Incorporation of N7-Platinated Guanines into Thermus Aquaticus (Taq) DNA Polymerase: Atomistic Insights from Molecular Dynamics Simulations

In this work, we elucidated some key aspects of the mechanism of action of the cisplatin anticancer drug, cis-[Pt(NH₃)₂Cl₂], involving direct interactions with free nucleotides. A comprehensive in silico molecular modeling analysis was conducted to compare the interactions of Thermus aquaticus (Taq) DNA polymerase with three distinct N7-platinated deoxyguanosine triphosphates: [Pt(dien)(N7-dGTP)] (1), cis-[Pt(NH₃)₂Cl(N7-dGTP)] (2), and cis-[Pt(NH₃)₂(H₂O)(N7-dGTP)] (3) {dien = diethylenetriamine; dGTP = 5'-(2'-deoxy)-guanosine-triphosphate}, using canonical dGTP as a reference, in the presence of DNA. The goal was to elucidate the binding site interactions between Taq DNA polymerase and the tested nucleotide derivatives, providing valuable atomistic insights. Unbiased molecular dynamics simulations (200 ns for each complex) with explicit water molecules were performed on the four ternary complexes, yielding significant findings that contribute to a better understanding of experimental results. The molecular modeling highlighted the crucial role of a specific α-helix (O-helix) within the fingers subdomain, which facilitates the proper geometry for functional contacts between the incoming nucleotide and the DNA template needed for incorporation into the polymerase. The analysis revealed that complex 1 exhibits a much lower affinity for Taq DNA polymerase than complexes 2-3. The affinities of cisplatin metabolites 2-3 for Taq DNA polymerase were found to be quite similar to those of natural dGTP, resulting in a lower incorporation rate for complex 1 compared to complexes 2-3. These findings could have significant implications for the cisplatin mechanism of action, as the high intracellular availability of free nucleobases might promote the competitive incorporation of platinated nucleotides over direct cisplatin attachment to DNA. The study's insights into the incorporation of platinated nucleotides into the Taq DNA polymerase active site suggest that the role of platinated nucleotides in the cisplatin mechanism of action may have been previously underestimated.

Platinum-Nucleos(t)ide Compounds as Possible Antimetabolites for Antitumor/Antiviral Therapy: Properties and Perspectives

Nucleoside analogues (NAs) are a family of compounds which include a variety of purine and pyrimidine derivatives, widely used as anticancer and antiviral agents. For their ability to compete with physiological nucleosides, NAs act as antimetabolites exerting their activity by interfering with the synthesis of nucleic acids. Much progress in the comprehension of their molecular mechanisms has been made, including providing new strategies for potentiating anticancer/antiviral activity. Among these strategies, new platinum-NAs showing a good potential to improve the therapeutic indices of NAs have been synthesized and studied. This short review aims to describe the properties and future perspectives of platinum-NAs, proposing these complexes as a new class of antimetabolites.

C-H Functionalisation for Hydrogen Isotope Exchange

The various applications of hydrogen isotopes (deuterium, D, and tritium, T) in the physical and life sciences demand a range of methods for their installation in an array of molecular architectures. In this Review, we describe recent advances in synthetic C-H functionalisation for hydrogen isotope exchange.

Insertion of terminal alkyne into Pt-N bond of the square planar [PtI2(Me2phen)] complex

The reactivity of [PtX₂(Me₂phen)] complexes (X = Cl, Br, I; Me₂phen = 2,9-dimethyl-1,10-phenanthroline) with terminal alkynes has been investigated. Although the dichlorido species [PtCl₂(Me₂phen)] exhibits negligible reactivity, the bromido and iodido derivatives lead in short time to the formation of five-coordinate Pt(ii) complexes of the type [PtX₂(Me₂phen)(η²-CH[triple bond, length as m-dash]CR)] (X = Br, I; R = Ph, n-Bu), in equilibrium with the starting reagents. Similar to analogous complexes with simple acetylene, the five coordinate species can also undergo dissociation of an halido ligand and formation of the transient square-planar cationic species [PtX(Me₂phen)(η²-CH[triple bond, length as m-dash]CR)]⁺. This latter can further evolve to give an unusual, sparingly soluble square planar product where the former terminal alkyne is converted into a :C[double bond, length as m-dash]C(H)(R) moiety with the α-carbon bridging the Pt(ii) core with one of the two N-donors of coordinated Me₂phen. The final product [PtX₂{κ²-N,C-(Z)-N[combining low line]1-N10-C[combining low line][double bond, length as m-dash]C(H)(R)}] (N1-N10 = 2,9-dimethyl-1,10-phenanthroline; X = Br, I) contains a Pt-N-C-C-N-C six-membered chelate ring in a square planar Pt(ii) coordination environment.

73Ge, 119Sn and 207Pb: general cooperative effects of single atom ligands on the NMR signals observed in tetrahedral [MXnY4-n] (M = Ge, Sn, Pb; 1 ≤ n ≤ 4; X, Y = Cl, Br, I) coordination compounds of heavier XIV group elements

An inverse linear relationship between ⁷³Ge, ¹¹⁹Sn and ²⁰⁷Pb NMR chemical shifts and the overall sum of ionic radii of coordinated halido ligands has been discovered in tetrahedral [MX_nY_4-n] (M = Ge, Sn, Pb; 1 ≤ n ≤ 4; X, Y = Cl, Br, I) coordination compounds. This finding is consistent with a previously reported correlation found in octahedral, pentacoordinate and square planar platinum complexes. The effect of the coordinated halido ligands acting on the metal as shielding conducting rings is therefore confirmed also by ⁷³Ge, ¹¹⁹Sn and ²⁰⁷Pb NMR spectroscopy.

Insertion of alkynes into Pt-X bonds of square planar [PtX2(N^N)] (X = Cl, Br, I) complexes

The reactivity with acetylene of [PtX2(Me2phen)] (X = Cl, Br, I) complexes has been investigated. Whereas the chlorido species [PtCl2(Me2phen)] exhibits negligible reactivity at short reaction times, the bromido and iodido species [PtBr2(Me2phen)] and [PtI2(Me2phen)] lead initially to formation of Pt(II) five-coordinate complexes, [PtX2(η(2)-CH≡CH)(Me2phen)], that evolve to four-coordinate alkenyl complexes of the type [PtX(η(1)-E-CH=CHX)(Me2phen)]. The alkenyl complexes, in the presence of excess acetylene, establish an equilibrium with the five-coordinate alkyne-alkenyl species [PtX(η(1)-E-CH=CHX)(η(2)-CH≡CH)(Me2phen)] (X = Br, I). The π-bonded acetylene can be exchanged with free olefins or C≡O, affording the new alkene-alkenyl or carbonyl-alkenyl complexes [PtX(η(1)-E-CH=CHX)(η(2)-olefin)(Me2phen)] and [PtX(η(1)-E-CH=CHX)(C≡O)(Me2phen)]. The five-coordinate geometry of the alkyne-alkenyl and alkene-alkenyl complexes was assessed from NMR data and is fully consistent with that of a previously determined X-ray structure of [PtBr(η(1)-E-CH[double bond, length as m-dash]CHBr)(η(2)-CH2=CH2)(Me2phen)].

General cooperative effects of single atom ligands on a metal: a195Pt NMR chemical shift as a function of coordinated halido ligands’ ionic radii overall sum

An inverse linear relationship between the experimentally observed¹⁹⁵Pt NMR signals and the overall sum of coordinated halido X ligands’ ionic radii was discovered in Pt(ii) and Pt(iv) complexes.