High-Field 1H and 31P NMR Studies on the Binding of the Anticancer Agent Mitoxantrone to d[CpGpApTpCpG]2

Abstract

A high-field ¹H and ³¹P-NMR study of the oligomer d[CpGp ApTpCpG]₂ was carried out in H₂2O and water signal suppression was employed in all ¹H NMR acquisitions. Particular attention was given to imino proton and ³¹P assignments. Two dimensional ³¹P-¹H shift correlation contours were particularly useful in ³¹P assignments and confirming previous ¹H assignments. Titrimetric addition of aliquots of the anticancer agent mitoxantrone resulted in selective and progressive chemical shifts with critical changes at stoichiometrics of 1:1 and 2:1 drug to DNA ratios. The results indicate ultimate intercalative binding of the drug at both C.G termini of the oligomer in accord with the previously determined C.G preference and with non-nearest neighbor intercalation.     

High-field 1H NMR studies of prostaglandin H2 and its decomposition pathways

Prostaglandin H2 displays at 500 MHz a detailed 1H-NMR in which all methylene groups are non-equivalent in C6D6 solution. The spectrum was assigned by analogy to isosteric structures. The dissymmetric perturbation and steric hindrance of the bicyclo [2.2.1] core caused by the side-chains provides a rationale for the selective fragmentations which PGH2 undergoes. Purified PGH2 is considerably more robust than previous literature accounts suggest. The following transformations were monitored by 1H-NMR: 1) O-O bond cleavage by Ph3P , 2) aqueous media fragmentation to PGE2 and PGD2, 3) base catalyzed fragmentation to ketoaldehydes , and 4) thermolysis attempts.     

1H and 31P NMR studies of the binding of low-affinity anions to Cu,Zn superoxide dismutase

Anions that do not coordinate to the catalytically active copper ion of Cu,Zn superoxide dismutase, but still affect the activity of the enzyme by weaker interactions with the protein moiety surrounding the active site (low affinity anions), uniformly perturbed the 1H NMR line of the NH group of the copper ligand His 46. This effect was detected on the enzyme having Co(II) substituted for the native Zn(II), in which the resonances of residues bound to the copper are detected because of the antiferromagnetic coupling between Cu(II) and Co(II). The interaction with the enzyme of phosphate, a good representative of low-affinity anions, was also studied by 31P NMR of the native enzyme and of enzyme samples covalently modified at all lysines or at the Arg 141, which is 5 A away from the copper. The results obtained indicate that Arg 141 is a likely candidate for binding of low-affinity anions in the vicinity of the copper and that the 1H NMR line of His 46 NH is diagnostic for such an interaction.     

Combined 1H and 31P NMR studies of cerebral metabolism in vivo

NMR spectroscopic methods have recently been developed for measurement of several concentrated cerebral metabolites in vivo. At present, 31P spectra from the brain permit detection of ATP, PCr, Pi, and certain sugar and lipid phosphates. The resonant frequency of Pi also provides a measure of cerebral pHi, and under some conditions ADP concentration can be calculated from information available in the 31P spectrum. The 1H spectrum of brain provides measurements of lactate, creatine, and several amino acids and choline-containing compounds. Both kinds of spectra can be obtained from the same subject. Our group at Yale used combined 31P and 1H methods to demonstrate that loss and recovery of phosphate energy stores and concomitant changes in cerebral amino acids during hypoglycemic coma in rodents could be observed in vivo. We then used the same methods to show that cerebral pHi can be normal while lactate is elevated in status epilepticus. NMR spectroscopy performed in vivo provides an array of chemically specific measurements unavailable by any other non-invasive method. It is thought to be entirely free of deleterious biological effects; hence, its potential for use in humans is considerable.     

Synthesis, complete 1H assignments and conformations of the self-complementary hexadeoxyribonucleotide [d(CpGpApTpCpG)]2 and its fragments by high field NMR.

The two deoxyribonucleotides [d(CpGpApTpCpG)]2 and [d(CpGpCpG)]2 were synthesized by the phosphotriester method. Their duplex form under the conditions of the 1H-nmr experiments was proven by end 32P labeling with T4 polynucleotide kinase followed by butt end joining employing the absolute specificity of T4 ligase for double stranded DNA and analysis using gel electrophoresis and autoradiography. Complete nmr assignment of the 1H chemical shifts and coupling constants was achieved. The assignments were secured using sequential decoupling, NOE difference measurements, and two-dimensional COSY and SECSY experiments. Spectrum simulation confirmed the experimental values of chemical shifts and coupling constants. The techniques for the assignment outlined together with 31P and 2-D heteronuclear shift correlation permit an approach to a systematic analysis of more complex single-strand and duplex oligodeoxyribonucleotides.     

