Hybrid ligand-alkylating agents targeting telomeric G-quadruplex structures

The synthesis, physico-chemical properties and biological effects of a new class of naphthalene diimides (NDIs) capable of reversibly binding telomeric DNA and alkylate it through an electrophilic quinone methide moiety (QM), are reported. FRET and circular dichroism assays showed a marked stabilization and selectivity towards telomeric G4 DNA folded in a hybrid topology. NDI-QMs' alkylating properties revealed a good reactivity on single nucleosides and selectivity towards telomeric G4. A selected NDI was able to significantly impair the growth of melanoma cells by causing telomere dysfunction and down-regulation of telomerase expression. These findings points to our hybrid ligand-alkylating NDIs as possible tools for the development of novel targeted anticancer therapies.     

Two new ternary complexes of copper(II) with tetracycline or doxycycline and 1,10-phenanthroline and their potential as antitumoral: cytotoxicity and DNA cleavage

This paper reports on the synthesis and characterization of two new ternary copper(II) complexes: [Cu(doxycycline)(1,10-phenanthroline)(H(2)O)(ClO(4))](ClO(4)) (1) and [Cu(tetracycline)(1,10-phenanthroline)(H(2)O)(ClO(4))](ClO(4)) (2). These compounds exhibit a distorted tetragonal geometry around copper, which is coordinated to two bidentate ligands, 1,10-phenanthroline and tetracycline or doxycyline, a water molecule, and a perchlorate ion weakly bonded in the axial positions. In both compounds, copper(II) binds to tetracyclines via the oxygen of the hydroxyl group and oxygen of the amide group at ring A and to 1,10-phenanthroline via its two heterocyclic nitrogens. We have evaluated the binding of the new complexes to DNA, their capacity to cleave it, their cytotoxic activity, and uptake in tumoral cells. The complexes bind to DNA preferentially by the major groove, and then cleave its strands by an oxidative mechanism involving the generation of ROS. The cleavage of DNA was inhibited by radical inhibitors and/or trappers such as superoxide dismutase, DMSO, and the copper(I) chelator bathocuproine. The enzyme T4 DNA ligase was not able to relegate the products of DNA cleavage, which indicates that the cleavage does not occur via a hydrolytic mechanism. Both complexes present an expressive plasmid DNA cleavage activity generating single- and double-strand breaks, under mild reaction conditions, and even in the absence of any additional oxidant or reducing agent. In the same experimental conditions, [Cu(phen)(2)](2+) is approximately 100-fold less active than our complexes. These complexes are among the most potent DNA cleavage agents reported so far. Both complexes inhibit the growth of K562 cells with the IC(50) values of 1.93 and 2.59 μmol L(-1) for compounds 1 and 2, respectively. The complexes are more active than the free ligands, and their cytotoxic activity correlates with intracellular copper concentration and the number of Cu-DNA adducts formed inside cells.     

Competition of Ligands and the 18-mer Binding Domain of the RHAU Helicase for G-Quadruplexes: Orthosteric or Allosteric Binding Mechanism?

Stabilizing the DNA and RNA structures known as G-quadruplexes (G4s) using specific ligands is a strategy that has been proposed to fight cancer. However, although G-quadruplex:ligand (G4:L) interactions have often been investigated, whether or not ligands are able to disrupt G-quadruplex:protein (G4:P) interactions remains poorly studied. In this study, using native mass spectrometry, we have investigated ternary G4:L:P complexes formed by G4s, some of the highest affinity ligands, and the binding domain of the RHAU helicase. Our results suggest that RHAU binds not only preferentially to parallel G4s, but also to free external G-quartets. We also found that, depending on the G4, ligands could prevent the binding of the peptide, either by direct competition for the binding sites (orthosteric inhibition) or by inducing conformational changes (allosteric inhibition). Notably, the ligand Cu–ttpy (ttpy=4′-tolyl-2,2′:6′,2′′-terpyridine) induced a conformational change that increased the binding of the peptide. This study illustrates that it is important to not only characterize drug–target interactions, but also how the binding to other partners is affected.     

