Acid-base and metal-ion-binding properties of 9-[2-(2-phosphonoethoxy)ethyl]adenine (PEEA), a relative of the antiviral nucleotide analogue 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA). An exercise on the quantification of isomeric complex equilibria in solution

Stability Constant and Potentiometric Sensitivity of Heavy Metal-Organic Fluorescent Compound Complexes: QSPR Models for Prediction and Design of Novel Coumarin-like Ligands

Industrial wastewater often consists of toxic chemicals and pollutants, which are extremely harmful to the environment. Heavy metals are toxic chemicals and considered one of the major hazards to the aquatic ecosystem. Analytical techniques, such as potentiometric methods, are some of the methods to detect heavy metals in wastewaters. In this work, the quantitative structure-property relationship (QSPR) was applied using a range of machine learning techniques to predict the stability constant (logβ_ML) and potentiometric sensitivity (PS_ML) of 200 ligands in complexes with the heavy metal ions Cu²⁺, Cd²⁺, and Pb²⁺. In result, the logβML models developed for four ions showed good performance with square correlation coefficients (R²) ranging from 0.80 to 1.00 for the training and 0.72 to 0.85 for the test sets. Likewise, the PSML displayed acceptable performance with an R² of 0.87 to 1.00 for the training and 0.73 to 0.95 for the test sets. By screening a virtual database of coumarin-like structures, several new ligands bearing the coumarin moiety were identified. Three of them, namely NEW02, NEW03, and NEW07, showed very good sensitivity and stability in the metal complexes. Subsequent quantum-chemical calculations, as well as physicochemical/toxicological profiling were performed to investigate their metal-binding ability and developability of the designed sensors. Finally, synthesis schemes are proposed to obtain these three ligands with major efficiency from simple resources. The three coumarins designed clearly demonstrated capability to be suitable as good florescent chemosensors towards heavy metals. Overall, the computational methods applied in this study showed a very good performance as useful tools for designing novel fluorescent probes and assessing their sensing abilities.

Machine learning-based analysis of overall stability constants of metal-ligand complexes

The stability constants of metal(M)-ligand(L) complexes are industrially important because they affect the quality of the plating film and the efficiency of metal separation. Thus, it is desirable to develop an effective screening method for promising ligands. Although there have been several machine-learning approaches for predicting stability constants, most of them focus only on the first overall stability constant of M-L complexes, and the variety of cations is also limited to less than 20. In this study, two Gaussian process regression models are developed to predict the first overall stability constant and the n-th (n > 1) overall stability constants. Furthermore, the feature relevance is quantitatively evaluated via sensitivity analysis. As a result, the electronegativities of both metal and ligand are found to be the most important factor for predicting the first overall stability constant. Interestingly, the predicted value of the first overall stability constant shows the highest correlation with the n-th overall stability constant of the corresponding M-L pair. Finally, the number of features is optimized using validation data where the ligands are not included in the training data, which indicates high generalizability. This study provides valuable insights and may help accelerate molecular screening and design for various applications.

Metal-Based Compounds in Antiviral Therapy

In recent years, the study of metal complexes and metal-based nanomaterials has aroused particular interest, leading to the promotion of new effective systems for the abatement of various viral diseases. Starting from the analysis of chemical properties, this review focuses on the employment of metal-based nanoparticles as antiviral drugs and how this interaction leads to a substantial enhancement in antiviral activity. The use of metal-based antiviral drugs has also spread for the formulation of antiviral vaccines, thanks especially to the remarkable adjuvant activities of some of the metal complexes. In particular, the small size and inert nature of Au- and Ag-based nanoparticles have been exploited for the design of systems for antiviral drug delivery, leading to the development of specific and safe therapies that lead to a decrease in side effects.

Coordination Chemistry of Nucleotides and Antivirally Active Acyclic Nucleoside Phosphonates, including Mechanistic Considerations

