Efficient and selective cleavage of RNA oligonucleotides by calix[4]arene-based synthetic metallonucleases

Di- and trinuclear copper(II) complexes of [12]aneN3 macrocycles anchored at the upper rim of cone calix[4]arenes in 1,2-, 1,3-, and 1,2,3-positions were investigated as cleaving agents of 6-, 7-, and 17-meric oligoribonucleotides. A kinetic investigation of the cleavage reactions was carried out using gel electrophoresis to separate and analyze reactants and products having a radioactive phosphate label in the terminal 5'-position. The degree of cooperation was assessed on the basis of a comparison with rates of cleavage by mononuclear controls. A remarkable selectivity of cleavage of the CpA phosphodiester bond was observed for all metal complexes, in sharp contrast with the UpU and UpG selectivity previously observed in the cleavage of diribonucleoside monophosphates by the same metal complexes. The highest rate acceleration, brought about in the cleavage of the 5'-pCpA bond in hexanucleotide 9 by 50 muM trinuclear complex 5-Cu3 (water solution, pH 7.4, 50 degrees C), amounts to 5 x 105-fold, as based on the estimated background reactivity of the CpA dimer. Selectivity in the cleavage of oligoribonucleotides by copper(II) complexes closely resembles that experienced by ribonuclease A and by a number of metal-independent RNase A mimicks. The possible role of the dianionic phosphate at the 5'-terminal positions as a primary anchoring site for the metal catalyst is discussed.     

Di- and trinuclear Zn2+ complexes of calix[4]arene based ligands as catalysts of acyl and phosphoryl transfer reactions

The calix[4]arene scaffold, blocked in the cone conformation by proper alkylation of the lower rim hydroxyls, was used as a convenient molecular platform for the design of bi- and trimetallic Zn2+ catalysts. The catalytic activity of the Zn2+ complexes of calix[4]arenes decorated at the 1,2-, 1,3-, and 1,2,3-positions of the upper rim with 2,6-bis[(dimethylamino)methyl]pyridine units were investigated in the cleavage of ester 6 and of the RNA model compound HPNP. High rate enhancements, up to 4 orders of magnitude, were observed in a number of catalyst-substrate combinations. Interestingly the order of catalytic efficiency among regioisomeric dinuclear complexes in the cleavage of ester 6 is 1,2-vicinal > 1,3-distal, but it is reversed in the reaction of HPNP. The higher efficiency of trinuclear compared to dinuclear complexes provides an indication of the cooperation of three Zn2+ ions in the catalytic mechanism.     

Phosphodiester cleavage of ribonucleoside monophosphates and polyribonucleotides by homo- and heterodinuclear metal complexes of a cyclohexane-based polyamino-polyol ligand

The ability of the dinuclear complexes of tdci [1,3,5-trideoxy-1,3,5-tris(dimethylamino)-cis-inositol] to promote the cleavage of the phosphodiester bonds of nucleoside 2',3'-cyclic monophosphates, dinucleoside monophosphates and polyribonucleotides has been studied. The homodinuclear copper(II) and zinc(II) complexes efficiently promote the hydrolysis of cyclic nucleotides. The second-order rate constant (k(2) approximately 0.44 M(-1) s(-1)) estimated for the cleavage of 2',3'-cAMP induced by dinuclear copper(II) complexes is about 107 times greater than that for the hydroxide-ion-catalysed reaction. The complex selectively cleaves the 2'O-P bond of 2',3'-cUMP and forms the 3'-product in 91 % yield. An equimolar mixture of copper(II), zinc(II) and tdci proved to be more efficient than either of the binary systems: a 7-20-fold rate enhancement was observed for the cleavage of 2',3'-cNMP substrates. The half-life for the hydrolysis of 2',3'-cAMP decreased from 300 days to five minutes at 25 degrees C when the concentration of each of the three components was 2.5 mM. In contrast to the copper(II) or zinc(II) complexes of tdci, the heterodinuclear species promoted the hydrolysis of several dinucleoside monophosphates. For two ApA isomers, cleavage of the 3',5'-bond was about 6.5 times faster than cleavage of the 2',5'-bond. On the basis of the kinetic data, a trifunctional mechanism is suggested for the heterodinuclear-complex-promoted cleavage of the phosphodiester bond. Double Lewis acid activation occurs when the metal ions bind to the phosphate oxygen atoms. In particular, a metal-bound hydroxide ion serves as a general base or a nucleophilic catalyst, and, presumably, a zinc(II)-bound aqua ligand behaves as a general acid and facilitates the departure of the leaving alkoxide group. The effect of the complexes on the hydrolysis of poly(U), poly(A) and type III native RNA was also investigated, and, for the first time, kinetic data on the cleavage of the phosphodiester bonds of polyribonucleotides by a dinuclear complex was obtained.     

