NMR spectroscopic and molecular modeling studies of protein-carbohydrate and protein-peptide interactions

Investigations of the conformations of carbohydrates, their analogues and their molecular mimics are described, with emphasis on structural and functional information that can be gained by NMR spectroscopic techniques in combination with molecular modeling. The transferred nuclear Overhauser effect (trNOE) has been employed to determine the bound conformations of carbohydrates and other bioactive molecules in complex with protein receptors. The corresponding experiments in the rotating frame (trROE) and selective editing experiments (e.g., QUIET-NOESY) are used to eliminate indirect cross-relaxation pathways (spin diffusion), thereby minimizing errors in the data used for calculation of conformations. Saturation transfer difference NMR experiments reveal detailed information about intermolecular contacts between ligand and protein. Computational techniques are integrated with NMR-derived information to construct structural models of these bioactive molecules and of their complexes with proteins. Recent investigations into the nature of molecular mimicry with regard to protein-ligand interactions are described, along with applications in determining the mode of action of enzyme inhibitors. The results are relevant for the design of the next generation of drug and vaccine candidates.     

A spectroscopic and molecular modeling study on novel pseudopeptides exhibiting biological activity.

A series of pseudopeptides, containing two fluorophores, such as naphthalene (N) and indole (I), and exhibiting interesting biological activity as tachykinin receptor antagonists, were investigated by electronic absorption, CD and steady-state fluorescence experiments. In polar solvents (e.g. methanol), bioactivity is coupled with a stacked, charge-separated complex between I and N, the amount of which depends on the stereochemical features and conformational mobility of the central scaffold in the molecules examined. This agrees with the idea that dipolar charged, spatially close, aromatic moieties are important topochemical elements in the mechanism of action of these receptor antagonists. Molecular mechanics calculations allowed us to build up hypothetical, low-energy conformations of a few representative pseudopeptides, whose structural features are consistent with the experimental findings.     

The cholinomimetic activity of alkyltrimethylammonium compounds in experiments on the isolated mollusk neuron and on frog and chicken skeletal muscle

As revealed by contractile reaction of frog and chick muscles and by changes in the membrane current of isolated molluscan neurone, cholinomimetic activity of alkyltrimethylammonium compounds (ATMC) in the highest in drugs with 4 and 5 methylene groups in a molecule. The decrease in the activity with the decrease in the number of methylene groups was more evident in chick muscle; the decrease in the activity due to the increase in the number of these groups was most significant in experiments on molluscan neurone. Analysis of membrane current fluctuations showed that elementary current does not depend, whereas channel open time only slightly depends on the number of methylene groups in ATMC. However, with the increase of the number of methylene groups above 4, gradual decrease was observed in the ability of ATMC to increase at low (threshold) concentrations the membrane current (response) in the neurone. This decrease in the potency of ATMC correlated with the increase in Q10 value for neuronal response and calculated Q10 value for the reaction rate of ATMC with cholinoreceptor. The decrease in the activity of these ATMC is presumably due to a longer duration of complex formation with cholinoreceptor because of the higher energy barrier. ATMC with 8 and 9 methylene groups at high (saturating) concentrations elicited significantly smaller neuronal response with higher Q10 value. It is suggested that this phenomenon is due to a longer duration of complex formation with cholinoreceptor because of a higher energy cost.     

NMR spectroscopic and molecular modeling investigations of the trans-sialidase from Trypanosoma cruzi

Nuclear magnetic resonance (NMR) spectroscopy was used to investigate the transfer of sialic acid from a range of sialic acid donor compounds to acceptor molecules, catalyzed by Trypanosoma cruzi trans-sialidase (TcTS). We demonstrate here that NMR spectroscopy is a powerful tool to monitor the trans-sialidase enzyme reaction for a variety of donor and acceptor molecules. The hydrolysis or transfer reactions that are catalyzed by TcTS were also investigated using a range of N-acetylneuraminosyl-based donor substrates and asialo acceptor molecules. These studies showed that the synthetic N-acetylneuraminosyl donor 4-methylumbelliferyl alpha-d-N-acetylneuraminide (MUN) is hydrolyzed by the enzyme approximately 3-5 times faster than either the disaccharide Neu5Acalpha(2,3)Galbeta1Me or the trisaccharide Neu5Acalpha(2,3)Lacbeta1Me. In the transfer reaction, we show that Neu5Acalpha(2,3)Lacbeta1Me is the most favorable substrate for TcTS and is a better substrate than the naturally-occurring N-acetylneuraminosyl donor alpha1-acid glycoprotein. In the case of MUN as the donor molecule, the transfer of Neu5Ac to different acceptors is significantly slower than when other N-acetylneuraminosyl donors are used. We hypothesize that when MUN is bound by the enzyme, the orientation and steric bulk of the umbelliferyl aglycon moiety may restrict the access for the correct positioning of an acceptor molecule. AutoDock studies support our hypothesis and show that the umbelliferyl aglycon moiety undergoes a strong pi-stacking interaction with Trp-312. The binding properties of TcTS towards acceptor (lactose) and donor substrate (Neu5Ac) molecules have also been investigated using saturation transfer difference (STD) NMR experiments. These experiments, taken together with other published data, have clearly demonstrated that lactose in the absence of other coligands does not bind to the TcTS active site or other binding domains. However, in the presence of the sialic acid donor, lactose (an asialo acceptor) was observed by NMR spectroscopy to interact with the enzyme's active site. The association of the asialo acceptor with the active site is an absolute requirement for the transfer reaction to proceed.     

