Studies of viomycin, an anti-tuberculosis antibiotic: copper(ii) coordination, DNA degradation and the impact on delta ribozyme cleavage activity.

Viomycin is a basic peptide antibiotic, which is among the most effective agents against multidrug-resistant tuberculosis. In this paper we provide the characteristics of its acid base properties, coordination preferences towards the Cu(ii) ions, as well as the reactivity of the resulting complexes against plasmid DNA and HDV ribozyme. Careful coordination studies throughout the wide pH range allow for the characterisation of all the Cu(ii)-viomycin complex species. The assignment of proton chemical shifts was achieved by NMR experiments, while the DTF level of theory was applied to support molecular structures of the studied complexes. The experiments with the plasmid DNA reveal that at the physiological levels of hydrogen peroxide the Cu(ii)-viomycin complex is more aggressive against DNA than uncomplexed metal ions. Moreover, the degradation of DNA by viomycin can be carried out without the presence of transition metal ions. In the studies of antigenomic delta ribozyme catalytic activity, viomycin and its complex are shown to modulate the ribozyme functioning. The molecular modelling approach allows the indication of two different locations of viomycin binding sites to the ribozyme.

Structural features and oxidative stress towards plasmid DNA of apramycin copper complex.

The interaction of apramycin with copper at different pH values was investigated by potentiometric titrations and EPR, UV-vis and CD spectroscopic techniques. The Cu(II)-apramycin complex prevailing at pH 6.5 was further characterized by NMR spectroscopy. Metal-proton distances derived from paramagnetic relaxation enhancements were used as restraints in a conformational search procedure in order to define the structure of the complex. Longitudinal relaxation rates were measured with the IR-COSY pulse sequence, thus solving the problems due to signal overlap. At pH 6.5 apramycin binds copper(II) with a 2 : 1 stoichiometry, through the vicinal hydroxyl and deprotonated amino groups of ring III. Plasmid DNA electrophoresis showed that the Cu(II)-apramycin complex is more active than free Cu(II) in generating strand breakages. Interestingly, this complex in the presence of ascorbic acid damages DNA with a higher yield than in the presence of H(2)O(2).

Metal ion effects on the cis/trans isomerization equilibrium of proline in short-chain peptides: a solution NMR study.

The effect of copper(II) ions on the probabilities of existence of the four detectable conformers of the tetrapeptide Tyr-Pro-Phe-Pro (beta-casomorphin 4) in [2H6]DMSO was investigated by 1H NMR spectroscopy. Integration of the Phe-NH signals provided the relative populations in the free state as tt/tc/ct/cc=28:34:29:9 at 293 K (c=cis, t=trans). Copper(II) was shown to bind to all four isomers, yielding complexes with two different structures, depending on the conformation of Pro(2). The interpretation of paramagnetic relaxation rates of Pro(2)-Halpha signals provided the corresponding isomeric probabilities in the metal-bound state as 13:36:20:31. The observed stabilization of the conformation with the lowest probability of existence (cc) may be relevant for the biological role of copper and other metal ions.

1H NMR relaxation investigation of inhibitors interacting with Torpedo californica acetylcholinesterase.

Two naphthyridines interacting with Torpedo californica acetylcholinesterase (AChE) were investigated. (1)H NMR spectra were recorded and nonselective, selective, and double-selective spin-lattice relaxation rates were measured. The enhancement of selective relaxation rates could be titrated by different ligand concentrations at constant AChE (yielding 0.22 and 1.53 mM for the dissociation constants) and was providing evidence of a diverse mode of interaction. The double-selective relaxation rates were used to evaluate the motional correlation times of bound ligands at 34.9 and 36.5 ns at 300 K. Selective relaxation rates of bound inhibitors could be interpreted also in terms of dipole-dipole interactions with protons in the enzyme active site.

Calcium-binding properties and molecular organization of bradykinin A solution 1H-NMR study.

The NMR features of bradykinin were investigated in dimethylsulfoxide containing 1% water. The temperature dependence of chemical shifts and ROESY maps were monitored for the major species where all X-Pro bonds are trans. The occurrence of a head-to-tail ionic interaction and intramolecular hydrogen bonds stabilizing a pseudo cyclic arrangement was inferred, a beta turn at the C-terminus being the main feature of the secondary structure. Calcium was shown to bind to the peptide with a dissociation constant Kd = 2.8 + 0.2 mm. 2Pro and 3Pro carbonyls, as well as the 9Arg carboxyl, were assigned as the metal-binding sites. A molecular model of the 1 : 1 metal-complex was obtained. In light of conformational changes experienced by the peptide upon interaction with calcium, a role for the metal was hypothesized in the process of conformational selection from the free to the receptor-bound state of bradykinin.

