RNA and Protein Determinants Mediate Differential Binding of miRNAs by a Viral Suppressor of RNA Silencing Thus Modulating Antiviral Immune Responses in Plants.

Many plant viruses express suppressor proteins (VSRs) that can inhibit RNA silencing, a central component of antiviral plant immunity. The most common activity of VSRs is the high-affinity binding of virus-derived siRNAs and thus their sequestration from the silencing process. Since siRNAs share large homologies with miRNAs, VSRs like the p19 may also bind miRNAs and in this way modulate cellular gene expression at the post-transcriptional level.

Betulin Sulfonamides as Carbonic Anhydrase Inhibitors and Anticancer Agents in Breast Cancer Cells.

Hypoxia-regulated protein carbonic anhydrase IX (CA IX) is up-regulated in different tumor entities and correlated with poor prognosis in breast cancer patients. Due to the radio- and chemotherapy resistance of solid hypoxic tumors, derivatives of betulinic acid (BA), a natural compound with anticancer properties, seem to be promising to benefit these cancer patients. We synthesized new betulin sulfonamides and determined their cytotoxicity in different breast cancer cell lines.

An Integrated Mass Spectrometry Based Approach to Probe the Structure of the Full-Length Wild-Type Tetrameric p53 Tumor Suppressor.

We present an integrated approach for investigating the topology of proteins through native mass spectrometry (MS) and cross-linking/MS, which we applied to the full-length wild-type p53 tetramer. For the first time, the two techniques were combined in one workflow to obtain not only structural insight in the p53 tetramer, but also information on the cross-linking efficiency and the impact of cross-linker modification on the conformation of an intrinsically disordered protein (IDP). P53 cross-linking was monitored by native MS and as such, our strategy serves as a quality control for different cross-linking reagents.

Structural analysis of guanylyl cyclase-activating protein-2 (GCAP-2) homodimer by stable isotope-labeling, chemical cross-linking, and mass spectrometry.

The topology of the GCAP-2 homodimer was investigated by chemical cross-linking and high resolution mass spectrometry. Complementary conducted size-exclusion chromatography and analytical ultracentrifugation studies indicated that GCAP-2 forms a homodimer both in the absence and in the presence of Ca(2+). In-depth MS and MS/MS analysis of the cross-linked products was aided by (15)N-labeled GCAP-2.

Transport of the areca nut alkaloid arecaidine by the human proton-coupled amino acid transporter 1 (hPAT1).

Objectives: The pyridine alkaloid arecaidine is an ingredient of areca nut preparations. It is responsible for many physiological effects observed during areca nut chewing. However, the mechanism underlying its oral bioavailability has not yet been studied.

Three-dimensional quantitative structure-activity relationship analyses of substrates of the human proton-coupled amino acid transporter 1 (hPAT1).

The proton-coupled amino acid transporter hPAT1 has recently gained much interest due to its ability to transport small drugs thereby allowing their oral administration. A three-dimensional quantitative structure-activity relationship (3D QSAR) study has been performed on its natural and synthetic substrates employing comparative molecular similarity indices analysis (CoMSIA) to investigate the structural requirements for substrates and to derive a predictive model that may be used for the design of new prodrugs. The cross-validated CoMSIA models have been derived from a training set of 40 compounds and the predictive ability of the resulting models has been evaluated against a test set of 10 compounds.

Physiological characterization of cadmium-exposed Chlamydomonas reinhardtii.

Chlamydomonas reinhardtii is a common model organism for investigation of metal stress. This green alga produces phytochelatins in the presence of metal ions. The influence of cadmium is of main interest, because it is a strong activator of phytochelatin synthase.

Cyclic tetraureas with variable flexibility--synthesis, crystal structures and properties.

Macrocyclic molecules containing several amide or urea functions may serve as anion receptors. We describe the synthesis of 32-membered macrocycles, in which four rigid xanthene units (X) and/or diphenyl ether units (D) as flexible analogues are linked via urea groups. All six possible combinations of these units (XXXX, XXXD, XXDD, XDXD, XDDD and DDDD) were synthesized and two examples were characterised by single-crystal X-ray analyses (DDDD and two structures for XXXD).

Cyclic triureas--synthesis, crystal structures and properties.

The synthesis of 24-membered macrocycles is described, in which rigid xanthene units (X) and/or diphenyl ether units (D) as flexible analogues are linked via urea groups. All four possible combinations (XXX, XXD, XDD, DDD) have been obtained with yields of 40-72% for the cyclisation step. In two cases, the respective cyclic hexamers (XXDXXD, XXXXXX) were also isolated.

Reasons for the exclusive formation of heterodimeric capsules between tetra-tolyl and tetra-tosylurea calix[4]arenes.

The selective heterodimerization of tetra-tolyl () and tetra-tosylurea () calixarenes, serendipitously found by Rebek et al. (R. K.

Recognition of 2-aminothiazole-4-acetic acid derivatives by the peptide transporters PEPT1 and PEPT2.

The H(+)/peptide cotransporters PEPT1 and PEPT2 have gained considerable interest in pharmaceutical sciences as routes for drug delivery. It is, therefore, of interest to develop uncommon artificial substrates for the two carriers. This study was initiated to investigate the binding affinity of 2-aminothiazole-4-acetic acid (ATAA) conjugates with amino acids to PEPT1 and PEPT2.

Hydrogen bonding in dimers of tritolyl and tritosylurea derivatives of triphenylmethanes.

