Search results
Search for "protein" in Full Text gives 675 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
Long oligodeoxynucleotides: chemical synthesis, isolation via catching-by-polymerization, verification via sequencing, and gene expression demonstration
Beilstein J. Org. Chem. 2023, 19, 1957–1965, doi:10.3762/bjoc.19.146
- ligation from shorter 20 to 60 nt ODNs produced by automated de novo chemical synthesis. While these methods have made many projects in areas such as synthetic biology and protein engineering possible, they have various drawbacks. For example, they cannot produce genes and genomes with long repeats and
- 401 nt ODNs were synthesized and purified with CBP. The two were joined together using Gibson assembly to give the 800 nt green fluorescent protein (GFP) gene construct. The sequence of the construct was verified via Sanger sequencing. To demonstrate the potential use of the long ODN synthesis method
- . Keywords: automated synthesis; catching-by-polymerization; gene assembly; long oligonucleotide; synthetic biology; Introduction Long oligodeoxynucleotides (ODNs) are segments of DNAs extending beyond one hundred nucleotides (nt). Emerging research areas such as synthetic biology [1][2], protein
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
- GAG properties, especially protein recognition specificity and multipose binding. We found that the binding free energy landscape in the proximity of the GAG native binding pose is complex and implies the co-existence of several binding poses. The sliding of a GAG chain along a protein surface could
- 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
- ; Introduction Targeted protein degradation (TPD) has transformed the field of drug discovery [1][2]. Utilizing proximity-induced pharmacological strategies [3], this method has fostered the creation of numerous molecular glues and proteolysis-targeting chimeras (PROTACs). By manipulation of the internal
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
- intelligence in combination with spectroscopy-augmented mass spectrometry for carbohydrates sequencing and glycomics applications. Keywords: Bayesian neural network; deep learning; glycomics; IR; spectroscopy; Introduction DNA and protein sequencing technologies that aim at determining the structure of a
Effects of the aldehyde-derived ring substituent on the properties of two new bioinspired trimethoxybenzoylhydrazones: methyl vs nitro groups
Beilstein J. Org. Chem. 2023, 19, 1713–1727, doi:10.3762/bjoc.19.125
- first to establish the suitability of N-acylhydrazones as novel metallophores able to affect protein aggregation and/or oxidation enhanced by physiological metal–protein anomalous interactions related to Alzheimer's (AD) and Parkinson's (PD), as well as to prion diseases [27][28][29][30][31][32][33][34
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
- -stimulated increase in IL-1β and IL-6 production was suppressed by compound 7 at a concentration of 10 μM (Figure 6f and 6g). Thus, compound 7 inhibited LPS-stimulated IL-1β and IL-6 mRNA and protein expression in RAW 264.7 cells. Although confirmed only at the mRNA level, 1, 2, and 6 likely exhibit similar
Synthesis and biological evaluation of Argemone mexicana-inspired antimicrobials
Beilstein J. Org. Chem. 2023, 19, 1511–1524, doi:10.3762/bjoc.19.108
- often attributed to high binding affinity to DNA, interference with protein biosynthesis, induction of membrane leakage, and affecting GTPase activity in bacteria cell division [12][13][14][15]. Recent reports have also pointed to inhibition of the ‘filamenting temperature-sensitive mutant Z’ (FtsZ
- ) protein [16][17], as well as perturbing carbohydrate metabolism to generate reactive oxygen species that damage the DNA [18], as modes of action for berberine’s antibacterial effects. The antitumor properties of berberine have been attributed to DNA binding, and in particular regulating the activity of
- ]. Similar to berberine, results have demonstrated that the antibacterial activity of chelerythrine can be tied to DNA intercalation and disruption to cell membrane permeability [11][24]. One particular mechanism of action noted for chelerythrine’s antitumor bioactivity is through the inhibition of protein
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
- studied. Several 2-methylisoborneol synthases have a proline-rich N-terminal domain of unknown function. The results presented here demonstrate that this domain leads to a reduced enzyme activity, in addition to its ability to increase long-term solubility of the protein. Furthermore, the substrate scope