NMR studies of [1-2H]glucose metabolism in Zymomonas mobilis

In complementary experiments the metabolism of [1-2H]glucose in H2O and of unlabelled glucose in 2H2O by Zymomonas mobilis was examined. The utilization of [1-2H]glucose by Z. mobilis was monitored by high-resolution 2H NMR. The deuterium-labelling pattern and stereochemistry of the ethanols produced from the metabolism of [1-2H]glucose and unlabelled glucose in 2H2O were determined by a combination of 13C and 1H NMR and selective enzyme action. The labelling patterns were explained in terms of enzyme mechanisms and stereospecificity, and metabolite enolization.     

1H and 31P NMR investigations of actinomycin D binding selectivity with oligodeoxyribonucleotides containing multiple adjacent d(GC) sites

Imino proton and 31P NMR studies were conducted on the binding of actinomycin D (ActD) to self-complementary oligodeoxyribonucleotides with adjacent 5'-GC-3' sites. ActD showed very high specificity for binding to GC sites regardless of oligomer length and surrounding sequence. For a first class of duplexes with a central GCGC sequence, a mixture of 1:1 complexes was observed due to the two different orientations of the ActD phenoxazone ring system. Analysis of 1H chemical shifts suggested that the favored 1:1 complex had the benzenoid side of the phenoxazone ring over the G base in the central base pair of the GCGC sequence. This is the first case in which an unsymmetrical intercalator has been shown to bind to DNA in both possible orientations. A unique 2:1 complex, with significantly different 1H and 31P chemical shifts relative to those of the 1:1 complexes, was formed with these same oligomers, again with the benzenoid side of the ActD molecule over the G base of the central GC base pair. There is considerable anticooperativity to binding of the second ActD in a GCGC sequence. In titrations of oligomers with the GCGC sequence, only the two 1:1 complexes are found up to ratios of one ActD per oligomer. Increasing the ActD concentration, however, resulted in stoichiometric formation of the unique 2:1 adduct. Spectrophotometric binding studies indicated that the apparent binding equilibrium constant for a GC site adjacent to a bound site is reduced by approximately a factor of 20 relative to the ActD binding constant to an isolated GC site.     

31P and 1H NMR studies of ethanolamine-linked phosphoglycerides metabolism in human T lymphocytes.

Aqueous and organic extracts of peripheral human T lymphocytes and of T lymphoblastoid cell lines have been examinated by 31P and 1H NMR spectroscopy in order to study the metabolism of ethanolamine (Etn) linked phosphoglycerides. The results show that the Etn concentration in the culture medium determines the composition of Etn-containing metabolites and phospholipids. The effect of phorbol esters, stimulating the synthesis and the breakdown of choline-containing phospholipids has been also studied. A phorbol 12-myristate 13-acetate (PMA) dependent membrane phosphatidylethanolamine hydrolysis, presumably mediated by protein kinase C activity, has been demonstrated.     

1H-NMR studies of a monointercalating drug into a d(CpGpApTpCpG)2 minihelix

The structure of the complex formed between the 7H-pyridocarbazole monomer [[(2-piperidyl)-2,1-ethane-yl] [10-methoxy-7H-pyrido[4,3-c]carbazolium] dimethane sulfonate] and the autocomplementary hexanucleotide d(CpGpApTpCpG)2 in aqueous solution is analyzed by 270- and 400-MHz 1H-nmr. The large upfield shifts observed for both the drug and the self-complementary hexanucleotide protons provide evidence for intercalated complexes. The observation of intermolecular nuclear Overhauser effects between drug and the hexanucleotide protons gives a privileged orientation of the drug in the intercalation site with the quaternarizing ethyl piperidine chain protruding in the major groove. Moreover, the data suggest an intercalation based on the neighbor exclusion site principle in the three alternating sequences.     

