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Search for "protein" in Full Text gives 622 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
The role of chemistry in the success of oligonucleotides as therapeutics
Beilstein J. Org. Chem. 2022, 18, 197–199, doi:10.3762/bjoc.18.22
- , both of them target mRNA to disrupt protein synthesis. In the following text we will refer both antisense oligonucleotides and siRNAs collectively as therapeutic oligonucleotides. More than 10 oligonucleotide drugs have received regulatory approval by the FDA and are now helping patients suffering from
Ready access to 7,8-dihydroindolo[2,3-d][1]benzazepine-6(5H)-one scaffold and analogues via early-stage Fischer ring-closure reaction
Beilstein J. Org. Chem. 2022, 18, 143–151, doi:10.3762/bjoc.18.15
- particular enzymes. Preliminary results indicate that scaffold C shows good affinity to proto-oncogene tyrosine-protein kinase Src, a well-known anticancer target [47], with IC50 = 0.26 µM and is a suitable candidate for further structural optimization. Paullone related indolobenzazepinone isomers. 7,12
Regioselective synthesis of methyl 5-(N-Boc-cycloaminyl)-1,2-oxazole-4-carboxylates as new amino acid-like building blocks
Beilstein J. Org. Chem. 2022, 18, 102–109, doi:10.3762/bjoc.18.11
- peptide-like structure. Heterocyclic amino acids and related compounds have been used to prepare synthetic DNA-encoded compound libraries for the discovery of small molecule protein ligands [23][24][25]. Recently, a highly specific and potent p38α kinase inhibitor containing a 3-amino-1-phenyl-1H-pyrazole
1,2-Naphthoquinone-4-sulfonic acid salts in organic synthesis
Beilstein J. Org. Chem. 2022, 18, 53–69, doi:10.3762/bjoc.18.5
- evaluated against their antioxidant activity and exhibited promising activity. Protein tyrosine phosphatase 1B (PTP1B) is essential in the dephosphorylation of the activated insulin receptor, and inhibition of this enzyme would be an excellent strategy for the treatment of type 2 diabetes. Ahn and co
- -workers [82] synthesized and evaluated several 1,2-naphthoquinones substituted at position C4 with alkyl- or arylamino groups for their inhibition of the PTP1B protein. Furthermore, to discover new effective anti-inflammatory and analgesic agents, Gouda and co-workers [83] synthesized various compounds in
The enzyme mechanism of patchoulol synthase
Beilstein J. Org. Chem. 2022, 18, 13–24, doi:10.3762/bjoc.18.2
- reinvestigate the biosynthesis of patchoulol (3) the synthetic gene for patchoulol synthase from P. cablin was cloned and expressed in Escherichia coli [8]. The purified protein (Figure S1 in Supporting Information File 1) converted FPP into 3 as the main product, besides several side products (see Figure S2 in
Peptide stapling by late-stage Suzuki–Miyaura cross-coupling
Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1
- stapling techniques to stabilise α-helical secondary structure motifs of peptides led to the design of modulators of protein–protein interactions, which had been considered undruggable for a long time. We disclose a novel approach towards peptide stapling utilising macrocyclisation by late-stage Suzuki
- + 7 for two helix turns, respectively, followed by Ru-catalysed cross-linking [7]. By this robust and reliable approach, a library of stapled peptides was generated influencing diverse α-helical dominated protein–protein interactions (PPI) spanning pathways involved in cancer, infectious diseases
- 1% in proteins, but is highly conserved in binding sites on protein surfaces mediating PPI [43], it is an attractive target for the development of selective diversifications. C–H activation of the indole C2 position by Pd-catalysis allows both selective arylation [44][45][46][47][48] and formation
Unsaturated fatty acids and a prenylated tryptophan derivative from a rare actinomycete of the genus Couchioplanes
Beilstein J. Org. Chem. 2021, 17, 2939–2949, doi:10.3762/bjoc.17.203
- days. Isolation of compounds 1–5 Compounds 1–5 were obtained from a culture fermented in A16 production medium with a composition of glucose 2%, Pharmamedia® (Traders Protein, Memphis, TN, USA) 1%, and CaCO3 0.5%. The pH of the medium was adjusted to 7.0 before autoclaving. At the end of fermentation
