Pyrazolylborate-Zinc Complexes of RNA Precursors and Analogues Thereof

Theoretical and Experimental Vibrational Characterization of Biologically Active Nd(III) Complex

The neodymium(III) complex of orotic acid (HOA) was synthesized and its structure determined by means of analytical and spectral analyses. Detailed vibrational analysis of HOA, sodium salt of HOA, and Nd(III)–OA systems based on both the calculated and experimental spectra confirmed the suggested metal–ligand binding mode. Significant differences in the IR and Raman spectra of the complex were observed as compared to the spectra of the ligand. The calculated vibrational wavenumbers, including IR intensities and Raman scattering activities, for the ligand and its Nd(III) complex were in good agreement with the experimental data. The vibrational analysis performed for the studied species, orotic acid, sodium salt of orotic acid, and its Nd(III) complex helped to explain the vibrational behaviour of the ligand’s vibrational modes, sensitive to interaction with Nd(III). In this paper we also report preliminary results about the cytotoxicity of the investigated compounds. The cytotoxic effects of the ligand and its Nd(III) complex were determined using the MTT method on different tumour cell lines. The screening performed revealed that the tested compounds exerted cytotoxic activity upon the evaluated cell lines.

Mixed-Metal (Platinum, Palladium), Mixed-Pyrimidine (Uracil, Cytosine) Self-Assembling Metallacalix[n]arenes: Dynamic Combinatorial Chemistry with Nucleobases and Metal Species

Reactions between the mononuclear mixed-nucleobase complex [Pt(en)(UH-N1)(CH2-N3)]+ (1; en: ethylenediamine; UH-N1: uracil monoanion bonded through the N1 atom; CH2-N3: neutral cytosine bonded through the N3 atom) and [Pd(II)(en)] or [Pd(II)(2,2'-bpy)] (2,2'-bpy: 2,2'-bipyridine) lead to libraries of compounds of different stoichiometries and different connectivities. In these compounds, the palladium entity binds to or cross-links either the N3 sites of uracil and/or the N1 sites of cytosine, following deprotonation of these positions to give uracil dianions (U) and cytosine monoanions (CH). Cyclic species, which can be considered as metallacalix[n]arenes, have been detected in several cases, with n being 4 and 8. The complexity of the compounds formed not only results from the possibility of the two different nucleobases in building block 1 engaging in different connectivities with the Pd entities, but also from the potential for the formation of oligomers of different sizes and different conformations; in the case of cyclic tetranuclear Pt(2)Pd(2) species, this can, in principle, lead to the various arrangements (cone, partial cone, 1,2-alternate, 1,3-alternate) known from calix[4]arene chemistry. A further complication arises from the fact that, depending on the mutual orientation of the exocyclic groups of the two nucleobases (O2 and O4 of uracil, O2 and N4 of cytosine), these sites can be engaged in additional chelation of [Pd(II)(en)] and [Pd(II)(2,2'-bpy)]. Thus, penta-, hexa-, and octanuclear complexes, Pt(2)Pd(3), Pt(2)Pd(4), and Pt(2)Pd(6), derived from cyclic Pt(2)Pd(2) tetramers have been isolated and characterized.

Modeling Zinc Enzyme Inhibition with Functional Thiolate Ligands

The blocking of zinc enzymes by thiolate-containing inhibitors was modeled by treating TpPh,MeZn-OH with functional thiols. The latter were chosen such that they contain an additional donor function (COOH, COOR, NH2, NHR, OH) in a position favorable for chelation. Of them, mercapto carboxylic acid esters were incorporated as thiolates. The corresponding mercapto carboxylic acids, however, used only their carboxylate function for coordination. Various mercapto amines, mercapto alcohols, and mercaptophenol were exclusively converted to thiolate ligands. The two modes of inhibitor attachment, terminal or chelating, were observed equally frequently. As a rule, they occur as alternatives for similar ligands. In case of 2-mercaptophenol they coexist in the crystalline state and in solution. Hydrogen bonding, both intra- and intermolecular, seems to be a decisive factor determining the inhibitor attachments. Its persistence in solution is underlined by the observation that TpPh,MeZn-hydroxythiophenolates are methylated about 2 orders of magnitude slower than TpPh,MeZn-SPh itself.