Synthesis, physico-chemical and DNA interaction studies of homo- and hetero-trinuclear complexes

Synthesis and characterization of three new trinuclear metal complexes of type Cu3, Cu2Zn and Cu2Ni have been achieved by assembling simple mononuclear complexes, namely 2,2'-bipyridyl 3,4-dihydroxo benzaldehyde copper(II) complex and diethylenetriamine complexes of copper(II), nickel(II) and zinc(II) ions, through the reaction of coordinated ligands. The FAB mass spectra for the complexes show fragmentation pattern in accordance with the molecular formula. The frozen electron paramagnetic resonance (EPR) spectrum of tricopper complex shows two sets of parallel lines with approximately 2:1 ratio. The simulation has been carried out by considering dipolar interaction between the two types of copper ions present in the complex. The trimetallic complexes, Cu3, Cu2Ni and Cu2Zn show strong intercalation type of interaction with Calf thymus DNA in 0.02 mol L(-1) of phosphate buffer containing 60 mmol sodium chloride at pH 7.0 at room temperature. The binding constant is found to be in the order Cu3相似文献   

Structure and DNA cleavage properties of two copper(II) complexes of the pyridine-pyrazole-containing ligands mbpzbpy and Hmpzbpya

The DNA-cleavage properties of the two copper(II) complexes, [Cu(mbpzbpy)Br(2)](H(2)O)(2.5) (1) and [Cu(mpzbpya)Cl](CH(3)OH) (2), obtained from the ligands 6,6'-bis(3,5-dimethyl-N-pyrazolmethyl)-2,2'-bipyridine) (mbpzbpy) and 6'-(3,5-dimethyl-N-pyrazolmethyl)-2,2'-bipyridine-6-carboxylic acid) (Hmpzbpya), respectively, are reported. Upon coordination to Cu(II) chloride in methanol, one arm of the ligand mbpzbpy is hydrolyzed to form mpzbpya. Under the same experimental conditions, the reaction of mbpzbpy with CuBr(2) does not lead to ligand hydrolysis. The ligand mpzbpya is coordinated to a copper(ii) ion generating a CuN(3)OCl chromophore, resulting in a distorted square-pyramidal environment, whereas with the N(4) mbpzbpy ligand, the Cu(II) ion is four-coordinated in a distorted square planar geometry. Both complexes promote the oxidative DNA cleavage of phiX174 phage DNA in the absence of reductant. The oxidative nature of the DNA cleavage reaction has been confirmed by religation and cell-transformation experiments. Studies using standard radical scavengers suggest the involvement of hydroxyl radicals in the oxidative cleavage of DNA. Although both compounds do convert form I (supercoiled) DNA to form II (nicked, relaxed form), only complex 1 is able to produce small amounts of form III (linearized DNA). This observation may be explained either by the attack of the copper(ii) complexes to only one single strand of DNA, or by a single cleavage event. Statistical analysis of relative DNA quantities present after the treatment with both copper(ii) complexes supports a random mode of DNA cleavage.     

Phosphodiester cleavage properties of copper(II) complexes of 1,4,7-triazacyclononane ligands bearing single alkyl guanidine pendants