Influence of the metal and chiral diamine on metal(II)salen catalysed, asymmetric synthesis of α-methyl α-amino acids

The influence of the metal ion and chiral diamine used to form a metal(salen) complex on the catalytic activity of the complex in the asymmetric benzylation of an alanine enolate was investigated. Only metal ions which could form square-planar complexes gave catalytically active complexes, and best results were obtained with metal ions from the first row of transition metals, particularly copper(II) and cobalt(II). Salen ligands derived from acyclic, chiral 1,2-diamines were found to generate poor catalysts, an effect which seems to correlate with the ability of the substituents within the diamine to adopt a conformation in which they are anti to one another. Complexes derived from a variety of 5- and 6-membered cyclic 1,2-diamines did form active catalysts, but the enantioselectivity was always far lower than that of the parent cyclohexane-1,2-diamine derived complex.     

The Mechanism of Cleavage of RNA Phosphodiesters by a Gold Nanoparticle Nanozyme

The cleavage of uridine 3’-phosphodiesters bearing alcohols with pK_a ranging from 7.14 to 14.5 catalyzed by AuNPs functionalized with 1,4,7-triazacyclononane-Zn(II) complexes has been studied to unravel the source of catalysis by these nanosystems (nanozymes). The results have been compared with those obtained with two Zn(II) dinuclear catalysts for which the mechanism is fairly understood. Binding to the Zn(II) ions by the substrate and the uracil of uridine was observed. The latter leads to inhibition of the process and formation of less productive binding complexes than in the absence of the nucleobase. The nanozyme operates with these substrates mostly via a nucleophilic mechanism with little stabilization of the pentacoordinated phosphorane and moderate assistance in leaving group departure. This is attributed to a decrease of binding strength of the substrate to the catalytic site in reaching the transition state due to an unfavorable binding mode with the uracil. The nanozyme favors substrates with better leaving groups than the less acidic ones.     

Crystal and electronic structures of magnesium(II), copper(II), and mixed magnesium(II)-copper(II) complexes of the quinoline half of styrylquinoline-type HIV-1 integrase inhibitors

