{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,11]],"date-time":"2026-10-11T02:29:55Z","timestamp":1791685795430,"version":"4.3.4"},"reference-count":197,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2022,4,19]],"date-time":"2022-04-19T00:00:00Z","timestamp":1650326400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>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\u2014that 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 Among such derivatives are acyclic nucleoside phosphonates (ANPs), where the sugar moiety has been replaced by an aliphatic chain (often also containing an ether oxygen atom) and the phosphate group has been replaced by a phosphonate carrying a carbon\u2013phosphorus bond to make the compounds less hydrolysis-sensitive.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\u2014i.e., polymerases accept the ANPs as substrates, leading to chain termination because of the missing 3\u2032-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\u2212 = adenine(N9)-CH2-CH2-O-CH2-PO32) [or its diphosphate (PMEApp4\u2212)] as a representative of the ANPs. Why is PMEApp4\u2212 a better substrate for polymerases than ATP4\u2212? There are three reasons: (i) PMEA2\u2212 with its anti-like conformation (like AMP2\u2212) 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 P\u03b1 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(\u03b1,\u03b2)-M(\u03b3)-coordinated at a triphosphate chain, transphosphorylation occurs (kinases, etc.), whereas metal ion binding in a M(\u03b1)-M(\u03b2,\u03b3)-type fashion is relevant for polymerases. It may be noted that with diphosphorylated PMEA, (PMEApp4\u2212), the M(\u03b1)-M(\u03b2,\u03b3) 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)\u2212 stacks, which occur in low concentration and where one half of the molecule undergoes the dephosphorylation reaction and the other half stabilizes the structure\u2014i.e., acts as the \u201cenzyme\u201d by bridging the two ATPs. In accord herewith, one may enhance the reaction rate by adding AMP2\u2212 to the [Cu2(ATP)]2(OH)\u2212 solution, as this leads to the formation of mixed stacked Cu3(ATP)(AMP)(OH)\u2212 species, in which AMP2\u2212 takes over the structuring role, while the other \u201chalf\u201d of the molecule undergoes dephosphorylation. It may be added that Cu3(ATP)(PMEA) or better Cu3(ATP)(PMEA)(OH)\u2212 is even a more reactive species than Cu3(ATP)(AMP)(OH)\u2212. \u2013 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\u2212), which leads to the formation of intramolecular stacks in M(ATP)(Trp)3\u2212 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.<\/jats:p>","DOI":"10.3390\/molecules27092625","type":"journal-article","created":{"date-parts":[[2022,4,19]],"date-time":"2022-04-19T22:07:26Z","timestamp":1650406046000},"page":"2625","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Coordination Chemistry of Nucleotides and Antivirally Active Acyclic Nucleoside Phosphonates, including Mechanistic Considerations"],"prefix":"10.3390","volume":"27","author":[{"given":"Astrid","family":"Sigel","sequence":"first","affiliation":[{"name":"Department of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0095-7246","authenticated-orcid":false,"given":"Helmut","family":"Sigel","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1307-7993","authenticated-orcid":false,"given":"Roland K. O.","family":"Sigel","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,4,19]]},"reference":[{"key":"ref_1","first-page":"1","article-title":"Interactions of Metal Ions with Nucleotides, Nucleid Acids, and Their Constituents","volume":"Volume 32","author":"Sigel","year":"1996","journal-title":"Metal Ions in Biological Systems"},{"key":"ref_2","first-page":"1","article-title":"Structural and Catalytic Roles of Metal Ions in RNA","volume":"Volume 9","author":"Sigel","year":"2011","journal-title":"Metal Ions in Life Sciences"},{"key":"ref_3","first-page":"1","article-title":"Interplay Between Metal Ions and Nucleic Acids","volume":"Volume 10","author":"Sigel","year":"2012","journal-title":"Metal Ions in Life Sciences"},{"key":"ref_4","first-page":"91","article-title":"General Conclusions from Solid State Studies of Nucleotide-Metal Ion Complexes","volume":"32","author":"Aoki","year":"1996","journal-title":"Met. 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