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Search for "proteins" in Full Text gives 508 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
Identification of the p-coumaric acid biosynthetic gene cluster in Kutzneria albida: insights into the diazotization-dependent deamination pathway
Beilstein J. Org. Chem. 2024, 20, 1–11, doi:10.3762/bjoc.20.1
- biosynthesis by heterologous expression of the cma cluster and in vitro enzyme assays using recombinant Cma proteins. The ATP-dependent diazotase CmaA6 catalyzed the diazotization of both 3-aminocoumaric acid and 3-aminoavenalumic acid using nitrous acid in vitro. In addition, the high efficiency of the CmaA6
- on an ava cluster-related BGC in Kutzneria albida JCM 3240. We showed that this BGC is involved in p-coumaric acid biosynthesis by heterologous expression in Streptomyces albus J1074 and several in vitro biochemical experiments using recombinant proteins. CmaA6 was shown to catalyze the diazotization
- confirmed that the cma cluster is responsible for p-coumaric acid (5) biosynthesis, in which the number of condensations of the malonyl units was one time less than that in the biosynthesis of avenalumic acid. In vitro analysis of recombinant Cma proteins To further understand the biosynthetic machinery
Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling
Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144
- proteins. The structural and functional heterogeneities of GAGs as well as their ability to bind specific proteins are determined by the sugar composition of the GAG, the size of the GAG chains, and the degree and pattern of sulfation. A deep understanding of the interactions in protein–GAG complexes is
- ) with three different proteins (basic fibroblast growth factor, acidic fibroblast growth factor, and cathepsin K). The main focus of our study was to evaluate whether the US approach is able to reproduce experimentally obtained structures, and how useful it can be for getting a deeper understanding of
- be a potential mechanism of GAG particular sequence recognition by proteins. Keywords: glycosaminoglycan; molecular docking; protein–glycosaminoglycan interaction specificity; RS-REMD; umbrella sampling; Introduction Glycosaminoglycans (GAGs) are long linear periodic anionic polydisperse
N-Boc-α-diazo glutarimide as efficient reagent for assembling N-heterocycle-glutarimide diads via Rh(II)-catalyzed N–H insertion reaction
Beilstein J. Org. Chem. 2023, 19, 1841–1848, doi:10.3762/bjoc.19.136
- ubiquitin-proteasome degradation system, it has been achieved to approach previously considered undruggable targets and conceive remedies for drug-resistant targets [4]. The given TPD's benefit over traditional inhibition; numerous proteins have been set for proteasomal degradation by transmuting accessible
- small molecule inhibitors into PROTACs. The RAS proteins, once seen as drug-resistant, became susceptible and a series of covalent inhibitors [5][6][7] were synthesized to bind to KRASG12C. The application of the PROTAC principle has demonstrated the feasibility of endogenous degradation of KRAS [8][9
GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data
Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134
- impact for the society in regard to the United Nations sustainable development goal [1]. The major roadblock to carbohydrate sequencing is intrinsically due to their unique molecular properties, among biopolymers. In contrast with proteins and DNA, which are linear polymers made of a limited number of
Sulfur-containing spiroketals from Breynia disticha and evaluations of their anti-inflammatory effect
Beilstein J. Org. Chem. 2023, 19, 1604–1614, doi:10.3762/bjoc.19.117
- potent compound 7 was found to significantly inhibit the production of IL-1β and IL-6 proteins, as revealed by the analysis of culture supernatants. Keywords: anti-inflammatory; Breynia disticha; RAW 264.7 cells; sesquiterpenoids; sulfur-containing compounds; Introduction Breynia disticha J.R.Forst
Radical chemistry in polymer science: an overview and recent advances
Beilstein J. Org. Chem. 2023, 19, 1580–1603, doi:10.3762/bjoc.19.116
- consists of a bundle of disc-tipped acellular thread called byssus, which connect the mussel to the surfaces of substrates [10]. A family of proteins called mussel foot proteins (mfp’s) distribute throughout the whole length of byssus while there is an extremely high concentration of mfp’s at the plaque
- amino acid sequence of mfp-1, mfp-3, and mfp-5 (Y: DOPA, K: lysine). B) Scheme showing examples of the adhesive and cohesive properties of catechol-containing proteins. R represents the remainder of the mfp’s. Scheme 3 redrawn from [10]. Activation–deactivation equilibrium in nitroxide-mediated
Cyclodextrins permeabilize DPPC liposome membranes: a focus on cholesterol content, cyclodextrin type, and concentration
Beilstein J. Org. Chem. 2023, 19, 1570–1579, doi:10.3762/bjoc.19.115
- cellular processes, (e.g., signaling transduction, proteins trafficking, etc.) [19]. However, many discrepancies could be found in the literature regarding the existence of lipid rafts in synthetic membranes, especially CHOL–lipid binary mixtures. Studies of DPPC:CHOL bilayers have elucidated the formation
Synthesis and biological evaluation of Argemone mexicana-inspired antimicrobials
Beilstein J. Org. Chem. 2023, 19, 1511–1524, doi:10.3762/bjoc.19.108
