A Novel Head-to-Head Conformer of d(GpG) Cross-linked by Pt:  New Light on the Conformation of Such Cross-links Formed by Pt Anticancer Drugs

Abstract

The critical DNA lesion accounting for the anticancer activity of cis-PtCl2(NH3)2 and its analogues [cis-PtX2A2: A2 = a diamine or two amines, X2 = anionic leaving ligand(s)] is an unusual intrastrand cis-Pt(d(GpG))A2 cross-link with Pt linking N7's of adjacent guanines (G). The only known cross-link form with two anti G's, HH1, has head-to-head (HH) bases. We provide NMR, HPLC, and mass spectral evidence for a second, distinct HH cis-Pt(d(GpG))A2 cross-link conformer, HH2, in BipPt(d(GpG)) (Bip = 2,2‘-bipiperidine, where the coordinated Bip has R, S, S, and R configurations at the asymmetric N, C, C, and N chelate ring atoms). The HH1 and HH2 BipPt(d(GpG)) conformers are formed both kinetically and thermodynamically in comparable amounts. The NMR results showed for both BipPt(d(GpG)) conformers that the bases were anti, anti HH, the 5‘-G sugar pucker was N, and the 3‘-G sugar pucker was S. The major difference between the HH1 and HH2 conformers is the propagation direction of the phosphodiester linkage. Molecular modeling calculations with NMR restraints on the HH1 and HH2 conformers indicate comparable energies and no unusual features that should have precluded prediction of the existence of the HH2 conformer. Calculations led to similar conclusions for the cis-Pt(d(GpG))(NH3)2 HH2 conformer. During the two decades of intense interest in this cross-link, this new form has gone unrecognized, although published results have suggested the presence of unknown conformers. Our results in this first report of a second anti, anti HH d(GpG) adduct place an entirely different perspective on the conformational diversity of cis-Pt(d(GpG))(NH3)2 in solution. Although the new HH2 conformation is unlikely to exist in a duplex at low temperature, the new form may be important in mutational events, in duplex breathing, or in duplex interactions with DNA damage recognition proteins and repair enzymes. Finally, the spectral features, especially the H8 NMR signals, of HH1 d(GpG) species in single strands and in duplexes are typically very different, results attributed to differences in both extent and direction of base canting. Bip is an example of a chirality controlling chelate (CCC) ligand that can influence canting. The HH1 conformer of BipPt(d(GpG)) is the first single-stranded species that has key spectral characteristics very similar to those of a typical duplex cross-linked species. Thus, even the HH1 conformer of BipPt(d(GpG)) is an unusual species.

Slowly Exchanging cis‐PtA2B2 Atropisomers with A2 = Chiral Diamine Ligands and B = 5,6‐Dimethylbenzimidazole

“…Assignment of the Δ and Λ conformations to the two HT rotamers and of the HH d and HH u bases in the HH rotamer was derived from the relative positions of the H2 (five-membered ring) and H4 (six-membered ring) protons with respect to the N-Me ax and N-Me eq (quasi-axial and quasi-equatorial N-Me groups of the carrier ligand, respectively) as revealed by the 1 H/ 1 H NOESY spectrum. [24] The latter experiment depends on the assignment of the proton resonances to the axial and equatorial N-Me's of the Me 4 DAB ligand. This assignment was made on the basis of a previous investigation carried out in these laboratories on the (S,S)-Me 4 DABPt(3Ј-GMP) 2 adduct, [23] showing that the equatorial N-Me resonances have 13 2+ are reported in Figure 5 and Figure only for wavelengths above 230 nm, while they are rather different for wavelengths below 230 nm.…”

DNA fragment conformations in adducts with Kiteplatin

“…15,16 All evidence indicates that the HH1 conformer is clearly dominant in cisplatin-(∼GpG∼) intrastrand adducts in which a platinated strand is in a DNA duplex. 11,[17][18][19][20][21][22][23][24][25][26] However, in the simple cis-(NH 3 ) 2 Pt(d(GpG)) model and in cis-(NH 3 ) 2 Pt(ssoligo) models (oligo = oligodeoxyribonucleotide, ss = single strand), the dynamic nature of these adducts complicates the † Electronic supplementary information (ESI) available: Tables S1 and S2: 1 H and 31 P NMR data at different temperatures of (cis-1,4-DACH)Pt(d(TGGT)). NMR spectroscopic analysis.…”

“…[4][5][6][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43][44] Watson-Crick base pairing reduces conformational dynamics in duplexes. [17][18][19][20][21][22][23][24][25][26] In cases in which the intrastrand cross-link clearly has an HH1 conformation, such as in cis-A 2 Pt(d-oligo) adducts (d-oligo = duplexed oligodeoxyribonucleotides; A 2 = two monodentate or one bidentate N donor carrier ligand), the H8 signals of the two Gs are not well separated (δ ∼ 0.3 ppm), with the 3′-G H8 upfield and the 5′-G H8 downfield. The 3′-G base is canted, and the 3′-G H8 is positioned near the anisotropic region of the 5′-G base.…”

“…17,[46][47][48]53,55,59,64 The stereochemistry of the Bip carrier ligand influences both the conformer distribution and the cross-link handedness. For example, ((R,S,S,R)-Bip)Pt(d(GpG)) was shown to have two abundant right-handed conformers (HH1 R, HH2 R), and ((S,R,R,S)-Bip)Pt(d(GpG)) was shown to have two abundant lefthanded conformers (HH1 L, ΔHT1 L).…”

Conformation of 2-Aminomethylpyrrolidine and 2-Aminomethylpiperidine in Ternary Platinum(II) Complexes: Regulation of Conformation of the Diamine by the Coexisting Ligand

“…11) Using NMR spectroscopy, a conformational study of platinum(II) complexes with pipda was undertaken two decades ago 12) and several studies using derivatives of its enantiomeric form have been reported recently in conjunction with the orientations of nucleosides that coordinate as the ligands. [13][14][15][16] For the platinum(II) complex with pyrda, several X-ray studies have also been reported. 17,18) However, the conformations of these diamines in metal complexes in solution and in the crystal state may not be the same.…”