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 Among such derivatives are acyclic nucleoside phosphonates (ANPs), where the sugar moiety has been replaced by an aliphatic chain (often also containing an ether oxygen atom) and the phosphate group has been replaced by a phosphonate carrying a carbon–phosphorus bond to make the compounds less hydrolysis-sensitive.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

A quantitative appraisal of the ambivalent metal ion binding properties of cytidine in aqueous solution and an estimation of the anti - syn energy barrier of cytidine derivatives

The recently defined % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX! % MathType!MTEF!2!1!+- % feaafaart1ev1aaatCvAUfeBSn0BKvguHDwzZbqefeKCPfgBGuLBPn % 2BKvginnfarmWu51MyVXgatuuDJXwAK1uy0HwmaeHbfv3ySLgzG0uy % 0Hgip5wzaebbnrfifHhDYfgasaacH8qrps0lbbf9q8WrFfeuY-Hhbb % f9v8qqaqFr0xc9pk0xbba9q8WqFfea0-yr0RYxir-Jbba9q8aq0-yq % -He9q8qqQ8frFve9Fve9Ff0dmeaabaqaciGacaGaaeqabaWaaeWaea % aakeaaciGGSbGaai4BaiaacEgacaWGlbWaa0baaSqaaiaab2eadaqa % daqaaiaabYeaaiaawIcacaGLPaaaaeaacaqGnbaaaaaa!411C! $$\log K^{{\text{M}}}_{{{\text{M}}{\left( {\text{L}} \right)}}}$$ versus % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX! % MathType!MTEF!2!1!+- % feaafaart1ev1aaatCvAUfeBSn0BKvguHDwzZbqefeKCPfgBGuLBPn % 2BKvginnfarmWu51MyVXgatuuDJXwAK1uy0HwmaeHbfv3ySLgzG0uy % 0Hgip5wzaebbnrfifHhDYfgasaacH8qrps0lbbf9q8WrFfeuY-Hhbb % f9v8qqaqFr0xc9pk0xbba9q8WqFfea0-yr0RYxir-Jbba9q8aq0-yq % -He9q8qqQ8frFve9Fve9Ff0dmeaabaqaciGacaGaaeqabaWaaeWaea % aakeaacaqGWbGaam4samaaDaaaleaacaqGibWaaeWaaeaacaqGmbaa % caGLOaGaayzkaaaabaGaaeisaaaaaaa!3F35! $${\text{p}}K^{{\text{H}}}_{{{\text{H}}{\left( {\text{L}} \right)}}}$$ straight-line plots for L = pyridine-type (PyN) and ortho-aminopyridine-type (oPyN) ligands now allow the evaluation in a quantitative manner of the stability of the 1:1 complexes formed between cytidine (Cyd) and Ca2+, Mg2+, Mn2+, Co2+, Ni2+, Cu2+, Zn2+ or Cd2+ (M2+); the corresponding stability constants, % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX! <![CDATA[% MathType!MTEF!2!1!+- % feaafeart1ev1aaatCvAUfeBSn0BKvguHDwzZbqefeKCPfgBGuLBPn % 2BKvginnfarmWu51MyVXgatuuDJXwAK1uy0HwmaeHbfv3ySLgzG0uy % 0Hgip5wzaebbnrfifHhDYfgasaacH8qrps0lbbf9q8WrFfeuY-Hhbb % f9v8qqaqFr0xc9pk0xbba9q8WqFfea0-yr0RYxir-Jbba9q8aq0-yq % -He9q8qqQ8frFve9Fve9Ff0dmeaabaqaciGacaGaaeqabaWaaeWaea % aakeaacaWGlbWaa0baaSqaaiaab2eadaqadaqaaiaaboeacaqG5bGa % aeizaaGaayjkaiaawMcaaaqaaiaab2eaaaaaaa!4027! $$K_{{\text{M}}\left( {{\text{Cyd}}} \right)}^{\text{M}}$$ , including the acidity constant, % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX! <![CDATA[% MathType!MTEF!2!1!+- % feaafeart1ev1aaatCvAUfeBSn0BKvguHDwzZbqefeKCPfgBGuLBPn % 2BKvginnfarmWu51MyVXgatuuDJXwAK1uy0HwmaeHbfv3ySLgzG0uy % 0Hgip5wzaebbnrfifHhDYfgasaacH8qrps0lbbf9q8WrFfeuY-Hhbb % f9v8qqaqFr0xc9pk0xbba9q8WqFfea0-yr0RYxir-Jbba9q8aq0-yq % -He9q8qqQ8frFve9Fve9Ff0dmeaabaqaciGacaGaaeqabaWaaeWaea % aakeaacaWGlbWaa0baaSqaaiaabIeadaqadaqaaiaaboeacaqG5bGa % aeizaaGaayjkaiaawMcaaaqaaiaabIeaaaaaaa!401D! $$K_{{\text{H}}\left( {{\text{Cyd}}} \right)}^{\text{H}}$$ , for the deprotonation of the (N3)H+ site had been determined previously under exactly the same conditions as the mentioned plots. Since the stabilities of the M(PyN)2+ and M(oPyN)2+ complexes of Ca2+ and Mg2+ are practically identical, it is concluded that complex formation occurs in an outer-sphere manner, and this is in accord with the fact that in the pK a range 3-7 metal ion binding is independent of % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX! % MathType!MTEF!2!1!