Search results
Search for "proteins" in Full Text gives 471 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
Trichloroacetic acid fueled practical amine purifications
Beilstein J. Org. Chem. 2022, 18, 225–231, doi:10.3762/bjoc.18.26
- from rotaxanes, cucurbit[8]uril, to supramolecular smart materials [11][12][13][14][15][16]. TCA is also known for its application in the precipitation of proteins through what is believed to be an unfolding of the proteins structures [17][18]. In this context, we hypothesized that TCA could be used to
Anomeric 1,2,3-triazole-linked sialic acid derivatives show selective inhibition towards a bacterial neuraminidase over a trypanosome trans-sialidase
Beilstein J. Org. Chem. 2022, 18, 208–216, doi:10.3762/bjoc.18.24
- (GE Healthcare). The column was washed with buffer A to remove unbound proteins followed by elution of bound proteins with buffer B (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 500 mM imidazole). Further purification was carried out by gel filtration chromatography (Superdex S200 16/600 column, GE Healthcare
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
- messenger (mRNA) to stop the synthesis of proteins using short strands of DNA, now known as antisense oligonucleotides, was first coined about 40 years ago [1]. Almost 20 years later, another endogenous mechanism, known as RNA interference (RNAi) was discovered when it was shown that short stretches of
- double-stranded nucleotides, which are called short interfering RNA or “siRNA,” can target mRNA and prevent it from being translated to make proteins [2]. While the mechanism by which antisense oligonucleotides (single stranded oligonucleotide) and siRNA (short RNA duplexes) work are completely different
Synthesis and late stage modifications of Cyl derivatives
Beilstein J. Org. Chem. 2022, 18, 174–181, doi:10.3762/bjoc.18.19
- histones [6][7][8][9][10]. Blockade of the deacylating process causes hyperacetylation of histones and unregulated gene activity, that results in untimely cell death. Eighteen different HDAC enzymes are known so far and they are divided into four classes based on structural homology with yeast proteins [11
Synthesis and bioactivity of pyrrole-conjugated phosphopeptides
Beilstein J. Org. Chem. 2022, 18, 159–166, doi:10.3762/bjoc.18.17
- merits, such as ease of design and tailoring (based on the known structures from proteins), good biocompatibility and degradability, and low immunogenicity. For example, recent works have demonstrated the potential of peptide assemblies for a wide range of applications, including drug delivery [8][9][10
1,2-Naphthoquinone-4-sulfonic acid salts in organic synthesis
Beilstein J. Org. Chem. 2022, 18, 53–69, doi:10.3762/bjoc.18.5
- with amino acids to be used as colorimetric indicators, Folin [45] developed a method based on naphthoquinone since there were records in the literature that indicated that naphthoquinones reacted with amines and proteins to form colored products. Among the tested o-naphthoquinones, he found that 1,2
Peptide stapling by late-stage Suzuki–Miyaura cross-coupling
Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1
- of biomolecules [35][36][37]. The approaches by Buchwald and Pentelute are suitable for selective, bioorthogonal labelling of cysteine- [38][39][40] and lysine-containing [41][42] peptides and proteins using stochiometric amounts of pre-formed Pd(II)-aryl complexes. They can further be applied for
- 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
Stepwise PEG synthesis featuring deprotection and coupling in one pot
Beilstein J. Org. Chem. 2021, 17, 2976–2982, doi:10.3762/bjoc.17.207
- peptides, proteins and nucleic acids and to evade undesired immune responses, monodisperse PEGs are required or highly desired [12][13]. To meet the needs of monodisperse PEGs, significant efforts have been made to develop stepwise methods for their synthesis [14][15][16][17][18][19][20][21][22][23][24][25
A photochemical C=C cleavage process: toward access to backbone N-formyl peptides
Beilstein J. Org. Chem. 2021, 17, 2932–2938, doi:10.3762/bjoc.17.202
- ” amide products can and does occur under physiological conditions, the rates of this hydrolysis are slow for the simple models in this study. Within more complex peptides or proteins, selectivity in photocleavage pathways may differ significantly, depending on local chemical environment. It is also worth
A tribute to Carsten Schmuck
Beilstein J. Org. Chem. 2021, 17, 2795–2798, doi:10.3762/bjoc.17.190
- exchange of scientific ideas and knowledge. Carsten continuously gave a lot of attention and constructive questions about fine details in targeted binding sites of biomacromolecules (various types of DNA and RNA, or proteins), as well as already known small molecules binding to these targets. Then, taking
