Cluster Ligands Research Articles

Supramolecular Architectures Featuring Stereoisomeric Cluster Complexes of the [Re6(μ3‐Se)8]2+ Core

AbstractFor Abstract see ChemInform Abstract in Full Text.

Reaction of Mixed-Ligand Iron–Sulfur Cluster [Fe4(Cp*)3(Ph2C2S2)(μ3-S)3(μ3-S2)] (Cp* = C5Me5) with Methyl Iodide. Synthesis, Structure, and Redox Behavior of [Fe4(Cp*)3(Ph2C2S2)(μ3-S)3(μ3-S2Me)

Abstract The reaction of the mixed-ligand iron–sulfur cluster [Fe4(Cp*)3(Ph2C2S2)(μ3-S)3(μ3-S2)] ([3]) (Cp* = C5Me5) with iodomethane gave a methylated cluster, [Fe4(Cp*)3(Ph2C2S2)(μ3-S)3(μ3-S2Me)]I ([4]I), in 60% yield. The anion exchange of [4]I with KPF6 gave [4]PF6 as a pure sample. A similar treatment of [3] using iodoethane afforded an ethylated cluster, [Fe4(Cp*)3(Ph2C2S2)(μ3-S)3(μ3-S2Et)]I ([5]I), and oxidized parent cluster [3]I. The reaction of [3] with 2-iodopropane did not give an alkylated cluster. An unreacted cluster [3] was recovered with a small amount of oxidized cluster [3]I. The molecular structure of [Fe4(Cp*)3(Ph2C2S2)(μ3-S)3(μ3-S2Me)] ([4]), which was obtained by the reduction of [4]PF6 with cobaltocene, was determined by an X-ray diffraction study. Crystallographic data are: Monoclinic, P21/a, a = 21.707(2) Å, b = 21.382(2) Å, c = 11.433(1) Å, β = 98.98(1)°, V = 5241.5(9) Å3, Z = 4, and R = 0.067 for 7412 reflections with |Fo| > 3σ(Fo). The methyl group transferred from MeI is located on the singly ligating sulfur atom in the disulfide ligand of the parent cluster [3]. A cyclic voltammogram of [4]PF6 in 0.1 mol dm−3 tetrabutylammonium tetrafluoroborate–CH3CN showed five reversible one-electron redox waves at E1/2 = +1.42 V, +0.92 V, +0.41 V, −0.38 V, and −1.22 V vs SCE, corresponding to 4+/3+, 3+/2+, 2+/1+, 1+/0, and 0/1− charged cluster couples, respectively. An irreversible two-electron reduction wave was also observed at Epc = −1.97 V vs SCE.

GPCR-tailored pharmacophore pattern recognition of small molecular ligands.

The goal of our work was to differentiate between patterns, which are responsible for the activity of small molecular ligands binding to G-protein coupled receptors (GPCRs) and molecules, which are pharmacologically active on other target classes. Second the aim was to go one step further and analyze the chemical space occupied by GPCR active ligands itself, to distinguish between the actives of different subclasses or even cluster ligands for single receptors. To achieve these objectives, we have built a database of small, organic molecules, which bind to GPCRs. Once this crucial foundation for pattern recognition has been laid, we needed to find a descriptor, which is able to detect the compulsory features responsible for activity within a molecule. In this matter we found that the well accepted pharmacophore descriptor served us well. Finally we needed to find a method to display the clustering or separation of the specific ligands. We found that self-organizing maps (SOMs) perform excellently in this task. We herein present the analysis of the chemical space of active compounds, depending on their biological target, the GPCRs. We will also discuss the techniques used to create the chemical spaces. The findings can be applied and have an impact at various stages of the drug discovery process.

A New N-Acetylgalactosamine Containing Peptide as a Targeting Vehicle for Mammalian Hepatocytes Via Asialoglycoprotein Receptor Endocytosis

Galactoside-containing cluster ligands have high affinity for asialoglycoprotein receptors (ASGP-r), which are found in abundance in mammalian parenchymal liver cells. These ligands may be conjugated with a therapeutic drug to improve the efficiency of delivery to diseased liver cells. This report describes a new synthetic route towards clustering glycopeptides containing N-acetyl-D-galactosamine (GalNAc). The building block Fmoc-alpha-(ah-Ac3GalNAc)-L-glutamate allowed access to the target compound YEEE(alpha-ah-GalNAc)(3), a structural mimic of YEE(ah-GalNAc)(3), via solid phase peptide synthesis (SPPS). Fatty acid, poly-lysine, fluorescein and biotin conjugates further demonstrate the facility of the described method. Using fluorescein labeling and 131I labeling, in vitro and in vivo assays confirmed that YEEE(alpha-ah-GalNAc)(3) possesses both specificity and affinity to the liver, similar to the agent YEE(ah-GalNAc)(3), which targets liver lesions. The synthesis described in this report represents a considerable improvement in synthesizing a ligand for ASGP-r by simplifying both the preparation of the starting material and the procedure for conjugating the galactosidase cluster to drugs.

