Determination of the stability constants and oxidation susceptibility of nickel(II) complexes with 2'-deoxyguanosine 5'-triphosphate and L-histidine

Thermodynamics-based rules of thumb to evaluate the interaction of chelators and kinetically-labile metal ions in blood serum and plasma

Metal ions play a very important role in nature and their homeostasis is crucial. A lot of metal-related chemical research activities are ongoing that concern metal-based drugs or tools, such as chelation therapy, metal- and metabolite sensors, metallo-drugs and prodrugs, PET and MRI imaging agents, etc. In most of these cases, the applied chelator/ligand (L) or metal-ligand complex (M-L) has at least to pass the blood plasma to reach the target. Hence it is exposed to several metal-binding proteins (mainly serum albumin and transferrin) and to all essential metal ions (zinc, copper, iron, etc.). This holds also for studies in cultured cells when fetal calf serum is used in the medium. There is a risk that the applied compound (L or M-L) in the serum is transformed into a different entity, due to trans-metallation and/or ligand exchange reactions. This depends on the thermodynamics and kinetics. For kinetically-labile complexes, the complex stability with all the ligands and all metal ions present in serum is decisive in evaluating the thermodynamic driving force towards a certain fate of the chelator or metal-ligand complex. To consider that, an integrative view is needed on the stability constants, by taking into account all the metal ions present and all the main proteins to which they are bound, as well as the non-occupied metal binding site in proteins. Only then, a realistic estimation of the complex stability, and hence its potential fate, can be done. This perspective aims to provide a simple approach to estimate the thermodynamic stability of labile metal-ligand complexes in a blood plasma/serum environment. It gives a guideline to obtain an estimation of the plasma and serum complex stability and metal selectivity starting from the chemical stability constants of metal-ligand complexes. Although of high importance, it does not focus on the more complex kinetic aspects of metal-transfer reactions. The perspective should help for a better design of such compounds, to perform test tube assays which are relevant to the conditions in the plasma/serum and to be aware of the importance of ternary complexes, kinetics and competition experiments.

Stability and structure of mixed-ligand metal ion complexes that contain Ni2+, Cu2+, or Zn2+, and Histamine, as well as adenosine 5'-triphosphate (ATP4-) or uridine 5'-triphosphate (UTP(4-): an intricate network of equilibria

With a view on protein-nucleic acid interactions in the presence of metal ions we studied the "simple" mixed-ligand model systems containing histamine (Ha), the metal ions Ni(2+), Cu(2+), or Zn(2+) (M(2+)), and the nucleotides adenosine 5'-triphosphate (ATP(4-)) or uridine 5'-triphosphate (UTP(4-)), which will both be referred to as nucleoside 5'-triphosphate (NTP(4-)). The stability constants of the ternary M(NTP)(Ha)(2-) complexes were determined in aqueous solution by potentiometric pH titrations. We show for both ternary-complex types, M(ATP)(Ha)(2-) and M(UTP)(Ha)(2-), that intramolecular stacking between the nucleobase and the imidazole residue occurs and that the stacking intensity is approximately the same for a given M(2+) in both types of complexes: The formation degree of the intramolecular stacks is estimated to be 20 to 50%. Consequently, in protein-nucleic acid interactions imidazole-nucleobase stacks may well be of relevance. Furthermore, the well-known formation of macrochelates in binary M(2+) complexes of purine nucleotides, that is, the phosphate-coordinated M(2+) interacts with N7, is confirmed for the M(ATP)(2-) complexes. It is concluded that upon formation of the mixed-ligand complexes the M(2+)-N7 bond is broken and the energy needed for this process corresponds to the stability differences determined for the M(UTP)(Ha)(2-) and M(ATP)(Ha)(2-) complexes. It is, therefore, possible to calculate from these stability differences of the ternary complexes the formation degrees of the binary macrochelates: The closed forms amount to (65±10)%, (75±8)%, and (31±14) % for Ni(ATP)(2-), Cu(ATP)(2-), and Zn(ATP)(2-), respectively, and these percentages agree excellently with previous results obtained by different methods, confirming thus the internal validity of the data and the arguments used in the evaluation processes. Based on the overall results it is suggested that M(ATP)(2-) species, when bound to an enzyme, may exist in a closed macrochelated form only, if no enzyme groups coordinate directly to the metal ion.

