Adenosine 3′,5′-monophosphate and guanosine 3′,5′-monophosphate: A simultaneous protein binding assay

The adenosine 3′,5′-monophosphate and guanosine 3′,5′-monophosphate contents of microliter quantities of urine can be determined simultaneously by combining individual protein binding assays for the two nucleotides. ³²P-labeled adenosine 3′,5′-monophosphate is bound to a protein from bovine skeletal muscle, while a lobster muscle protein preparation is utilized for binding of ³H-labeled guanosine 3′,5′-monophosphate.     

2′,3′-cAMP hydrolysis by metal-dependent phosphodiesterases containing DHH, EAL, and HD domains is non-specific: Implications for PDE screening

The recent report of 2′,3′-cAMP isolated from rat kidney is the first proof of its biological existence, which revived interest in this mysterious molecule. 2′,3′-cAMP serves as an extracellular adenosine source, but how it is degraded remains unclear. Here, we report that 2′,3′-cAMP can be hydrolyzed by six phosphodiesterases containing three different families of hydrolytic domains, generating invariably 3′-AMP but not 2′-AMP. The catalytic efficiency (k_cat/K_m) of each enzyme against 2′,3′-cAMP correlates with that against the widely used non-specific substrate bis(p-nitrophenyl)phosphate (bis-pNPP), indicating that 2′,3′-cAMP is a previously unknown non-specific substrate for PDEs. Furthermore, we show that the exclusive formation of 3′-AMP is due to the P-O2′ bond having lower activation energy and is not the result of steric exclusion at enzyme active site. Our analysis provides mechanistic basis to dissect protein function when 2′,3′-cAMP hydrolysis is observed.     

Enzymatic characteristics of two novel Myxococcus xanthus enzymes, PdeA and PdeB, displaying 3′,5′- and 2′,3′-cAMP phosphodiesterase, and phosphatase activities

Myxococcus xanthus PdeA and PdeB, enzymes homologous to class III 3′,5′-cyclic nucleotide phosphodiesterases, hydrolyzed 3′,5′- and 2′,3′-cyclic AMP (cAMP) to adenosine, and also demonstrated phosphatase activity toward nucleoside 5′-tri-, 5′-di-, 5′- and 3′-monophosphates with highest activities for nucleoside 5′-monophosphates. The substrate specificities of PdeA and PdeB show no similarity to that of any known cNMP phosphodiesterase, nucleotidase, or phosphatase. The enzyme activities of PdeA and PdeB were stimulated by 50 μM Mn²⁺ or Co²⁺. The K_m values of PdeA and PdeB for 3′,5′-cAMP, 2′,3′-cAMP, 5′-ATP, and 5′-AMP were in the low micromolar range (1.4-12.5  μM).     

Anionic effects on the formation of tridentate 4′-chloro-2,2′:6′,2″-terpyridine copper(II) complexes having 1:1 or 1:2 ratio of metal and ligand and their crystal symmetry

A facile synthetic procedure has been used to prepare one five-coordinate and four six-coordinate copper(II) complexes of 4′-chloro-2,2′:6′,2″-terpyridine (tpyCl) ligand with different counterions (, , , , and ) in high yields. They are formulated as [Cu(tpyCl-κ³N,N′,N′′)(SO₄-κO)(H₂O-κO)] · 2H₂O (1), trans-[Cu(tpyCl-κ³N,N′,N″)(NO₃-κO)₂(H₂O-κO)] (2), [Cu(tpyCl-κ³N,N′,N″)₂](BF₄)₂ (3), [Cu(tpyCl-κ³N,N′,N″)₂](PF₆)₂ (4) and [Cu(tpyCl-κ³N,N′,N″)₂](ClO₄)₂ (5) and versatile interactions in supramolecular level including coordinative bonding, O-H?O, O-H?Cl, C-H?F, and C-H?Cl hydrogen bonding, π-π stacking play essential roles in forming different frameworks of 1-5. It is concluded that the difference of coordination abilities of the counterions used and the experimental conditions codominate the resulting complexes with 1:1 or 1:2 ratio of metal and ligand.     