+- % feaafaart1ev1aaatCvAUfeBSn0BKvguHDwzZbqefeKCPfgBGuLBPn % 2BKvginnfarmWu51MyVXgatuuDJXwAK1uy0HwmaeHbfv3ySLgzG0uy % 0Hgip5wzaebbnrfifHhDYfgasaacH8qrps0lbbf9q8WrFfeuY-Hhbb % f9v8qqaqFr0xc9pk0xbba9q8WqFfea0-yr0RYxir-Jbba9q8aq0-yq % -He9q8qqQ8frFve9Fve9Ff0dmeaabaqaciGacaGaaeqabaWaaeWaea % aakeaacaWGlbWaa0baaSqaaiaabIeadaqadaqaaiaabcfacaqG5bGa % aeOtaaGaayjkaiaawMcaaaqaaiaabIeaaaaaaa!4013! $$K^{{\text{H}}}_{{{\text{H}}{\left( {{\text{PyN}}} \right)}}}$$ or % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX! % MathType!MTEF!2!1!+- % feaafaart1ev1aaatCvAUfeBSn0BKvguHDwzZbqefeKCPfgBGuLBPn % 2BKvginnfarmWu51MyVXgatuuDJXwAK1uy0HwmaeHbfv3ySLgzG0uy % 0Hgip5wzaebbnrfifHhDYfgasaacH8qrps0lbbf9q8WrFfeuY-Hhbb % f9v8qqaqFr0xc9pk0xbba9q8WqFfea0-yr0RYxir-Jbba9q8aq0-yq % -He9q8qqQ8frFve9Fve9Ff0dmeaabaqaciGacaGaaeqabaWaaeWaea % aakeaacaWGlbWaa0baaSqaaiaabIeadaqadaqaaiaad+gacaqGqbGa % aeyEaiaab6eaaiaawIcacaGLPaaaaeaacaqGibaaaaaa!4107! $$K^{{\text{H}}}_{{{\text{H}}{\left( {o{\text{PyN}}} \right)}}}$$ . Ca(Cyd)2+ and Mg(Cyd)2+ are more stable than the corresponding (outer-sphere) M(PyN)2+ complexes and this means that the C2 carbonyl group of Cyd must participate, next to N3 which is most likely outer-sphere, in metal ion binding, leading thus to chelates; these have formation degrees of about 50% and 35%, respectively. Co(Cyd)2+ and Ni(Cyd)2+ show no increased stability based on the % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX! <![CDATA[% MathType!MTEF!2!1!+- % feaafeart1ev1aaatCvAUfeBSn0BKvguHDwzZbqefeKCPfgBGuLBPn % 2BKvginnfarmWu51MyVXgatuuDJXwAK1uy0HwmaeHbfv3ySLgzG0uy % 0Hgip5wzaebbnrfifHhDYfgasaacH8qrps0lbbf9q8WrFfeuY-Hhbb % f9v8qqaqFr0xc9pk0xbba9q8WqFfea0-yr0RYxir-Jbba9q8aq0-yq % -He9q8qqQ8frFve9Fve9Ff0dmeaabaqaciGacaGaaeqabaWaaeWaea % aakeaaciGGSbGaai4BaiaacEgacaaMe8Uaam4samaaDaaaleaacaqG % nbWaaeWaaeaacaWGVbGaaeiuaiaabMhacaqGobaacaGLOaGaayzkaa % aabaGaaeytaaaakiaaysW7caqG2bGaaeyzaiaabkhacaqGZbGaaeyD % aiaabohacaaMe8UaaeiCaiaadUeadaqhaaWcbaGaaeisamaabmaaba % Gaam4BaiaabcfacaqG5bGaaeOtaaGaayjkaiaawMcaaaqaaiaabIea % aaGccaaMe8UaaeiCaiaabYgacaqGVbGaaeiDaiaabohacaGG7aaaaa!5E07! $$\log \;K^{{\text{M}}}_{{{\text{M}}{\left( {o{\text{PyN}}} \right)}}} \;{\text{versus}}\;{\text{p}}K^{{\text{H}}}_{{{\text{H}}{\left( {o{\text{PyN}}} \right)}}} \;{\text{plots}};$$ hence, the (C2)O group does not participate in metal ion binding, but the inner-sphere coordination to N3 is strongly inhibited by the (C4)NH2 group. In the M(Cyd)2+ complexes of Mn2+, Cu2+, Zn2+ and Cd2+, this inhibiting effect on M2+ binding at N3 is partially compensated by participation of the (C2)O group in complex formation and the corresponding chelates have formation degrees between about 30% (Zn2+) and 83% (Cu2+). The different structures of the mentioned chelates are discussed in relation to available crystal structure analyses. (1) There is evidence (crystal structure studies: Cu2+, Zn2+, Cd2+) that four-membered rings form, i.e. there is a strong M2+ bond to N3 and a weak one to (C2)O. (2) By hydrogen bond formation to (C2)O of a metal ion-bound water molecule, six-membered rings, so-called semichelates, may form. (3) For Ca2+ and Mg2+, and possibly Mn2+, and their Cyd complexes, six-membered chelates are also likely with (C2)O being inner-sphere (crystal structure) and N3 outer-sphere. (4) Finally, for these metal ions also complexes with a sole outer-sphere interaction may occur. All these types of chelates are expected to be in equilibrium with each other in solution, but, depending on the metal ion, either the one or the other form will dominate. Clearly, the cytidine residue is an ambivalent binding site which adjusts well to the requirements of the metal ion to be bound and this observation is of relevance for single-stranded nucleic acids and their interactions with metal ions. In addition, the anti-syn energy barrier has been estimated as being in the order of 6-7.5kJ/mol for cytidine derivatives in aqueous solution at 25°

