Cis-trans isomerization in cyclosporin C dissolved in acetonitrile.

Cyclosporin is an 11-amino acid cyclic peptide with pharmacologically valuable properties which has a variety of actual and potential applications. Its activity relies on the cell membrane permeability which, in turn, depends on the structure of cyclosporin and its ability to change the conformation. In this work, conformational exchange processes occurring in cyclosporin C were studied using one- and two-dimensional nuclear magnetic resonance spectroscopy. The free energy barrier separating two major conformers observed in polar solution (acetonitrile) was found to be 77 ± 2 kJ/mol. Less populated conformation states are also present in the solution, which agrees with the ease of formation of multiple forms revealed by MD simulations of cyclosporin C.

Comparison of cyclosporin variants B-E based on their structural properties and activity in mitochondrial membranes.

Cyclosporins B, C, D, and E were characterized by NMR spectroscopy, and backbone flexibility was studied by molecular dynamics simulation. Structures of the molecules were characterized by nuclear Overhauser effect spectroscopy, which revealed that the studied peptides have many common features. Molecular dynamics simulation showed that the backbone of cyclosporin E is relatively more rigid than in other peptides. Calcium-dependent swelling of liver mitochondria under the influence of four considered compounds was also investigated. Three of them were found to have the activity similar to cyclosporin A, inhibiting opening of the mitochondrial pore at concentrations within 100-300 nM. However, cyclosporin E did not show any biological effect at concentrations up to 1 µM. Results of this study agree with the idea on the correlation between the peptide chain flexibility and its bioavailability.

Polyurethane ionomers based on amino ethers of ortho-phosphoric acid.

The etherification of ortho-phosphoric acid with triethanolamine and polyoxypropylene glycol is studied. The reaction process is accompanied by the formation of hyperbranched amino ethers of ortho-phosphoric acid terminated by hydroxyl groups. A specific feature of the chemical structure of the compounds obtained is the existence of ion pairs in their structure separated in space. The reaction of the etherification of ortho-phosphoric acid with glycols becomes possible through the use of tertiary amines. The amino ethers of ortho-phosphoric acid are investigated as a polyol component for the synthesis of polyurethanes with high adhesion characteristics and strength properties. The experimental results presented allow us to relate polyurethanes obtained on the basis of ortho-phosphoric acid amino ethers to polymers of ionomeric nature.

Evidence of oligomerization of bovine insulin in solution given by NMR.

The protein hormone insulin exists in several forms in nature, and a large number of modified sequences are used in pharmacy. They differ by physicochemical properties and efficiency of biological action. Pancreatic bovine insulin was studied in an acidic solution by nuclear magnetic resonance spectroscopy. [Formula: see text]H and [Formula: see text]C NMR signal assignment of backbone and side chains was made by analysis of a set of 2D spectra obtained on a sample with natural isotope abundance. The presence of certain secondary structure elements was revealed on a qualitative level based on nuclear Overhauser effect spectroscopy, which are similar to those observed in the crystal structure. The C-terminus of the B-chain possessed a remarkable flexibility. The molecule was shown to exist in exchange with oligomers based on its self-diffusion coefficient and correlation time measurements performed at different concentrations. Certain signals in the NOESY and HSQC spectra are consistent with the presence of minor conformers; this is an obstacle in simulating the molecular structure under the conditions used in the experiment.

Interaction of different statins with model membranes by NMR data.

Hydroxy-methyl-glutaryl-coenzyme A (HMG-CoA) reductase inhibitors or statins reduce the amount of low-density lipoprotein (LDL) cholesterol, which is known as a well-established risk factor for atherosclerosis. Despite the fact that statins have a common pharmacologic target essential to sterol biosynthesis, their efficacy, safety, and potential non-LDL actions vary significantly for different statins. There is a hypothesis that pharmacological features of statins depend on their location in cell membrane, but to the present day there is a lack of information in literature on interactions of statins with the surface of the cell membrane in liquid media. The results of NMR experiments showed that all studied statins form intermolecular complexes with models of cell membranes (dodecylphosphocholine micelles) in water solution. Locations of pravastatin, simvastatin, fluvastatin and cerivastatin on model membranes were established by NOESY NMR data. Distinctions in their positions can explain differences in pharmacological properties of studied compounds.