Iron-catalyzed domino coupling reactions of π-systems
Beilstein J. Org. Chem. 2021, 17, 2848–2893, doi:10.3762/bjoc.17.196
GlycoBioinformatics
Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184
- one of the authors of this article, Fadda, used glyco-adapted molecular dynamics to explain in a separate publication [4] how the COVID-19 spike protein recognition element requires N-linked glycosylation to be exposed. Another approach to understanding glyco-interactions is described in a review
- protein O-linked glycome based on the specificity of mammalian glycoenzymes, in order to generate a theoretical glycolipid glycome. One of the main tasks of glycobioinformatics is to convert analytical data obtained from biological samples (cell lysates, tissues, isolated proteins) into glycoscience
- transcription factors using next-generation sequencing expression data of glycoenzymes in cancer cell lines. The latter paper uses knowledge from current open access glycomic databases to curate and validate glycan structures reported on proteins in the Protein Data Bank (PDB) database. Overall, the wide
Synthesis of new bile acid-fused tetrazoles using the Schmidt reaction
Beilstein J. Org. Chem. 2021, 17, 2611–2620, doi:10.3762/bjoc.17.174
- solubilizers, bile acids are now recognized as metabolism regulators through specific receptors: farnesoid X receptor (FXR) and Takeda G protein receptor 5 (TGR5) [1][2][3]. Research efforts to find ligands for these receptors initiated several synthetic studies where bile acids are being used as a starting
α-Ketol and α-iminol rearrangements in synthetic organic and biosynthetic reactions
Beilstein J. Org. Chem. 2021, 17, 2570–2584, doi:10.3762/bjoc.17.172
- compound was less active at inhibiting protein translation [14]. Triumphalone (41) and isotriumphalone (42) represent a class of oxidized phloroglucinol natural products isolated from the Australian plant Melaleuca triumphalis. In their total synthesis of these two compounds in racemic form, Nishimura et
Cryogels: recent applications in 3D-bioprinting, injectable cryogels, drug delivery, and wound healing
Beilstein J. Org. Chem. 2021, 17, 2553–2569, doi:10.3762/bjoc.17.171
- pores of the gel. These cell-attracting properties suggest that the use of cryogelated GelMA as a method for cell-integrated scaffolding and protein release for applications in biomaterials-based therapy is a viable option. Similar work was carried out by Lai et al. [79], whereby the polymerisation of
- such as antimicrobial properties. A work reported by Koshy et al. in 2018 was testing the use of injectable nanocomposite cryogels for versatile protein-drug delivery [37]. Injectable and porous cryogels were prepared using a bio-orthogonal click chemistry crosslinking approach with alginate employing
- , degradation, and protein adsorption properties, demonstrating potential as a haemostatic dressing. The healing of wounds to skin tissue takes place over a much shorter time scale than the regeneration of bone tissue in fractures and breaks [118][119]. It has been reported that the majority of skin tissue
Targeting active site residues and structural anchoring positions in terpene synthases
Beilstein J. Org. Chem. 2021, 17, 2441–2449, doi:10.3762/bjoc.17.161
- , turning SmTS1 from a sesterterpene into a diterpene synthase. This article gives rational explanations for these findings that may generally allow for protein engineering of other terpene synthases to improve their catalytic efficiency or to change their functions. Keywords: biosynthesis; enzyme
- expression plasmids for the G184L and A222V enzyme variants. All SmTS1 derivatives were expressed, purified and adjusted to the same protein concentration (80 μg mL−1), with the exception of the R228L variant that was obtained with very low yields in the soluble fraction and thus not further studied
- activity. Similar observations were recently made for spiroalbatene synthase from Allokutzneria albata, in which the otherwise highly conserved Ser within the NSE triad is naturally substituted by Gly. In this case, the G229S enzyme variant did not yield any soluble protein, possibly because the