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 (ATP4−). 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 (M2+is Co2+, Ni2+, or Cu2+) 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 (AMP2−), 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 Cu2+ coordinated to phen and the phosphonate group of 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA2−) 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

Metal Ion-Coordinating Properties in Aqueous Solution of the Antivirally Active Nucleotide Analogue (S)-9-[3-Hydroxy-2-(phosphonomethoxy)propyl]adenine (HPMPA). Quantification of Complex Isomeric Equilibria

Acyclic nucleoside phosphonates are of medical relevance and deserve detailed chemical characterization. We focus here on ( S )‐9‐[3‐hydroxy‐2‐(phosphonomethoxy)propyl]adenine (HPMPA) and include for comparison 9‐[2‐(phosphonomethoxy)ethyl]adenine (PMEA), as well as the nucleobase‐free (phosphonomethoxy)ethane (PME) and ( R )‐hydroxy‐2‐(phosphonomethoxy)propane (HPMP). The acidity constants of H 3 (HPMPA) + were determined and compared with those of the related phosph(on)ate derivatives; they are also needed to understand the properties of the metal ion complexes. Given that in vivo nucleotides and their analogues participate in reactions typically as divalent metal ion (M 2+ ) complexes, the stability constants of the M(H;HPMPA) + and M(HPMPA) species with M 2+ = Mg 2+ , Ca 2+ , Sr 2+ , Ba 2+ , Mn 2+ , Co 2+ , Ni 2+ , Cu 2+ , Zn 2+ , and Cd 2+ were measured. Comparisons between the results for HPMPA 2- and the previous data for PMEA 2- , HPMP 2- and PME 2- revealed that for most M(HPMPA) complexes the enhanced stability (the enhancement relative to the stability of a simple phosphonate‐M 2+ coordination), can solely be explained by the formation of 5‐membered chelates involving the ether oxygen. These chelates occur in equilibrium with simple ′open′ phosphonate‐M 2+ species, the phosphonate group being the primary binding site. The only exceptions are the M(HPMPA) complexes of Ni 2+ , Cu 2+ , and Zn 2+ , which show an additional stability enhancement; in these instances not only the indicated 5‐membered chelates are formed, but M 2+ coordinates in addition to N3 of the adenine residue forming a 7‐membered chelate ring. This observation regarding N3 is important because it emphasizes the metal ion affinity of this site (which is often ignored). Note that in the DNA double helix N3 is exposed to the solvent in the minor groove. The stability data for the monoprotonated M(H;HPMPA) + complexes suggest that these carry H + at the phosphonate group whereas M 2+ is partly at the nucleobase and partly also at the phosphonate group. The ratios of these isomers depend on the metal ion involved, e.g., for Cu(H;HPMPA) the ratio of the isomers is about 1:1