A new target in AIDS therapy development is HIV-1 integrase (IN). It was proven that HIV-1 IN required divalent metal cations to achieve phosphodiester bond cleavage of DNA. Accordingly, all newly investigated potent IN inhibitors contain chemical fragments possessing a high ability to chelate metal cations. One of the promising leads in the polyhydroxylated styrylquinolines (SQLs) series is (E)-8-hydroxy-2-[2-(4,5-dihydroxy-3-methoxyphenyl)-ethenyl]-7-quinoline carboxylic acid (1). The present study focuses on the quinoline-based progenitor (2), which is actually the most probable chelating part of SQLs. Conventional and synchrotron low-temperature X-ray crystallographic studies were used to investigate the chelating power of progenitor 2. Mg2+ and Cu2+ cations were selected for this purpose, and three types of metal complexes of 2 were obtained: Mg(II) complex (4), Cu(II) complex (5) and mixed Mg(II)-Cu(II) complexes (6 and 7). The analysis of the crystal structure of complex 4 indicates that two tridentate ligands coordinate two Mg2+ cations, both in octahedral geometry. The Mg-Mg distance was found equal to 3.221(1) A, in agreement with the metal-metal distance of 3.9 A encountered in the crystal structure of Escherichia coli DNA polymerase I. In 5, the complex is formed by two bidentate ligands coordinating one copper ion in tetrahedral geometry. Both mixed Mg(II)-Cu(II) complexes, 6 and 7 exhibit an original arrangement of four ligands linked to a central heterometallic cluster consisting of three octahedrally coordinated magnesium ions and one tetrahedrally coordinated copper ion. Quantum mechanics calculations were also carried out in order to display the electrostatic potential generated by the dianionic ligand 2 and complex 4 and to quantify the binding energy (BE) during the formation of the magnesium complex of progenitor 2. A comparison of the binding energies of two hypothetical monometallic Mg(II) complexes with that found in the bimetallic magnesium complex 4 was made.     

Spectrophotometric determination of traces of metallic ions and their mixtures with 3-methyl-1,2-cyclopentanodione dithiosemicarbazone: II. Bismuth,copper, and cobalt

The properties of bismuth, copper, and cobalt complexes of 3-methyl-1,2-cyclopentanodione dithiosemicarbazone and the optimal conditions for their formation are described. The complexes were used with success in the photometric determination of traces of bismuth, copper, and cobalt. Nine procedures are proposed for the accurate analysis of Bi(III)-Cu(II), Bi(III)-Co(II), Zn(II)-Cu(II), Cd(II)-Cu(II), Hg(II)-Cu(II), Zn(II)-Co(II), Cd(II)-Co(II), Hg(II)-Co(II), and Cu(II)-Co(II) mixtures. Satisfactory results were obtained.     

New palladium(II)-catalyzed asymmetric 1,2-dibromo synthesis

[reaction: see text] The oxidation of olefins by chiral monometallic and bimetallic Pd(II)-Cu(II) catalysts in bromide-containing aqueous-THF reaction mixtures produced chiral 1,2-dibromides. With alpha-olefins, the ee's were about 95% while most of the internal alkenes gave somewhat lower enantioselectivities ( approximately 80%).     

Polymer supported catalysts for oxidation of phenol and cyclohexene using hydrogen peroxide as oxidant

Polymer supported transition metal complexes of N,N′-bis (o-hydroxy acetophenone) hydrazine (HPHZ) Schiff base were prepared by anchoring its amino derivative Schiff base (AHPHZ) on cross-linked (6 wt%) polymer beads and then loading iron(III), copper(II) and zinc(II) ions in methanol. The loading of HPHZ Schiff base on polymer beads was 3.436 mmol g⁻¹ and efficiency of complexation of polymer anchored HPHZ Schiff base for iron(III), copper(II) and zinc(II) ions was 83.21, 83.40 and 83.17%, respectively. The efficiency of complexation of unsupported HPHZ Schiff base for these metal ions was lower than polymer supported HPHZ Schiff base. The structural information obtained by spectral, magnetic and elemental analysis has suggested octahedral and square planar geometry for iron(III) and copper(II) ions complexes, respectively, with paramagnetic behavior, but zinc(II) ions complexes were tetrahedral in shape with diamagnetic behavior. The complexation with metal ions has increased thermal stability of polymer anchored HPHZ Schiff base. The catalytic activity of unsupported and polymer supported HPHZ Schiff base complexes of metal ions was evaluated by studying the oxidation of phenol (Ph) and epoxidation of cyclohexene (CH). The polymer supported metal complexes showed better catalytic activity than unsupported metal complexes. The catalytic activity of metal complexes was optimum at a molar ratio of 1:1:1 of substrate to oxidant and catalyst. The selectivity for catechol (CTL) and epoxy cyclohexane (ECH) in oxidation of phenol and epoxidation of cyclohexene was better with polymer supported metal complexes in comparison to unsupported metal complexes. The energy of activation for oxidation of phenol (22.8 kJ mol⁻¹) and epoxidation of cyclohexene (8.9 kJ mol⁻¹) was lowest with polymer supported complexes of iron(III) ions than polymer supported Schiff base complexes of copper(II) and zinc(II) ions.     