- Organic Chemistry at the UDE. It was a privilege in 2010 to start the nucleus of our later Collaborative Research Center 1093 with him, which we called “Supramolecular Chemistry on Proteins” and which he directed as Vice Speaker, with great enthusiasm. In 2011, Carsten organized the first “SupraChem
GlycoBioinformatics
Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184
- proteomic data into a glycomic context by harvesting information about glyco-related genes and proteins. Glycobioinformatics requires additional information about the expressed glycan, including but not limited to monosaccharide composition, full or partial sequence including linkage and branching structure
- tightly connected to mainstream bioinformatics. For example, databases and tools from genomics can be used for gaining information about genes encoding for glycosyltransferases, glycosidases, and glycan-binding proteins (lectins), and search engines initially designed for the detection of
- 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
Synthetic strategies toward 1,3-oxathiolane nucleoside analogues
Beilstein J. Org. Chem. 2021, 17, 2680–2715, doi:10.3762/bjoc.17.182
- ; separation of racemic nucleosides; stereoselectivity; Introduction Among all the biomolecules in an organism, nucleic acids, namely DNA and RNA, have the unique role of storing the genetic code – the nucleotide sequence that specifies the amino acid sequence of proteins that is essential for life on Earth
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
- produce them from biocompatible materials make these materials ideal for cell culture and tissue engineering [12][16][38][42]. Furthermore, post-synthesis modifications can be performed to enhance attachment from certain objects, for example proteins from the extracellular matrix (ECM) in tissue
- , although mild inflammation occurred during in vivo tests, however this is a common occurrence with biomaterials as shown by Mikos et al. [78]. Finally, the cryogel was capable of a controlled release of proteins. This allowed for a more controlled integration and movement of cells interconnecting with
- pore size range was between 50–300 μm, and small concentrations of laponite found in the gel wall helped with sustained release of a number of proteins with diverse properties [37]. Injectable nanocomposite cryogels have also appeared in research as a method to combat cancer. Bauleth-Ramos et al. used
In-depth characterization of self-healing polymers based on π–π interactions
Beilstein J. Org. Chem. 2021, 17, 2496–2504, doi:10.3762/bjoc.17.166
- ]. This specific process is based on reversible interactions, which are integrated in the chemical structure of the proteins of the thread [5]. Zinc–histidine metal complexes which are part of the protein’s structure enable the material to regenerate its mechanical performance after a damage event [1][6
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
- 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
- -phenylarsenoxide-based agents. This can also lead to deactivation of the drug as these organoarsenic drugs react readily with blood proteins, in particular transferrin [10]. In order to limit premature inactivation of the arsenic drugs, a range of nanoparticles have been developed to enhance stability, thus
- peptides and proteins have been linked to nanotechnology. DQA and TPP are both cationic and lipophilic molecules and therefore able to easily pass the mitochondrial membrane [15][16][17][18][19]. TPP is the most-studied mitochondrial targeting agent and has shown to accumulate 1000 times more in 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
- in the docking studies. Keywords: chronic myeloid leukemia; 1,3-dipolar cycloaddition; imatinib; (phenylamino)pyrimidine-pyridine; 1,2,3-triazole; Introduction Changes in tyrosine kinase proteins (TKPs), either by mutation or chromosomal translocation, can turn them into potent oncogenes
Constrained thermoresponsive polymers – new insights into fundamentals and applications
Beilstein J. Org. Chem. 2021, 17, 2123–2163, doi:10.3762/bjoc.17.138
- synthetic polymers, thermoresponsivity can also be observed in biological structures and their derivatives. While LCST behavior is more frequently studied in synthetic polymers, the occurrence of UCST behavior predominates in aqueous solutions of proteins [302][303]. The thermoresponse of natural proteins
Progress and challenges in the synthesis of sequence controlled polysaccharides
Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129
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