Alteration of molecular conformations and spectral properties for nickel(II), zinc(II) and copper(II) complexes having 3,8-di(thiophen-2′,2′′-yl)-1,10-phenanthroline ligands

Four transition metal complexes of 3,8-di(thiophen-2′,2″-yl)-1,10-phenanthroline (dtphen), formulated as [Ni(dtphen)₂(H₂O)₂]·(ClO₄)₂ (1), [Zn(dtphen)₂(H₂O)]·(ClO₄)₂ (2) [Cu(dtphen)₂(H₂O)]·(ClO₄)₂ (3), [Cu(dtphen)(phen)₂]·(ClO₄)₂ (4) (phen = 1,10-phenanthroline) with different metal-to-ligand ratios, were synthesized and characterized herein. The X-ray single-crystal diffraction studies of 1-4 exhibit that different molecular configurations for the dtphen ligand can be observed where the side thiophene rings adopt the trans/trans, trans/cis, trans/disorder and cis/cis conformations relative to the central 1,10-phenanthroline unit in different compounds. Fluorescence emission spectra of 1-4 in methanol show that the fluorescence emission of 2 is much stronger than the other three metal complexes, which is mainly due to its full d¹⁰ electronic configuration of Zn(II) ion.     

Synthesis and structural characterization of three hydrogen-bonding connected supramolecular complexes of nickel, zinc and copper with 1,3-diphenyl-4-(salicylidene hydrazide)-acetyl-pyrazolone-5 and 2,2′-bipyridine

A new set of supramolecular complexes, [Ni(DPAP-SHZ)(2,2′-bipy)CH₃OH] (1), [Zn(DPAP-SHZ)(2,2′-bipy)CH₃OH] (2) and [Cu(DPAP-SHZ)(2,2′-bipy)] · 2CH₂Cl₂ (3) (DPAP-SHZ = 1,3-diphenyl-4-(salicylidene hydrazide)-acetyl-pyrazolone-5, 2,2′-bipy = 2,2′-bipyridine) have been synthesized and characterized by elemental analysis, TG-DTA, IR spectroscopy and X-ray crystallography. The X-ray diffraction analyses of the complexes show that the Ni(II) ion and Zn(II) ion centers are six-coordinated while the Cu(II) ion center is five-coordinated. The three supramolecular complexes contain the same ligands, namely DPAP-SHZ and 2,2′-bipy. However, their hydrogen bonds are significantly different, and this variation apparently is responsible for the dissimilar structures of the three supramolecular complexes.     

A series of metal-organic frameworks constructed with 2,2′-bipyridine-3,3′-dicarboxylate: Syntheses, structures, and physical properties

To determine the influence of metal ion and the auxiliary ligand on the formation of metal-organic frameworks, six new coordination polymers, {[Mn₂(bpdc)(bpy)₃(H₂O)₂] · 2ClO₄ · H₂O}_n (1), {[Mn(bpdc)(dpe)] · CH₃OH · 2H₂O}_n (2), {[Cu(bpdc)(H₂O)₂]}_n (3), {[Zn(bpdc)(H₂O)₂]}_n (4), {[Cd(bpdc)(H₂O)₃] · 2H₂O}_n (5), and {[Co(bpdc)(H₂O)₃] · 0.5dpe · H₂O}_n (6) (H₂bpdc = 2,2′-bipyridine-3,3′-dicarboxylic acid, bpy = 2,2′-bipyridine, dpe = 1,2-di(4-pyridyl) ethylene), have been synthesized and characterized. Compound 1 forms 1D helical chain structure containing two unique Mn^II ions. In 2, the bridging ligand dpe links Mn-bpdc double zigzag chains to generate a layer possesses rectangular cavities. In 3, bpdc²⁻ ligand connects to three metal centers forming a 2D network. Different from the above compounds, 4 displays a 1D double-wavelike chain. Compound 5 features a helical chain. Compound 6 also displays a helical chain with guest molecule dpe existing in the structure. These diverse structures illustrate rational adjustment of metal ions and the second ligand is a good method for the further design of helical compounds with novel structures and properties. In addition, the magnetic properties of 2, 3 and 6, the thermal stabilities and photoluminescence properties of 4 and 5 were also studied.     

