4,5-Bis(diphenylphosphinoyl)-1,2,3-triazole ligand: Studies on metal complex formations in liquid-liquid distribution systems

The formation reactions of hydrophobic metal complexes of divalent typical element and transition metal ions with a novel chelating ligand containing N and O donor atoms, 4,5-bis(diphenylphosphinoyl)-1,2,3-triazole (L^TH), were investigated by the liquid-liquid distribution method carried out on metal ions between chloroform and aqueous solutions. The liquid-liquid distribution reaction formulae of metal ions via the formation of hydrophobic metal complexes were revealed, along with their equilibrium constants. Three types of hydrophobic mononuclear and binuclear metal complexes distributed into chloroform solutions were found, namely, ML₂ (M = Mg²⁺, Zn²⁺, Pb²⁺; L = L^T−), ML₂(HL) (M = Cd²⁺, Mn²⁺), and M₂L₃(OH) (M = Co²⁺, Ni²⁺, Cu²⁺). Linear free energy relationships were found between the equilibrium constants of the liquid-liquid distribution reactions and the stability constants of 1:1 complexes consisting of a divalent metal ion and a glycinate. These relationships suggest the chelate formation of N,O-coordination with a heterocyclic five-membered ring in the metal complexes with L^TH.     

Spectroscopic and magnetic properties of diethyl (pyridin-4-ylmethyl)phosphate (4-pmOpe) ligand with perchlorate transition metal salts. Crystal structure of [Cu(4-pmOpe)2(ClO4)2]

The perchlorate M(II) (M = Cu, Ni, Co) complexes with the diethyl (pyridin-4-ylmethyl)phosphate (4-pmOpe) ligand of the composition [M(4-pmOpe)₂ (H₂O)₂](ClO₄)₂ (M = Ni, Co) and [Cu(4-pmOpe)₂(ClO₄)₂] were prepared and studied. The ligand contains two donor atoms, i.e. pyridine nitrogen and phosphoryl oxygen atoms. In particular, the crystal structure of [Cu(4-pmOpe)₂(ClO₄)₂] was determined by the X-ray method. Its structure consists of a one-dimensional polymeric chain in which copper(II) ions are N,O-bridged by two 4-pmOpe organic ligands in a trans arrangement. Two perchlorate ions occupy the fifth and the sixth coordination sites. The Cu?Cu distance is 9.180 Å. The crystal packing is determined by the weak intermolecular C-H?O hydrogen contacts. The coordination compounds were identified and characterized by elemental analysis, spectroscopic and magnetic studies. Spectroscopic and magnetic results of the copper(II) compound are presented in the light of the crystal structure. The magnetic data indicate very weak intra- and interchain magnetic exchange interactions (J^’ = −0.43 and zJ^’ = 0.29 cm⁻¹, respectively). The spectroscopic and magnetic properties of the Co(II) and Ni(II) complexes indicate octahedral and polymeric structure of both compounds in which 4-pmOpe ligand also acts as N,O-bridge between metal ions.     

Synthesis and characterization of new ternary Cu(II)-polyamines-ATP complexes

Four new complexes of Cu(II) of stoichiometry [Cu(ATP)(polyamine)] containing as ligands the polyamines (PA) ethylenediamine, 1,3-diaminopropane, spermidine or spermine and adenosine 5′triphosphate were prepared from aqueous solution at pH 6. The synthesis, characterization, thermogravimetric, vibrational spectroscopy, electron paramagnetic resonance analyses are described and show that these complexes have similar molecular structures. The infrared spectra and the thermal analysis are briefly discussed based on the peculiarities of the complexes. The IR spectra of the ligands and their copper complexes were used to assign the various groups and compare the shifts due to complexation. The EPR parameters values for the complexes show that Cu(II) is complexed in a similar way in the four complexes. Similarity in the coordination mode of complexes in solid state has been determined and discussed. The data obtained suggest that the four complexes present one water molecule of hydration and are complexed through two oxygen atoms from ATP and through two nitrogen atoms of each polyamine.     

Synthesis, spectroscopy and thermal behavior of new lead(II) complexes derived from S-methyl/benzyldithiocarbazates (SMDTC/SBDTC): X-ray crystal structure of [Pb(SMDTC)(NO3)2]