Considering that practically all reactions that involve nucleotides also involve metal ions, it is evident that the coordination chemistry of nucleotides and their derivatives is an essential corner stone of biological inorganic chemistry. Nucleotides are either directly or indirectly involved in all processes occurring in Nature. It is therefore no surprise that the constituents of nucleotides have been chemically altered-that is, at the nucleobase residue, the sugar moiety, and also at the phosphate group, often with the aim of discovering medically useful compounds. Among such derivatives are acyclic nucleoside phosphonates (ANPs), where the sugar moiety has been replaced by an aliphatic chain (often also containing an ether oxygen atom) and the phosphate group has been replaced by a phosphonate carrying a carbon-phosphorus bond to make the compounds less hydrolysis-sensitive. Several of these ANPs show antiviral activity, and some of them are nowadays used as drugs. The antiviral activity results from the incorporation of the ANPs into the growing nucleic acid chain-i.e., polymerases accept the ANPs as substrates, leading to chain termination because of the missing 3'-hydroxyl group. We have tried in this review to describe the coordination chemistry (mainly) of the adenine nucleotides AMP and ATP and whenever possible to compare it with that of the dianion of 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA2- = adenine(N9)-CH2-CH2-O-CH2-PO32) [or its diphosphate (PMEApp4-)] as a representative of the ANPs. Why is PMEApp4- a better substrate for polymerases than ATP4-? There are three reasons: (i) PMEA2- with its anti-like conformation (like AMP2-) fits well into the active site of the enzyme. (ii) The phosphonate group has an enhanced metal ion affinity because of its increased basicity. (iii) The ether oxygen forms a 5-membered chelate with the neighboring phosphonate and favors thus coordination at the Pα group. Research on ANPs containing a purine residue revealed that the kind and position of the substituent at C2 or C6 has a significant influence on the biological activity. For example, the shift of the (C6)NH2 group in PMEA to the C2 position leads to 9-[2-(phosphonomethoxy)ethyl]-2-aminopurine (PME2AP), an isomer with only a moderate antiviral activity. Removal of (C6)NH2 favors N7 coordination, e.g., of Cu2+, whereas the ether O atom binding of Cu2+ in PMEA facilitates N3 coordination via adjacent 5- and 7-membered chelates, giving rise to a Cu(PMEA)cl/O/N3 isomer. If the metal ions (M2+) are M(α,β)-M(γ)-coordinated at a triphosphate chain, transphosphorylation occurs (kinases, etc.), whereas metal ion binding in a M(α)-M(β,γ)-type fashion is relevant for polymerases. It may be noted that with diphosphorylated PMEA, (PMEApp4-), the M(α)-M(β,γ) binding is favored because of the formation of the 5-membered chelate involving the ether O atom (see above). The self-association tendency of purines leads to the formation of dimeric [M2(ATP)]2(OH)- stacks, which occur in low concentration and where one half of the molecule undergoes the dephosphorylation reaction and the other half stabilizes the structure-i.e., acts as the "enzyme" by bridging the two ATPs. In accord herewith, one may enhance the reaction rate by adding AMP2- to the [Cu2(ATP)]2(OH)- solution, as this leads to the formation of mixed stacked Cu3(ATP)(AMP)(OH)- species, in which AMP2- takes over the structuring role, while the other "half" of the molecule undergoes dephosphorylation. It may be added that Cu3(ATP)(PMEA) or better Cu3(ATP)(PMEA)(OH)- is even a more reactive species than Cu3(ATP)(AMP)(OH)-. - The matrix-assisted self-association and its significance for cell organelles with high ATP concentrations is summarized and discussed, as is, e.g., the effect of tryptophanate (Trp-), which leads to the formation of intramolecular stacks in M(ATP)(Trp)3- complexes (formation degree about 75%). Furthermore, it is well-known that in the active-site cavities of enzymes the dielectric constant, compared with bulk water, is reduced; therefore, we have summarized and discussed the effect of a change in solvent polarity on the stability and structure of binary and ternary complexes: Opposite effects on charged O sites and neutral N sites are observed, and this leads to interesting insights.

Acid–base properties of an antivirally active acyclic nucleoside phosphonate: (S)-9-[3-hydroxy-2-(phosphonomethoxy)propyl]adenine (HPMPA)

Protonation equilibria for the parent compound of three highly potent antivirals have been studied by 1H NMR spectroscopy.

Solution properties of metal ion complexes formed with the antiviral and cytostatic nucleotide analogue 9-[2-(phosphonomethoxy)ethyl]-2-amino-6-dimethylaminopurine (PME2A6DMAP)

