Cisplatin-DNA cross-link retro models with a chirality-neutral carrier ligand: evidence for the importance of "second-sphere communication"

We employ retro models, cis-PtA2G2 (A2 = a diamine, G = guanine derivative), to assess the cross-linked head-to-head (HH) form of the cisplatin-DNA d(GpG) adduct widely postulated to be responsible for the anticancer activity. Retro models are designed to have minimal dynamic motion to overcome problems recognized in models derived from cisplatin [A2 = (NH3)2]; the latter models are difficult to understand due to rapid rotation of G bases about the Pt-N7 bond in solution and the dominance of the head-to-tail (HT) form in the solid. Observation of an HH form is unusual for cis-PtA2G2 models. Recently, we found the first HH forms for a cis-PtA2G2 model with A2 lacking NH groups in a study of new Me2ppzPtG2 models. (Me2ppz, N,N'-dimethylpiperazine, has inplane bulk which reduces dynamic motion by clashing with the G O6 as the base rotates into the coordination plane from the ground state position approximately perpendicular to this plane G = 5'-GMP and 3'-GMP.) The finding of an HH form (albeit in a mixture with HT forms) with both G H8 signals unusually downfield encouraged us to study additional Me2ppzPtG2 analogues in order to explain the unusual spectral features and to identify factors that influence the relative stability of HT and HH forms. Molecular modeling techniques suggest HH structures with the H8's close to the deshielding region of the z axis of the magnetically anisotropic Pt atom, explaining the atypical shift pattern. When G = 1-Me-5'-GMP, we obtained NMR evidence that the HH rotamer has a high abundance (34%) and that the three rotamers have nearly equal abundance. These findings and the observation that the relative HT distributions varied little or not at all as a function of pH when G = Guo, 1-MeGuo, or 1-Me-5'-GMP are consistent with two of our earlier proposals concerning phosphate groups in HT forms of cis-PtA2(GMP)2 complexes. We proposed that a G phosphate group can form hydrogen bonds with the cis G N1H ("second-sphere" communication) and (for 5'-phosphate) A2 NH groups. The new results with 1-Me-5'-GMP led us to propose a new role for a 5'-phosphate group; it can also favor the HH form by counteracting the natural preference for the G bases to adopt an HT orientation. Finally, the HH form was also sufficiently abundant to allow observation of a distinct 195Pt NMR signal (downfield of the resonance observed for the HT forms) for several complexes. This is the first report of an HH 195Pt NMR signal for cis-PtA2G2 complexes.     

Mass spectral identification and positional mapping of aflatoxin B1—Guanine adducts in oligonucleotides

The biological consequences of a carcinogen—DNA adduct are defined by the structure of the lesion and its position within the genome. Electrospray ionization ion trap mass spectrometry (ESI-ITMS) is shown here to be a sensitive and rapid approach capable of defining both of these parameters. Three isomeric oligonucleotides of the sequence 5′-CCGGAGGCC modified by the potent human carcinogen aflatoxin B₁ (AFB₁) at different guanines were analyzed by ESI-ITMS. All three samples possessed the same molecular ion confirming the presence of an intact aflatoxin moiety in each oligonucleotide. In addition, each sample displayed a characteristic fragmentation pattern that permitted unambiguous identification of the site of modification within the sequence. Furthermore, an AFB₁-modified oligonucleotide was converted under alkaline conditions to its more stable formamidopyrimidine (FAPY) derivative. Analysis of this sample revealed the presence of a molecular ion corresponding to the presence of the FAPY adduct and a distinctive fragmentation pattern that paralleled the known chemical stability of the FAPY metabolite. This approach should be of general use in the determination of not only the nature and site of covalent modifications, but also the chemical stability of DNA adducts.     

Factors influencing conformer equilibria in retro models of cisplatin-DNA adducts as revealed by moderately dynamic (N,N'-dimethyl-2,3-diaminobutane)PtG(2) retro models (G = a guanine derivative)