Acetato and formato copper(II) complexes with 4,4′-dimethyl-2,2′-bipyridine and 5,5′-dimethyl-2,2′-bipyridine: Synthesis, crystal structure, magnetic properties and EPR results. A new 1D polymeric water chain

By the reactions of Cu(AcO)₂·H₂O and Cu(HCOO)₂·4H₂O with 4,4′-dimethyl-2,2′-bipyridine and 5,5′-dimethyl-2,2′-bipyridine the compounds [Cu(AcO)₂(4,4′-Me₂-2,2′-bipy)]·1/2H₂O (1), [Cu(AcO)₂(5,5′-Me₂-2,2′-bipy)(H₂O)] (2), [Cu(HCOO)(μ-HCOO)(4,4′-Me₂-2,2′-bipy)]_n·nH₂O (3) and [Cu(HCOO)(μ-HCOO)(5,5′-Me₂-2,2′-bipy)]_n·2nH₂O (4) were obtained. In the acetate complexes, 1 and 2, the geometry around copper is distorted octahedral and square pyramidal, respectively. Dimeric units of different geometry are formed in both cases through hydrogen bonds in which non-coordinated (in 1) and coordinated (in 2) water molecules are involved. The structures of 3 and 4 consist of polymeric monodimensional chains of square pyramidal copper units linked by axial-equatorial syn-anti (3) or anti-anti (4) bridging formate groups. Water molecules form hydrogen bonds with formate groups of the same chain in compound 3. In compound 4 the water molecules link the polymeric contiguous chains of complex through hydrogen bonds with oxygen atoms of formate groups and they are also linked between them, forming monodimensional water chains which run parallel to the complex chains. Sheets parallel to the ac plane are formed by alternating chains of water and polymeric complex. Magnetic properties and EPR spectra for these compounds have been studied.     

Preparation and photophysical studies of copper(I) and ruthenium(II) complexes of 4,4′-bis(3,5-dimethoxyphenyl)-6,6′-dimethyl-2,2′-bipyridine

We report the synthesis of a new ligand, 4,4′-bis(3,5-dimethoxyphenyl)-6,6′-dimethyl-2,2′-bipyridine, optimised for binding to copper(I) and with pendant functionality that can eventually be developed into metallodendritic structures. The synthesis and photophysical properties of complexes with copper(I) and ruthenium(II) are reported. The solid state structure of the complex [Cu(1)₂][PF₆] · MeCN (1 = 4,4′-bis(3,5-dimethoxyphenyl)-6,6′-dimethyl-2,2′-bipyridine) is also described.     

Binding of 2′-Amino-2′-Deoxycytidine-5′-Triphosphate to Norovirus Polymerase Induces Rearrangement of the Active Site

Crystal structures of a genogroup II.4 human norovirus polymerase bound to an RNA primer-template duplex and the substrate analogue 2′-amino-2′-deoxycytidine-5′-triphosphate have been determined to 1.8 Å resolution. The alteration of the substrate-binding site that is required to accommodate the 2′-amino group leads to a rearrangement of the polymerase active site and a disruption of the coordination shells of the active-site metal ions. The mode of binding seen for 2′-amino-2′-deoxycytidine-5′-triphosphate suggests a novel molecular mechanism of inhibition that may be exploited for the design of inhibitors targeting viral RNA polymerases.     

Preparation and photophysical properties of precursors of inorganic macromolecules. Mono and binuclear complexes of Ru(II) and terpyridine derivatized with thiophene and 4-(5-bromothiophene) groups