The acidity constants of protonated 9-[2-(phosphonomethoxy)ethyl]-2-amino-6-dimethylaminopurine (H3(PME2A6DMAP)+) are considered, and the stability constants of the M(H;PME2A6DMAP)+ and M(PME2A6DMAP) complexes (M2+ = Mg2+, Ca2+, Sr2+, Ba2+, Mn2+, Co2+, Ni2+, Cu2+, Zn2+, or Cd2+) were measured by potentiometric pH titrations in aqueous solution (25 °C; I = 0.1 mol/L, NaNO3). In the M(H;PME2A6DMAP)+ species, H+ and M2+ (mainly outersphere) are at the phosphonate group; this is relevant for phosphoryl-diester bridges in nucleic acids because, in the present system, there is no indication for a M2+–purine binding. This contrasts, for example, with the complexes formed by 9-[2-(phosphonomethoxy)ethyl]adenine, M(H;PMEA)+, where M2+ is mainly situated at the adenine residue. Application of log [Formula: see text] vs. [Formula: see text] plots for simple phosph(on)ate ligands, R–PO32− (R being a residue that does not affect M2+ binding), proves that all M(PME2A6DMAP) complexes have larger stabilities than what would be expected for a M2+–phosphonate coordination. Comparisons with M(PME–R) complexes, where R is a noncoordinating residue of the (phosphonomethoxy)ethane chain, allow one to conclude that the increased stability is due to the formation of five-membered chelates involving the ether–oxygen of the –CH2–O–CH2–PO32− residue: the percentages of formation of these M(PME2A6DMAP)cl/O chelates, which occur in intramolecular equilibria, vary between 20% (Sr2+, Ba2+) and 50% (Zn2+, Cd2+), up to a maximum of 67% (Cu2+). Any M2+ interaction with N3 or N7 of the purine moiety, as in the parent M(PMEA) complexes, is suppressed by the (C2)NH2 and (C6)N(CH3)2 substituents. This observation, together with the previously determined stacking properties, offers an explanation why PME2A6DMAP2– has remarkable therapeutic effects.

Comparison of the π-stacking properties of purine versus pyrimidine residues. Some generalizations regarding selectivity

Aromatic-ring stacking is pronounced among the noncovalent interactions occurring in biosystems and therefore some pertinent features regarding nucleobase residues are summarized. Self-stacking decreases in the series adenine > guanine > hypoxanthine > cytosine ~ uracil. This contrasts with the stability of binary (phen)(N) adducts formed by 1,10-phenanthroline (phen) and a nucleobase residue (N), which is largely independent of the type of purine residue involved, including (N1)H-deprotonated guanine. Furthermore, the association constant for (phen)(A)(0/4-) is rather independent of the type and charge of the adenine derivative (A) considered, be it adenosine or one of its nucleotides, including adenosine 5'-triphosphate (ATP(4-)). The same holds for the corresponding adducts of 2,2'-bipyridine (bpy), although owing to the smaller size of the aromatic-ring system of bpy, the (bpy)(A)(0/4-) adducts are less stable; the same applies correspondingly to the adducts formed with pyrimidines. In accord herewith, [M(bpy)](adenosine)(2+) adducts (M(2+) is Co(2+), Ni(2+), or Cu(2+)) show the same stability as the (bpy)(A)(0/4-) ones. The formation of an ionic bridge between -NH3 (+) and -PO3 (2-), as provided by tryptophan [H(Trp)(±)] and adenosine 5'-monophosphate (AMP(2-)), facilitates recognition and stabilizes the indole-purine stack in [H(Trp)](AMP)(2-). Such indole-purine stacks also occur in nature. Similarly, the formation of a metal ion bridge as occurs, e.g., between Cu(2+) coordinated to phen and the phosphonate group of 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA(2-)) dramatically favors the intramolecular stack in Cu(phen)(PMEA). The consequences of such interactions for biosystems are discussed, especially emphasizing that the energies involved in such isomeric equilibria are small, allowing Nature to shift such equilibria easily.

Intrinsic acid-base properties of a hexa-2'-deoxynucleoside pentaphosphate, d(ApGpGpCpCpT): neighboring effects and isomeric equilibria