Typical cis-PtA(2)G(2) models of key DNA lesions formed by cis-type Pt anticancer drugs are very dynamic and difficult to characterize (A(2) = diamine or two amines; G = guanine derivative). Retro models have A(2) carrier ligands designed to decrease dynamic motion without eliminating any of three possible conformers with bases oriented head-to-tail (two: DeltaHT and LambdaHT) or head-to-head (one: HH). All three were found in NMR studies of eight Me(2)DABPtG(2) retro models (Me(2)DAB = N,N'-dimethyl-2,3-diaminobutane with S,R,R,S and R,S,S,R configurations at the chelate ring N, C, C, and N atoms, respectively; G = 5'-GMP, 3'-GMP, 5'-IMP, and 3'-IMP). The bases cant to the left (L) in (S,R,R,S)-Me(2)DABPtG(2) adducts and to the right (R) in (R,S,S,R)-Me(2)DABPtG(2) adducts. Relative to the case in which the bases are both not canted, canting will move the six-membered rings closer in to each other ("6-in" form) or farther out from each other ("6-out" form). Interligand interactions between ligand components near to Pt (first-first sphere communication = FFC) or far from Pt (second-sphere communication = SSC) influence stability. In typical cases at pH < 8, the "6-in" form is favored, although the larger six-membered rings of the bases are close. In minor "6-out" HT forms, the proximity of the smaller five-membered rings could be sterically favorable. Also, G O6 is closer to the sterically less demanding NH part of the Me(2)DAB ligand, possibly allowing G O6-NH hydrogen bonding. These favorable FFC effects do not fully compensate for possibly stronger FFC dipole effects in the "6-in" form. SSC, phosphate-N1H cis G interactions favor LambdaHT forms in 5'-GMP and 5'-IMP complexes and DeltaHT forms in 3'-GMP and 3'-IMP complexes. When SSC and FFC favor the same HT conformer, it is present at >90% abundance. In six adducts [four (S,R,R,S)-Me(2)DABPtG(2) and (R,S,S,R)-Me(2)DABPtG(2) (G = 3'-GMP and 3'-IMP)], the minor "6-out" HT form at pH approximately 7 becomes the major form at pH approximately 10, where G N1H is deprotonated, because the large distance between the negatively charged N1 atoms minimizes electrostatic repulsion and probably because the G O6-(NH)Me(2)DAB H-bond (FFC) is strengthened by N1H deprotonation. At pH approximately 10, phosphate-negative N1 repulsion is an unfavorable SSC term. This factor disfavors the LambdaHT R form of two (R,S,S,R)-Me(2)DABPtG(2) (G = 5'-GMP and 5'-IMP) adducts to such an extent that the "6-in" DeltaHT R form remains the dominant form even at pH approximately 10.     

Observation of an Unusual Molecular Switching Device. The Position of One 1,2-Dimethylimidazole Switched "On" or "Off" the Rotation of the Other 1,2-Dimethylimidazole in cis,cis,cis-Ru(II)Cl(2)(Me(2)SO)(2)(1,2-dimethylimidazole)(2)

Some cis,cis,cis-RuX(2)(Me(2)SO)(2)(1,2-Me(2)Im)L complexes [L = 1,2-Me(2)Im (1,2-dimethylimidazole) or Me(3)Bzm (1,5,6-trimethylbenzimidazole), X = Cl or Br, and Me(2)SO = S-bonded DMSO] have been synthesized and their rotamers studied in CDCl(3). From 2D NMR data, cis,cis,cis-RuCl(2)(Me(2)SO)(2)(1,2-Me(2)Im)(Me(3)Bzm) has 1,2-Me(2)Im in position "a" (cis to both Me(2)SO's and cis to "b") and Me(3)Bzm in position "b" (trans to one Me(2)SO and cis to the other). There are two stable atropisomers [head-to-tail (HT, 84%) and head-to-head (HH, 16%), defining the aromatic H of Ru-N-C-H as head for both ligands]. Me(3)Bzm has the same orientation in both atropisomers. In this orientation, the unfavorable interligand steric interactions of Me(3)Bzm with the Me(2)SO and 1,2-Me(2)Im ligands appear to be countered by favorable electrostatic attraction between the delta+ N(2)CH moiety of Me(3)Bzm and the delta- cis Cl ligands. The 1,2-Me(2)Im lacks a delta+ N(2)CH group, and its orientation is dominated by steric effects of the 2-Me group. The NMR spectrum of cis,cis,cis-RuCl(2)(Me(2)SO)(2)(1,2-Me(2)Im)(2) is consistent with four rotamers in restricted rotation about both Ru-N bonds: two HH and two HT. 2D NMR techniques (NOESY and ROESY) afforded complete proton signal assignments. The ligand disposition could be assessed from the large chemical shift dispersion of some 1,2-Me(2)Im ligand signals (Delta 0.86-1.52 ppm) arising from cis-1,2-Me(2)Im shielding modulated by deshielding influences of the cis halides. The relative stability of the four rotamers correlates best with steric interactions between the 2-Me groups and the Me(2)SO ligands. The most favorable conformer (46%) is the HH rotamer with both 2-Me groups pointing away from the Me(2)SO ligands. The least favorable conformer (14%) was also HH, but the methyl groups in this case point toward the Me(2)SO ligands. In the HT conformers of intermediate stability ( approximately 20%), one 2-Me group is toward and the other is away from the Me(2)SO ligands. The exchange cross-peaks in the 2D spectra are unusually informative about the dynamic processes in solution; the spectra provide evidence that the rotamers interchange in a definite pattern of succession. Thus, all conceivable exchange pathways are not available. 1,2-Me(2)Im "b" can rotate regardless of the orientation of 1,2-Me(2)Im "a". 1,2-Me(2)Im "a" can rotate only when "b" has the orientation with its 2-Me group directed away from "a". Thus, 1,2-Me(2)Im "b" can switch 1,2-Me(2)Im "a" rotation on or off.     