31P and 2H NMR studies of structure and motion in bilayers of phosphatidylcholine and phosphatidylethanolamine

The structural and motional properties of mixed bilayers of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) have been examined by using wide-line 31P, 14N, and 2H NMR. 2H and 14N NMR data showed that in mixed bilayers containing both PC and PE the conformations of the head-group moieties are essentially identical with those observed for bilayers containing a single phospholipid species. Equimolar amounts of cholesterol induce also only a small change in head-group conformation. 31P T1 relaxation measurements (at 300 MHz) at various temperatures of bilayers containing phospholipids with a mixture of phosphocholine and phosphoethanolamine head-groups and unsaturated fatty acid residues revealed in all cases a clearly defined minimum corresponding to the condition omega O tau C-1 approximately 1. For all phospholipid mixtures studied, the 31P T1 relaxation was homogeneous over the whole powder spectrum and could be fitted to a single-exponential decay. The 31P vs temperature profiles were analyzed by a simple correlation model following the analysis of Seelig et al. (1981) [Seelig, J., Tamm, L., Hymel, L., & Fleischer, S. (1981) Biochemistry 20, 3922-3932]. Rotational diffusion of the phosphate moiety in bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) was slower than that of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and the activation energy was increased by a factor of 1.7 to 31.4 kJ mol-1.(ABSTRACT TRUNCATED AT 250 WORDS)     

Aluminum binding to phosphatidylcholine lipid bilayer membranes: 27Al and 31P NMR spectroscopic studies

27Al and 31P nuclear magnetic resonance (NMR) spectroscopies were used to investigate aluminum interactions at pH 3.4 with model membranes composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). A solution state 27Al NMR difference assay was developed to quantify aluminum binding to POPC multilamellar vesicles (MLVs). Corresponding one-dimensional (1D) fast magic angle spinning (MAS) 31P NMR spectra showed that aluminum induced the appearance of two new isotropic resonances for POPC shifted to -6.4 ppm and -9.6 ppm upfield relative to, and in slow exchange with, the control resonance at -0.6 ppm. Correlation of the (27)Al and (31)P NMR binding data revealed a 1:2 aluminum:phospholipid stoichiometry in the aluminum-bound complex at -9.6 ppm and a 1:1 aluminum:phospholipid stoichiometry in that at -6.4 ppm. Slow MAS 31P NMR spectra demonstrated shifts in the anisotropic chemical shift tensor components of the aluminum-bound POPC consistent with a close coordination of aluminum with phosphorus. A model of the aluminum-bis-phospholipid complex is proposed on the basis of these findings.     

Reassessment of structural characteristics of the d(CGCG)2:actinomycin D complex from complete 1H and 31P NMR

Complexes formed between Actinomycin D (ActD) and the tetranucleotides d(AGCT)2 and d(CGCG)2 were studied in detail by one and two-dimensional 1H and 31P NMR. The 31P two dimensional chemical exchange experiment, at room temperature on saturated complexes (1:1), showed unambiguously that the asymmetrical phenoxazone ring binds to the unique GC site under the two possible orientations in the d(AGCT)2 tetranucleotide but adopts a single orientation in the d(CGCG)2 tetranucleotide. For the d(CGCG)2:Act D saturated complex, complete assignments of all protons and phosphorus signals of the two-nucleotide strands, as well as of the two cyclic pentapeptide chains has allowed us to study in details the conformational features of the complex from NOE and coupling constants analysis. The tetranucleotide remains in a right-handed duplex, but the sugar puckers are modified for residues at the intercalation site. A uniform C2' endo pucker is observed for residues on the strand facing the quinoid side of the phenoxazone ring while a C2' endo-C3-endo equilibrium about 60% of C2' endo is proposed for the two residues on the strand facing the benzenoid side of the phenoxazone ring. In contrast to previous studies on ActD-DNA interactions, we have been able to measure the 3J phosphorus-proton coupling constants at the intercalation site but also adjacent to it, showing that 31P chemical shifts are not simply related to the backbone conformation. Molecular mechanics calculations, using empirical distances deduced from NOE effects as restrained distances during minimizations, led to a model differing mainly from those previously published by orientation of the N methyl groups of both N-Methyl-Valines.     

1H NMR studies of mastoparan binding by calmodulin

Association with the cytoactive tetradecapeptide mastoparan perturbs the downfield 1H NMR spectrum of the calmodulin-Ca42+ complex. Changes occur in the resonances assigned to His-107 and Tyr-138. Composite peaks assigned to Phe-16 and Phe-89 and to Phe-68 and Tyr-99 are also affected. Both the upfield and downfield 1H NMR spectra contain evidence for spectroscopically distinct intermediates in Ca2+ binding by the calmodulin-mastoparan complex.     