Efficient synthesis of polyfunctionalized carbazoles and pyrrolo[3,4-c]carbazoles via domino Diels–Alder reaction
Beilstein J. Org. Chem. 2021, 17, 2425–2432, doi:10.3762/bjoc.17.159
- alkaloids and pharmacologically active compounds representing a broad spectrum of important bioactivities such as anticancer, antituberculosis, anti-protein kinase C, antipsychotic, and antioxidative activities [1][2][3][4][5]. For some examples, carprofen is a nonsteroidal anti-inflammatory pharmaceutical
Post-functionalization of drug-loaded nanoparticles prepared by polymerization-induced self-assembly (PISA) with mitochondria targeting ligands
Beilstein J. Org. Chem. 2021, 17, 2302–2314, doi:10.3762/bjoc.17.148
- ]. PENAO triggers cell apoptosis by targeting the ANT protein, which is located in the mitochondria. More specifically, PENAO binds to the thiols located on the ANT peptide loops Cys57 and Cys257, which results in the formation of stable cyclic dithioarsinite complexes [5]. Arsenic drugs do not only bind
- to mitochondrial protein, but also chelates other cysteine-containing species. Several hundred good binding sites for trivalent arsenicals in each organ have been proposed [6][7], and more than 50 arsenic-binding proteins could be identified and analysed by Zhang et al. [8] and Yan et al. [9] using p
- non-specific protein absorption. Su et al. [40] investigated the effects of a protein corona on active and passive targeting using 20 different types of PEGylated gold nanoparticles, which were decorated with cyclic RGD (arginylglycylaspartic acid) peptides. As a result, the active targeting
(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
- chromosome known as Philadelphia (Ph). Ph is the result of the reciprocal chromosomal conversion between the proto-oncogene Abl1 of chromosome 9 and the BCR gene on chromosome 22 [3][4]. Research activity on compounds able to act as protein tyrosine kinase inhibitors (TKIs), which has intensified since the
- TKIs that are even more potent than IMT, such as nilotinib [6][7]. These drugs act as inhibitors at the ATP binding site in the inactive form of BCR-Abl-1, preventing the binding of the protein to ATP in a competitive manner and resulting in the interruption of the substrate phosphorylation process and
- Virtual Docker v6.0 (MVD) program was used to predict the complexes and energies of interaction between the enzyme BCR-Abl 1 and inhibitors 2c, 2d, and 2g. The crystallographic structures of the enzyme BCR-Abl-1, complexed with IMT, were extracted from the Protein Data Bank (PDB code: 3PYY) [37]. The
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
- (Traders Protein) 1%, CaCO3 0.5%, and Diaion® HP-20 (Mitsubishi Chemical Corporation) 1% in distilled water of pH 7.0). The inoculated flasks were placed on a rotary shaker (200 rpm) at 30 °C for 7 days. For the production of nomimicin D (3), the seed culture (3 mL) was transferred into 20 500 mL K-1 flasks
Constrained thermoresponsive polymers – new insights into fundamentals and applications
Beilstein J. Org. Chem. 2021, 17, 2123–2163, doi:10.3762/bjoc.17.138
- , the developed GA-polyHMPA initially exhibits UCST responsiveness, but can subsequently be slowly biodegraded to a fully water-soluble polymer (polyHMPA) via hydrolysis. Initial in vivo studies of a sustained release of either a hydrophilic model protein or a hydrophobic dye entrapped within the
An initiator- and catalyst-free hydrogel coating process for 3D printed medical-grade poly(ε-caprolactone)
Beilstein J. Org. Chem. 2021, 17, 2095–2101, doi:10.3762/bjoc.17.136
- mechanical properties, cytocompatibility, biodegradability, and good printing properties [8][14][15], it is a hydrophobic polymer and immersion into fluids can result in air bubble capture within the scaffold structure, biofouling and non-specific cell interactions [16]. Protein adsorption and denaturation
On the application of 3d metals for C–H activation toward bioactive compounds: The key step for the synthesis of silver bullets