Three new metal-coordinating ligands, L(1)·4HCl [1-(2-guanidinoethyl)-1,4,7-triazacyclononane tetrahydrochloride], L(2)·4HCl [1-(3-guanidinopropyl)-1,4,7-triazacyclononane tetrahydrochloride], and L(3)·4HCl [1-(4-guanidinobutyl)-1,4,7-triazacyclononane tetrahydrochloride], have been prepared via the selective N-functionalization of 1,4,7-triazacyclononane (tacn) with ethylguanidine, propylguanidine, and butylguanidine pendants, respectively. Reaction of L(1)·4HCl with Cu(ClO(4))(2)·6H(2)O in basic aqueous solution led to the crystallization of a monohydroxo-bridged binuclear copper(II) complex, [Cu(2)L(1)(2)(μ-OH)](ClO(4))(3)·H(2)O (C1), while for L(2) and L(3), mononuclear complexes of composition [Cu(L(2)H)Cl(2)]Cl·(MeOH)(0.5)·(H(2)O)(0.5) (C2) and [Cu(L(3)H)Cl(2)]Cl·(DMF)(0.5)·(H(2)O)(0.5) (C3) were crystallized from methanol and DMF solutions, respectively. X-ray crystallography revealed that in addition to a tacn ring from L(1) ligand, each copper(II) center in C1 is coordinated to a neutral guanidine pendant. In contrast, the guanidinium pendants in C2 and C3 are protonated and extend away from the Cu(II)-tacn units. Complex C1 features a single μ-hydroxo bridge between the two copper(II) centers, which mediates strong antiferromagnetic coupling between the metal centers. Complexes C2 and C3 cleave two model phosphodiesters, bis(p-nitrophenyl)phosphate (BNPP) and 2-hydroxypropyl-p-nitrophenylphosphate (HPNPP), more rapidly than C1, which displays similar reactivity to [Cu(tacn)(OH(2))(2)](2+). All three complexes cleave supercoiled plasmid DNA (pBR 322) at significantly faster rates than the corresponding bis(alkylguanidine) complexes and [Cu(tacn)(OH(2))(2)](2+). The high DNA cleavage rate for C1 {k(obs) = 1.30 (±0.01) × 10(-4) s(-1) vs 1.23 (±0.37) × 10(-5) s(-1) for [Cu(tacn)(OH(2))(2)](2+) and 1.58 (±0.05) × 10(-5) s(-1) for the corresponding bis(ethylguanidine) analogue} indicates that the coordinated guanidine group in C1 may be displaced to allow for substrate binding/activation. Comparison of the phosphate ester cleavage properties of complexes C1-C3 with those of related complexes suggests some degree of cooperativity between the Cu(II) centers and the guanidinium groups.     

Synthesis and characterization of 8-aminoquinolines,substituted by electron donating groups,as high-affinity copper chelators for the treatment of Alzheimer's disease

The deregulation of copper homeostasis generates copper–amyloid aggregation and strongly participates in neuron damage in the brains of patients with Alzheimer's disease. Therefore, copper chelators able to regulate copper homeostasis should be considered as potential therapeutic agents. On the basis of a bidentate amine side chain attached at the 2-position of an 8-aminoquinoline motif, a series of low-molecular-weight copper chelators have been designed to act as specific tetradentate Cu(II) chelators. The affinity of these ligands for Cu(II) and their selectivity for Cu(II) with respect to Zn(II) are reported. These ligands provide a square planar tetradentate coordination sphere that should be suitable to extract copper (II) from copper–amyloid complexes, and are therefore expected to regulate copper homeostasis in vivo.     

Role of cofactors in folding of the blue-copper protein azurin

Many proteins in living cells coordinate cofactors, such as metal ions, to attain their activity. Since the cofactors in such cases often can interact with their corresponding unfolded polypeptides in vitro, it is important to unravel how cofactors modulate protein folding. In this review, I will discuss the role of cofactors in folding of the blue-copper protein Pseudomonas aeruginosa azurin. In the case of both copper (Cu(II) and Cu(I)) and zinc (Zn(II)), the metal can bind to unfolded azurin. The residues involved in copper (Cu(II) and Cu(I)) coordination in the unfolded state have been identified as Cys112, His117, and Met121. The affinities of Cu(II), Cu(I), and Zn(II) are all higher for the folded than for the unfolded azurin polypeptide, resulting in metal stabilization of the native state as compared to the stability of apo-azurin. Cu(II), Zn(II), and several apo forms of azurin all fold in two-state kinetic reactions with roughly identical polypeptide-folding speeds. This suggests that the native-state beta-barrel topology, not cofactor interactions or thermodynamic stability, determines azurin's folding barrier. Nonetheless, copper binds much more rapidly (i.e., 4 orders of magnitude) to unfolded azurin than to folded azurin. Therefore, the fastest route to functional azurin is through copper binding before polypeptide folding; this sequence of events may be the relevant biological pathway.     

