(N7)-Platination and its effect on (N1)H-acidification in nucleoside phosphate derivatives

Sigel, Astrid; Operschall, Bert P.; Griesser, Rolf; Song, Bin; Okruszek, And̀rzej; Odani, Akira; Katsuta, Tsuguno; Lippert, Bernhard; Sigel, Helmut

doi:10.1016/j.ica.2016.02.048

Cited by 5 publications

(4 citation statements)

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“…[36,44] The pH sensitivity of nucleotides plays vital role for coordination abilities of nucleotides, stability of supramolecular complexes. [37][38][39][40][41][42][43][44][45][46]48] The metal recognition through N-binding sites of monophosphate nucleotide shows different binding sites due to endocyclic nitrogen. The Nitrogen N6 is favourably coordinated with metals ( Mn, Cd, Pt, Ni) at basic pH = 8-9.…”

Section: Resultsmentioning

confidence: 99%

“…The Nitrogen N6 is favourably coordinated with metals ( Mn, Cd, Pt, Ni) at basic pH = 8-9. [37,38,43,41,44,46] 2D layers are produced in complexes by the bridging ligand bpe and solvent molecules through comprehensive π-π interactions and hydrogen bonding in 3D supramolecular frameworks. These interactions occur between the phosphate oxygen atom, organized solvent molecules, purine base (guanine) and ribose sugar hydroxy ( gure 2, S3).…”

Section: Resultsmentioning

confidence: 99%

“…[37,[38][39][40][41] While nitrogen points in GMP nucleotide coordinated with metal in slightly basic conditions. [36,42,43,44,45,46] From above studies it is found that GMP coordination complexes with cadmium metal in crystalline state can be constructed by tuning the pH. The previous studies of nucleotide coordination supramolecular complexes different factors, synthesis methods were studied.…”

Section: Introductionmentioning

confidence: 99%

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PH Controlled the Supramolecular Assemblies of Two Guanosine Monophosphate Cadmium Metal Coordination Complexes: Structure and Chirality

Iqbal

Khan

et al. 2021

Preprint

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In biological systems Chirality is important property from small molecules to macromolecules. The construction of homochiral coordination supramolecules in crystal and helical delivers the connection of molecular and macromolecular chirality. Complexity and properties in the presence of cadmium ion and bpe auxiliary ligand for bio-molecular guanosine-5- monophosphate disodium salt (GMP) was studied. The two Complexes 1 and 2 have been investigated the impact of auxiliary ligand bpe, hydroxy group on the sugar motif and pH for coordination of GMP ligands. The interaction of mixed ligands for growth and advancement of chiral complexes was controlled by the alteration of pH values for coordination of guanosine-5-monophosphate nucleotide with cadmium Cd (II) metal. The chirality of complexes 1 and 2 was studied with solid circular dichroism (CD) spectroscopy, including supramolecular chirality and extended auxiliary ligand (EAC) combining with the crystal structure analysis. The various hydrogen bonding and auxiliary ligand are the special means of transporting chirality from isolated molecules to dynamic supramolecular three-dimensional designs of GMP nucleotide crystals. The research results will be benefit to the controlling supramolecular assembly with well-defined structure and properties.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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PH Controlled the Supramolecular Assemblies of Two Guanosine Monophosphate Cadmium Metal Coordination Complexes: Structure and Chirality

Iqbal

Khan

et al. 2021

Preprint

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“…In the preceding part of this review, we have repeatedly seen that metal ions interact with N7 of a purine residue and affect such the structure and function of DNA and RNA molecules [172]. A simple example is the coordination of Pt(II) to N7, which acidifies the (N1)H + site in nucleoside phosphate derivates [173], though to varying extents bio-metals [174] are expected to have the same effect. However, metal ions bind in RNA and DNA not only to N7 but in rare cases also to N1 or N3-e.g., Mg(II) binds in an innersphere to the N3 position of a guanine residue within an adenine riboswitch aptamer (Mg105 to G6-N3) [175,176].…”

Section: Discussionmentioning

confidence: 98%

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

Sigel

2022

Molecules

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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.

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Merging Metal–Nucleobase Chemistry With Supramolecular Chemistry

Lippert

Miguel

2018

Advances in Inorganic Chemistry

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(N7)-Platination and its effect on (N1)H-acidification in nucleoside phosphate derivatives

Cited by 5 publications

References 103 publications

PH Controlled the Supramolecular Assemblies of Two Guanosine Monophosphate Cadmium Metal Coordination Complexes: Structure and Chirality

PH Controlled the Supramolecular Assemblies of Two Guanosine Monophosphate Cadmium Metal Coordination Complexes: Structure and Chirality

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

Merging Metal–Nucleobase Chemistry With Supramolecular Chemistry

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