Beilstein J. Org. Chem. 2021, 17, 1849–1938, doi:10.3762/bjoc.17.126
Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides
Beilstein J. Org. Chem. 2021, 17, 1828–1848, doi:10.3762/bjoc.17.125
- complement and improved nuclease resistance. Additionally, a 20-mer PS-ASO with nine incorporations of modification 34 near the 3’-end was introduced into A549 cells via the electroporation method to induce c-raf mRNA and protein knockdown. Improved activity of the modified PS-ASO relative to the unmodified
- lymphoma 2 (bcl-2) protein levels were examined. All PS-ASOs gave improved downregulation relative to the control (scrambled sequence), but only PS-ASOs carrying the nucleotides modified with spermine (i.e., monomer 49) or pentaamine (i.e., monomer 50) induced improved downregulation of gene expression
- protein interactions compared to the phosphodiester backbone [104]. In an effort to reduce the overall negative charge of the backbone, also a large number of different artificially linked backbone ONs has been synthesized, and a selected number of these can be seen in Table 8 and Table 9. The latter
Natural products in the predatory defence of the filamentous fungal pathogen Aspergillus fumigatus
Beilstein J. Org. Chem. 2021, 17, 1814–1827, doi:10.3762/bjoc.17.124
- -melanin. Additionally, the surfactant protein D (SP-D), a soluble C-type lectin receptor (CLR), is also able to recognise DHN-melanin and opsonize it to increase the immune response. However, MelLec receptors are only present on some endothelial and myeloid cells [156][157]. Fumigaclavines Fumigaclavine C
- [72]. It was further shown to be cytotoxic and inhibiting cell cycle progression at G2/M phase [163]. Fumitremorgin C was shown to effect mammalian cells and inhibit the breast cancer resistance protein which imparts multidrug resistance and thus resistance to chemotherapeutics in breast cancer
Sustainable manganese catalysis for late-stage C–H functionalization of bioactive structural motifs
Beilstein J. Org. Chem. 2021, 17, 1733–1751, doi:10.3762/bjoc.17.122
- protein–ligand binding properties as well as biological activities of small molecules, potentially leading to dramatic increases in potency, and thus has been widely explored in drug discovery [54][55][56]. Late-stage C–H methylation has recently been investigated using iron and cobalt catalysts as
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
- the activity of promoter and enhancer regions through cap analysis of gene expression (CAGE), TF motif instances, and expression quantitative trait loci (eQTL) to evaluate weights (evidence scores) for TF–gene isoform relationships; and iii) integration of TF-binding motifs, protein–protein
- using ST6GALNAC3-6 and also ST8SIA1/3/5. 4) Dolichol pathway: This results in the formation of the dolichol-linked 14-monosaccharide precursor oligosaccharide. This glycan is cotranslationally transferred en bloc onto Asn-X-Ser/Thr sites of the newly synthesized protein as it enters the endoplasmic
- reticulum. The enzymes involved is such synthesis include the ALG (asparagine-linked N-glycosylation) enzymes and additional proteins (part of OSTA and OSTB) involved in the transfer of the glycan to the nascent protein. 5) Complex N-glycans: This pathway includes glycogenes responsible for processing the N
Volatile emission and biosynthesis in endophytic fungi colonizing black poplar leaves
Beilstein J. Org. Chem. 2021, 17, 1698–1711, doi:10.3762/bjoc.17.118
- , and heterologously expressed in Escherichia coli. To determine mono-, sesqui-, and diterpene-forming activity, the bacterial raw protein extracts were assayed with the substrates GPP, FPP, and GGPP, each in the presence of the co-substrate magnesium chloride. Both protein extracts containing the
- flow desalting column (GE Healthcare, Chicago, IL, USA) and eluted in extraction buffer. Enzyme assays were performed in a Teflon-sealed, screw-capped 1 mL GC glass vial containing 50 μL of the heterologously expressed protein and 50 µL assay buffer containing 50 μM substrate (GPP, (E,E)-FPP, or (E,E,E
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