The intrinsic acid-base properties of the hexa-2'-deoxynucleoside pentaphosphate, d(ApGpGpCpCpT) [=(A1∙G2∙G3∙C4∙C5∙T6)=(HNPP)⁵⁻] have been determined by ¹H NMR shift experiments. The pKa values of the individual sites of the adenosine (A), guanosine (G), cytidine (C), and thymidine (T) residues were measured in water under single-strand conditions (i.e., 10% D₂O, 47 °C, I=0.1 M, NaClO₄). These results quantify the release of H⁺ from the two (N7)H⁺ (G∙G), the two (N3)H⁺ (C∙C), and the (N1)H⁺ (A) units, as well as from the two (N1)H (G∙G) and the (N3)H (T) sites. Based on measurements with 2'-deoxynucleosides at 25 °C and 47 °C, they were transferred to pKa values valid in water at 25 °C and I=0.1 M. Intramolecular stacks between the nucleobases A1 and G2 as well as most likely also between G2 and G3 are formed. For HNPP three pKa clusters occur, that is those encompassing the pKa values of 2.44, 2.97, and 3.71 of G2(N7)H⁺, G3(N7)H⁺, and A1(N1)H⁺, respectively, with overlapping buffer regions. The tautomer populations were estimated, giving for the release of a single proton from five-fold protonated H₅(HNPP)(±) , the tautomers (G2)N7, (G3)N7, and (A1)N1 with formation degrees of about 74, 22, and 4%, respectively. Tautomer distributions reveal pathways for proton-donating as well as for proton-accepting reactions both being expected to be fast and to occur practically at no "cost". The eight pKa values for H₅(HNPP)(±) are compared with data for nucleosides and nucleotides, revealing that the nucleoside residues are in part affected very differently by their neighbors. In addition, the intrinsic acidity constants for the RNA derivative r(A1∙G2∙G3∙C4∙C5∙U6), where U=uridine, were calculated. Finally, the effect of metal ions on the pKa values of nucleobase sites is briefly discussed because in this way deprotonation reactions can easily be shifted to the physiological pH range.

Extent of intramolecular π-stacks in aqueous solution in mixed-ligand copper(II) complexes formed by heteroaromatic amines and several 2-aminopurine derivatives of the antivirally active nucleotide analog 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA)

The acidity constants of twofold protonated, antivirally active, acyclic nucleoside phosphonates (ANPs), H(2)(PE)(±), where PE(2-)=9-[2-(phosphonomethoxy)ethyl]adenine (PMEA(2-)), 2-amino-9-[2-(phosphonomethoxy)ethyl]purine (PME2AP(2-)), 2,6-diamino-9-[2-(phosphonomethoxy)ethyl]purine (PMEDAP(2-)), or 2-amino-6-(dimethylamino)-9-[2-(phosphonomethoxy)ethyl]purine (PME(2A6DMAP)(2-)), as well as the stability constants of the corresponding ternary Cu(Arm)(H;PE)(+) and Cu(Arm)(PE) complexes, where Arm=2,2'-bipyridine (bpy) or 1,10-phenanthroline (phen), are compared. The constants for the systems containing PE(2-)=PMEDAP(2-) and PME(2A6DMAP)(2-) have been determined now by potentiometric pH titrations in aqueous solution at I=0.1M (NaNO(3)) and 25°; the corresponding results for the other ANPs were taken from our earlier work. The basicity of the terminal phosphonate group is very similar for all the ANP(2-) species, whereas the addition of a second amino substituent at the pyrimidine ring of the purine moiety significantly increases the basicity of the N(1) site. Detailed stability-constant comparisons reveal that, in the monoprotonated ternary Cu(Arm)(H;PE)(+) complexes, the proton is at the phosphonate group, that the ether O-atom of the -CH(2)-O-CH(2)-P(O)(2)(-)(OH) residue participates, next to the P(O)(2)(-)(OH) group, to some extent in Cu(Arm)(2+) coordination, and that π-π stacking between the aromatic rings of Cu(Arm)(2+) and the purine moiety is rather important, especially for the H·PMEDAP(-) and H·PME(2A6DMAP)(-) ligands. There are indications that ternary Cu(Arm)(2+)-bridged stacks as well as unbridged (binary) stacks are formed. The ternary Cu(Arm)(PE) complexes are considerably more stable than the corresponding Cu(Arm)(R-PO(3)) species, where R-PO(3)(2-) represents a phosph(on)ate ligand with a group R that is unable to participate in any kind of intramolecular interaction within the complexes. The observed stability enhancements are mainly attributed to intramolecular-stack formation in the Cu(Arm)(PE) complexes and also, to a smaller extent, to the formation of five-membered chelates involving the ether O-atom present in the -CH(2)-O-CH(2)-PO(3)(2-) residue of the PE(2-) species. The quantitative analysis of the intramolecular equilibria involving three structurally different Cu(Arm)(PE) isomers shows that, e.g., ca. 1.5% of the Cu(phen)(PMEDAP) system exist with Cu(phen)(2+) solely coordinated to the phosphonate group, 4.5% as a five-membered chelate involving the ether O-atom of the -CH(2)-O-CH(2)-PO(3)(2-) residue, and 94% with an intramolecular π-π stack between the purine moiety of PMEDAP(2-) and the aromatic rings of phen. Comparison of the various formation degrees of the species formed reveals that, in the Cu(phen)(PE) complexes, intramolecular-stack formation is more pronounced than in the Cu(bpy)(PE) species. Within a given Cu(Arm)(2+) series the stacking intensity increases in the order PME2AP(2-) <PMEA(2-) <PMEDAP(2-) <PME(2A6DMAP)(2-). One could speculate that the reduced stacking intensity of PME2AP(2-), together with a different H-bonding pattern, could well lead to a different orientation of the 2-aminopurine moiety (compared to the adenine residue) in the active site of nucleic acid polymerases and thus be responsible for the reduced antiviral activity of PME2AP compared with that of PMEA and the other ANPs containing a 6-amino substituent.

