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Search for "clustering" in Full Text gives 47 result(s) in Beilstein Journal of Organic Chemistry.
Repurposing the anticancer drug cisplatin with the aim of developing novel Pseudomonas aeruginosa infection control agents
Beilstein J. Org. Chem. 2018, 14, 3059–3069, doi:10.3762/bjoc.14.284
- -Hochberg) adjusted P-value smaller than 0.05. The raw sequence reads were normalized by size factors, then Log2(N + 1) transformed. Hierarchical clustering analysis was performed using the transformed reads, and a heat-map was drawn for the differentially expressed genes between the cisplatin treated cells
Carbohydrate inhibitors of cholera toxin
Beilstein J. Org. Chem. 2018, 14, 484–498, doi:10.3762/bjoc.14.34
- galactosides have millimolar Kds and little interaction can be detected for simple sialosides [20]. The distance separating the binding sites is similar for all members of the AB5 toxin family and is believed to be instrumental in clustering the glycolipid ligands in such a way that membrane curvature is
The use of 4,4,4-trifluorothreonine to stabilize extended peptide structures and mimic β-strands
Beilstein J. Org. Chem. 2017, 13, 2842–2853, doi:10.3762/bjoc.13.276
- criterion, almost 50% of the 4a and 4b conformations are globally extended, whereas less than 30% of the other sequence conformations are in that case (Table 6). The most prevalent conformations of each peptide were determined by clustering their conformational ensembles, using the “gromos” method
Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience
Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114
Synthesis of multi-lactose-appended β-cyclodextrin and its cholesterol-lowering effects in Niemann–Pick type C disease-like HepG2 cells
Beilstein J. Org. Chem. 2017, 13, 10–18, doi:10.3762/bjoc.13.2
- . Stokmaier et al. revealed that the binding affinity of galactose to ASGPR elevated 100–1000 fold from mono- to triantennary galactose structures, probably due to clustering effects [22]. The dissociation constant of monosaccharide with ASGPR was 10–4 M, whereas those of triantennary and tetraantennary
- [15][16]. Therefore, the binding affinity of multi-Lac-β-CD (DSL5.6) to ASGPR is likely to be much higher than that of mono-Lac-β-CD. In fact, multi-Lac-β-CD (DSL5.6) has a quite low dissociation constant (2.6 × 10−8 M) with PNA, probably a result of its clustering effect in ASGPR recognition. The
Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides
Beilstein J. Org. Chem. 2016, 12, 1250–1268, doi:10.3762/bjoc.12.120
- been determined. This is often due to the lack of suitable candidate enzymes, especially in eukaryotic pathways where gene clustering is less common. Otherwise, it could reflect the challenges associated with expression of functional soluble protein or the generation of a suitable substrate for
Is conformation a fundamental descriptor in QSAR? A case for halogenated anesthetics
Beilstein J. Org. Chem. 2016, 12, 760–768, doi:10.3762/bjoc.12.76
- ), another with negative scores in PC1 and around null scores in PC2 (compounds with moderate-to-low activities), and the third one at negative scores in PC1 and very positive scores in PC2 (compounds with low activities). Variables X1876 and X5979 in the loadings plot are responsible for clustering these
Enabling technologies and green processes in cyclodextrin chemistry
Beilstein J. Org. Chem. 2016, 12, 278–294, doi:10.3762/bjoc.12.30
- interaction and may promote the formation of metal nanoparticle clustering. Cu(I)-based system have been used in alkyne/azide [3 + 2] cycloadditions, while Pd(II)-based catalysts have been used in C–C couplings reactions (Scheme 7) [34]. An example of water-soluble β- and γ-CD/chitosan derivatives have been
Assembly of synthetic Aβ miniamyloids on polyol templates
Beilstein J. Org. Chem. 2015, 11, 2646–2653, doi:10.3762/bjoc.11.284
- and 11 is possible (Figure 6). Addition of 0.7 equivalents of boronic acid to the dimeric template 9 intentionally leads to incomplete esterification and identifies the C-terminal site B as the slightly preferred esterification site. This technique is relevant for identifying hydrophobic clustering of
Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations
Beilstein J. Org. Chem. 2015, 11, 2459–2473, doi:10.3762/bjoc.11.267
- along the trajectory, we obtained the most stable geometry in vacuo. The simulations show a weak clustering of the hydrophobic thioalkyl groups and an extensive pattern of hydrogen bonds at the polar rim involving the adjacent OH groups (Figure 1a), yielding a cylindrical molecular shape with similar