Pyrazolylborate−Zinc Alkoxide Complexes. 3. Acid−Base Reactions

The alkoxides TpPh,MeZn-OR (R = Me, Et, i-Pr) undergo acid-base reactions with all hydrogen compounds whose acidity is higher than that of the corresponding alcohol ROH. Thus, anion exchange occurs with the common acids acetic acid, acetohydroxamic acid, acetylacetone, phenol, and ethylmercaptan. Alkoxide exchange is observed using methanol, ethanol, and trifluoroethanol. With the NH acids cyanamide, trifluoroacetamide, and pyrazoles, the corresponding anions are attached to zinc, and likewise beta- and gamma-lactams, a thiazolidinedione, and the cyclic sulfimide saccharin are deprotonated. Of the CH acids acetonitrile forms the Tp*Zn-cyanomethanide. Acetone is deprotonated by the cyanomethanide complex and incorporated as the Tp*Zn-beta-ketoiminate.

Recruitment of divalent metal ions by incorporation of 4-thio-2'-deoxythymidine or 4-thio-2'-deoxyuridine into DNA

The modified nucleosides 4-thio-2'-deoxyuridine (s4dU) and 4-thio-2'-deoxythymidine (s4dT) are incorporated into dinucleosides, and s4dT is incorporated into a DNA hairpin loop to provide divalent metal ion binding sites. Binding of two different metal ions to these sites is studied, including Cd(II) as an NMR spectroscopy probe and Cu(II) as a reactive metal ion for DNA cleavage. Binding of Cd(II) to 4-thiouridine (s4U) and s4dT nucleosides, s4dU- and s4dT-containing dinucleosides, and a hairpin loop oligonucleotide containing s4dT is monitored by following the change in UV-vis absorbance of the thionucleosides at 340 nm and 21 degrees C in solutions containing 20.0-40 mM buffer, 1.00 M NaCl, and 15.0 mM BaCl2. Cd(II) binds to the N3 deprotonated form of s4dT with a binding constant (K = 1.1 x 10(4) M(-1)) that is similar to that for Cd(II) binding to d(Tps4T) (K = 9.2 x 10(3) M(-1)). Apparent binding constants (Kapp) at pH 7.7 of Cd(II) to dinucleosides d(Gps4T), d(s4TpG), and d(Gps4U) are similar to those of their respective nucleosides s4U and s4dT, suggesting that neither the phosphate diester nor the second nucleoside has a major effect on Cd(II) binding. Binding of Cd(II) to s4U and d(Gps4U) is studied by use of 113Cd NMR and 1H NMR spectroscopy, respectively. Binding strength and stoichiometry of the Cd(II) complex with d(Gps4U) as studied by 1H NMR spectroscopy are similar to that obtained by UV-vis spectroscopy. Cd(II) binds strongly to s4dT in the loop portion of a DNA hairpin loop (Kapp = 2.7 x 10(3) M(-1) at pH 7.7). However, the hairpin loop is moderately destabilized by Cd(II) binding, with a decrease in T(m) of 14 degrees C in the presence of 10.0 mM Cd(II) as determined by optical melting experiments. Cu(II) oxidizes s4dT to form the disulfide of s4dT, limiting the usefulness of further studies with Cu(II).

Uracilato and 5-halouracilato complexes of Cu(II), Zn(II) and Ni(II). X-ray structures of [Cu(uracilato-N1)2(NH3)2]·2(H2O), [Cu(5-chlorouracilato-N1)2(NH3)2](H2O)2, [Ni(5-chlorouracilato-N1)2(en)2]·2H2O and [Zn(5-chlorouracilato-N1)(NH3)3]·(5-chlorouracilato-N1)·(H2O)

Four new complexes of uracilato and 5-halouracilato with the divalent metal ions Cu(II), Zn(II) and Ni(II) were obtained and structurally characterized. [Cu(uracilato- N(1))(2)(NH(3))(2)].2(H(2)O) (1) and [Cu(5-chlorouracilato-N(1))(2)(NH(3))(2)](H(2)O)(2) (2) complexes present distorted square planar co-ordination geometry around the metal ion. Although an additional axial water molecule is present [Cu(II)-OH(2)=2.89 A (for 1) and 2.52 A (for 2)] in both cases, only in the complex 2 would be considered in the limit of a bond distance. The Zn(II) in [Zn(5-chlorouracilato-N(1))(NH(3))(3)].(5-chlorouracilato-N(1)).(H(2)O) presents a tetrahedral co-ordination with three ammonia molecules and the N(1) of the corresponding uracilato moiety. A non-coordinated uracilato molecule is present as a counterion and a recognition between co-ordinated and free ligands, by means a tandem of H-bonds, should be mentioned. Finally, the complex [Ni(5-chlorouracilato-N(1))(2)(en)(2)] (H(2)O)(2) (where en is ethylenediamine) presents a typical octahedral trans co-ordination with additional hydrogen bonds between 5-chlorouracilato and the NH(2) groups of ethylenediamine units.