Stereodynamics of some pyridoxine derivatives.

The conformational properties of three pyridoxine derivatives were studied by 1 H dynamic NMR spectroscopy. Conformational exchange caused by a rotation of 2-nytrophenyl group around one single C-C bond, of 2,4-dinitrophenyl substituent around two single C-O bonds, and twist-twist transformations of the seven-membered ketal cycle was observed by NMR experiments at low temperatures. Meanwhile, the conformational exchange of the acetal ring remains fast in the NMR timescale even at 198 K. The energy barriers for all observed conformational exchange processes were determined by the lineshape analysis of dynamic NMR spectra. The activation barriers of the 2-nitrophenyl group rotation were almost the same for all studied compounds, about 40-41 kJ/mol. The energy barriers of the conformational exchange processes of the 2,4-nitrophenyl group and the ketal cycle increased significantly up to 10 kJ/mol in comparison with previously studied compounds with similar structure. Copyright © 2016 John Wiley & Sons, Ltd.

Antimicrobial peptide protegrin-3 adopt an antiparallel dimer in the presence of DPC micelles: a high-resolution NMR study.

A tendency to dimerize in the presence of lipids was found for the protegrin. The dimer formation by the protegrin-1 (PG-1) is the first step for further oligomeric membrane pore formation. Generally there are two distinct model of PG-1 dimerization in either a parallel or antiparallel ß-sheet. But despite the wealth of data available today, protegrin dimer structure and pore formation is still not completely understood. In order to investigate a more detailed dimerization process of PG-1 and if it will be the same for another type of protegrins, in this work we used a high-resolution NMR spectroscopy for structure determination of protegrin-3 (RGGGL-CYCRR-RFCVC-VGR) in the presence of perdeuterated DPC micelles and demonstrate that PG-3 forms an antiparallel NCCN dimer with a possible association of these dimers. This structural study complements previously published solution, solid state and computational studies of PG-1 in various environments and validate the potential of mean force simulations of PG-1 dimers and association of dimers to form octameric or decameric ß-barrels.

Structure of pravastatin and its complex with sodium dodecyl sulfate micelles studied by NMR spectroscopy.

The aim of this work was to study the mechanisms of interaction between pravastatin and cell membranes using model membranes (sodium dodecyl sulfate micelles) by nuclear magnetic resonance spectroscopy methods. On the basis of the nuclear magnetic resonance experiments, it was established that pravastatin can form intermolecular complexes with sodium dodecyl sulfate micelles by the interaction of its hydrophilic groups with the polar surface of the micelle. Conformational features of pravastatin molecule were also studied.

High-resolution NMR structure of the antimicrobial peptide protegrin-2 in the presence of DPC micelles.

PG-1 adopts a dimeric structure in dodecylphosphocholine (DPC) micelles, and a channel is formed by the association of several dimers but the molecular mechanisms of the membrane damage by non-α-helical peptides are still unknown. The formation of the PG-1 dimer is important for pore formation in the lipid bilayer, since the dimer can be regarded as the primary unit for assembly into the ordered aggregates. It was supposed that only 12 residues (RGGRL-CYCRR-RFCVC-V) are needed to endow protegrin molecules with strong antibacterial activity and that at least four additional residues are needed to add potent antifungal properties. Thus, the 16-residue protegrin (PG-2) represents the minimal structure needed for broad-spectrum antimicrobial activity encompassing bacteria and fungi. As the peptide conformation and peptide-to-membrane binding properties are very sensitive to single amino acid substitutions, the solution structure of PG-2 in solution and in a membrane mimicking environment are crucial. In order to find evidence if the oligomerization state of PG-1 in a lipid environment will be the same or not for another protegrins, we investigate in the present work the PG-2 NMR solution structure in the presence of perdeuterated DPC micelles. The NMR study reported in the present work indicates that PG-2 form a well-defined structure (PDB: 2MUH) composed of a two-stranded antiparallel ß-sheet when it binds to DPC micelles.

Determination of preferred conformations of ibuprofen in chloroform by 2D NOE spectroscopy.