Synthesis of periphery-functionalized dendritic molecules using polylithiated dendrimers as starting material

A general method for the functionalization of Si-Cl terminated carbosilane dendritic molecules via organolithium or organomagnesium reagents is described. Quantitative exchange of the bromine atoms of 4-bromophenyl-functionalized dendrimers affords polylithiated species that are valuable starting materials for further functionalization, e.g., into pyridyl alcohols. The latter were successfully applied as catalyst precursors in a ruthenium-mediated ring-closure metathesis reaction.     

Dramatic 5'-residue effect on conformer distribution of short oligonucleotide retro models of the cisplatin-DNA cross-link: implications for the Lippard and cross-link distorted base pair steps present in cisplatin-DNA duplex adducts

The cisplatin anticancer drug preferentially attacks the GG sequence of DNA duplexes. Virtually all DNAs containing the key G*G* lesion (G* = N7 platinated G) have large distortions in the cross-link (G*G*) base pair (bp) step and also in the adjacent Lippard (XG*) bp step, making the adducts very different from B-form DNA in the XG*G* region. The XG*G* strand in duplexes also differs in several ways from single-strand (ss) models with G*G* and XG*G* sequences. In the duplex, the X residue has an N sugar, the 5'-G* and 3'-G* bases have slight "R" canting (3'-G* H8 atom toward the 5'-G* base), and there is no or weak H-bonding by the NH3 ligands. In most XG*G* ss models, X has an S sugar, the 5'-G* base normally cants strongly toward the 3'-G* base (L canting), and the NH3 forms an H-bond. Well-defined ss models exist in the solid state, but dynamic motion obscures the properties of the ss models in solution. In this work, we employ retro models (better defined, less dynamic ss models) to understand the differences between duplex and ss models. The retro models in this study lack carrier ligand NH's, thus eliminating H-bonding. To correlate previous ss solid-state models with our solution work, we constructed hybrid molecules by overlaying parts of known structures. The combined model and experimental information indicates that the X N-pucker is not favorable in L-canted ss models, that X residue steric effects (not H-bonding) favor L canting in ss models, that X N-pucker is needed for favorable WC hydrogen bonding and stacking interactions in duplexes, and that X N-pucker minimizes X base clashes with bases in the complementary strand in duplexes. The R canting minimizing clashes between the X and G* residues of the Lippard bp step (independent of X pucker) and the repositioning of the X residue base caused by the change from S-pucker to N-pucker together lead to the unusual features of the Lippard bp step in the duplex.     

Synthesis and Characterization of Rhenium(V) Oxo Complexes with a New Thiol-Amide-Thiourea Ligand System. X-ray Crystal Structure of [1-Phenyl-3-[2-((2-thioacetyl)amino)ethyl]thioureato]oxorhenium(V)

General methods for preparing Re(V)O complexes with a novel series of thiol-amide-thiourea (TATU) ligands, a new class of N(2)S(2) chelates, were developed. The TATU ligands, the first multidentate systems designed with a bidentate thiourea moiety, have been used to prepare the first high-valent transition metal complexes with bidentate thiourea coordination. Direct reaction of N-(2-aminoethyl)-2-((triphenylmethyl)thio)acetamide (1) with phenyl, 4-methoxyphenyl, 4-chlorophenyl, and methyl isothiocyanate afforded ready access to the corresponding S-protected TATU ligands in one step. A two-step preparation of the N,N-dimethylthiourea TATU ligand derived from 1 was also developed. Deprotection of thiols in trifluoroacetic acid with triethylsilane followed by a ligand exchange reaction with Re(V)O precursors yielded neutral ReO(TATU) complexes. The structure of [1-phenyl-3-[2-((2-thioacetyl)amino)ethyl]thioureato]oxorhenium(V) (6a) was determined by X-ray diffraction methods. Crystal data for 6a: C(11)H(12)N(3)O(2)ReS(2), fw 468.6, orthorhombic, Pca2(1); a = 22.605(5) ?, b = 13.029(3) ?, c= 9.698(2) ?; V = 2856.3(11) ?(3); Z = 8. The coordination environment of 6a was pseudo-square-pyramidal with a deprotonated thiol S, deprotonated amide N, deprotonated thiourea N, and thiocarbonyl S coordinated in the basal plane and the oxo ligand in the apical position. The thiourea function forms a four-membered chelate ring in the multidentate TATU ligands. The two N-C and the S-C bond distances within the monodeprotonated thiourea moiety were typical of bonds with multiple-bond character. Solution (1)H NMR data for all five complexes were consistent with the solid-state structure of 6a. A broad singlet attributable to the uncoordinated NH group of thiourea was observed for the monosubstituted thiourea complexes but was not present for the N,N-dimethylthiourea derivative. Instead, two singlets of equal intensity were observed for the two methyl groups, indicating that there is restricted rotation around the C-N(CH(3))(2) bond and an extended pi system in the thiourea moiety. The four-membered ring might cause difficulty because the M-S distance would be relatively long in an undistorted ligand. This may be the reason such chelate ligands have not been previously investigated. However, the N-C-S angle narrows to approximately 105 degrees, permitting a Re-S bond with a typical bond length to be formed. We conclude that such a ring represents a versatile new building block to create multidentate ligands.