The DNA sequence at echinomycin binding sites determines the structural changes induced by drug binding: NMR studies of echinomycin binding to [d(ACGTACGT)]2 and [d(TCGATCGA)]2

The complexes formed between the cyclic octadepsipeptide antibiotic echinomycin and the two DNA octamers [d(ACGTACGT)]2 and [d(TCGATCGA)]2 have been investigated by using one- and two-dimensional proton NMR spectroscopy techniques. The results obtained for the two complexes are compared to each other, to the crystal structures of related DNA-echinomycin complexes, and to enzymatic and chemical footprinting results. In the saturated complexes, two echinomycin molecules bind to each octamer by bisintercalation of the quinoxaline moieties on either side of each CpG step. Binding of echinomycin to the octamer [d(ACGTACGT)]2 is cooperative so that only the two-drug complex is observed at lower drug-DNA ratios, but binding to [d(TCGATCGA)]2 is not cooperative. At low temperatures, both the internal and terminal A.T base pairs adjacent to the binding site in the [d(ACGTACGT)]2-2 echinomycin complex are Hoogsteen base paired (Gilbert et al., 1989) as observed in related crystal structures. However, as the temperature is raised, the internal A.T Hoogsteen base pairs are destabilized and are observed to be exchanging between the Hoogsteen base-paired and an open (or Watson-Crick base-paired) state. In contrast, in the [d(TCGATCGA)]2-2 echinomycin complex, no A.T Hoogsteen base pairs are observed, the internal A.T base pairs appear to be stabilized by drug binding, and the structure of the complex does not change significantly from 0 to 45 degrees C. Thus, the structure and stability of the DNA in echinomycin-DNA complexes depends on the sequence at and adjacent to the binding site. While we conclude that no single structural change in the DNA can explain all of the footprinting results, unwinding of the DNA helix in the drug-DNA complexes appears to be an important factor while Hoogsteen base pair formation does not.     

Bisintercalation of ditercalinium into a d(CpGpApTpCpG)2 minihelix: a 1H- and 31P-NMR study

The structure of the complex formed in aqueous solution between ditercalinium, a bisintercalating drug, and the self-complementary hexanucleotide d(CpGpApTpCpG)2 is investigated by 400-MHz 1H-nmr and 162-MHz 31P-nmr. Whatever the drug to helix ratio, ditercalinium occurred in the bound form, whereas free and complexed hexanucleotide are in slow exchange. This allows unambiguous resonance assignment through two-dimensional chemical exchange experiments. The strong upfield shifts measured on most aromatic protons on both drug and bases as well as on DNA imino protons are consistent with bisintercalation of the dimer. Nuclear Overhauser effects observed between drug and nucleotide protons give a defined geometry for complexation, and suggest a DNA conformational change upon drug binding.     

Comparative 31P and 1H NMR studies on rat astrocytes and C6 glioma cells in culture.

Rat astroglial cells in primary culture (95% enrichment) and C6 glioma cells were adapted to grow on microcarrier beads. In vivo 31P NMR spectra were collected from cell-covered beads perfused in the NMR tube. The NMR-visible phosphorylated metabolite contents of both cell types were determined using saturation factors calculated from the values of longitudinal relaxation times determined for C6 cells using progressive saturation experiments. On the other hand, the amounts of phosphorylated metabolites in cells were determined from proton decoupled 31P NMR spectra of cell perchloric acid extracts. The results indicate that the NTP and Pi contents of the normal and tumoral cells were similar, whereas the PCr level was higher in C6 cells and the NDP and phosphomonoester levels higher in astrocytes. The comparison of 1H NMR spectra of cell perchloric acid extracts evidenced larger inositol and alanine contents in C6 cells, whereas larger taurine and choline (and choline derivatives) contents were found in astrocytes. The Glu/Gln ratio was very different, 3.5 and 1 in C6 cells and astrocytes, respectively. In both cases, the more intense resonance in the 1H NMR spectrum was assigned to glycine. Based on the comparison of the metabolite content of a tumoral and a normal cell of glial origin, this work emphasizes the usefulness of a multinuclear NMR study in characterizing intrinsic differences between normal and tumoral cells.