The preparation and characterization of mono and binuclear complexes of Ru(II) with a newly synthesized derivate of the terpyridine ligand, 4^′-(5-bromothiophene)-2,2^′,6^′,2″-terpyridine, are communicated. In the binuclear complex, 2,5-bis(2,2^′,6^′,2″-terpyridine-4^′yl)thiophene was used as a bridge between two Ru(II) centers. The new compounds were characterized by H NMR, UV-Vis and IR spectroscopies. Bands at ∼500 nm for the Ru(II) to terpyridine charge transfer transition and absorption bands at λ<400 nm assigned to intraligand transitions, π^*←π, centered in the tpy moiety were observed in the UV-Vis spectra of the complexes. Irradiation of the complexes in CH₃CN at 337 or 500 nm induced luminescence with maxima at ∼670 nm and lifetimes τ?10² ns. Time-resolved absorption spectroscopy revealed the formation of long-lived species during the decay of the metal to ligand charge transfer excited states. The intermediates were tentatively assigned as unstable products of ligand-substitution or orthometalation excited state reactions.     

Synthesis, structure and DNA cleavage activity of two 4,4′-dimethyl-2,2′-bipyridyl manganese(II) complexes

Two new mononuclear Mn(II) complexes, Mn(dmbpy)₂(OCN)₂ (1) and Mn(dmbpy)₂(dca)₂ (2) (dmbpy = 4,4′-dimethyl-2,2′-bipyridine, dca = dicyanamide), have been synthesized and characterized by IR, elemental analysis, and single crystal X-ray analysis. Both complexes have similar molecular structures. The coordination sphere of the Mn(II) ion in 1 or 2 is a seriously distorted octahedron formed by two dmbpy ligands and two OCN⁻ or dca anions in cis positions. For both complexes, the most striking feature is that the mononuclear molecules are linked together by plentiful weak C-H?N hydrogen bonds into a compact 3D supramolecular structure. DNA cleavage studies show that the complexes can promote plasmid DNA cleavage in the presence of H₂O₂ under physiological conditions, and their cleavage activities are obviously both pH value and complex concentration-dependent. The cleavage mechanism between the complexes and plasmid DNA is likely to involve hydroxyl radicals as reactive oxygen species.     

Exploring water-soluble Pt(II) complexes of diethylenetriamine derivatives functionalized at the central nitrogen. Synthesis, characterization, and reaction with 5′-GMP

The aims of our program are to develop coordination complexes that can be used as selective probes, fluorescent agents and inorganic medicinal agents. In order to accomplish this, the design, synthesis, characterization and X-ray structure of new water-soluble monofunctional Pt(II) complexes with useful spectroscopic properties for assessing metal binding to biomolecules were investigated. Two diethylenetriamine (dien) derivatives, 2-(bis(2-aminoethyl)amino)acetic acid (acdien) and N′-[7-(acetamido)-4-(trifluoromethyl)coumarin]diethylenetriamine (atfcdien), were used. The latter was designed to allow the fluorophore group, 7-amino-4-(trifluoromethyl)coumarin (atfc), to be attached to metal centers through the dien moiety. ¹H NMR spectroscopy and X-ray crystallography were employed to characterize the [Pt(atfcdien)Br][Pt(Me₂SO)Br₃] (8a) and [Pt(acdien)Br]Br (9a) complexes. ¹H NMR and fluorescence spectroscopic methods were used to characterize the [Pt(atfcdien)Br]Br (8b) and [Pt(acdien)Br]Br (9a) complexes. ¹H NMR studies of the monofunctional [Pt(acdien)Br]Br (9a) complex conducted to examine its interaction with guanosine 5′-monophosphate (5′-GMP) in D₂O solutions revealed one downfield-shifted H8 and one downfield-shifted H1′ signal, consistent with 5′-GMP binding via N7 and fast rotation about the Pt-N7 bond.     

4,4′-Bis(tert-butyl)-2,2′-bipyridinedichlorometal(II) - Synthesis, structure and EPR spectroscopy