- complicated by both berberine and chelerythrine having multiple pathways associated with their antimicrobial activity [11][12][13][14][15][16][17][18][24]. In an effort to better understand the differences seen with our variants, we chose to focus on their effects on leakage of intercellular proteins, as
Functions of enzyme domains in 2-methylisoborneol biosynthesis and enzymatic synthesis of non-natural analogs
Beilstein J. Org. Chem. 2023, 19, 1452–1459, doi:10.3762/bjoc.19.104
- cloned individually, heterologously expressed as N-terminally His-tagged proteins in Escherichia coli and purified (Supporting Information File 1, Figure S1). Also full length 2MIBS from S. coelicolor was obtained in the same way. The relative production of 1 from 2-Me-GPP was tested in triplicate
Functional characterisation of twelve terpene synthases from actinobacteria
Beilstein J. Org. Chem. 2023, 19, 1386–1398, doi:10.3762/bjoc.19.100
- ). The genes coding for all fifteen enzymes were amplified by PCR from genomic DNA, cloned and expressed in Escherichia coli. The purified recombinant proteins (Figure S1, Supporting Information File 1) were used in test incubations with geranyl pyrophosphate (GPP), farnesyl pyrophosphate (FPP
Synthesis of ether lipids: natural compounds and analogues
Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96
- ) that exhibit promising anticancer properties renew the interest in this class of compounds. Indeed, ether lipid represent a new and promising class of compounds featuring the capacity to modulate selectively the activity of some membrane proteins or, for other compounds, feature antiproliferative
- with biomembranes via supramolecular interactions with the lipids and proteins that are embedded in these membranes. We can hypothesis that their mechanism of action occurs via a direct interaction with membrane proteins or by a modification of the biophysical properties of the membranes. It must be
- noted that the design of new bioactive ELs is an alternative to others strategies (e.g., small molecules, antibodies) to modulate membrane proteins functions. Recent results from our group [41][42] and others renew the interest to develop new ether lipids with promising perspectives to address the
Intermediates and shunt products of massiliachelin biosynthesis in Massilia sp. NR 4-1
Beilstein J. Org. Chem. 2023, 19, 909–917, doi:10.3762/bjoc.19.69
- photosynthesis, respiration or nitrogen fixation, in which iron-containing proteins are engaged in electron transfer reactions. In fact, the transition metal is perfectly suited for shifting electrons due to its ability to easily interconvert between a reduced ferrous (Fe2+) and an oxidized ferric state (Fe3
Asymmetric tandem conjugate addition and reaction with carbocations on acylimidazole Michael acceptors
Beilstein J. Org. Chem. 2023, 19, 881–888, doi:10.3762/bjoc.19.65
- solubility in water. Among exceptional properties belongs to easy post-transformation of acylimidazoles to common carbonyl analogs. These tunable properties allow the use of acylimidazoles in chemical biology research, which includes chemical synthesis of proteins/peptides, structure analysis, and functional
Synthesis of imidazo[1,2-a]pyridine-containing peptidomimetics by tandem of Groebke–Blackburn–Bienaymé and Ugi reactions
Beilstein J. Org. Chem. 2023, 19, 727–735, doi:10.3762/bjoc.19.53
- ], olprinon (cardiotonic agent for the treatment of acute heart failure) [18], GSK812397 (with anti-human immunodeficiency virus (HIV) properties) [19] (Figure 1). In light of the numerous viral epidemics and even pandemics, antiviral drugs that can inhibit the activity of proteins and enzymes encoded by
Palladium-catalyzed enantioselective three-component synthesis of α-arylglycine derivatives from glyoxylic acid, sulfonamides and aryltrifluoroborates
Beilstein J. Org. Chem. 2023, 19, 719–726, doi:10.3762/bjoc.19.52
- production of drugs, fertilizers, (biodegradable) polymers or nutritional supplements [2]. More importantly, α-amino acids form the backbone of all proteins and enzymes are therefore essential for almost all biological processes. In the last twenty years non-proteinogenic and chemically synthesized unnatural
Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme
Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40
- in the cell membrane. Keywords: dipeptidyl peptidase enzyme; excimer; molecular dynamics simulations; phenanthridine; polynucleotide; pyrene; Introduction The design of small molecules that can selectively bind and discriminate different biomolecular structures (polynucleotides vs proteins, DNA or
- emission change upon binding to proteins, and a cyanine fluorescence that was selective for polynucleotides. Moreover, the FRET pair of chromophores was activated upon binding to biomolecules [18]. Continuing our previous work, two phenanthridine–pyrene conjugates Phen-Py-1 and Phen-Py-2 (Scheme 1
An efficient metal-free and catalyst-free C–S/C–O bond-formation strategy: synthesis of pyrazole-conjugated thioamides and amides
Beilstein J. Org. Chem. 2023, 19, 231–244, doi:10.3762/bjoc.19.22
- pharmaceutical ingredients [48] such as fenclosic acid, fentiazac, and febuxostate. Similarly, in contemporary chemistry, the amide functionality is one of the most studied functional groups. Specifically, this moiety is vital for the formation of the backbone of structural proteins and enzymes [49]. The amide