Factors affecting the cholinomimetic activity of alkyltrimethylammonium compounds in experiments on isolated neurons of the mollusk Planorbarius corneus

It has been shown that the elementary current is independent whereas the duration of channel opening is slightly dependent on the number of methylene groups (from 1 to 9) in the molecule of alkyltrimethylammonium compounds. However, substances with more than 4 methylene groups exhibit lower cholinomimetic activity (i.e. the ability to increase the membrane current) and higher values of Q10 for the reaction with cholinoreceptor. It is suggested that lower activity of these compounds is due to a low rate of formation of a complex with cholinoreceptor because of the higher potential energy barrier.     

13C NMR spectra of some naturally occurring binaphthoquinones and related compounds

¹³C NMR chemical shift assignments have been shown to be diagnostic for the establishment of the dimeric linkage of some naturally occurring binaphthoquinones. The unsymmetric ¹³C and ¹H spin-spin coupled pattern observed in the ¹H coupled ¹³C NMR spectrum of plumbagin for C-6 has also been noticed earlier with the related compound juglone. The nature of these effects has been substantiated for the first time using benzene induced solvent shifts and D₂O exchange. ¹³C chemical shift assignments of plumbagin reported earlier for C-6 and C-8 have been revised.     

Conjugated and cross-conjugated mesomeric betaines. Correlation of electroreduction with structure and physiological activity

Electroreduction studies were performed on several cross-conjugated mesomeric betaines containing the fused pyrazolium (2) and fused imidazolium (3) ring systems. Studies at acidic pH were of principal interest. Substituent effects for 2 were in line with prior findings, and reduction potentials were comparatively negative (-0.96 to -1.34 V). Reduction potentials fit the modified Hammett equation. Compound 3 was more readily reduced (-0.88 V). The related psi-oxatriazoles (6) gave values in the range of -0.85 to -1.22 V. The electrochemical characteristics are compared with those of the mesoionic sydnones (4) and sydnoneimines (5). These mesoionic compounds were generally reduced at more positive potentials than 2 and 3. A relationship between electroreduction and physiological activity is proposed. The overall results are in keeping with the hypothesis of widespread participation of iminium-type species in biological systems.     

Conformation of kainic acid in solution from molecular modelling and NMR spectra

Conformational behaviour of kainic acid in aqueous solution was elucidated by molecular mechanics and dynamics. The pucker of the five-membered ring in kainic acid was examined and compared with that of model compounds. In cyclopentane there is no barrier to pseudorotation, so that all puckered states coexist. In pyrrolidinium, the presence of a hetero-atom in the ring introduces a small barrier (about 0.6 kcal mol(-1)) to pseudorotation, separating two stable regions, A and B, which are equivalent by symmetry. In proline, the presence of the carboxylate group on C2 removes the symmetry but two stable conformational minima, A and B, remain. In kainic acid, the presence of side-chains on C3 and C4 introduces complications resulting in additional sub-minima in both regions, A and B. In solution, kainic acid is a complex mixture of conformers with comparable energies, because of the combination of several stable states of the pyrrolidinium ring with the torsional degrees of freedom arising from the two side-chains. The individual geometries, energies, and estimates of relative populations of these conformers were obtained from molecular dynamics simulations. The calculations were validated by a comparison of predicted inter-proton distances and vicinal proton coupling constants with the experimental quantities derived from NMR spectra.     