Delineation of conformational and structural features of the amikacin-Cu(II) complex in water solution by 13C-NMR spectroscopy.

The copper (II) complex of amikacin in water solution at pH 5.5 was investigated by 13C-NMR. The temperature dependence of spin-lattice relaxation rates was measured and fast exchange conditions were shown to apply. The motional correlation time of the complex was approximated by the pseudo-isotropic rotational correlation time of free amikacin in water solution (tau c = 0.17 ns at 300 K). Formation of a pseudo-tetrahedral 1:1 complex was demonstrated by relaxation rates analysis and also by UV-Vis spectrophotometry. Two amino nitrogens of amikacin, together with the amide nitrogen and the hydroxyl in the hydroxyl-aminopropyl carbonyl side chain, were assigned as the copper-binding sites and a model of the complex was built by using copper-carbon distances obtained by NMR analysis as input parameters.

1H NMR studies on the interaction of beta-carboline derivatives with human serum albumin.

1H NMR studies were performed on two beta-carboline derivatives interacting with human serum albumin. The spin-lattice relaxation rates of the two derivatives, having side chains of different length and polarity, were used to demonstrate a diverse motional behavior in solution together with slightly different relaxation pathways. Single- and double-selective excitation made it possible to evaluate dynamics in the free and protein-bound states. Occurrence of a relatively long hydrophilic chain interacting with the proton-acceptor nitrogen of the beta-carboline moiety was shown to yield lower association constants, slower dissociation rates, and diverse interacting modes with the indole hydrophobic site of the protein.

Conformational features of charged dibucaine in solution as investigated by 13C- and 1H-NMR.

Conformational features of charged dibucaine in [2H6]DMSO were elucidated by measuring 13C and 1H spin-lattice relaxation rates and 1H-(1H) and 13C-(1H) nuclear Overhauser effects. The reorientational correlation time of the aromatic moiety was evaluated at 0.16 ns at room temperature and side chains were observed to display segmental motion. Relevant distances were calculated by isolating dipolar interaction terms of 1H-1H or 13C-1H pairs. The 'preferred' conformation in solution was shown to present several analogies, but also some differences, with the structures obtained by solid state experiments, energy calculations and LIS data.

Interaction of Daunomycin with Dipalmitoylphosphatidylcholine Model Membranes. A 1H NMR Study

1H NMR parameters were obtained for daunomycin in water solution in the free state as well as in the presence of dipalmitoylphosphatidylcholine model membranes. Spin-lattice relaxation rates were measured under nonselective, single-selective, and double-selective irradiation modes, and 2D NOESY spectra were obtained at several values of the mixing time. Proton-proton distances were calculated and the motional correlation time was evaluated in both the free and bound states. NMR parameters were used to show that ring A and the glucosamine moiety of daunomycin strongly interact with the external surface of the bilayer, while the rest of the molecule penetrates the membrane without crossing it. The structures of both free and bound daunomycin were obtained and compared by using molecular modeling.

1H-NMR and 13C-NMR investigation of complexes of Mn2+ with ocytocin analogues in (2H6)dimethylsulfoxide.

Several ocytocin analogues were synthesised by substitution of the Pro residue with sarcosine or N-methylalanine, the glutamine residue with threonine and one of the cysteines with 2-mercaptopropionic acid. All the derivatives were investigated by NMR in dimethylsulfoxide solutions and evidence was obtained for similar preferred conformations in the solution free state. All peptides were shown to form complexes with Mn2+ in solution by the strong paramagnetic effects experienced by several proton resonances. Two structures could be determined, one formed by peptides containing threonine and the other by the remaining peptides. The two structures were delineated by molecular modelling using the Mn(2+)-proton distances obtained by NMR as restraints.

Amiodarone affects membrane water permeability properties of human erythrocytes and rat mitochondria.

Dose-dependent water exchange times and intracellular water contents were measured by NMR (nuclear magnetic resonance) in erythrocytes and mitochondria interacted with the anti-anginal and anti-arrhytmic agent, amiodarone. Addition of the drug up to 26 microM yielded 80% enhancement of the water exchange rate in erythrocytes at 37 degrees C and 41% enhancement at 22 degrees C with 40% and 9%, respectively, increases in the intracellular water content. Similar enhancements were obtained in mitochondria at 22 degrees C. The data suggests a somewhat higher affinity of amiodarone to mitochondrial than to erythrocyte membranes.

2D NMR Methods for Structural Delineation of Copper(II) Complexes of Penicillin and Pilocarpine.

A method was developed for delineating the structure of paramagnetic metal complexes. The selective disappearance of cross-peaks in proton-carbon shift correlated 2D NMR maps was shown to uniquely depend upon the scalar and/or dipolar interaction between ligand nuclei and the unpaired electron(s), thus providing a means of identifying binding sites. Copper(II) was shown to form metal complexes with both Penicillin (PNC) and Pilocarpine (PLC) and the structure of the two 1:2 complexes in water solution at physiological pH were determined.