Pyrazolylborate-zinc-nucleobase-complexes, 2:(1) preparations and structures of Tp(Cum,Me)Zn and Tp(Ph,Me)Zn complexes

The interactions of the nine most significant nucleobases (thymine, uracil, dihydrouracil, cytosine, adenine, guanine, diaminopurine, xanthine, hypoxanthine, in their deprotonated forms) with zinc and with themselves in pyrazolylborate zinc complexes Tp(Cum,Me)Zn-base and Tp(Ph,Me)Zn-base are described. Except for guanine, the complexes Tp*Zn-base could be isolated in all cases. Structure determinations could be performed for seven of the eight product types. Except for dihydrouracil and xanthine, the zinc ion is attached to that nitrogen of the base which in nucleosides bears the sugar moiety. In the solid state, all zinc-bound nucleobases are involved in hydrogen bonding interactions. Except for xanthine, this includes homo base pairing across a crystallographic inversion center.

Pyrazolylborate-zinc-nucleobase-complexes, 3:(1) base pairing studies

In solution, the pyrazolylborate-zinc-nucleobase complexes show self-association and base pairing with external nucleobases. The self-association was studied quantitatively for Tp(Cum,Me)Zn-hypoxanthinate and Tp(Cum,Me)Zn-thyminate; the dimerization constants K(D) are 63 +/- 8 and 0.2 +/- 0.1 M(-1), respectively. Of the external nucleobases, 9-ethyladenine forms stable base pairs with the thyminate, uracilate, and xanthinate complexes, 9-isobutylguanine only with the cytosinate complex, 1-methylthymine with the adeninate and diaminopurinate complexes, and 1-methyluracil with the diaminopurinate complex. The association constant for the base pair Tp(Cum,Me)Zn-thyminate:9-ethyladenine was determined by NMR methods as K = 66 +/- 10 M(-1). Structure determinations of the crystalline adducts have confirmed the base pairing for Tp(Cum,Me)Zn-thyminate:9-ethyladenine, Tp(Cum,Me)Zn-cytosinate:9-isobutylguanine, and Tp(Cum,Me)Zn-xanthinate:9-ethyladenine. Both Watson-Crick and Hoogsteen base pairs have been observed. In the solid state, extended base pairing leads to quartet and polymer arrangements.

A sterically hindered N,N,O tripod ligand and its zinc complex chemistry

The new ligand bis(2-picolyl)(2-hydroxy-3,5-di-tert-butylbenzyl)amine (HL) was prepared from bis(2-picolyl)amine and 2,4-di-tert-butyl-6-(chloromethyl)phenol. It acts as a tetradentate N,N,O tripod ligand ensuring 5-fold coordination in all its zinc complexes L.Zn-X. The central complex of the series was [L.Zn(OH(2))]ClO(4) (1) obtained from zinc perchlorate. Together with the more labile complex L.Zn-C(2)H(5) (2), obtained from diethyl zinc, it was used as a starting material for ligand substitutions. In the presence of bases, 1 was converted to L.Zn-OH (3), [L.Zn(py)]ClO(4) (4), and [(L.Zn)(3)(mu(3)-CO(3))]ClO(4) (5). Metathetical reactions produced the neutral complexes L.Zn-X with X = Br (6), OAc (7), OC(6)H(5) (8), SC(6)H(5) (9), OP(O)(OPh)(2) (10), p-nitrophenolate (11), 1-methyluracilate (12), o-formylphenolate (13), and o-hydroxymethylphenolate (14). Structure determinations of 1, 5, 7, 10, 11, 13, and 14 confirmed the strictly monodentate attachment of all units X in L.Zn-X. The hydrolytic cleavage of tris(p-nitrophenyl) phosphate by 1 was investigated preparatively and kinetically. L.Zn-OH was found to be the hydrolytically active nucleophile. The second-order rate constant for the cleavage reaction was found to be slightly lower than the values for related systems, reflecting the steric hindrance in the tert-butyl-substituted ligand L.