Lead(II) complexes of S-methyldithiocarbazate (SMDTC), [Pb(SMDTC)(NO₃)₂] (1) and S-benzyldithiocarbazate (SBDTC), [Pb(SBDTC)(NO₃)₂] (2) have been synthesized for the first time and characterized by elemental analysis, IR and TGA techniques. The complexes were obtained by addition of the appropriate ligand to an aqueous ethanolic solution of lead(II) nitrate in 1:1 molar ratio. The X-ray crystal structure of complex 1 has been determined by single crystal X-ray diffractometry. In complex 1, lead(II) is in a nine coordinated sphere with seven oxygen atoms of the nitrate groups and thione sulfur, β-nitrogen of neutral bidentate NS chelating ligand. Three nitrate groups act as bidentate chelating whereas the fourth nitrate group is coordinating to the central lead(II) and at the same time it bridges with neighboring lead(II) atom. Coordination geometry of the central lead(II) atom has a tricapped trigonal prismatic arrangement with streochemically inactive lone pair. The lead atoms are linked into polymeric chains and these chains form twin polymeric ribbons linked through bridging oxygen atoms. The N-H?O hydrogen bond network between N_SMDTC and O_nitrate atom leads to self-assembled molecular conformation and stabilizes the crystal structure. The complex 2 with similar spectral and thermal behavior is expected to have a tricapped trigonal prismatic structure. The thermal behavior studies shows that the complexes start to decompose at relatively low temperature (ca. 110 °C) to give PbS residue.     

Shape complementarity of protein-protein complexes at multiple resolutions

Biological complexes typically exhibit intermolecular interfaces of high shape complementarity. Many computational docking approaches use this surface complementarity as a guide in the search for predicting the structures of protein-protein complexes. Proteins often undergo conformational changes to create a highly complementary interface when associating. These conformational changes are a major cause of failure for automated docking procedures when predicting binding modes between proteins using their unbound conformations. Low resolution surfaces in which high frequency geometric details are omitted have been used to address this problem. These smoothed, or blurred, surfaces are expected to minimize the differences between free and bound structures, especially those that are due to side chain conformations or small backbone deviations. Despite the fact that this approach has been used in many docking protocols, there has yet to be a systematic study of the effects of such surface smoothing on the shape complementarity of the resulting interfaces. Here we investigate this question by computing shape complementarity of a set of 66 protein-protein complexes represented by multiresolution blurred surfaces. Complexed and unbound structures are available for these protein-protein complexes. They are a subset of complexes from a nonredundant docking benchmark selected for rigidity (i.e. the proteins undergo limited conformational changes between their bound and unbound states). In this work, we construct the surfaces by isocontouring a density map obtained by accumulating the densities of Gaussian functions placed at all atom centers of the molecule. The smoothness or resolution is specified by a Gaussian fall-off coefficient, termed "blobbyness." Shape complementarity is quantified using a histogram of the shortest distances between two proteins' surface mesh vertices for both the crystallographic complexes and the complexes built using the protein structures in their unbound conformation. The histograms calculated for the bound complex structures demonstrate that medium resolution smoothing (blobbyness = -0.9) can reproduce about 88% of the shape complementarity of atomic resolution surfaces. Complexes formed from the free component structures show a partial loss of shape complementarity (more overlaps and gaps) with the atomic resolution surfaces. For surfaces smoothed to low resolution (blobbyness = -0.3), we find more consistency of shape complementarity between the complexed and free cases. To further reduce bad contacts without significantly impacting the good contacts we introduce another blurred surface, in which the Gaussian densities of flexible atoms are reduced. From these results we discuss the use of shape complementarity in protein-protein docking.     

Binding of HIV-1 TAR mRNA to a peptide nucleic acid oligomer and its conjugates with metal-ion-binding multidentate ligands

A peptide nucleic acid (PNA) oligomer and a series of PNA conjugates featuring covalently attached pendant 1,4,7,10-tetraazacyclododecane (cyclen) or bis((pyridin-2-yl)methyl)amine (DPA) moieties have been synthesized that are complementary to regions of the HIV-1 TAR messenger RNA stem-loop. Thermal denaturation studies, in conjunction win with native gel shift assays, suggest that the PNAs “invade” TAR to produce a mixture of two 1:1 PNA–TAR adducts, tentatively assigned as an “open-duplex” structure, in which the TAR stem-loop dissociates and the PNA hybridizes with its RNA complement via Watson–Crick base-pairing, and a triplex-type structure, in which the initially displaced RNA segment is bound to the PNA:RNA duplex through Hoogsteen base-pairing. Thermal denaturation experiments with the TAR sequence and single-stranded RNA and DNA oligonucleotides, both in the presence and in the absence of Zn²⁺ ions, show that the introduction of cyclen or DPA ligand arms into the PNA oligomer leads to a small but reproducible increase in the T _m values. This is attributed to hydrogen-bonding and/or electrostatic interactions between protonated forms of cyclen/DPA and the cognate RNA or DNA oligonucleotide targets. Contrary to expectations, the addition of Zn²⁺ ions did not further enhance duplex formation through binding of Zn(II)–cyclen or Zn(II)–DPA moieties to the complementary RNA or DNA. Native gel shift assays further confirmed the stability increase of the metal-free cyclen- and DPA-modified PNA hybrids as compared with a control PNA sequence. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Two Cooperating Helices Constitute the Lipid-binding Domain of the Bacterial SRP Receptor

