Refinement of the NMR structures of alpha-conotoxin MI using molecular dynamics simulation with explicit solvent water and a full molecular force field

Three NMR structures of alpha-conotoxin MI, a potent antagonist of the nicotinic acetylcholine receptor, have been refined using molecular dynamics (MD) simulation with explicit water. Although the convergence of the NMR structures of alpha-conotoxin MI was not sufficient to provide detailed structural features, the average structures obtained from MD simulations converged to one conformation, providing structural characteristics. The resulting structure was also found to be consistent with the results of amide proton-exchange experiments. These results demonstrate that MD simulation with explicit solvent water is very useful in refining NMR structures.     

Nondestructive identification of colloidal molecular sieves stabilized in water

The encapsulation of small quaternary ammonium ions in zeolite frameworks could be used as a base for investigation of the crystallization process of colloidal (nanosized) molecular sieves stabilized in water with Raman and (13)C NMR spectroscopic methods. The organic-framework interactions in colloidal microporous materials with LTA, FAU, BEA, and MFI topology have been considered; the results show that the crystallinity of nanosized particles with monomodal particle size distribution stabilized in water can be examined using the vibrational and magnetic resonance spectral features of the organic template molecules occluded in the specific pores and cages in the zeolite framework. The molecular packing effect and restricted mobility due to specific organic/framework interactions result in shifts and substantial broadening of the (13)C NMR signals, as well as in changes of the positions and the relative intensities of the Raman peaks. The spectroscopic methods are very efficient for analyzing the crystalline structures of nanosized molecular sieves stabilized in aqueous suspensions due to no restrictions related to the particle size.     

Metabolic products of microorganisms. Stereochemistry of lankamycin

The stereochemical structure of the macrolide antibiotic lankamycin could be completed by an extended NMR.-analysis of the degradation products III, IV, VI and VIII.     

Conformational study of fosinopril sodium in solution using NMR and molecular modeling

Two conformers of fosinopril sodium in methanol were unambiguously established using 2D NMR methods and variable‐temperature NMR experiments. Differences in their conformational structure were shown to be related to the rotational energy barrier about the amide bond and hydrophobic interaction. The relationship between the 3D structure and activity is discussed. It is suggested that the trans‐conformer may be more biologically active owing to its stacking structure and strong hydrophobic interaction and the cis‐conformer could be more easily hydrolyzed because of its extended structure. Copyright © 2003 John Wiley & Sons, Ltd.     

Guest encapsulation in a water-soluble molecular capsule based on ionic interactions

We report on the synthesis and characterization of a water-soluble molecular capsule based on multiple ionic interactions. The assembly has been studied by means of 1H NMR, ESI-MS spectroscopy, and isothermal titration calorimetry (ITC), showing an association constant in water, Ka, of 3.3 x 104 M-1. The achieved water solubility of the system opens the possibility of using this supramolecular assembly for molecular recognition in pure water. Encapsulation studies have been performed and are reported in this Communication.     

NMR study of pradimicin derivative BMY-28864 and its interaction with calcium ions in D2O

The dynamic structure of the antifungal antibiotic pradimicin BMY-28864 in D2O and its interaction with calcium ions were analyzed using one- and two-dimensional 1H nuclear magnetic resonance (NMR). Spectra indicate extensive self-association of molecules in the solution. Two-component spectra were observed simultaneously in a very dilute solution, suggesting equilibrium of two aggregative states. The addition of CaCl2 caused a number of changes in NMR spectra. Therefore we concluded that pradimicin BMY-28864 could form a complex with the Ca2+ ion, causing a movement of the equilibrium. The position of the bound calcium ion is determined indirectly by observing how the NMR shift affects protons that are close to the binding site. The stoichiometry of Ca2+ ion to the Pradimicin molecule for the Ca(2+)-saturated complex is verified to be 1:2. Signal broadening and changes in chemical shift in the 1H NMR spectroscopy of BMY-28864 are assumed to be related to changes in the molecular aggregate conformation.     