Complex formation of cadmium with sugar residues, nucleobases, phosphates, nucleotides, and nucleic acids

Cadmium(II), commonly classified as a relatively soft metal ion, prefers indeed aromatic-nitrogen sites (e.g., N7 of purines) over oxygen sites (like sugar-hydroxyl groups). However, matters are not that simple, though it is true that the affinity of Cd(2+) towards ribose-hydroxyl groups is very small; yet, a correct orientation brought about by a suitable primary binding site and a reduced solvent polarity, as it is expected to occur in a folded nucleic acid, may facilitate metal ion-hydroxyl group binding very effectively. Cd(2+) prefers the guanine(N7) over the adenine(N7), mainly because of the steric hindrance of the (C6)NH(2) group in the adenine residue. This Cd(2+)-(N7) interaction in a guanine moiety leads to a significant acidification of the (N1)H meaning that the deprotonation reaction occurs now in the physiological pH range. N3 of the cytosine residue, together with the neighboring (C2)O, is also a remarkable Cd(2+) binding site, though replacement of (C2)O by (C2)S enhances the affinity towards Cd(2+) dramatically, giving in addition rise to the deprotonation of the (C4)NH(2) group. The phosphodiester bridge is only a weak binding site but the affinity increases further from the mono- to the di- and the triphosphate. The same also holds for the corresponding nucleotides. Complex stability of the pyrimidine-nucleotides is solely determined by the coordination tendency of the phosphate group(s), whereas in the case of purine-nucleotides macrochelate formation takes place by the interaction of the phosphate-coordinated Cd(2+) with N7. The extents of the formation degrees of these chelates are summarized and the effect of a non-bridging sulfur atom in a thiophosphate group (versus a normal phosphate group) is considered. Mixed ligand complexes containing a nucleotide and a further mono- or bidentate ligand are covered and it is concluded that in these species N7 is released from the coordination sphere of Cd(2+). In the case that the other ligand contains an aromatic residue (e.g., 2,2'-bipyridine or the indole ring of tryptophanate) intramolecular stack formation takes place. With buffers like Tris or Bistris mixed ligand complexes are formed. Cd(2+) coordination to dinucleotides and to dinucleoside monophosphates provides some insights regarding the interaction between Cd(2+) and nucleic acids. Cd(2+) binding to oligonucleotides follows the principles of coordination to its units. The available crystal studies reveal that N7 of purines is the prominent binding site followed by phosphate oxygens and other heteroatoms in nucleic acids. Due to its high thiophilicity, Cd(2+) is regularly used in so-called thiorescue experiments, which lead to the identification of a direct involvement of divalent metal ions in ribozyme catalysis.

Understanding the acid-base properties of adenosine: the intrinsic basicities of N1, N3 and N7

Adenosine (Ado) can accept three protons, at N1, N3, and N7, to give H(3) (Ado)(3+) , and thus has three macro acidity constants. Unfortunately, these constants do not reflect the real basicity of the N sites due to internal repulsions, for example, between (N1)H(+) and (N7)H(+). However, these macroconstants are still needed for the evaluations and the first two are taken from our own earlier work, that is, pK(H)(H(3))((Ado)) = -4.02 and pK(H)(H(2))((Ado)) = -1.53; the third one was re-measured as pK(H)(H)((Ado)) = 3.64 ± 0.02 (25 °C; I=0.5 M, NaNO(3)), because it is the main basis for evaluating the intrinsic basicities of N7 and N3. Previously, contradicting results had been published for the micro acidity constant of the (N7)H(+) site; this constant has now been determined in an unequivocal manner, and that of the (N3)H(+) site was obtained for the first time. The micro acidity constants, which describe the release of a proton from an (N)H(+) site under conditions for which the other nitrogen atoms are free and do not carry a proton, decrease in the order pk(N7-N1)(N7(Ado)N1·H)) = 3.63 ± 0.02 > pk(N7-N1)(H·N7(Ado)N1) = 2.15 ± 0.15 > pk(N3-N1,N7)(H·N3(Ado)N1,N7) =1.5 ± 0.3, reflecting the decreasing basicity of the various nitrogen atoms, that is, N1>N7>N3. Application of the above-mentioned microconstants allows one to calculate the percentages (formation degrees) of the tautomers formed for monoprotonated adenosine, H(Ado)(+) , in aqueous solution; the results are 96.1, 3.2, and 0.7% for N7(Ado)N1·H(+), (+)H·N7(Ado)N1, and (+)H·N3(Ado)N1,N7, respectively. These results are in excellent agreement with theoretical DFT calculations. Evidently, H(Ado)(+) exists to the largest part as N7(Ado)N1·H(+) having the proton located at N1; the two other tautomers are minority species, but they still form. These results are not only meaningful for adenosine itself, but are also of relevance for nucleic acids and adenine nucleotides, as they help to understand their metal ion-binding properties; these aspects are briefly discussed.