Design and spectroscopic characterization of peptide models for the plastocyanin copper-binding loop

The Cu(II)- and Co(II)-binding properties of two peptides, designed on the basis of the active site sequence and structure of the blue copper protein plastocyanin, are explored. Peptide BCP-A, Ac-Trp-(Gly)(3)-Ser-Tyr-Cys-Ser-Pro-His-Gln-Gly-Ala-Gly-Met-(Gly )(3)-His-(Gly)(2)-Lys-CONH(2), conserves the Cu-binding loop of plastocyanin containing three of the four copper ligands and has a flexible (Gly)(3) linker to the second His ligand. Peptide BCP-B, Ac-Trp-(Gly)(3)-Cys-Gly-His-Gly-Val-Pro-Ser-His-Gly-Met-Gly-CONH(2), contains all four blue copper ligands, with two on either side of a beta-turn. Both peptides form 1:1 complexes with Cu(II) through His and Cys ligands. BCP-A, the ligand loop, binds to Cu(II) in a tetrahedrally distorted square plane with axial solvent ligation, while BCP-B-Cu(II) has no tetrahedral distortion in aqueous solution. In methanolic solution, distortion of the square plane is evident for both BCP-Cu(II) complexes. Tetrahedral Co(II) complexes are observed for both peptides in aqueous solution but with 4:2 peptide:Co(II) stoichiometries as estimated by ultracentrifugation. Cu(II) reduction potentials for the aqueous peptide-Cu(II) complexes were measured to be +75 +/- 30 mV vs NHE for BCP-A-Cu(II) and -10 +/- 20 mV vs NHE for BCP-B-Cu(II). The results indicate that the plastocyanin ligand loop can act as a metal-binding site with His and Cys ligands in the absence of the remainder of the folded protein but, by itself, cannot stabilize a type 1 copper site, emphasizing the role of the protein matrix in protecting the Cu binding site from solvent exposure and the Cys from oxidation.     

Bis(dipyridophenazine)copper(II) complex as major groove directing synthetic hydrolase

The copper(II) complex [Cu(dppz)(2)Cl]Cl () has been prepared, structurally characterized and its DNA binding and cleavage properties studied (dppz, dipyridophenazine). Crystal structure of 1xdppzxH(2)O shows the presence of the monocationic copper(II) complex containing two dppz ligands and one chloride in the five coordinate structure. While one bidentate chelating dppz ligand occupies the basal plane, the other dppz ligand shows an axial/equatorial mode of bonding. The chloride ligand binds at the basal plane. The complex crystallizes with dppz and water as lattice molecules. The dppz moieties in the metal-bound and free forms are involved in pi-pi stacking interactions. The one-electron paramagnetic complex shows a visible spectral d-d band at 707 nm in DMF and displays quasireversible cyclic voltammetric response for the Cu(II)/Cu(I) couple near 0.1 V vs. SCE in DMF-0.1 M TBAP. The complex which is an avid binder to calf thymus DNA giving a binding constant (K(b)) value of 2.0 x 10(4) M(-1) in DMF-Tris buffer, cleaves supercoiled pUC19 DNA in an oxidative manner in the presence of mercaptopropionic acid (MPA) as a reducing agent or on photo irradiation at 312 nm. Control experiments show major groove binding and DNA cleavage via the formation of hydroxyl radical in the presence of MPA and by singlet oxygen in the photocleavage reaction. The complex exhibits significant hydrolytic cleavage of DNA in the dark in the absence of any additives at a rate of approximately 3.0 h(-1). The hydrolytic nature of the DNA cleavage is evidenced from the T4 ligase experiments converting the nicked circular form to its original supercoiled form quantitatively. Complex presents a rare example of copper-based major groove directing efficient synthetic hydrolase.     