Bitterness evaluation of medicines for pediatric use by a taste sensor

The purpose of this study was to evaluate the bitterness of 18 different antibiotic and antiviral drug formulations, widely used to treat infectious diseases in children and infants, in human gustatory sensation tests and using an artificial taste sensor. Seven of the formulations were found to have a bitterness intensity exceeding 1.0 in gustatory sensation tests (evaluated against quinine as a standard) and were therefore assumed to have an unpleasant taste to children. The bitterness intensity scores of the medicines were examined using suspensions in water or an acidic sports drink. In the case of three macrolide antibiotic formulations containing erythromycin (ERYTHROCIN dry syrup), clarithromycin (CLARITH dry syrup for pediatric), and azithromycin (ZITHROMAC fine granules for pediatric use), the bitterness intensities of suspensions in acidic sports drinks were dramatically enhanced compared with the corresponding scores of suspensions in water. This enhancement could be predicted using the taste sensor. On the other hand, a reduction of bitterness intensity was observed for an acidic sports drink suspension of an amantadine product (SYMMETREL fine granules) compared with an aqueous suspension. This reduction in bitterness could also be predicted using the taste sensor output value. Thus, the taste sensor could predict whether or not suspension in an acidic sports drink would enhance or reduce the bitterness intensity of pediatric drug formulations, compared with suspensions in water.     

Poly(ethylene glycol)-b-poly(epsilon-caprolactone) and PEG-phospholipid form stable mixed micelles in aqueous media

Novel mixed polymeric micelles formed from biocompatible polymers, poly(ethylene glycol)-b-poly(epsilon-caprolactone) (PEG(5000)-b-PCL(x)) and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-methoxy poly(ethylene glycol) (PEG-DSPE), possess small size and high thermodynamic stability, raising their potential as long circulating carriers in the context of delivery of antineoplastic and antibiotic drugs. Formation of mixed polymeric micelles was confirmed using size exclusion chromatography and 1H NMR NOESY. Steady-state fluorescence measurements revealed depressed critical micellar concentrations indicative of a cooperative interaction between component hydrophobic blocks, which was quantified using the pseudophase model for micellization. Steady-state fluorescence measurements indicated that the mixed polymeric micelle cores possess intermediate micropolarity and high microviscosity. Pulsed field gradient spin-echo measurements were used to characterize micellar diffusion coefficients, which agree well with those obtained using dynamic light scattering. NOE spectra suggested that the hydrophobic polymer segments from individual components are in close proximity, giving evidence for the formation of a relatively homogeneous core. Contrary to one-component PEG(5000)-b-PCL(x) micelles, the mixed polymeric micelles could incorporate clinically relevant levels of the poorly water soluble antibiotic, amphotericin B (AmB). AmB encapsulation and release studies revealed an interesting composition-dependent interaction of the drug with the mixed polymeric micelle core.     

Determination of the three-dimensional, solution-phase structure of the macrolide antibiotic oxolide in CD2Cl2 and D2O from NMR constraints

The three-dimensional structure of the antibiotic oxolide, (9S,11S)-11-amino-9-deoxo-11,12-deoxy-9,12-epoxyerythromycin, was determined in CD2Cl2 through constrained molecular mechanics with constraints derived from proton NMR. The calculations yielded a well-defined global minimum. Data acquired for oxolide in D2O, although not as complete, indicate that the antibiotic adopts the same conformation in water.     

Organic anion recognition of naphthalenesulfonates by steroid-modified beta-cyclodextrins: enhanced molecular binding ability and molecular selectivity

Two beta-cyclodextrin (beta-CD) derivatives bearing steroid groups (1 and 2) were synthesized by the condensation of mono(6-aminoethylamino-6-deoxy)-beta-CD with cholic acid and deoxycholic acid, respectively, and their original conformations and binding behavior to the organic anion of naphthalenesulfonate derivatives were investigated by using 1H NMR spectroscopy and spectrofluorometric titration in combination with computational methods. The 2D NMR experiments reveal that the steroid groups attached to the beta-CD rim could be deeply embedded in the beta-CD cavity to form the intramolecular (for 1) or intermolecular (for 2) inclusion complexes in aqueous solution. Upon complexation with naphthalenesulfonate derivatives, modified beta-CDs display two obviously different binding modes, that is, the competitive inclusion mode and the induced-fit inclusion mode, which is consistent with the results of molecular modeling study. The two modes and the strict size/shape fitting relationship between the hosts and guests reasonably explain the different binding behaviors and molecular selectivity of host beta-CDs 1 and 2 toward the naphthalenesulfonate guests. Therefore, the cholic acid- or deoxycholic acid-modified beta-CDs could effectively recognize the size/shape of guest molecules as compared with the parent beta-CD, giving good molecular selectivity up to 24.9 for the disodium 2,6-naphthalenedisulfonate/disodium 1,5-naphthalenedisulfonate pair by the host 1.     