The crystal structure of the homodimer formed by the tritolylurea 3a proves the existence of a belt of six bifurcated hydrogen bonds between both NH and the O=C groups of the adjacent urea residues. For the tritosylurea 3b, four additional three-center hydrogen bonds, also involving the SO2 oxygen, are found in the crystalline state. Molecular dynamics simulations in a chloroform box confirm these patterns of the hydrogen bonds and the resulting elongation of the dimer 3b.

Structural requirements for the substrates of the H+/peptide cotransporter PEPT2 determined by three-dimensional quantitative structure-activity relationship analysis.

The renal type H(+)/peptide cotransporter PEPT2 has a substantial influence on the in vivo disposition of dipeptides and tripeptides as well as peptide-like drugs within the body, particularly in kidney, lung, and the brain. The comparative molecular similarity indices analysis (CoMSIA) method was applied to identify those regions in the substrate structures that are responsible for recognition and for differences in affinity. We have developed a comprehensive 3D quantitative structure-activity relationship (3D-QSAR) model based on 83 compounds that is able to explain and predict the binding affinities of new PEPT2 substrates.

Orientational preferences of aromatic guests in dimeric capsules of tetraurea calix[4]arenes--MD and NMR studies.

Molecular dynamics (MD) simulations have been performed for complexes of a dimeric capsule of a tetraurea calixarene with a series of twelve aromatic guests. A distinct orientational preference and a restriction of the internal mobility was found which depend on the size and electronic properties of the guests. The results are in agreement with the CIS values obtained from (1)H NMR spectroscopic measurements and with complexation selectivities obtained by competition experiments.

Unusual conformations of 1,3-dialkoxythiacalix[4]arenes in the solid state.

The structures of three syn-1,3-dialkoxythiacalix[4]arenes with unusual conformations in the solid state are reported. The pinched cone conformation of syn-2(2),4(2)-dihydroxy-1(2),3(2)-bis(prop-2-enyloxy)thiacalix[4]arene, C30H24O4S4, (3a), is stabilized by two intramolecular hydrogen bonds, remarkably formed from both OH groups to the same ether O atom. In syn-2(2),4(2)-dihydroxy-1(5),2(5),3(5),4(5)-tetranitro-1(2),3(2)-bis(prop-2-enyloxy)thiacalix[4]arene acetone disolvate, C30H20N4O12S4.

Three-dimensional quantitative structure-activity relationship analyses of beta-lactam antibiotics and tripeptides as substrates of the mammalian H+/peptide cotransporter PEPT1.

The utilization of the membrane transport protein PEPT1 as a drug delivery system is a promising strategy to enhance the oral bioavailability of drugs. Since very little is known about the substrate binding site of PEPT1, computational methods are a meaningful tool to gain a more detailed insight into the structural requirements for substrates. Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies using the comparative molecular similarity indices analysis (CoMSIA) method were performed on a training set of 98 compounds.

Hydrogen bonded dimers of triurea derivatives of triphenylmethanes.

Tri-(2-alkoxy-5-ureido-phenyl)methanes represent a novel self-complementary motif forming hydrogen bonded homo- and heterodimers in nonpolar, aprotic solvents as evidenced by 1H NMR and ESI-mass spectra and by the formation of heterodimers. MD simulations suggest the formation of hydrogen bonds of different strength in agreement with NMR data. The dimerization does not interfere with that of tetraurea calix[4]arenes.

Preferred dimerization of tetra-tolyl- and tetra-tosylurea derivatives of flexible and rigidified calix[4]arenes.

The dimerization of tetratolyl- and tetratosyl-urea derivatives 1 and 2, derived from a tetrapentoxy calix[4]arene in the cone conformation and of the corresponding tetra-urea derivatives 3 and 4, in which the cone conformation is rigidified by the two crown-3 tethers, have been studied. All six possible equimolar mixtures were examined by 1H NMR using CDCl3 and CD2Cl2 as solvents. While no heterodimers are found for the combinations 1/3 and 2/4 in either solvent, all remaining combinations lead to the (exclusive) formation of heterodimers in CD2Cl2.

Preparation and conformation of dioxocalix[4]arene derivatives.

CrO(3) oxidation experiments conducted on atropisomeric forms of 2 (2(paco), 2(1,3)(-)(alt), and 2(1,2)(-)(alt)) indicate that under the reaction conditions only methylene groups located between pairs of geminal rings oriented in an anti disposition are oxidized to carbonyls. NMR data suggest that the tetrahydroxydioxocalix[4]arenes 7 and 9 adopt the partial cone and 1,2-alternate conformations, respectively. In the crystal structure of 7.

Sterically and guest-controlled self-assembly of calix[4]arene derivatives.

In solvents such as chloroform or benzene, tetraurea calix[4]arenes 1 form dimeric capsules in which one solvent molecule is usually included as guest. To explore the structural requirements for the formation of such hydrogen-bonded dimers we replaced one p-tolylurea residue by a simple acetamide function. The resulting calix[4]arene 2 a, substituted at its wide rim with one acetamide and three p-tolylurea functions, assumes a C(1)-symmetrical conformation in apolar solvents as shown by (1)H NMR, which is not compatible with the usual capsule.

3-Oxa-6,8-diaza-1,2:4,5-dibenzocycloocta-1,4-dien-7-one: a three-dimensional network assembled by hydrogen-bonding, pi-pi and edge-to-face interactions.

The title compound, C(13)H(10)N(2)O(2), is the first structure in which the urea moiety is incorporated into an eight-membered ring. Two molecules are found in the asymmetric unit, which are almost identical in their conformation and their hydrogen-bond pattern. The carbonyl O atom acts as a double acceptor for the NH groups of two adjacent molecules.