- and the MD run lasted for 500 ps, in view of the much faster relaxation due to the random collisions with the solvent. Here, the aCD assumes the typical truncated-cone shape taken by cyclodextrins in the solid state, but in the present case this feature is further enhanced by the clustering of the H
- weaker than in vacuo because of the competing interaction of the polar groups with the water molecules. In the initial minimizations, only minor changes were observed, mainly involving some clustering and partial shielding of the H groups to minimize contact with water. After the MD runs, only relatively
Regulation of integrin and growth factor signaling in biomaterials for osteodifferentiation
Beilstein J. Org. Chem. 2015, 11, 773–783, doi:10.3762/bjoc.11.87
- receptors and result in optimal cell survival and migration signals. Growth factor-mediated activation of the receptors leads to clustering of integrins and activation of integrin signaling [8][17]. In a word, the crosstalk between integrins and growth factor receptors is bidirectional that integrins may
- on the denser parts shall be smaller than 70 nm, thereby allowing integrin clustering and assembly focal adhesions to induce cell spreading. In a similar concept, a controlled nanodisordered pattern, which is not highly ordered but not random either, induces rapid osteogenesis from skeletal stem
- limited. As a result, cells are self-renewed without loss of phenotype [32]. In a recent study, how nanoscale clustering of integrin ligands alters the mechano-regulation of integrins has been revealed with the assistance of molecular tension fluorescence microscopy [33]. In the step of nascent adhesion
Glycodendrimers: tools to explore multivalent galectin-1 interactions
Beilstein J. Org. Chem. 2015, 11, 739–747, doi:10.3762/bjoc.11.84
- of glycoconjugates (TF antigen Mucin-1) on adjacent cells which directly facilitates aggregation; and (ii) clustering of receptors (TF antigen Mucin-1) which exposes adhesion molecules that interact with adhesion molecules on neighboring cells to cause aggregation. All four generations of the
Probing multivalency in ligand–receptor-mediated adhesion of soft, biomimetic interfaces
Beilstein J. Org. Chem. 2015, 11, 720–729, doi:10.3762/bjoc.11.82
- ligands are typically oligomers consisting of multiple subunits of varying complexity. When binding to receptors this leads to a receptor clustering or so-called glycocluster effect. However, multivalency even goes further: For example when cells form contact layers of surface anchored carbohydrates the
Multivalent scaffolds induce galectin-3 aggregation into nanoparticles
Beilstein J. Org. Chem. 2014, 10, 1570–1577, doi:10.3762/bjoc.10.162
- Warren Avenue, Detroit, Michigan 48201, USA 10.3762/bjoc.10.162 Abstract Galectin-3 meditates cell surface glycoprotein clustering, cross linking, and lattice formation. In cancer biology, galectin-3 has been reported to play a role in aggregation processes that lead to tumor embolization and survival
- binding of galectins, as demonstrated in galectin binding studies with neuroblastoma cells [25]. Here, we demonstrate that glycodendrimers bearing lactose can be used to form large, discrete aggregates of galectin-3. Since, as noted above, glycan clustering and galectin-3-mediated aggregations have been
- formation as previously postulated [18][31][36]. Ongoing studies on the aggregate stoichiometry should provide valuable insight on this matter. Overall, the results presented here indicate that clustering and aggregation events should be considered in addition to carbohydrate binding affinity for galectin-3
Conformation of dehydropentapeptides containing four achiral amino acid residues – controlling the role of L-valine
Beilstein J. Org. Chem. 2014, 10, 660–666, doi:10.3762/bjoc.10.58
- investigated peptides were defined by using the XPLOR-NIH [32] program. The average values obtained for dihedral angles after the clustering of received conformers are presented in Table 3. In the case of peptides 1 and 2 the results of the calculations suggest that peptides could adopt two types of bent
- conformations, whereas for peptide 3 only one well-defined bent conformation could be found. Selected φ and ψ dihedral angles were excluded during clustering analysis for all investigated peptides. When we tried to group the obtained conformers according to all torsion angles of the main chain, the analysis did