- hurdle that needs to be addressed before ASOs can find more widespread use [3][9][10][11][14]. A lack of efficient delivery of ASOs can be caused by various reasons such as degradation [15][16], insufficient endosomal escape [17], glomerular filtration [18], or binding to one or more proteins [19][20
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
- termed glycogenes [1][2]. These glycogenes include the glycosyltransferases, glycosidases, sulfotransferases, transporters, etc. The expression of these glycogenes is in turn driven by the action of a class of proteins called transcription factors (TFs). These TFs regulate gene expression by binding
- may regulate pathways related to sialylation, hyaluronan synthesis, as well as chondroitin and dermatan sulfate elongation. Here, STAT1, 4, and 5 proteins were enriched in the IL-21 signaling pathway. Luminal breast cancer types are known to express STAT1 and 3 as well as STATs 2 and 4. STAT5 is known
- [24][25]. It has been found to be upregulated in breast cancer with respect to normal-like. PRDM1, also known as Blimp-1, is a transcriptional repressor, and its upregulation in cancer is known to dysregulate other proteins [26]. The increase poly-LacNAc structures have been shown to play roles in
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
- structures of sesquiterpenes emitted from endophytic fungi (Table 2) isolated from black poplar leaves. Terpene synthase activity of CxTPS1 and CxTPS2. A) Genes were heterologously expressed in Escherichia coli and partially purified proteins were assayed with GPP, (E,E)-FPP, or (E,E,E)-GGPP as substrates in
- -springene (14). B) Structures of the enzyme products of CxTPS1 and CxTPS2, including (E)-β-caryophyllene (1) which was the only terpene detected from Cladosporium sp. cultures. Dendrogram analysis (rooted tree) of CxTPS1 and CxTPS2 (bold) from Cladosporium sp. and characterized TPS proteins and their main
- amino acid substitutions per site. The alpha-domain of maize TPS4 [62] was chosen as an outgroup. TPS proteins from different Ascomycota are highlighted according to their different lifestyle: endophytic (purple), pathogenic (orange) and saprophytic (green). Fungal endophytes identified from leaves of
Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications
Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116
- negative charge on PNA’s backbone. Electrostatic repulsion of the negatively charged phosphates dominates the conformational properties and structure of nucleic acids. In contrast to proteins that prefer to fold in compact structures, DNA and RNA inherently prefer extended conformations that minimize the
- electrostatic repulsion. The maintenance and function of long double-stranded DNA (dsDNA) is achieved through complex mechanisms involving histones and other proteins. Large non-coding RNAs (e.g., ribosomes) manage electrostatic repulsion using positively charged RNA-binding proteins and cations (e.g
- covalent conjugation of PNA to delivery enhancing compounds. Cell-penetrating peptides derived from natural proteins: The initial success of PNA delivery involved PNA conjugates taken up by receptor-mediated endocytosis. Pardridge and co-workers successfully demonstrated in vivo delivery and blood-brain
Antiviral therapy in shrimp through plant virus VLP containing VP28 dsRNA against WSSV
Beilstein J. Org. Chem. 2021, 17, 1360–1373, doi:10.3762/bjoc.17.95
- of interest [12][13][14][15][16]. The antiviral response of RNAi is triggered by double-stranded RNA (dsRNA) to block the synthesis of a specific viral protein, in the case of WSSV the targets being the structural proteins VP19, VP24, VP26, and VP28, as they are involved in cell recognition, virus
- entry, binding and assembly of the virion. Previous studies have shown that silencing these structural proteins in WSSV challenge assays, increases shrimp survival [10][11][17][18][19][20][21]. The VP28 glycoprotein plays an important role in systemic infection by interacting with cell membrane proteins
- , and it is one of the most abundant proteins along with VP26 (≈60%) in the external WSSV surface [21][22]. The RNAi trials using an intramuscular injection (IM) have shown that VP28 glycoprotein is the target of choice to block WSSV infection in shrimp [14][23][24]. However, RNAi intramuscular (IM
Icilio Guareschi and his amazing “1897 reaction”
Beilstein J. Org. Chem. 2021, 17, 1335–1351, doi:10.3762/bjoc.17.93
- work is testified by Willstätter, who in his memoirs refers to Guareschi as “alkaloid chemist” [28]. Ptomaines (from the Greek πτωμα, cadaver) are anaerobic bacterial degradation products of proteins and choline-containing phospholipids. The formation of these is associated with putrefaction of animal
Other Beilstein-Institut Open Science Activities