Xanthosine 5'-monophosphate (XMP). Acid-base and metal ion-binding properties of a chameleon-like nucleotide

The four acidity constants of threefold protonated xanthosine 5'-monophosphate, H(3)(XMP)(+), reveal that in the physiological pH range around 7.5 (X - H x MP)(3-) strongly dominates and not XMP(2-) as commonly given in textbooks and often applied in research papers. Therefore, this nucleotide, which participates in many metabolic processes, should be addressed as xanthosinate 5'-monophosphate as is stated in this critical review. Micro acidity constant schemes allow quantification of intrinsic site basicities. In 9-methylxanthine nucleobase deprotonation occurs to more than 99% at (N3)H, whereas for xanthosine it is estimated that about 30% are (N1)H deprotonated and for (X - H x MP)(3-) it is suggested that (N1)H deprotonation is further favored, especially in macrochelates where the phosphate-coordinated M(2+) interacts with N7. The formation degree of these macrochelates in the (X - H x MP x M)(-) species of Co(2+), Ni(2+), Cu(2+), Zn(2+) or Cd(2+) amounts to 90% or more. In the monoprotonated (M x X - H x MP x H)(+/-) complexes, M(2+) is located at the N7/[(C6)O] unit as the primary binding site and it forms macrochelates with the P(O)(2)(OH)(-) group to about 65% for nearly all metal ions considered (i.e., including Ba(2+), Sr(2+), Ca(2+), Mg(2+)); this indicates outer-sphere binding to P(O)(2)(OH)(-). Finally, a new method quantifying the chelate effect is applied to the M(X - H x MP)(-) species, stabilities and structures of mixed-ligand complexes are considered, and the stability constants for several M(X - H x DP)(2-) and M(X - H x TP)(3-) complexes are estimated (112 references).

Comparison of the surprising metal-ion-binding properties of 5- and 6-uracilmethylphosphonate (5Umpa2- and 6Umpa2-) in aqueous solution and crystal structures of the dimethyl and di(isopropyl) esters of H2(6Umpa)

5- and 6-Uracilmethylphosphonate (5Umpa(2-) and 6Umpa(2-)) as acyclic nucleotide analogues are in the focus of anticancer and antiviral research. Connected metabolic reactions involve metal ions; therefore, we determined the stability constants of M(Umpa) complexes (M(2+)=Mg(2+), Ca(2+), Mn(2+), Co(2+), Cu(2+), Zn(2+), or Cd(2+)). However, the coordination chemistry of these Umpa species is also of interest in its own right, for example, the phosphonate-coordinated M(2+) interacts with (C4)O to form seven-membered chelates with 5Umpa(2-), thus leading to intramolecular equilibria between open (op) and closed (cl) isomers. No such interaction occurs with 6Umpa(2-). In both M(Umpa) series deprotonation of the uracil residue leads to the formation of M(Umpa-H)(-) complexes at higher pH values. Their stability was evaluated by taking into account the fact that the uracilate residue can bind metal ions to give M(2)(Umpa-H)(+) species. This has led to two further important insights: 1) In M(6Umpa-H)-cl the H(+) is released from (N1)H, giving rise to six-membered chelates (degrees of formation of ca. 90 to 99.9 % with Mn(2+), Co(2+), Cu(2+), Zn(2+), or Cd(2+)). 2) In M(5Umpa-H)$-cl the (N3)H is deprotonated, leading to a higher stability of the seven-membered chelates involving (C4)O (even Mg(2+) and Ca(2+) chelates are formed up to approximately 50 %). In both instances the M(Umpa-H)-op species led to the formation of M(2)(Umpa-H)(+) complexes that have one M(2+) at the phosphonate and one at the (N3)(-) (plus carbonyl) site; this proves that nucleotides can bind metal ions independently at the phosphate and the nucleobase residues. X-ray structural analyses of 6Umpa derivatives show that in diesters the phosphonate group is turned away from the uracil residue, whereas in H(2)(6Umpa) the orientation is such that upon deprotonation in aqueous solution a strong hydrogen bond is formed between (N1)H and PO(3) (2-); replacement of the hydro gen with M(2+) gives the M(6Umpa-H)-cl chelates mentioned.