Targeted guanine oxidation by a dinuclear copper(II) complex at single stranded/double stranded DNA junctions

A dinuclear copper(II) complex [Cu(II)2(PD'O-)(H2O)2](ClO4)3 (5) with terminal Cu(II)-H(2)O moieties and a Cu...Cu distance of 4.13 A (X-ray structure) has been synthesized and characterized by EPR spectroscopy (ferromagnetic coupling observed) and cyclic voltammetry. Dizinc(II) and mononuclear copper(II) analogues [Zn(II)2(PD'O-)(H2O)2]3+ (7) and [Cu(II)(mPD'OH)(H2O)]2+ (6), respectively, have also been synthesized and structurally characterized. Reacting 5/MPA/O(2) (MPA = 3-mercaptopropionic acid) with DNA leads to a highly specific oxidation of guanine (G) at a junction between single- and double-stranded DNA. Mass spectrometric analysis of the major products indicates a gain of +18 and +34 amu relative to initial DNA strands. The most efficient reaction requires G at the first and second unpaired positions of each strand extending from the junction. Less reaction is observed for analogous targets in which the G cluster is farther from the junction or contains less than four Gs. Consistent with our previous systems, the multinuclear copper center is required for selective reaction; mononuclear complex 6 is not effective. Hydrogen peroxide as a substitute for MPA/O2 also does not lead to activity. Structural analysis of a [Cu(II)2(PD'O-)(G)]3+ complex (8) and dizinc analogue [Zn(II)(2)(PD'O-)(G)](ClO4)3 (9) (G = guanosine) reveals coordination of the G O6 and N7 atoms with the two copper (or zinc) centers and suggests that copper-G coordination likely plays a role in recognition of the DNA target. The Cu2-O2 intermediate responsible for guanine oxidation appears to be different from that responsible for direct-strand scission induced by other multinuclear copper complexes; the likely course of reaction is discussed.     

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.     

Synthesis, DNA-binding, cleavage, and cytotoxic activity of new 1,7-dioxa-4,10-diazacyclododecane artificial receptors containing bisguanidinoethyl or diaminoethyl double side arms

Novel 1,7-dioxa-4,10-diazacyclododecane artificial receptors with two pendant aminoethyl (3) or guanidinoethyl (4) side arms have been synthesized. Spectroscopy, including fluorescence and CD spectroscopy, of the interactions of 3, 4, and their copper(II) complexes with calf thymus DNA indicated that the DNA binding affinity of these compounds follows the order Cu(2+)-4>Cu(2+)-3>4>3, and the binding constants of Cu(2+)-3 are Cu(2+)-4 are 7.2x10(4) and 8.7x10(4) M(-1), respectively. Assessment by agarose gel electrophoresis of the plasmid pUC 19 DNA cleavage activity in the presence of the receptors showed that the complexes Cu(2+)-3 and Cu(2+)-4 exhibit powerful supercoiled DNA cleavage efficiency. Kinetic data of DNA cleavage promoted by Cu(2+)-3 and Cu(2+)-4 under physiological conditions fit to a saturation kinetic profile with kmax values of 0.865 and 0.596 h(-1), respectively, which give about 10(8)-fold rate acceleration over uncatalyzed supercoiled DNA. This acceleration is due to efficient cooperative catalysis of the copper(II) center and the functional (diamino or bisguanidinium) groups. In-vitro cytotoxic activities toward murine melanoma B16 cells and human leukemia HL-60 cells were also examined: Cu(2+)-4 shows the highest activity with IC(50) values of 1.62x10(-4) and 1.19x10(-5) M, respectively.     