- Gly(1) and Val(2) as well as Val(2) and ΔZPhe(3) (see Table S7 in Supporting Information File 1). This observation seems to be confirmed by the result of the XPLOR calculation. Figure 3 shows two consecutive bents for both clusters 2a and 2b, which were found after clustering the results of the XPLOR
Mannose-decorated cyclodextrin vesicles: The interplay of multivalency and surface density in lectin–carbohydrate recognition
Beilstein J. Org. Chem. 2012, 8, 1543–1551, doi:10.3762/bjoc.8.175
- a substantially lower rate of agglutination. These observations can be explained on the basis of a clustering of mannose residues in the mixed glycocalyx of guest 2 and “inert” guest 6: clusters of guest 2 could offer multivalent “adhesive patches” for ConA even if the average surface coverage of
- guest 2 is far below 50%. The low rate of agglutination could be a consequence of a slow rearrangement of the glycocalyx, i.e., a “receptor-induced clustering” of mannose in the presence of ConA. Conclusion In this study we described a biomimetic model for the glycocalyx of a cell membrane based on
Design of a novel tryptophan-rich membrane-active antimicrobial peptide from the membrane-proximal region of the HIV glycoprotein, gp41
Beilstein J. Org. Chem. 2012, 8, 1172–1184, doi:10.3762/bjoc.8.130
- the hydrophilic residues clustering on one face of the peptide, while hydrophobic residues appear on the opposite face [3]. This amphipathic structure allows the peptide to embed itself into the interfacial region of a phospholipid membrane and it anchors the peptide to the surface of the bilayer
Similarity analysis, synthesis, and bioassay of antibacterial cyclic peptidomimetics
Beilstein J. Org. Chem. 2012, 8, 1146–1160, doi:10.3762/bjoc.8.128
- [38]. Clustering of the structures in such a multidimensional space is the natural choice for similarity analysis. Clustering Clustering is a widely used technique that has found application in the selection of compounds for screening, analysis of substructure search output, and the prediction of
- molecular properties [49]. The “k-means method” implemented in Statistica software is effective in clustering results for many practical applications, and was used to classify the current data set. All types of descriptors are calculated by using the CODESSA Pro program and the descriptor matrix is
- generated, which served as an input for the cluster-analysis module in STATISTICA software. The use of descriptors in this study can give differing clustering patterns [50]. The first step in the structure clustering is the generation of a matrix containing similarity values of descriptors for all pairs of
Low-generation dendrimers with a calixarene core and based on a chiral C2-symmetric pyrrolidine as iminosugar mimics
Beilstein J. Org. Chem. 2012, 8, 951–957, doi:10.3762/bjoc.8.107
- [14]. Multivalent calixarenes functionalised with carbohydrate units (glycocalixarenes) [15] have been extensively reported in the literature and represent examples of sugar clustering on macrocyclic structures [16][17]. Thanks to the “glycoside cluster effect” [18][19][20], glycocalixarenes can
High-affinity multivalent wheat germ agglutinin ligands by one-pot click reaction
Beilstein J. Org. Chem. 2012, 8, 819–826, doi:10.3762/bjoc.8.91
- mode to WGA. The best divalent WGA ligand is C4 (IC50 0.6 µM), which binds 1000 times stronger to WGA than N,N’-diacetylchitobiose (500 times per chitobiose residue). As expected, clustering of carbohydrate epitopes with higher WGA binding affinity not only leads to multivalent ligands with higher
Planar-bilayer activities of linear oligoester bolaamphiphiles
Beilstein J. Org. Chem. 2011, 7, 1562–1569, doi:10.3762/bjoc.7.184
- impossible to rationalize in any simple way as the activities themselves are multifacetted and do not admit simple explanations. In our systematic application of the “activity-grid” method to published records we found that, from the great number of unique architectures, there is an overall clustering
Coupled chemo(enzymatic) reactions in continuous flow
Beilstein J. Org. Chem. 2011, 7, 1449–1467, doi:10.3762/bjoc.7.169
- clustering the enzymes of a given metabolic pathway. Moreover, the clustered enzymes usually form supramolecular complexes enabling so-called “substrate channeling”, where intermediates of sequential metabolic steps are not released into the cytoplasm, but instead are “channeled” from one enzyme to another
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