Protein targeting by the bacterial signal recognition particle requires the specific interaction of the signal recognition particle (SRP)-ribosome-nascent chain complex with FtsY, the bacterial SRP receptor. Although FtsY in Escherichia coli lacks a transmembrane domain, the membrane-bound FtsY displays many features of an integral membrane protein. Our data reveal that it is the cooperative action of two lipid-binding helices that allows this unusually strong membrane contact. Helix I comprises the first 14 amino acids of FtsY and the second is located at the interface between the A- and the N-domain of FtsY. We show by site-directed cross-linking and binding assays that both helices bind to negatively charged phospholipids, with a preference for phosphatidyl glycerol. Despite the strong lipid binding, helix I does not seem to be completely inserted into the lipid phase, but appears to be oriented parallel with the membrane surface. The two helices together with the connecting linker constitute an independently folded domain, which maintains its lipid binding even in the absence of the conserved NG-core of FtsY. In summary, our data reveal that the two consecutive lipid-binding helices of FtsY can provide a membrane contact that does not differ significantly in stability from that provided by a transmembrane domain. This explains why the bacterial SRP receptor does not require an integral β-subunit for membrane binding.     

Preparation, circular dichroism induced helical conformation and optical property of chitosan acid salt complexes for biomedical applications

The efficient procedure for preparation of chitosan acid complexes containing aspartic acid, benzilic acid and terephthalic acid moieties in isopropyl alcohol under mild condition has been demonstrated. The ionic complexation between chitosan and the acid is confirmed by FTIR and ¹H NMR spectroscopy. The circular dichroism (CD) spectra of chitosan/aspartic acid complex showed negative (at λ = 312) band, chitosan/benzilic acid and chitosan/terephthalic complexes showed positive (at λ = 286 and 315 nm) band in DMSO, indicating that the polymers adopted helical (left-handed and last two right-handed) secondary structure. The inversion of the CD pattern in chitosan acid salt complexes suggests that there is a change in the chiral structure of the polymer system. Some physical properties and surface morphology were analyzed by X-ray diffraction (XRD), differential scanning calorimetry (DSC), thermogravimetry (TG) and scanning electron microscopy (SEM). Optical properties of chitosan derivatives are evaluated by photoluminescence (PL) spectroscopy which showed red shift. The introduction of acid moieties into chitosan increases the solubility in most of the organic solvents, which opens new perspectives for the employment of chitosan-based biohybrid in biomedical applications.     

DNA photocleavage activity of cobalt(III) polypyridyl complexes containing dpq ligand

Four cobalt(III) polypyridyl complexes, [Co(phen)_3−n(dpq)_n]³⁺ (phen = 1,10-phenanthroline, dpq = dipyrido[3,2-f:2′,3′-h]-quinoxaline) (n = 0, 1, 2, and 3) were synthesized and the influences of the dpq ligand on the photophysical properties, electrochemical properties, DNA binding affinities, as well as photonuclease activities of the complexes, were examined in detail. The presence of dpq ligand increases the DNA binding affinities of the corresponding complexes remarkably with respect to [Co(phen)₃]³⁺. With the sequential substitution of phen ligand by dpq ligand, the ¹O₂ quantum yields of the corresponding complexes are enhanced greatly. As a result, the photonuclease activities follow the order of [Co(dpq)₃]³⁺ > [Co(phen)(dpq)₂]³⁺ > [Co(phen)₂(dpq)]³⁺ ? [Co(phen)₃]³⁺. It was found all the examined complexes can generate OH upon UV irradiation, and OH is also involved in DNA photocleavage as reactive oxygen species.     

Synthesis, characterization and deepening in the comprehension of the biological action mechanisms of a new nickel complex with antiproliferative activity

Thiosemicarbazones are versatile organic compounds that present considerable pharmaceutical interest because of a wide range of properties. In our laboratory we synthesised some new metal-complexes with thiosemicarbazones derived from natural aldehydes which showed peculiar biological activities. In particular, a nickel complex [Ni(S-tcitr)₂] (S-tcitr = S-citronellalthiosemicarbazonate) was observed to induce an antiproliferative effect on U937, a human histiocytic lymphoma cell line, at low concentrations (IC₅₀ = 14.4 μM). Therefore, we decided to study the interactions of this molecule with various cellular components and to characterise the induced apoptotic pathway. Results showed that [Ni(S-tcitr)₂] causes programmed cell death via down-regulation of Bcl-2, alteration of mitochondrial membrane potential and caspase-3 activity, regardless of p53 function. The metal complex is not active on G₀ cells (i.e. fresh leukocytes) but is able to induce perturbation of the cell cycle on stimulated lymphocytes and U937 cells, in which a G₂/M block was detected. It reaches the nucleus where it induces, at low concentrations (2.5-5.0 μM), DNA damage, which could be partially ascribed to oxidative stress. [Ni(S-tcitr)₂] is moreover able to strongly reduce the telomerase activity. Although the biological target of this metal complex is still unknown, the reported data suggest that [Ni(S-tcitr)₂] could be a good model for the synthesis of new metal thiosemicarbazones with specific biological activity.