Synthesis of ditopic ligands for the selective extraction of copper(II) nitrate and crystal structures of their Cu(II) complexes

We have synthesized two ditopic ligands for selective extraction of copper(II) nitrate. We also synthesized one cation-only binding analog for comparison. All three ligands were characterized by conventional techniques. Competitive two-phase metal ion solvent extraction experiments were performed at 25 °C over a period of 24 h. These ligands showed significant selectivity for Cu(II) ions, having the ditopic ligands extract 81 and 73% of the Cu(II) ions in a solution of different metal ions {Ni(II), Co(II), Cu(II), Zn(II), Cd(II), Pb(II)} at pH 5.09. Competitive transport experiments (water/chloroform/water) were undertaken employing each ligand separately as the ionophore in the membrane (chloroform) phase. No metal ion transport was observed, but a large concentration of Cu(II) was present in the membrane phase. Competitive anion extraction and transport were carried out with the ditopic ligands, yielding selective extraction and transport of nitrate. Furthermore, a pH isotherm of the best ditopic ligand (H₂L²) with Cu(II) was determined from pH 1.0 to 6.0, producing a pH_½ value of approximately 2.6. Finally, crystal structures of the ditopic ligands complexed with Cu(II) were determined and refined. The coordination geometry around the metal centers are distorted square planar and the Cu(II)-donor bond lengths fall within the normal range.     

Copper(II) complexes with bioactive carboxyamide: synthesis, characterization and biological activity

Complexes of Cu(II) with bioactive carboxyamide ligands N',N'-bis(3-carboxy-1-oxoprop-2-enyl)2-amino-N-arylbenzamidine, N',N'-bis(3-carboxy-1-oxopropanyl)2-amino-N-arylbenzamidine and N',N'-bis(3-carboxy-1-oxophenelenyl)2-amino-N-arylbenzamidine have been synthesized and characterized by various physico-chemical techniques. Mass spectrum explains the successive degradation of the molecular species in solution and justifies ML complexes. Vibrational spectra indicate coordination of amide and carboxylate oxygen of the ligands along with water molecules. Electronic spectra and magnetic susceptibility measurements reveal octahedral geometry for Cu(II) complexes. The EPR of the reported complex show g( parallel)>g( perpendicular)>2.0023 and G value within the range 2.08-4.49 are consistent with [Formula: see text] ground state in an octahedral geometry. The voltammogram of the copper(II) complex shows a quasi-reversible redox process and a simple one electron process assignable to the Cu(II)/Cu(I) couple. Kinetic and thermodynamic parameters were computed from the thermal data using Coats and Redfern method, which confirm first order kinetics. The bio-efficacy of the ligands and its copper complexes have been examined against the growth of bacteria and pathogenic fungi in vitro to evaluate their antimicrobial potential. The results indicate that the ligand and its metal complexes possess notable antimicrobial properties.     

Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands

Ligands with the capability to bind G-quadruplexes (G4s) specifically, and to control G4 structure and behaviour, offer great potential in the development of novel therapies, technologies and functional materials. Most known ligands bind to a pre-formed topology, but G4s are highly dynamic and a small number of ligands have been discovered that influence these folding equilibria. Such ligands may be useful as probes to understand the dynamic nature of G4 in vivo, or to exploit the polymorphism of G4 in the development of molecular devices. To date, these fascinating molecules have been discovered serendipitously. There is a need for tools to predict such effects to drive ligand design and development, and for molecular-level understanding of ligand binding mechanisms and associated topological perturbation of G4 structures. Here we study the G4 binding mechanisms of a family of stiff-stilbene G4 ligands to human telomeric DNA using molecular dynamics (MD) and enhanced sampling (metadynamics) MD simulations. The simulations predict a variety of binding mechanisms and effects on G4 structure for the different ligands in the series. In parallel, we characterize the binding of the ligands to the G4 target experimentally using NMR and CD spectroscopy. The results show good agreement between the simulated and experimentally observed binding modes, binding affinities and ligand-induced perturbation of the G4 structure. The simulations correctly predict ligands that perturb G4 topology. Metadynamics simulations are shown to be a powerful tool to aid development of molecules to influence G4 structure, both in interpreting experiments and to help in the design of these chemotypes.