Due to the better solubility of the 4,4′-substituted bipyridine ligand a series of 4,4′-bis(tert-butyl)-2,2′-bipyridinedichlorometal(II) complexes, [M(tbbpy)Cl₂], with M = Cu, Ni, Zn, Pd, Pt was synthesised and characterised. The blue copper complex 4,4′-bis(tert-butyl)-2,2′-bipyridinedichlorocopper(II) was isolated in two different polymorphic forms, as prisms 1 with a solvent inclusion and solvent-free as needles 2. Both structures were determined by X-ray structure analysis. They crystallise in the monoclinic space group P2₁/c with four molecules in the unit cell, but with different unit cells and packing motifs. Whereas in the prisms 1, with the unit cell parameters a = 12.1613(12), b = 10.6363(7), c = 16.3074(15) Å, β = 94.446(8)°, the packing is dominated by intra- and intermolecular hydrogen bonds, in the needles 2, with a = 7.738(1), b = 18. 333(2), c = 13.291(3) Å, β = 97.512(15)°, only intramolecular hydrogen bonds appear and the complex molecules are arranged in columns which are stabilised by π-π-stacking interactions. In both complexes the copper has a tetrahedrally distorted coordination sphere. These copper complexes were also studied by EPR spectroscopy in solution, as frozen glass and diamagnetically diluted powder with the analogue [Pd(tbbpy)Cl₂] as host lattice.     

Formation of coordination polymer and molecular complex of 4,4′-bipyridyl-N,N′-dioxide of manganese and zinc

A 1D-coordination polymer [{Mn₃(C₆H₅COO)₆(BPNO)₂(MeOH)₂}(MeOH)₂]_n (1) having benzoate as the anionic ligand and 4,4′-bipyridyl-N,N′-dioxide (BPNO) as bridging ligand is synthesized by reacting benzoic acid with manganese(II) acetate tetrahydrate followed by reaction with 4,4′-bipyridyl-N N′-dioxide. The bridging bidentate BPNO ligands in this coordination polymer along with the benzoate bridges hold the repeated units. The chain like structure in one dimension by benzoate bridges are connected to each other through the μ³-η²:η¹ bridges of BPNO ligands. This coordination polymer can be transformed to a molecular complex [Mn(H₂O)₆](C₆H₅COO)_2.4BPNO (2). In this complex the BPNO remains outside the coordination sphere but they are hydrogen bonded to water molecules to form self assembled structure. The reaction of 3,5-pyrazoledicarboxylic acid (L₁H2) and BPNO with manganese(II) acetate or zinc(II) acetate led to molecular complexes with composition [M₂(L₁)₂(H₂O)₆].BPNO·xH₂O {where M = Mn(II) (3), Zn(II)(4)}. These molecular complexes of BPNO are characterised by X-ray crystallography. The complexes 3-4 are binuclear carboxylate complexes having M₂O₂ core formed from carboxylate ligands with two metal ions.     

Validation of a novel in vitro assay using ultra performance liquid chromatography–mass spectrometry (UPLC/MS) to detect and quantify hydroxylated metabolites of BDE-99 in rat liver microsomes

The purpose of this study was to develop and validate an ultra performance liquid chromatography–mass spectrometry (UPLC/MS) method to investigate the hepatic oxidative metabolism of 2,2′,4,4′,5-pentabromodiphenyl ether (BDE-99), a widely used flame retardant and ubiquitous environmental contaminant. Hydroxylated metabolites were extracted using liquid-to-liquid extraction, resolved on a C₁₈ column with gradient elution and detected by mass spectrometry in single ion recording mode using electrospray negative ionization. The assay was validated for linearity, accuracy, precision, limit of quantification, range and recovery. Calibration curves were linear (R² ≥ 0.98) over a concentration range of 0.010–1.0 μM for 4-OH-2,2′,3,4′,5-pentabromodiphenyl ether (4-OH-BDE-90), 5′-OH-2,2′,4,4′,5-pentabromodiphenyl ether (5′-OH-BDE-99) and 6′-OH-2,2′,4,4′,5-pentabromodiphenyl ether (6′-OH-BDE-99), and a concentration range of 0.0625–12.5 μM for 2,4,5-tribromophenol (2,4,5-TBP). Inter- and intra-day accuracy values ranged from −2.0% to 6.0% and from −7.7% to 7.3%, respectively, and inter- and intra-day precision values ranged from 2.0% to 8.5% and from 2.2% to 8.6% (n = 6), respectively. The limits of quantification were 0.010 μM for 4-OH-BDE-90, 5′-OH-BDE-99 and 6′-OH-BDE-99, and 0.0625 μM for 2,4,5-TBP. Recovery values ranged between 85 and 100% for the four analytes. The validated analytical method was applied to identify and quantify hydroxy BDE-99 metabolites formed in vitro. Incubation of BDE-99 with rat liver microsomes yielded 4-OH-BDE-90 and 6′-OH-BDE-99 as major metabolites and 5′-OH-BDE-99 and 2,4,5-TBP as minor metabolites. To our knowledge, this is the first validated UPLC/MS method to quantify hydroxylated metabolites of PBDEs without the need of derivatization.     