Transition metal-directed self-assembly of calix[4]arene based dithiocarbamate ligands

The transition metal-directed self-assembly of dithiocarbamate ligand functionalized upper and lower rim calix[4]arenes affords novel dimeric bimetallic bis(calix[4]arene) species as determined by a combination of analytical methods including X-ray crystallography. An exception is a zinc(II) dithiocarbamate upper rim calix[4]arene assembly which is monomeric in nature. Electrochemical investigations reveal the bimetallic copper(II) bis(calix[4]arene) systems can electrochemically sense dihydrogen phosphate and carboxylate anions via significant cathodic perturbations of the respective copper(II)/(III) dithiocarbamate oxidation wave.     

Synthesis, structure and spectroscopy of new thiopyrone and hydroxypyridinethione transition-metal complexes

The coordination chemistry of several O,S mixed donor ligands, namely thiopyrone and hydroxypyridinethione chelators, with a variety of middle and late first-row transition-metal ions is described. Complexes of 3-hydroxy-2-methyl-4-thiopyrone (thiomaltol) with cobalt(II), copper(II) and zinc(II); 3-hydroxy-1,2-dimethyl-4(1H)-pyridinethione (3,4-HOPTO) with iron(III), nickel(II), copper(II) and zinc(II); and 3-hydroxy-1-methyl-2(1H)-pyridinethione (3,2-HOPTO) with iron(III), nickel(II), copper(II) and zinc(II) have been synthesized and characterized. The structures, absorbance spectroscopy, cyclic voltammetry and superconducting quantum interferometer device (SQUID) measurements of selected metal complexes, as well as ligand protonation constants, are reported. Most of the metal complexes show coordination geometries indicative of a strong trans influence by the O,S chelators. The data presented herein provide the most detailed study of the transition-metal coordination chemistry of both thiopyrone and hydroxypyridinethione O,S donor ligands to date, and provide the basis for the investigation of these ligands in realm of biological inorganic chemistry.     

Guanidine‐Based Polymer Brushes Grafted onto Silica Nanoparticles as Efficient Artificial Phosphodiesterases

Polymer brushes grafted to the surface of silica nanoparticles were fabricated by atom‐transfer radical polymerization (ATRP) and investigated as catalysts in the cleavage of phosphodiesters. The surfaces of silica nanoparticles were functionalized with an ATRP initiator. Surface‐initiated ATRP reactions, in varying proportions, of a methacrylate moiety functionalized with a phenylguanidine moiety and an inert hydrophilic methacrylate species afforded hybrid nanoparticles that were characterized with potentiometric titrations, thermogravimetric analysis, and SEM. The activity of the hybrid nanoparticles was tested in the transesterification of the RNA model compound 2‐hydroxypropyl para‐nitrophenylphosphate (HPNP) and diribonucleoside monophosphates. A high catalytic efficiency and a remarkable effective molarity, thus overcoming the effective molarities previously observed for comparable systems, indicate the existence of an effective cooperation of the guanidine/guanidinium units and a high level of preorganization in the nanostructure. The investigated system also exhibits a marked and unprecedented selectivity for the diribonucleoside sequence CpA. The results presented open up the way for a novel and straightforward strategy for the preparation of supramolecular catalysts.     