Metal-ion-coordinating properties of the dinucleotide 2'-deoxyguanylyl(5'-->3')-2'-deoxy-5'-guanylate (d(pGpG)3-): isomeric equilibria including macrochelated complexes relevant for nucleic acids

The interaction between divalent metal ions and nucleic acids is well known, yet knowledge about the strength of binding of labile metal ions at the various sites is very scarce. We have therefore studied the stabilities of complexes formed between the nucleic acid model d(pGpG) and the essential metal ions Mg2+ and Zn2+ as well as with the generally toxic ions Cd2+ and Pb2+ by potentiometric pH titrations; all four ions are of relevance in ribozyme chemistry. A comparison of the present results with earlier data obtained for M(pUpU)- complexes allows the conclusion that phosphate-bound Mg2+ and Cd2+ form macrochelates by interaction with N7, whereas the also phosphate-coordinated Pb2+ forms a 10-membered chelate with the neighboring phosphate diester bridge. Zn2+ forms both types of chelates with formation degrees of about 91% and 2.4% for Zn[d(pGpG)]cl/N7 and Zn[d(pGpG)]-cl/PO, respectively; the open form with Zn2+ bound only to the terminal phosphate group, Zn[d(pGpG)]-op, amounts to about 6.8 %. The various intramolecular equilibria have also been quantified for the other metal ions. Zn2+, Cu2+, and Cd2+ also form macrochelates in the monoprotonated M[H;d(pGpG)] species (the proton being at the terminal phosphate group), that is, the metal ion at N7 interacts to some extent with the P(O)2(OH)- group. Thus, this study demonstrates that the coordinating properties of the various metal ions toward a pGpG unit in a nucleic acid differ: Mg2+, Zn2+, and Cd2+ have a significant tendency to bridge the distance between N7 and the phosphate group of a (d)GMP unit, although to various extents, whereas Pb2+ (and possibly Ca2+) prefer a pure phosphate coordination.

Towards the mechanism of trimeric purine nucleoside phosphorylases: Stopped-flow studies of binding of multisubstrate analogue inhibitor — 2-amino-9-[2-(phosphonomethoxy)ethyl]-6-sulfanylpurine

The binding of multisubstrate analogue inhibitor - 2-amino-9-[2-(phosphonomethoxy)ethyl]-6-sulfanylpurine (PME-6-thio-Gua) to purine nucleoside phosphorylase from Cellulomonas sp. at 20 degrees C, in 20 mM Hepes buffer with ionic strength adjusted to 50 mM using KCl, at several pH values between 6.5 and 8.2, was investigated using a stopped-flow spectrofluorimeter. The kinetic transients registered after mixing a protein solution with ligand solutions of different concentrations were simultaneously fitted by several association reaction models using nonlinear least-squares procedure based on numerical integration of the chemical kinetic equations appropriate for given model. It is concluded that binding of a PME-6-thio-Gua molecule by each of the binding sites is sufficiently well described by one-step process, with a model assuming interacting binding sites being more probable than a model assuming independent sites. The association rate constants derived from experimental data, assuming one step binding and independent sites, are decreasing with an increase in pH, changing from 30 to 6 microM(-1)s(-1) per binding site. The dissociation rate constants are in the range of 1-3 s(-1), and they are rather insensitive of changes in pH. Interestingly, for each pH value, the one-step binding model with interacting sites results in the association rate constant per site 1.5-4 times smaller for the binding of the first ligand molecule than that for the binding of the second one. Decrease of association constants with pH indicate that the enzyme does not prefer binding of the naturally occurring anionic form of the 6-thioguanine ring (pK(a) 8.7) resulting from a dissociation of N(1)-H. This finding supports the mechanism in which hydrogen bond interaction of N(1)-H with Glu204 (Glu 201 in mammalian PNPs) is crucial in the catalytic process. Results obtained also indicate that, in contrast to transition-state analogues, for which binding is followed by a conformational change, binding of multisubstrate analogue inhibitors to trimeric PNPs is a one-step process.