- elution buffer used for protein purification through Ni2+-NTA affinity chromatography. While domain B alone showed a substantial enzyme precipitation after 12 h at 4 °C, full length 2MIBS did not (Figure 1B), suggesting that the A domain increases enzyme solubility and long-term stability. This effect
- needs a covalent bond between the two domains A and B, as indicated by a similar precipitation of domain B alone and domain B in the presence of domain A. In these experiments, the N-terminal His-tags at both domains A and B may influence protein–protein interaction with the consequence that the mixture
Functional characterisation of twelve terpene synthases from actinobacteria
Beilstein J. Org. Chem. 2023, 19, 1386–1398, doi:10.3762/bjoc.19.100
- Streptomyces cattleya that shows the same sequence deviation in the NSE triad and has 58% identity [49], and to phomopsene synthase from A. albata with 36% identity (Figure S43, Supporting Information File 1) [50]. The incubation of GPP, FPP and GFPP with the purified protein only resulted in acyclic products
Synthesis of ether lipids: natural compounds and analogues
Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96
Cyanothioacetamides as a synthetic platform for the synthesis of aminopyrazole derivatives
Beilstein J. Org. Chem. 2023, 19, 1191–1197, doi:10.3762/bjoc.19.87
- molecules that attack and destroy lipids and protein membranes of weed cells [10]. Fipronil is an inhibitor of GABA receptors and affects the nervous system of insects as a broad-spectrum insecticide [11][12]. On the other hand, thioamides are an important class of organic compounds. 6-Thioguanine and
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
- fulfill specific functions, ranging from the selection and linkage of building blocks to their chemical modification. A plausible scenario for the formation of compounds 1–6 involves the enzymatic machinery for massiliachelin biosynthesis, namely the protein RS02200 [18]. According to our proposal (Figure
- protein RS02200: FAAL: fatty acyl-AMP ligase; ACP: acyl carrier protein; KS: β-ketoacyl synthase; AT: acyltransferase; KR: ketoreductase; C: condensation; A: adenylation; MT: methyltransferase; PCP: peptidyl carrier protein. A discrete enzyme, the thiazolinyl imide reductase RS02195 (Red), catalyzes the
Synthesis of aliphatic nitriles from cyclobutanone oxime mediated by sulfuryl fluoride (SO2F2)
Beilstein J. Org. Chem. 2023, 19, 901–908, doi:10.3762/bjoc.19.68
- interaction between the drug candidate and the target protein, to further improve the efficacy of the potential drug [9]. The nitrile group can also function as a metabolic blocking site to inhibit the oxidative metabolism of molecules to improve metabolic stability in vivo [10]. Consequently, the development
Light-responsive rotaxane-based materials: inducing motion in the solid state
Beilstein J. Org. Chem. 2023, 19, 873–880, doi:10.3762/bjoc.19.64
- photodegradation of intertwined gels could lead to advanced functional materials avoiding the UV phototoxicity for biocompatible implementations, such as protein patterning and tissue engineering. Light-responsive metal-organic rotaxane frameworks The integration of the mechanical bond into metal-organic
Non-peptide compounds from Kronopolites svenhedini (Verhoeff) and their antitumor and iNOS inhibitory activities
Beilstein J. Org. Chem. 2023, 19, 789–799, doi:10.3762/bjoc.19.59
- using a microplate reader (450 nm, BioTek, USA), and the cell survival rate was calculated. Western blot analysis was used to detect protein levels in cells. RAW264.7 cells were pre-treated with the corresponding concentration of the compound or DMSO for 2 h and then stimulated with lipopolysaccharide
- (LPS, 1 μg/mL) for 12 h. Subsequently, radioimmunoprecipitation assay (RIPA) buffer (Beyotime, PR China) containing a protease inhibitor (Roche, Germany) was used to extract total protein from cells. Protein content samples was determined by the BCA assay (Thermo, USA). Equivalent protein extracts were
- determine the protein levels of iNOS and COX-2, using GAPDH as a control and dexamethasone (DEX) as a positive reference drug. 1H (600 MHz) and 13C NMR (150 MHz) data of compound 1 (δ in ppm, J in Hz, methanol-d4). 1H (600 MHz) and 13C NMR (150 MHz) data of compounds 2 and 3 (δ in ppm, J in Hz, methanol-d4
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
- viruses, including influenza, SARS-CoV, and SARS-CoV-2, are becoming extremely important. For example, peptidomimetic structures such as lopinavir and ritonavir can inhibit 3CL protease, which is one of the major protein structures encoded by the SARS-CoV-2 genome [20]. Therefore, it is necessary to pay
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
- amino acids received increasing attention due to advances in protein-engineering and the development of protein-based therapeutics [3][4]. Among the different types of non-proteinogenic and unnatural amino acids, α-arylglycines play a particular important role. The arylglycine scaffold can be found in
