Competitive formation of DNA linkage isomers by a trinuclear platinum complex and the influence of pre-association

Abstract

2D [1H, 15N] HSQC NMR spectroscopy has been used to monitor the reaction of fully 15N-labelled [{trans-PtCl(NH3)2}2(μ-trans-Pt(NH3)2 {NH2(CH2)6NH2}2)]4+ (BBR3464 (15N-1)) with the 14-mer duplex (5’-{d(ATACATG(7)G(8)TACATA)}-3’. 5’-{d(TATG(18)TACCATG(25)TAT)}-3’ or I) at pH 5.4 and 298 K, to examine the possible formation of 1,4 and 1,5-GG adducts in both 5′ –5′ and 3′ –3′ directions. In a previous study, the binding of the dinuclear 1,1/t,t to I showed specific formation of the 5′ –5′ 1,4 G(8)G(18) cross-link, whereas in this case a mixture of adducts were formed. Initial 1H NMR spectra suggested the presence of two pre-associated states aligned in both directions along the DNA. The pre-association was studied in the absence of covalent binding, by use of the “non-covalent” analog [{trans-Pt(NH3)3}2(μ-trans-Pt(NH3)2 {NH2(CH2)6NH2}2)]6+ (AH44, 0). Chemical shift changes of DNA protons combined with NOE connectivities between CH2 and NH3 protons of 0 and the adenine H2 protons on I show that that two different molecules of 0 are bound in the minor groove. Molecular dynamic simulations were performed to study the interaction of 0 at the two pre-association sites using charges derived from density functional theory (DFT) calculations. Structures where the central platinum is located in the minor groove and the aliphatic linkers extend into the major groove, in opposite directions, often represent the lowest energy structures of the snapshots selected. In the reaction of 15N-1 and I, following the pre-association step, aquation occurs to give the mono aqua monochloro species 2, with a rate constant of 3.43 ± 0.03 × 10−5s−1. There was evidence for two monofunctional adducts (3, 4) bound to the 3′ (G8) and 5′ (G7) residues and the asymmetry of the 1H,15N peak for 3 suggested two conformers of the 3′ adduct, aligned in different directions along the DNA. The rate constant for combined monofunctional adduct formation (0.6 ± 0.1 M−1) is ca. 2-fold lower for 1 compared to 1,1/t,t, whereas the rate constant for conversion of the combined monofunctional species to combined bifunctional adducts (5) (8.0 ± 0.2 × 10−5s−1) is two-fold higher.

Molecular methods for assessment of non-covalent metallodrug–DNA interactions

“…The initial orientation of BBR3464 on DNA mediated by electrostatic interactions transiently engaging with phosphate groups in the minor groove is an important feature which dictates not only isomer directionality but also the final conformation of covalently-bound interstrand crosslinks (1,4 versus 1,6) because in some cases the covalent adduct can be formed directly but in others, diffusion off the DNA is necessary for covalent binding to occur. These subtleties can be followed by 2D { 1 H, 15 N} HSQC NMR 30,31…”

Probing Disaccharide Binding to Triplatin as Models for Tumor Cell Heparan Sulfate (GAG) Interactions

“…The energy of interaction showed that the interaction SI-PPC···1HPN is thermodynamically favorable, expressing negative mean of Gibbs’ free energy values along the simulated trajectory. Upon initial molecular recognition, the next step in the reaction will be monofunctional binding of one Pt unit to the biomolecule, as seen for the binding of triplatin to DNA. , The molecular dynamics (MD) simulations of compounds I - 3 , II-3x , and II-3y were therefore performed, where these are monofunctional carboxylate bound adducts of triplatin with the two disaccharides. For II , both 1 C 4 ( x ) and 2 S 0 ( y ) ring conformations for the IdoA­(2S) residue were modeled, noting that for the 1:1 triplatinNC/FPX adduct, the conformational ratio of the 1 C 4 / 2 S 0 forms of the FPX residue IdoA­(2S) is altered from ca.…”

Solution studies on DNA interactions of substitution-inert platinum complexes mediated via the phosphate clamp

“…The results were consistent with those found for 15 N-BBR3464. 6,20 Upon addition of the dodecamers a downfield shift of 0.07-0.13 ppm for both peaks is observed in the proton dimension at pH 7, Table 1. The fact that the protons of the Pt-15 NH 3 as well as the Pt-15 NH 2 CH 2units are affected to the same extent indicates that both groups are equally involved in the binding process.…”