Novel Oxygen Chirality Induced by Asymmetric Coordination of an Ether Oxygen Atom to a Metal Center in a Series of Sugar-Pendant Dipicolylamine Copper(II) Complexes

Six sugar-pendant 2,2'-dipicolylamine (DPA) ligands (L1-3 and L'1-3) have been prepared. OH-protected and unprotected D-glucose, D-mannose, and D-xylose were attached to a DPA moiety via an O-glycoside linkage. X-ray crystallography of the copper(II) complexes (1-5) with these ligands revealed that the anomeric oxygen atom is coordinated to the metal center in the solid state, generating a chiral center at the oxygen atom. The CD spectra of these copper complexes in methanol or aqueous solution exhibit Cotton effects in the d-d transition region, which indicates that the ether oxygen atoms remain coordinated to the metal center and the oxygen-atom chirality is preserved even in solution. For complexes 1 and 2, the inverted oxygen-atom chirality and chelate-ring conformation in the solid state are well correlated with the mirror-image CD spectra in methanol solution. The concomitant inversion of the asymmetric configuration around the copper center was also observed in a methanol solution of complex 3 and a pyridine solution of complex 2. The square-pyramidal/octahedral copper(II) centers also exhibited characteristic absorption and CD spectra.

Evidence for intramolecular aromatic-ring stacking in the physiological pH range of the monodeprotonated xanthine residue in mixed-ligand complexes containing xanthosinate 5′-monophosphate (XMP)

The stability constants of the mixed-ligand complexes formed between Cu(Arm)2+ [Arm = 2,2'-bipyridine (Bpy) or 1,10-phenanthroline (Phen)], and the di- or trianion of xanthosine 5'-monophosphoric acid [= XMP(2-) or (XMP - H)(3-)] were determined by potentiometric pH titration in aqueous solution (25 degrees C; I = 0.1 M, NaNO3). Those for the monoanion, i.e., the Cu(Arm)(H;XMP)+ complexes, could only be estimated; for these species it is concluded that the metal ion is overwhelmingly bound at N7 and the proton resides at the phosphate group. Similarly, in the Cu(Arm)(XMP)+/- [= Cu(Arm)(X - H.MP.H)+/-] complexes Cu(Arm)2+ is also at N7 but the xanthine residue has lost a proton whereas the phosphate group still carries one, i.e., stacking plays, if at all, only a very minor role, yet, the N7-bound Cu(Arm)2+ appears to form an outer-sphere macrochelate with P(O)2(OH)-, its formation degree being about 60%. All this is different in the Cu(Arm)(XMP - H)- complexes, which are formed by the (XMP - H)(3-) species, that occur at the physiological pH of 7.5 and for which previously evidence has been provided that in a tautomeric equilibrium the xanthine moiety loses a proton either from (N1)H or (N3)H. In Cu(Arm)(XMP - H)- the phosphate group is the primary binding site for Cu(Arm)2+ and the observed increased complex stability is mainly due to intramolecular stack (st) formation between the aromatic-ring systems of Phen or Bpy and the monodeprotonated xanthine residue of (XMP - H)(3-); e.g., the stacked Cu(Phen)(XMP - H) isomer occurs with approximately 76%. Regarding biological systems the most important result is that at physiological pH the xanthine moiety has lost a proton from the (N1)H/(N3)H sites forming (XMP - H)(3-) and that its anionic xanthinate residue is able to undergo aromatic-ring stacking.

Nucleoside 5'-triphosphates: self-association, acid-base, and metal ion-binding properties in solution

Adenosine 5'-triphosphate (ATP(4-)) and related nucleoside 5'-triphosphates (NTP(4-)) serve as substrates in the form of metal ion complexes in enzymic reactions taking part thus in central metabolic processes. With this in mind, the coordination chemistry of NTPs is critically reviewed and the conditions are defined for studies aiming to describe the properties of monomeric complexes because at higher concentrations (>1 mM) self-stacking may take place. The metal ion (M(2+)) complexes of purine-NTPs are more stable than those of pyrimidine-NTPs; this stability enhancement is attributed, in accord with NMR studies, to macrochelate formation of the phosphate-coordinated M(2+) with N7 of the purine residue and the formation degrees of the resulting isomeric complexes are listed. Furthermore, the formation of mixed-ligand complexes (including also those with buffer molecules), the effect of a reduced solvent polarity on complex stability and structure (giving rise to selectivity), the use of nucleotide analogues as antiviral agents, and the effect of metal ions on group transfer reactions are summarized.