Conformational features of erythrocyte-bound chloroquine from double-selective 1H NMR relaxation.

The interaction between the antimalarial drug chloroquine and red blood cells was investigated by measuring 1H NMR spin-lattice relaxation rates upon double-selective excitation of dipolarly connected spin pairs within the ligand molecule. Geometric and dynamic features were inferred, for the free as well as for the bound ligand, by the cross-relaxation terms between protons at fixed and time-dependent distances, respectively. A change in orientation of the side chain in respect of the aromatic moiety was shown to result from the binding interaction.

NMR investigations of Mn(II)-leucine-enkephalin complexes in [2H6]-DMSO solution.

Structural and kinetic features of the Mn(II)-Leu-enkephalin binding equilibria were delineated by measuring 13C and 1H NMR spin-lattice relaxation rates. The temperature dependence of such rates showed that some carbons were experiencing slow exchange regimes such that kinetic parameters at room temperature could be calculated (k(off) = 1400 sec-1, delta H* = 12.0 kcal/mol, delta S* = -9.9 e.u.). The paramagnetic rates of fast exchanging carbons were interpreted by the Solomon-Bloembergen-Morgan theory to provide structural parameters. The terminal carboxyl and amino groups were shown to be the binding sites. The motional correlation time (tau c = 0.6 nsec at 298 K) was calculated by measuring selective and double-selective 1H spin-lattice relaxation rates for the free peptide. The number of coordinated ligands was evaluated by considering the distance of the Leu CO in the complex at 2.54 A, as shown by molecular models. Finally, carbon-Mn(II) distances were calculated and the molecular model of the 1:1 complex was built.

Nuclear magnetic resonance spectrometric investigations of calcium antagonist drugs. III: Conformational and dynamic features of diltiazem in solution.

Conformational features of diltiazem in D2O have been delineated by measuring 13C and 1H NMR parameters. The data obtained by interpretation of spin-lattice relaxation rates and 13C-[1H] nuclear Overhauser effects were used to build a model of the most probable arrangement in solution. The molecular motion of the two aromatic rings and of the thiazepinic ring is anisotropic, and the assumption that the molecule is an ellipsoid undergoing Brownian motion leads to calculation of the diffusion constants for the rotation around the longer axis and the shorter axis. The dimethylaminoethyl chain seems folded back, and it displays the typical features of segmental motion; in the same way, the methoxy- and the acetyloxymethyls behave like free rotors.

Nuclear magnetic resonance investigations of calcium antagonist drugs. II: Conformational and dynamic features of verapamil in [2H6]DMSO.

Conformational features of verapamil in [2H6]DMSO have been delineated by measuring 13C and 1H NMR parameters. Spin-lattice relaxation rates were interpreted within the frame of an extended alkane chain with segmental motions hampered by the aromatic substituents at both ends. The effective correlation times were all evaluated in the range 0.16-0.22 ns at 293 K. The aromatic rings were found to lie somewhat out-of-plane with the alkane chain. The NMR data were used to construct a Dreiding model of the most probable spatial arrangement and a molecular modeling system was utilized to represent the "preferred" conformation of verapamil in solution.

Selective 1H-NMR relaxation investigations of membrane-bound drugs in vitro. 3. Calcium-entry blockers and adenosine.

Selective proton relaxation rates (SPRR) were measured for selected protons of nimodipine or diltiazem in the presence of neutrophils, allowing detection of binding to the cell membrane. Fast exchange exchange of drug molecules between bound and free environments was shown to be the main factor determining the enhancement of SPRR, whereas viscosity effects could be neglected. The SPRR enhancement was almost completely cancelled out by the presence of adenosine as a cosolute in a dose-dependent fashion, leading to the suggestion that the endogenous mediator 'adenosine' affects binding of calcium-entry blockers to the neutrophil surface.

1H-NMR studies on the self-association of chloroquine in aqueous solution.

The concentration dependences of 1H-NMR chemical shifts and spin-lattice relaxation rates were measured for chloroquine in aqueous solution. The weak self-association constant was evaluated according to a dimerization equilibrium with the formation of self-stacked adducts (Kd = 4.52 +/- 0.68 l mol-1). The motional correlation times were evaluated for the monomer and the dimer by measuring intramolecular dipolar cross-relaxation rates of aromatic vicinal protons (tau cm = 0.06 ns and tau cd = 0.26 ns). The geometry of the stacked dimer was elucidated by measuring intermolecular dipolar cross-relaxation rates and interpreted in terms of partial superposition of quinoline moieties.