Revisiting the bromination of 3β-hydroxycholest-5-ene with CBr4/PPh3 and the subsequent azidolysis of the resulting bromide, disparity in stereochemical behavior
Beilstein J. Org. Chem. 2023, 19, 91–99, doi:10.3762/bjoc.19.9
- epithelial cells as well as in hepatocytes. As hydrophobic molecule, it circulates in the blood stream engulfed in carrier lipoproteins of two types, high density lipoproteins (HDL) or good proteins and low-density lipoproteins (LDL) or bad proteins [4][5]. People with a total blood cholesterol over 125–200
Digyalipopeptide A, an antiparasitic cyclic peptide from the Ghanaian Bacillus sp. strain DE2B
Beilstein J. Org. Chem. 2022, 18, 1763–1771, doi:10.3762/bjoc.18.185
- hydrophilic biological environments. Repeated studies on the bioactivity of lipopeptides have shown that the primary mechanism of action of these peptides involves interactions with the double layer of lipids and proteins that constitute the cell membrane [24][25][26]. This mechanism of action is important
Inline purification in continuous flow synthesis – opportunities and challenges
Beilstein J. Org. Chem. 2022, 18, 1720–1740, doi:10.3762/bjoc.18.182
- -workers developed a vortex fluidic device with an immobilized metal affinity chromatography (IMAC) resin to purify proteins in continuous flow mode [46]. This technology is highly efficient (run time ca. 10 minutes), reproducible, and scalable (stable over 5 days of processing) for soluble proteins
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
- and decoration of a NP scaffold. In comparison to biosynthetic assembly lines, intermediates are not permanently covalently bound to carrier proteins in discrete, multi-enzymatic assemblies. In both biosynthetic principles, the NP backbone is first assembled by core enzymes and then further modified
- ]. trans-AT PKSs are much more complex than cis-AT PKS systems as they harbor non-elongating modules, cryptic domains and seemingly superfluous domains. Moreover, they frequently employ a number of trans-acting modifying enzymes, are characterized by modules that are split between proteins and they often
- alignments with known genes and domains using algorithms like BLAST (Figure 4) [42]. BLAST detects similar sequences to a given query sequence [42]. The first version of the tool BAGEL utilized BLAST analysis, among others, to identify putative BGCs of bacteriocins (= antimicrobial peptides and proteins) [43
Microelectrode arrays, electrosynthesis, and the optimization of signaling on an inert, stable surface
Beilstein J. Org. Chem. 2022, 18, 1488–1498, doi:10.3762/bjoc.18.156
- detection methods in the subsequent binding studies. The polymer network is not permeable to molecules tethered to its surface or proteins in solution. The synthetic problem was solved by using the electrodes in an array to generate chemical reagents and catalysts and then confining those reagents and
- 5) [21]. Gαi1 was selected as a positive control for subsequent studies because it can be expressed easily, has roughly 55% homology with the much more difficult to express Gαq [15], and chimeric proteins are available that have Gαi1 modified with a Gαq binding site for YM and FR [22]. R6A was
Characterization of a new fusicoccane-type diterpene synthase and an associated P450 enzyme
Beilstein J. Org. Chem. 2022, 18, 1396–1402, doi:10.3762/bjoc.18.144
- efficient modulators of 14-3-3 protein–protein interactions (PPIs) [3][4]. 14-3-3 PPIs, which refer to the binding interactions of 14-3-3 proteins with hundreds of “client” proteins, are associated with many diseases, such as cancer and neurodegenerative diseases [3][4]. As a result, lots of attempts
On drug discovery against infectious diseases and academic medicinal chemistry contributions
Beilstein J. Org. Chem. 2022, 18, 1355–1378, doi:10.3762/bjoc.18.141
- antibacterial research department of GSK reported the results of their genome-driven seven-year long quest for original antibiotics. This target-based approach actually failed although 300 bacterial genes had been considered and 70 high-throughput screening campaigns, focusing on the corresponding proteins, had
- of antivirals which solely target the dengue virus via the inhibition of an essential interaction between the viral proteins NS3 and NS4B [200]. Still in the domain of infectious diseases, there are two very advanced public-based endeavors aiming at providing drugs against malaria which are
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
- , 5600 MB Eindhoven, Netherlands 10.3762/bjoc.18.137 Abstract The 14-3-3 protein family, one of the first discovered phosphoserine/phosphothreonine binding proteins, has attracted interest not only because of its important role in the cell regulatory processes but also due to its enormous number of
- interactions with other proteins. Here, we use a computational approach to predict the binding sites of the designed hybrid compound featuring aggregation-induced emission luminophores as a potential supramolecular ligand for 14-3-3ζ in the presence and absence of C-Raf peptides. Our results suggest that the
- discovered phosphoserine/phosphothreonine binding proteins. In total seven isoforms of the 14-3-3 family are known to date (β, ε, γ, τ, θ, σ, and ζ) in mammals [1]. They are forming homo and heterodimers with a profile shaped like the Greek letter “ω” [2]. 14-3-3 proteins have attracted interest due to their
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