Solution of an anti-inflammatory drug ibuprofen ((RS)-2-(4-isobutylphenyl) propionic acid) in chloroform was studied by nuclear magnetic resonance spectroscopy. A set of 2D NOESY spectra was analyzed in order to obtain atom-atom distances. Since ibuprofen is known to exist as an ensemble of different conformations, these distances are averaged over the ensemble. To compare experimental and calculated distances, three models of averaging were concerned. Our data allowed to determine the dominant conformers of ibuprofen dissolved in chloroform. The population of conformers in the saturated solution leads to a certain crystal morphology formed within the nucleation process. Observed and calculated (13)C chemical shifts (at the DFT/B3LYP/6-311+G(2d,p) level) were in good agreement.

Dynamic NMR study of cyclic derivatives of pyridoxine.

A series of pyridoxine derivatives was investigated by (1) H and 2D nuclear overhauser enhancement spectroscopy (NOESY) NMR. The free energies of activation for the pyridyl-oxygen rotation of the 2,4-dinitrophenyl ether of the seven-membered acetals of pyridoxine were measured by dynamic NMR. A conformational exchange between the chair and twist forms of the seven-membered acetal ring was confirmed by dynamic NMR and STO3G computations.

[Structure of amyloid-beta peptides in a complex with model membranes].

Structures of amyloid-beta peptides Aß1-40, Aß10-35, Aß13-23 and Aß16-22 in a complex with model membranes in solution were obtained on the analysis of NMR experimental data. It has been established that the process of peptide-micelle complex formation occurs through the amino acid residues L17, F19, F20 and G29-M35.

[NMR screening of potential inhibitors of Citrobacter freundii methionine].

Methionine γ-lyase [EC 4.4.1.11] participates in a methionine catabolism at a number of bacteria and protozoa eukaryotes, including pathogenic microorganisms. Lack of this enzyme at mammals allows consider it as a perspective target for rational antibacterial drug design. Currently in medical practice there are no the preparations based on an inhibition of methionine γ-lyase activity. We present results of the search of potential inhibitors of the enzyme using the NMR screening techniques based on identification of compounds, which able to bind specifically to their biological target. Study included a stage of in silico virtual screening of the library of commercially available compounds and subsequent experimental selection of the leading compounds, capable to interact with enzyme. Identification of binding was carried out by means of saturation transfer difference (STD) spectroscopy and WaterLOGSY technique. At the final stage the experimental assessment of inhibiting ability of the selected compounds in the reaction of γ-elimination of L-methionine catalyzed by methionine γ-lyase was carried out. Binding constants of two leading compounds were determined using the WaterLOGSY method. The research expands structural group of potential inhibitors of methionine γ-lyase and allows approach to the design of the inhibitors with higher efficacy.

A novel liquid crystalline system for partial alignment of polar organic molecules.

A new system for partial alignment of polar organic molecules to measure residual dipolar couplings in NMR consists of a 1:1 or a 2:1 mixture of water and DMSO including 3-13% n-alkylpentaethylene glycol as the surfactant. Temperature and concentration dependence of the alignment system are investigated and, as examples, the 13C,1H residual dipolar couplings for the amino acid methionine 1 and for an alpha-methylene-gamma-butyrolactone 2 have been obtained and are compared with those obtained from the alignment media consisting of n-alkylpentaethylene glycol, n-alkyl alcohol and water.

Changes in the nitrocellulose molecule induced by sulfate-reducing bacteria Desulfovibrio desulfuricans 1,388. The enzymes participating in this process.

The appearance of unsubstituted glucopyranose residues in nitrocellulose (NC) induced by Desulfovibrio desulfuricans was established by (13)C-NMR spectroscopy. After contact with bacterial cells, the degree of substitution by nitro groups in NC decreased from 2.59 to 2.40. The bacteria possess intra- and extracellular nitroesterase activities, which are responsible for denitration of the polymer. The presence of NC in the growth medium influences the extracellular nitroesterase activity. It is shown that inhibition of enzymatic activity in the presence of NC is caused by appearance of nitrates in the culture medium. Nitrate and nitrite reductases of dissimilatory type reduce nitrates. The data suggest consideration of bacteria belonging to the Desulfovibrio genus as the initial agent in utilization of an unnatural polymer--nitrocellulose--in a microbial consortium.