Metal Ion Complexes of Nuceloside Phosphorothioates Reflecting the Ambivalent Properties of Lead (II)

This Perspective outlines the coordinating properties of lead( II ), to some extent in comparison with related metal ions like Ca 2+ , Zn 2+ or Cd 2+ . It is worth noting that the affinity of Pb 2+ towards phosphate residues corresponds to that of Cu 2+ . Furthermore, the binding tendency of Pb 2+ towards thiophosphate groups as present in methyl thiophosphate (MeOPS 2− ) or uridine 5′- O -thiomonophosphate (UMPS 2− ) is compared with that of the parent ligands, that is, methyl phosphate (CH 3 OPO 3 2− ) and uridine 5′-monophosphate (UMP 2− ). The replacement of an O by a S atom makes the monoprotonated thiophosphate group considerably more acidic [compared to ROP(O) 2 − (OH)], but at the same time its affinity for Pb 2+ increases tremendously: more than 99% of Pb 2+ is S-bound. This is very different if the coordinating properties of uridylyl-(5′→3′)-[5′]-uridylate (pUpU 3− ) and P -thiouridylyl-(5′→3′)-[5′]-uridylate (pUp (S) U 3− ) are compared. The phosphate-coordinated Pb 2+ forms a 10-membered chelate with one of the two terminal O atoms of the phosphodiester linkage, which reaches a formation degree of about 90% in Pb(pUpU) − . However, in Pb(pUp (S) U) − the formation degree of the chelate is reduced to about half in accordance with the fact that now only one terminal O atom is available in the thiophosphate diester bridge, that is, Pb 2+ coordinates to this O showing no affinity for S in ROP(O)(S) − OR′. These observations are ascribed to the properties of the Pb 2+ lone pair, which shapes the Pb 2+ coordination sphere; its role is discussed further in this Perspective and a caveat is made regarding Pb 2+ binding to a thiophosphate diester linkage

Extent of the Acidification by N7-Coordinated cis-Diammine-Platinum(II) on the Acidic Sites of Guanine Derivatives

Coordination of two monoprotonated 2'-deoxyguanosine 5'-monophosphate species, H(dGMP)−, via N7 to cis-(NH2)2Pt2+ gives the complex cis-(NH2)2Pt(H·dGMP)2 which is a four-protonic acid. The corresponding acidity constants were measured by potentiometric pH titrations (25℃; I = 0.1 M, NaNO3). The first two protons are released from the two -P(O)2(OH)− groups (PKa/1= 5.57; PKa/2 = 6.29) and the next two protons are from the H(N1) sites of the guanine residues (PKa/3 = 8.73; PKa/4 = 9.48). The micro acidity constants of the various sites are also evaluated. Comparison of these data with those determined for the three-protonic H2(dGMP)± (PKa/1 = 2.69 for the H+(N7) site; PKa/2 = 6.29 for -P(O)2(OH)− ;PKa/3 = 9.56 for H(N1)) shows that on average the N-7-coordinated Pt2+ acidifies the phosphate protons by Δ pKa = 0.36 and the H(N1) sites by Δ pKa = 0.46. These results are further compared with those obtained previously for cis-(NH2)2Pt(L)2, where L = 9-ethylguanine or monoprotonated 2'-deoxycytidine 5'-monophosphate. Conclusions regarding platinated DNA are also presented