The key role of hydrogen bonding in the nuclearity of three copper(II) complexes with hydrazone-derived ligands and nitrogen donor heterocycles

Three new Cu(II) complexes of formula [Cu(L¹)(pyz)(CH₃OH)]ClO₄ (1), [Cu(L¹)(4,4′-bpy)(ClO₄)]·0.5H₂O (2) and [{Cu(L²)(ClO₄)}₂(μ-4,4′-bpy)] (3) have been synthesised by using pyrazine (pyz) and 4,4′-bipyridine (4,4′-bpy) and tridentate O,N,O-donor hydrazone ligands, L¹H and L²H, obtained by the condensation of 1,1,1-trifluoro-2,4-pentanedione with salicyloylhydrazide and benzhydrazide, respectively. The ligands and their complexes have been characterized by elemental analyses, FT-IR, and UV-Vis spectroscopies. Single crystal X-ray structure analysis evidences the metal ion in a slightly deformed square pyramidal geometry in all the complexes. However complexes 1 and 2 are mononuclear with pyz and 4,4′-bpy, respectively, showing an unusual monodentate behavior, while complex 3 is dinuclear with 4,4′-bpy adopting the typical bridging coordination mode. Self assembly of the complex units by hydrogen bonding interactions produces one-dimensional arrangement in each crystal packing. The magnetic characterization of complex 3 indicates a weak antiferromagnetic exchange interaction between the Cu(II) ions (J = −0.96 cm⁻¹) mediated through the long 4,4′-bpy bridge. Electrochemical behavior of the complexes is also discussed.     

DFT study of the interaction of cytidine and 2′-deoxycytidine with Li, Na, and K: effects of metal cationization on sugar puckering and stability of the N-glycosidic bond

Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li⁺, Na⁺, and K⁺ with cytidine and 2′-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li⁺ to Na⁺ and K⁺ for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.5, 55.2, and 41.8 and for 2′-deoxycytidine, 82.8, 57.4, and 42.2 kcal/mol, respectively. It is also interesting to mention that linear correlations between calculated MIA values and the atomic numbers (Z) of the above metal ions were found. The influence of metal cationization on the coordination modes and the strength of the N-glycosidic bond in cytosine nucleosides have been studied. In all cases, the N1-C1′ bond distance changes upon introducing a positive charge in the nucleosides. It has been found that metal binding significantly changes the values of the phase angle of pseudorotation P in the sugar unit of these nucleosides. With respect to the sugar ring, metal binding changes the values of the glycosyl torsion angle and sugar ring conformation. The present calculations in the gas phase provide the first clues on the intrinsic chemistry of these systems and may be of value for studies of the influence of metal cations on the conformational behavior and function of nucleic acids.     

Histamine modified 2′-deoxyriboadenosine - Potential copper binding site in DNAzymes

Copper(II) complexes of histamine modified 2′-deoxyriboadenosine (N-[(9-β-D-2′-deoxyribofuranosylpurin-6-yl)-carbamoyl]histamine) ligand were studied by potentiometric, UV-visible and EPR techniques. The imidazole residue of the ligand was described as the main binding site forming mono-, bis-(ligand) and dimer complexes, but the interactions between adenosine nitrogen N(1) and carbamoyl nitrogen atoms and the copper(II) ion also were detected. This is the first report evaluating the coordinating ability of such a modified adenosine ligand towards copper(II) ion. Our findings suggest that histamine modified 2′-deoxyriboadenosine could chelate efficiently copper(II) ions if it were incorporated into DNAzyme sequence.