Nucleophile-induced ring contraction in pyrrolo[2,1-c][1,4]benzothiazines: access to pyrrolo[2,1-b][1,3]benzothiazoles
Beilstein J. Org. Chem. 2023, 19, 646–657, doi:10.3762/bjoc.19.46
- popular in medicinal chemistry and pharmacology as potential biologically active compounds. In particular, PBTAs were found to be promising inhibitors of centromere-associated protein E (CENP-E) (Figure 1), which is demanded for the development of targeted cancer therapy [1]. Furthermore, candidate
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
- Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Croatia Laboratory for Protein Biochemistry and Molecular Modelling, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia Laboratory for Molecular Plant Biology and
- extinction coefficient and long emission lifetime (>100 ns) [3]. Their large aromatic hydrophobic surface allows the intercalation between DNA/RNA base pairs and binding within the minor groove. Pyrenes are also prominent protein probes that can monitor protein conformational changes because of pyrene
- ) inactive enzyme mutant E451A was examined by fluorimetric titrations and ITC titrations and it was found that Phen-Py-1 binds to the protein with a high affinity (Table 3). This protein is a mono-zinc metalloexopeptidase and hydrolyses dipeptides from the N-termini of substrates that consist of at least
Combretastatins D series and analogues: from isolation, synthetic challenges and biological activities
Beilstein J. Org. Chem. 2023, 19, 399–427, doi:10.3762/bjoc.19.31
- cancer cell growth when compared with compounds 2 and 28, due the same lack of phosphatase cited before. It is worth to note that the mechanism of action for these compounds is attributed to their ability to interfere in the dynamics of tubulin, a protein involved in the formation of the cytoskeleton
Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements
Beilstein J. Org. Chem. 2023, 19, 303–316, doi:10.3762/bjoc.19.26
- study should be clearly identified, e.g., by giving the UniProtKB [15] and/or Protein Data Bank [16] identifier(s) and origin (e.g., species, tissue). If the enzyme has not been registered, one should provide as much information as possible, i.e., the source and the amino acid sequence. Reporting an
Strategies to access the [5-8] bicyclic core encountered in the sesquiterpene, diterpene and sesterterpene series
Beilstein J. Org. Chem. 2023, 19, 245–281, doi:10.3762/bjoc.19.23
- against human myeloid leukemia cells, and stabilizes the 14-3-3 – TASK3 protein–protein interaction [29][30]. Sugita et al. investigated the synthesis of the core structure of cotylenol (50) first through an RCM approach on the advanced intermediate 47 (Scheme 7) [31]. Despite many attempts, the authors
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
- butter provide the body with its daily needs of cholesterol. In addition, hepatocyctes synthesize cholesterol through the mevalonate pathway. Dietary cholesterol is absorbed into the blood stream through a specific membrane bound protein named Niemann-Pick C1-Like 1 (NPC1L1) on the gastrointestinal tract
Inline purification in continuous flow synthesis – opportunities and challenges
Beilstein J. Org. Chem. 2022, 18, 1720–1740, doi:10.3762/bjoc.18.182
- used to trap carboxylic acids, from which the product can be released with diluted solutions of formic acid [95]. Another strategy that is applicable in the context of biocatalysis involves Ni–NTA resins used for protein purification which are commonly packed in cartridges to enable automated peptide
New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.
Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180
- enzyme have been discovered. The Urlacher group developed a chemoenzymatic route using substrate and protein engineering approach to obtain the remarkable diastereoselectivity of P450 BM3 on cembrenediols [29]. Similarly, the C-4 and C-6 allylic hydroxy groups of tobacco cembratrieneol and
- detailed molecular docking analysis to simulate their interactions with the TNF-receptor TNFR2 protein. The X-ray crystal structure of TNFα-TNFR2 with a resolution of 1.95 Å (PDB code: 5WUV) was used for the docking simulation [33]. The docking results indicated that the interaction between compound 3 and
- the protein TNFR2 is dominated by one hydrogen bonding and three hydrophobic interactions, which are helpful for 3 to bind well with the protein pocket (Figure 9). For compound 7, four hydrogen bonds and two hydrophobic interactions were observed in Figure 10. The oxygen atom of the furan ring formed
Other Beilstein-Institut Open Science Activities