Isolation and NMR spectroscopic characterization of sialic acid compounds and hemofiltrate of chronic uremia patients

Eight sialyloligosaccharides have been isolated from the hemofiltrate of a patient with end stage renal disease using reverse osmosis, gel filtration, ion-exchange and high-performance liquid chromatography. The structures were predominantly elucidated by one- and two-dimensional 1H- and 13C-NMR spectroscopy: 1 NeuAc alpha 2-3Gal beta 1-4Glc; 2 NeuAc alpha 2-6Gal beta 1-4Glc; 3 NeuAc alpha 2-3Gal beta 1-4GlcNAc; 4 NeuAc-alpha 2-6Gal beta 1-4GlcNAc; 5 NeuAc alpha 2-3Gal beta 1-4-GlcNAc alpha 1-P; 6 NeuAc alpha 2-6Gal beta 1-4GlcNAc alpha 1-P; 7 NeuAc alpha 2-3Gal beta 1-3GalNAc alpha 1-P; 8 NeuAc alpha 2-8NeuAc. While compounds 1-7 are also components of normal human urine, di-N-acetyl-D-neuraminic acid (8) could be isolated for the first time from biological material. The origin and possible clinical relevance of these compounds have to be proved in further investigations.     

Improved quality of 1H NMR spectroscopic data for enhanced metabolic profiling of low molecular weight metabolites in human serum

NMR based metabolic profiling of blood samples in epidemiological studies can be used for molecular phenotyping and biomarker discovery. Often metabolic changes in blood are more subtle and demand a high quality spectrum especially when looking at low molecular weight compounds. In order to improve ¹H NMR spectroscopic data we compared different serum sample preparation methods. Application of phosphate buffer reduces chemical shift variation, enhances resolution of signal multiplicity, facilitates visual inspection of NMR spectra and annotation of signals compared to traditionally used saline. For analysis of low molecular weight compounds we found that standard 1D spectra of ultrafiltrated serum samples show enhanced spectral quality of small metabolites as compared to transverse relaxation edited spectra (also called Carr–Purcell–Meiboom–Gill, CPMG) spectra of unfiltered serum samples due to improved signal-to-noise ratio. Thus, NMR signals attributable to different amino acids and other small metabolites could readily be detected in spectra of ultrafiltrated serum, but remained invisible in the corresponding CPMG spectra. An OPLS model of fasting blood glucose showed an increase of Q² when using spectra from ultrafiltrated serum (Q² = 0.261) compared to using CPMG spectra (Q² = 0.173). Similar results were observed for OPLS models of BMI (Q² = 0.253 and Q² = 0.216, respectively). Furthermore, a reduction in model dimensionality was observed when using ultrafiltrated serum data. In conclusion we recommend sample preparation of serum samples in phosphate buffer instead of saline. Ultrafiltration of serum samples prior to NMR analysis is beneficial especially for low concentrated small metabolites.     

Phytotoxic activity of Cleome arabica L. and its principal discovered active compounds

The aim of this study was to assess the phytotoxic potential of Cleome arabica L, as well as to isolate the main bioactive compounds. Phytotoxicity was evaluated on germination and seedling growth of Lactuca sativa, Raphanus sativus, Peganum harmala and Silybum marianum, through testing aqueous and organic extracts of different C. arabica organs (roots, shoots, siliquae and seeds). Results showed that siliquae methanol extract caused the greatest negative effect on lettuce germination and growth. For the bioactive subfractions (petroleum ether, ethyl acetate and methanol–water), the ethyl acetate induced highly significant reduction, showing 100% inhibition of lettuce growth at 6 g/L. The bioactive ethyl acetate subfraction was chromatographed and subjected to NMR techniques. Based on bio-guided chromatographic fractionation, five bioactive allelochemical compounds were isolated from ethyl acetate extract of siliquae of C. arabica. The most inhibitory compound on lettuce seedling growth was elucidated as 11-α-acetylbrachy-carpone-22(23)-ene.     

A novel strategy for site-directed chemical reactions in single stranded DNA--absorption and NMR spectroscopic studies of model compounds.

A new and simple model enabling a chemical species to be brought to a preselected site in single strand DNA is reported. Two oligonucleotides containing a propanediol linkage were hybridized to their complementary sequences with an extra-base opposite the propanediol derivative. Absorption studies results shown that the addition of a bisacridine derivative strongly increased the stabilities of both duplexes when added in a 1:1 ratio. NMR studies on one of these duplexes brought evidence of the intercalation of the bisacridine at the position involving the propanediol linkage. These results suggest that this system could be used to target a specific reaction at a preselected position using the bisacridine derivative as carrier for the reactive species.     

Application of rare-earth elements as labels in studying bilogically active compounds. II. Luminescence spectra and structure of europium complexes for use as shift reagents in NMR studies]

The luminescence spectra and solubility of several europium complexes are investigated. The conditions put upon the complex structure for its successful use as a shift reagent are discussed. Some water-soluble europium complexes with pyridoxaliden amino acids are shown to be fit as possible shift reagents.