Enhanced sampling molecular dynamics simulations and solution-phase experiments come together to demonstrate the diverse effects of G4-interactive small molecules.     

Binding affinities for models of biologically available potential Cu(II) ligands relevant to Alzheimer's disease: an ab initio study

A systematic study of the binding affinities of the model biological ligands X: = (CH3)2S, CH3S-, CH3NH2, 4-CH3-imidazole (MeImid), C6H5O-, and CH3CO2- to (NH3)i(H2O)3-iCu(II)-H2O (i = 3, 2, 1, 0) complexes has been carried out using quantum chemical calculations. Geometries have been obtained at the B3LYP/ 6-31G(d) level of theory, and binding energies, Delta, relative to H2O as a ligand, have been calculated at the B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) level. Solvation effects have been included using the COSMO model, and the relative binding free energies in aqueous solution (Delta) have been determined at pH 7 for processes that are pH dependent. CH3S- (Delta = -16.0 to -53.5 kJ mol(-1)) and MeImid (Delta = -18.5 to -35.2 kJ mol(-1)) give the largest binding affinities for Cu(II). PhO- and (CH3)2S are poor ligands for Cu(II), Delta = 20.6 to -9.7 and 19.8 to -3.7 kJ mol(-1), respectively. The binding affinities for CH3NH2 range from -0.8 to -15.0 kJ mol(-1). CH3CO2- has Cu(II) binding affinities in the ranges Delta = -13.5 to -32.4 kJ mol(-1) if an adjacent OH bond is available for hydrogen bonding and Delta = 10.1 to -4.6 kJ mol(-1) if this interaction is not present. In the context of copper coordination by the Abeta peptide of Alzheimer's disease, the binding affinities suggest preferential binding of Cu(II) to the three histidine residues plus a lysine or the N-terminus. For a 3N1O Cu(II) ligand arrangement, it is more probable that the oxygen ligand comes from an aspartate/glutamate residue side chain than from the tyrosine at position 10. Methionine appears unlikely to be a Cu(II) ligand in Abeta.     

Hydrolytic protein cleavage mediated by unusual mononuclear copper(II) complexes: X-ray structures and solution studies

The crystal structures and redox and UV-vis/EPR spectroscopic properties of two new mononuclear copper(II) complexes, [Cu(HL1)Cl2] (1) and [Cu(L1)Cl] (2), prepared through the reaction between copper(II) chloride and the ligand 2-[(bis(pyridylmethyl)amino)methyl]-4-methyl-6-formylphenol (HL1) under distinct base conditions, are reported along with solution studies. Also, we demonstrate that these CuII complexes are able to cleave unactivated peptide bonds from bovine serum albumin (BSA) and the thermostable enzyme Taq DNA polymerase at micromolar concentration, under mild pH and temperature conditions. The cleavage activity seems to be specific with defined proteolytic fragments appearing after protein treatment. The location of the specific cleavage sites was tentatively assigned to solvent-accessible portions of the protein. These are two of the most active Cu(II) complexes described to date, since their cleavage activity is detected in minutes and evidence is here presented for a hydrolytic mechanism mediating protein cleavage by these complexes.     