Synthesis,characterization, fluorescence imaging,and cytotoxicity studies of a uracil‐based azo derivative and its metal complexes

A uracil‐based heterocyclic azo derivative was prepared by coupling diazotized 5‐aminouracil with 2‐naphthol. This ligand, viz., 1‐(2,4‐dioxopyrimidine‐5‐yl)‐azo‐naphth‐2‐ol (HNAP), was used as a precursor for the synthesis of a series of complexes with manganese(II), cobalt(II), nickel(II), copper(II), and zinc(II) ions. Various physicochemical measurements UV–Visible, Infrared (IR), ¹H NMR, ¹³C Nuclear Magnetic Resonance (NMR), and electron spin resonance (ESR) spectral studies were employed to characterize the ligand and the metal complexes. The ligand showed good selectivity toward Mn²⁺ over the other metal ions with a detection limit of 1.36 μM. This probe was used for the confocal fluorescence imaging of Mn²⁺ ions in Michigan Cancer Foundation‐7 (MCF‐7) cells. The ligand and the metal complexes were tested for their cytotoxicity on the MCF‐7 cell line. It was observed that complexation of HNAP with the metal ions exhibited a promising cytotoxicity.     

DNA cleavage by the photocontrolled cooperation of Zn(II) centers in an azobenzene-linked dizinc complex

We synthesized a new photoactive dinuclear zinc(II) complex by linking two zinc centers with a ligand containing an azobenzene chromophore and investigated the DNA cleavage activities of its trans and cis forms. The trans structure of the dinuclear zinc complex was determined by X-ray crystallography, where each zinc center is situated in an octahedral coordination environment comprised of three nitrogen atoms from the ligand and three oxygen atoms from two nitrate ions. The dinuclear zinc complex containing the azobenzene chromophore was photoisomerizable between the trans and cis forms. The binding affinities of the trans and cis complexes with calf thymus (CT)-DNA were similar. Although the DNA cleavage activity of the trans complex was negligible, the cis complex was able to cleave DNA. We attribute the efficient activity of the cis complex to the cooperation of the two closely located zinc centers and the inactivity of the trans complex to the two metal centers positioned far away from each other. The DNA cleavage activity of the cis complex exhibited a pH-dependent bell-shaped profile, which has been observed in the hydrolytic cleavage of DNA by zinc complexes. The DNA cleavage activity was not inhibited by a major groove binder, methyl green, but decreased significantly by a minor groove binder, 4',6-diamidino-2-phenylindole, indicating that the dinuclear zinc complex binds to the minor groove of DNA. The present work shows the importance of the cooperation of two zinc ions for hydrolytic DNA cleavage, which can be photoregulated by linking the two metal centers with a photoisomerizable spacer, such as an azobenzene chromophore.     

Synthesis, Characterization, and Antibacterial Activity of Complexes of (1S,2S)-N,N-1,2-Diphenylethylene- bis -(5-imino-1-phenyl-1,3-hexanedione)

 The synthesis and characterization of homobimetallic complexes of VO(IV), Cr(II), Co(II), Ni(II), and Cu(II) with the chiral Schiff base (1S,2S)-N,N-1,2-Diphenylethylene-bis-(5-imino-1-phenyl-1,3-hexa-nedione) is reported. The metal ions occupy both compartments of the ligand; water molecules fill the coordination spheres to provide an octahedral environment around the central atoms. The antibacterial activity of both mono- and bimetallic complexes against a number of Gram-positive as well as Gram-negative bacteria has been tested and is discussed.     

Studies on the reaction kinetics and the mechanism of hydrolysis of bis(4-nitrophenyl)phosphate (BNPP) by hydroxamic acid complexes containing benzo-15-crown-5

