17 protein sequences associated with 12 genomes. After analyzing these genomes with AntiSMASH [3], we identified 150 different BGCs of specialized metabolites from different biosynthetic classes. The RiPPs accounted for 36% of these (54 clusters). A total of 14 BGCs
- two transporter protein peptidases, which we named CloT1 and CloT2 (Figure 2). The amino acid sequences of the C39 peptidase domain of CloT1 and CloT2, further identified as CloPt1 and CloPt2, were subjected to BLAST analysis, revealing a strong primary sequence conservation with all homologous
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