Effect of steric encumbrance of tris(3-phenylpyrazolyl)borate on the structure and properties of ternary copper(II) complexes having N,N-donor heterocyclic bases

Complexes of formulation [Cu(Tp(Ph))(L)](ClO(4)) (1-4), where Tp(Ph) is anionic tris(3-phenylpyrazolyl)borate and L is N,N-donor heterocyclic base, viz. 2,2'-bipyridine (bpy, 1), 1,10-phenanthroline (phen, 2), dipyridoquinoxaline (dpq, 3), and dipyridophenazine (dppz, 4), are prepared from a reaction of copper(II) acetate.hydrate with KTp(Ph) and L in CH(2)Cl(2) and isolated as perchlorate salts. The complexes are characterized by analytical, structural, and spectral methods. The crystal structures of complexes 1-4 show the presence of discrete cationic complexes having the metal, Tp(Ph), and L in a 1:1:1 ratio and a noncoordinating perchlorate anion. The complexes have a square-pyramidal 4 + 1 coordination geometry in which two nitrogens of L and two nitrogens of the Tp(Ph) ligand occupy the basal plane and one nitrogen of Tp(Ph) binds at the axial site. Complexes 3 and 4 display distortion from the square-pyramidal geometry. The Cu-N distances for the equatorial and axial positions are approximately 2.0 and 2.2 A, respectively. The phenyl groups of Tp(Ph) form a bowl-shaped structure that encloses the [CuL] moiety. The steric encumbrance is greater for the bpy and phen ligands compared to that for dpq and dppz. The one-electron paramagnetic complexes (mu approximately equal to 1.8 mu(B)) exhibit axial EPR spectra in CH(2)Cl(2) glass at 77 K giving g(parallel) and g(perpendicular) values of approximately 2.18 (A(parallel) = 128 G) and approximately 2.07. The data suggest a [d(x(2)-y(2))](1) ground state. The complexes are redox-active and display a quasireversible cyclic voltammetric response for the Cu(II)/Cu(I) couple near 0.0 V versus SCE with an i(pc)/i(pa) ratio of unity in CH(2)Cl(2) or DMF-0.1 M TBAP. The E(1/2) values of the couple vary in the order 4 > 3 > 2 > 1. A profound effect of steric encumbrance caused by the Tp(Ph) ligand is observed in the reactivity of 1-4 with the calf thymus (CT) and supercoiled (SC) DNA. Complexes 2-4 show similar binding to CT DNA. The propensity for the SC DNA cleavage varies as 4 > 3 > 2. The bpy complex does not show any significant binding or cleavage of DNA. Mechanistic investigations using distamycin reveal minor groove binding for 2 and 3 and a major groove binding for 4. The scission reactions that are found to be inhibited by hydroxyl radical scavenger DMSO are likely to proceed through sugar hydrogen abstraction pathways.     

Reaction of beta-diketiminate copper(II) complexes and Na2S2

Reaction of beta-diketiminate copper(II) complexes and Na2S2 resulted in formation of (mu-eta2:eta2-disulfido)dicopper(II) complexes (adduct formation) or beta-diketiminate copper(I) complexes (reduction of copper(II)) depending on the substituents of the supporting ligands. In the case of sterically less demanding ligands, adduct formation occurred to provide the (mu-eta2:eta2-disulfido)dicopper(II) complexes, whereas reduction of copper(II) took place to give the corresponding copper(I) complexes with sterically more demanding beta-diketiminate ligands. Spectroscopic examinations of the reactions at low temperature using UV-vis and ESR as well as kinetic analysis have suggested that a 1 : 1 adduct LCuII-S-SNa with an end-on binding mode is initially formed as a common intermediate, from which different reaction pathways exist depending on the steric environment of the metal-coordination sphere provided by the ligands. Thus, with the sterically less demanding ligands, rearrangement of the disulfide adduct from end-on to side-on followed by self-dimerisation occurs to give the (mu-eta2:eta2-disulfido)dicopper(II) complexes, whereas such an intramolecular rearrangement of the disulfide co-ligand does not take place with the sterically more demanding ligands. In this case, homolytic cleavage of the CuII-S bond occurs to give the reduced copper(I) product. The steric effects of the supporting ligands have been discussed on the basis of detailed analysis of the crystal structures of the copper(II) starting materials.