A hydroxamic acid (HL) containing benzo-15-crown-5 and their copper(II), zinc(II), cobalt(II) and manganese(II) complexes have been synthesized and studied as catalysts for the cleavage of bis(4-nitrophenyl)phosphate (BNPP). The catalytic properties of these complexes and the kinetics and mechanism of BNPP hydrolysis have been investigated. The kinetic mathematical model of BNPP cleavage catalyzed by these complexes has been proposed. The effects of reaction temperature and metal ion in the complexes on the rate of BNPP catalytic hydrolysis have been discussed. The results show that the hydroxamic acid complexes containing benzo-15-crown-5 exhibit high activity in the BNPP catalyzed hydrolysis; the pseudo-first-order-rate constants of BNPP hydrolysis catalyzed by the complexes increase along with the increases of pH of the buffer solution from 7.50 to 9.50; the activity of different metal ions decreases in the order: Co²⁺ > Cu²⁺ > Zn²⁺ > Mn²⁺; the pseudo-first-order-rate constants of BNPP hydrolysis catalyzed by the complexes is 2.24 × 10⁵ ~ 3.24 × 10⁵ times as large as that of spontaneous hydrolysis of BNPP.     

Catalytic activities of polymer‐supported metal complexes in oxidation of phenol and epoxidation of cyclohexene

The metal complexes of N, N′‐bis (o‐hydroxy acetophenone) propylene diamine (HPPn) Schiff base were supported on cross‐linked polystyrene beads. The complexation of iron(III), copper(II), and zinc(II) ions on polymer‐anchored HPPn Schiff base was 83.4, 85.7, and 84.5 wt%, respectively, whereas the complexation of these metal ions on unsupported HPPn Schiff base was 82.3, 84.5, and 83.9 wt%. The iron(III) complexes of HPPn Schiff base were octahedral in geometry, whereas copper(II) and zinc(II) ions complexes were square planar and tetrahedral. Complexation of metal ions increased the thermal stability of HPPn Schiff base. Catalytic activity of metal complexes was tested by studying the oxidation of phenol and epoxidation of cyclohexene in the presence of hydrogen peroxide. The polymer‐supported HPPn Schiff base complexes of iron(III) ions showed 73.0 wt% conversion of phenol and 90.6 wt% conversion of cyclohexene at a molar ratio of 1:1:1 of substrate to catalyst and hydrogen peroxide, but unsupported complexes of iron(III) ions showed 63.8 wt% conversion for phenol and 83.2 wt% conversion for cyclohexene. The product selectivity for catechol (CTL) and epoxy cyclohexane (ECH) was 93.1 and 98.3 wt%, respectively with supported HPPn Schiff base complexes of iron(III) ions but was lower with HPPn Schiff base complexes of copper(II) and zinc(II) ions. Activation energy for the epoxidation of cyclohexene and phenol conversion with unsupported HPPn Schiff base complexes of iron(III) ions was 16.6 kJ mol^?1 and 21.2 kJ mol^?1, respectively, but was lower with supported complexes of iron(III) ions. Copyright © 2007 John Wiley & Sons, Ltd.     

Photocontrol of spatial orientation and DNA cleavage activity of copper(II)-bound dipeptides linked by an azobenzene derivative

Copper(II) ion-bound CysGly dipeptides linked by an azobenzene derivative were photoisomerized between the trans and cis forms. The two copper(II) ion centers were positioned close to each other in the cis form, whereas they were far away from each other in the trans form. The copper complex in the cis form exhibited DNA cleavage activity, whereas the activity in the trans form was negligible. The DNA cleavage activity of the cis form is attributed to the cooperation of the closely located copper(II) centers. The present results show the photocontrol of the cooperation of metal ions for DNA cleavage.     

Syntheses and structures of Mn(II), Co(II), and Zn(II) complexes of 1,3-diterpyridyl-substituted p-tert-butylcalix[4]arene

The calix[4]arene-based podand which incorporates two terpyridine functions in 1,3-alternate positions with flexible propylene spacers at lower rim has been prepared and subjected to complexation studies with some transition metal ions. Single-crystal structures of Mn(II), Co(II), and Zn(II) complexes were determined by X-ray diffraction. These metal complexes are formed with a 2?:?1 ratio of metal and ligand. Coordination of each metal is five-coordinate distorted trigonal-bipyramidal geometry by three nitrogen atoms from a terpyridyl unit and two chloride atoms.