NMR solvent shifts of adenine in aqueous solution from hybrid QM/MM molecular dynamics simulations

We present first principles calculations of the NMR solvent shift of adenine in aqueous solution. The calculations are based on snapshots sampled from a molecular dynamics simulation, which were obtained via a hybrid quantum-mechanical/mechanical modeling approach, using an all-atom force field (TIP3P). We find that the solvation via the strongly fluctuating hydrogen bond network of water leads to nontrivial changes in the NMR spectra of the solutes regarding the ordering of the resonance lines. Although there are still sizable deviations from experiment, the overall agreement is satisfactory for the 1H and 15N NMR shifts. Our work is another step toward a realistic first-principles prediction of NMR chemical shifts in complex chemical environments.     

A novel mechanism of antibiotic resistance: study of the complex state of peptides with bacterial Staphylococcus aureus ribosomes

Two antibiotic resistance peptides, the E-peptide (MRLFV) and the K-peptide (MRFFV) conferring macrolide and ketolide resistance, respectively, were studied in the complex state with bacterial Staphylococcus aureus ribosomes after a conformational analysis by NMR spectroscopy and molecular modeling of the unbound molecules. T2 (CPMG) measurements were used to characterize equilibrium binding of antibiotic resistance peptides to bacterial ribosomes. Additionally, interactions of antibiotic resistance peptide to ribosomes were investigated using two-dimensional transferred nuclear Overhauser effect spectroscopy (TRNOESY), resulting in bound structures compatible with the experimental NMR data.     

Different types of water in the film formation process of latex dispersions as detected by solid-state nuclear magnetic resonance spectroscopy

 The properties of polymer films prepared from latex dispersions are influenced by the drying or film formation process. In order to investigate this process, various systems of aqueous latex dispersions were dried until a specific solid content was reached. The samples investigated were based on vinyl acetate, vinyl acetate/ethylene and pure acrylics employing different surfactants and polyelectrolytes as stabilisers of the dispersions. The role of water in these partially dried films was investigated using ¹H and ²H solid-state NMR spectroscopy. Different types of water could be distinguished in the spectra. The drying latex films were found to contain interfacial external water, water at ionic and nonionic groups at surfactants in the polymer/water interface and also water inside the swollen polymer. These different types of water were examined separately using various NMR techniques. Received: 22 October 1999/Accepted in revised form: 19 November 1999     

含活泼质子水溶性化合物的核磁共振结构解析

利用核磁共振对在水溶剂易溶且含活泼质子的化合物的结构进行解析.实验中将待测样品直接溶解于二次去离子水中,并利用外标进行锁场.这样既保证了核磁共振实验的正常进行,同时避免了实验中氘代试剂对活泼质子的置换效应,为化合物中活泼质子的定位提供了直接的依据.为了保证外标锁场实验核磁共振谱图的质量,本工作采用了溶剂峰压制的核磁共振实验技术,获取了一组高质量的1D、2D谱图,并在此基础上顺利完成了对头孢米诺盐的结构确定.     

Encapsulation of small polar guests in molecular apple peels

Three aromatic oligoamides have been prepared that have alternating 1,6-diaminopyridine and 1,6-pyridinedicarboxylic acid units at the center of the sequence and two 8-amino-2-quinolinecarboxylic acid units at each extremity. The three oligomers differ in the number--3, 5, or 7-of pyridine units in the sequence. They were designed to adopt helically folded conformations in solution and in the solid state. The sequence of monomers was chosen so that the diameter of the helix is larger in the center than at each extremity, and hence they resemble helically wrapped apple peels. According to modeling studies, the pyridine units were expected to define a polar hollow within the helix that is large enough to accommodate small polar guests, whereas the quinoline units at each end of the oligomeric sequences were expected to completely cap the hollow and transform the helix cavities into a closed shell that may act as a capsule. Crystallographic studies demonstrate that the oligomers do fold into helices that define a cavity isolated from the surrounding medium in the solid state. Depending on the number of pyridine rings, one or two water molecules are bound within the capsules. The crystal structure of a capsule fragment shows that MeOH can also be hosted by the largest oligomer. Solution NMR studies confirm that binding of water also occurs in solution with the same stoichiometry as observed in the solid state. The capsules have distinct signals depending on whether they are empty, half-full, or full, and these species are in slow exchange on the NMR timescale at low temperature. Indeed, the binding and release of water molecules requires a significant conformational distortion of the helix that slows down these processes. The addition of small polar molecules such as methanol, hydrazine, hydrogen peroxide, or formic acid to the largest capsule leads to the observation of new sets of NMR signals of the capsules that were assigned to complexes with these guests. However, water appears to be the preferred guest.     