Comparison of the acid-base properties of ribose and 2'-deoxyribose nucleotides

The extent to which the replacement of a ribose unit by a 2'-deoxyribose unit influences the acid-base properties of nucleotides has not hitherto been determined in detail. In this study, by potentiometric pH titrations in aqueous solution, we have measured the acidity constants of the 5'-di- and 5'-triphosphates of 2'-deoxyguanosine [i.e., of H(2)(dGDP)(-) and H(2)(dGTP)(2-)] as well as of the 5'-mono-, 5'-di-, and 5'-triphosphates of 2'-deoxyadenosine [i.e., of H(2)(dAMP)(+/-), H(2)(dADP)(-), and H(2)(dATP)(2-)]. These 12 acidity constants (of the 56 that are listed) are compared with those of the corresponding ribose derivatives (published data) measured under the same experimental conditions. The results show that all protonation sites in the 2'-deoxynucleotides are more basic than those in their ribose counterparts. The influence of the 2'-OH group is dependent on the number of 5'-phosphate groups as well as on the nature of the purine nucleobase. The basicity of N7 in guanine nucleotides is most significantly enhanced (by about 0.2 pK units), while the effect on the phosphate groups and the N1H or N1H(+) sites is less pronounced but clearly present. In addition, (1)H NMR chemical shift change studies in dependence on pD in D(2)O have been carried out for the dAMP, dADP, and dATP systems, which confirmed the results from the potentiometric pH titrations and showed the nucleotides to be in their anti conformations. Overall, our results are not only of relevance for metal ion binding to nucleotides or nucleic acids, but also constitute an exact basis for the calculation, determination, and understanding of perturbed pK(a) values in DNAzymes and ribozymes, as needed for the delineation of acid-base mechanisms in catalysis.

Characterization of copper(II) interactions with sinefungin, a nucleoside antibiotic: combined potentiometric, spectroscopic and DFT studies

Interactions between sinefungin and copper(II) ions were investigated. Stoichiometry and stability constants of the metal-free system and two mononuclear complexes present in solution were determined on the basis of potentiometric data analysis. The results were compared to the Cu(II)-ornithine system due to structural similarities between both molecules. Combined spectroscopic and theoretical studies allowed for determination of coordination pattern for the Cu(II)-sinefungin complexes. At acidic pH, copper is bound in “glycine-like” coordination mode, identical with that of ornithine. This involves α-amino group and the carboxyl oxygen. At higher pH, a “bis-complex” is formed by two sinefungin molecules. The second ligand binds in equatorial position displacing two water molecules, what results in the stable {2N,2O} coordination. Both axial positions are supposed to be occupied by N1 nitrogen donors of adenine moiety, what is confirmed by DFT calculations. They interact indirectly with copper(II) through water molecules as the result of dominant syn conformation of purine.

Comparative studies of coordination properties of puromycin and puromycin aminonucleoside towards copper(II) ions

Protonation equilibria of puromycin (PM) and puromycin aminonucleoside (PAN) and their coordination by copper(II) ion were studied in solution by potentiometry, electronic absorption spectroscopy (UV-Vis), circular dichroism (CD), electron paramagnetic resonance (EPR) and mass spectrometry. For puromycin four mononuclear complexes were found, with stoichiometries Cu(PM)2+, CuH(-1)(PM)+, CuH(-2)(PM) and CuH(-3)(PM)(-). In each of them the Cu(II) ion was bound in the peptidic-like manner, the differences of stoichiometries are a consequence of subsequent deprotonations of the sugar C2'-OH group and the coordinated water molecule. The coordination mode for puromycin aminonucleoside was aminosugar-like. Two dimeric complexes, Cu2H(-1)(PAN)2(2+) and Cu2H(-2)(PAN)2+, and one monomeric CuH(-2)(PAN)2 were found. The N6,N6-dimethyladenine moiety of PAN was not involved in the coordination process due to steric hindrance.

Acid-base, coordination and oxidative properties of systems containing ATP, L-histidine and Ni(II) ions

Potentiometric measurements of ATP-His system proved an existence of five adducts in the solution with stoichiometries ranging from H(5)(ATP)(His) to H(ATP)(His)(4-). Their formation is a consequence of electrostatic interactions only. In the ternary Ni(II)-ATP-His system, two complex species NiH(ATP)(His)(2-) and Ni(ATP)(His)(3-), were found. In the former, stacking interaction between the aromatic moiety of ATP and the imidazole ring of l-histidine is crucial to the adduct stability. All studied systems are able to generate single strand lesions of plasmid DNA in the presence of hydrogen peroxide. However, only binary systems produce linear form of DNA, which is a consequence of the accumulation of the single-stranded breaks.