Solvent-stabilized molecular capsules

Pyrrogallolarenes 2 were prepared by acid-catalyzed condensation of pyrrogallol with aldehydes. Compound 2a crystallizes from a methanol solution of quinuclidine hydrochloride to give a dimeric molecular capsule surrounding one disordered quinuclidinium cation. The molecules of 2a are connected by direct hydrogen bonds and by bridging methanol and water molecules. The chloride anion is positioned outside the capsule and is hydrogen bonded to the hydroxy groups of 2a. The shortest distance between the cation and anion was found to be 6.7 A. Crystallization of 2b from aqueous acetonitrile resulted in a dimeric capsule linked by a polar belt of 16 hydrogen bonding water molecules. Four acetonitrile molecules occupy the cavity of this dimeric capsule and assume two binding sites that differ in hydrogen bonding and electronic environment. Compounds 2 also form hydrogen-bonded dimeric molecular capsules in alcohols and aqueous acetonitrile solutions. These assemblies readily encapsulate tetramethylammonium, tetramethylphosphonium, quinuclidinium, and tropylium cations to give complexes stable on the NMR time scale at 233 K.     

Nanostructure of open water-channel reversed micelles. I. 1H NMR spectroscopy and molecular modeling

A recently proposed model for the rodlike reversed micelles of nickel(II) bis(2-ethylhexyl)phosphate is examined in greater detail using 1H NMR spectroscopy and molecular modeling. 1H NMR spectra show that the solubilized water molecules are situated in a different environment compared with the water molecules in classical (AOT) reversed micelles. Geometry optimization and molecular dynamics simulation clearly indicate that the water molecules are not located in the interior core of the reversed micelles, but instead the water molecules exist in compartments or channels in the surface of these rodlike reversed micelles, thereby confirming the open water-channel model of reversed micelles. Molecular modeling was also employed to examine the effects of surfactant molecular structure, cosurfactant, solvent aromaticity, and temperature on the nanostructure of the reversed micellar aggregates. It is significant that molecular modeling provides an interpretation of the nanostructure of reversed micellar aggregates that is consistent with a variety of known experimental observations reported in the liquid/liquid extraction literature. These findings show that the structure of reversed micelles is much richer at the nanoscale level than previously recognized.     

A 13CNMR study of the carbohydrate portion of ristocetin A

A ¹³C NMR study of the antibiotic ristocetin A establishes two changes which must be made to the structures hitherto accepted for the carbohydrate portion of the antibiotic.     

RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case

Nuclear magnetic resonance (NMR) provides structural and dynamic information reflecting an average, often non-linear, of multiple solution-state conformations. Therefore, a single optimized structure derived from NMR refinement may be misleading if the NMR data actually result from averaging of distinct conformers. It is hypothesized that a conformational ensemble generated by a valid molecular dynamics (MD) simulation should be able to improve agreement with the NMR data set compared with the single optimized starting structure. Using a model system consisting of two sequence-related self-complementary ribonucleotide octamers for which NMR data was available, 0.3 ns particle mesh Ewald MD simulations were performed in the AMBER force field in the presence of explicit water and counterions. Agreement of the averaged properties of the molecular dynamics ensembles with NMR data such as homonuclear proton nuclear Overhauser effect (NOE)-based distance constraints, homonuclear proton and heteronuclear ¹H–³¹P coupling constant (J) data, and qualitative NMR information on hydrogen bond occupancy, was systematically assessed. Despite the short length of the simulation, the ensemble generated from it agreed with the NMR experimental constraints more completely than the single optimized NMR structure. This suggests that short unrestrained MD simulations may be of utility in interpreting NMR results. As expected, a 0.5 ns simulation utilizing a distance dependent dielectric did not improve agreement with the NMR data, consistent with its inferior exploration of conformational space as assessed by 2-D RMSD plots. Thus, ability to rapidly improve agreement with NMR constraints may be a sensitive diagnostic of the MD methods themselves.