Supramolecular architectures featuring stereoisomeric cluster complexes of the [Re6(μ3‐Se)8]2+ core

AbstractThe [Re6(μ3‐Se)8]2+ core‐containing cluster complexes of the general formula [Re6(μ3‐Se)8(PEt3)4L2]2+ (both trans‐ and cis‐isomers) site‐differentiated with inert PEt3 and functional L ligands that are capable of hydrogen bonding or secondary (with respect to primary coordination with the cluster core) metal‐ligand coordination interactions have been prepared. The applications of such stereospecific cluster isomers as building blocks for supramolecular construction have been studied. A great variety of multicluster arrays mediated by intercluster hydrogen bonding or cluster ligand coordination with secondary metal ions have been obtained and structurally characterized. The findings from this research clearly establish the superior utility of these novel building blocks for the creation of structurally sophisticated architectures and possibly functional materials.

Control of the ratio of functional and non-functional ligands in clusters of the type Zr6O4(OH)4(carboxylate)12for their use as building blocks for inorganic–organic hybrid polymers

The methacrylate ligands of the cluster Zr6O4(OH)4(methacrylate)12 undergo degenerate exchange with methacrylic acid in solution. Addition of propionic or isobutyric acid allows partial or complete exchange of the methacrylate ligands for propionate or isobutyrate. The mixed-carboxylate cluster Zr6O4(OH)4(OMc)8(isobutyrate)4(BuOH) was independently prepared by reaction of Zr(OnBu)4 with a mixture of methacrylic acid and isobutyric acid. The structures of Zr6O4(OH)4(OMc)8(isobutyrate)4(BuOH) and Zr6O4(OH)4(isobutyrate)12(H2O) consist of an octahedral Zr6(μ3-O)4(μ3-OH)4 core with one of the carboxylate ligands being monodentate. The H2O or ROH molecule is coordinated to the neighbouring zirconium atom and, at the same time, hydrogen bonded to the monodentate carboxylate. A mechanism for the carboxylate exchange is suggested based on the structural observations.

Coordination polymer incorporating maleonitriledithiolate copper clusters: electrocrystallization synthesis and crystal structure of (NPr4)2[Cu(MeCN)]2[Cu8(i-mnt)6].(MeCN)0.5.(THF)0.25.

(NPr4)2[Cu(MeCN)]2[Cu8(i-mnt)6].(MeCN)0.5.(THF)0.25 is prepared by electrocrystallization of a solution of (NPr(4))(4)[Cu(I)(8)(i-mnt)(6)]; the crystal structure consists in bidimensional layers characterised by coordination of copper atoms by the cyano groups of the iso-maleonitriledithiolate ligand of the octa-copper cluster.

Interaction of platelets with liposomes containing dodecapeptide sequence from fibrinogen.

Liposomes with a covalently bound synthetic peptide containing the dodecapeptide sequence HHLGGAKQAGDV, the putative platelet interaction site at gamma(400-411) of fibrinogen (dodecapeptide-liposomes), were prepared. These liposomes enhanced platelet aggregation and specifically adhered to platelets activated on the collagen surface. Dodecapeptide-liposomes released encapsulated materials upon interacting with platelets activated on the collagen surface. The rate of content release was dependent on the peptide surface density, indicating that the interaction between the dodecapeptide-liposomes and platelets activated on the collagen surface induces clustering of the surface-coupled ligands at the binding site on the receptor matrix to facilitate release of the internal contents through the liposome membranes. The level of lipid mixing between the dodecapeptide-liposomes and platelets activated on the collagen surface was relatively low, however it was increased in liposome preparations containing octa-arginine, the (R)8 GDV sequence, while content release was maintained at the same level as that of the dodecapeptide-liposomes. The level of content release and lipid mixing for liposome preparations containing the RGD sequence as a ligand (RGD-liposomes) upon interacting with platelets activated on the collagen surface was extremely low. Both the level of the content release and lipid mixing, however, were enhanced in liposome preparations containing octa-arginine, the (R)8 RGD sequence. Dodecapeptide-liposomes and RGD-liposomes were not internalized by activated platelets. On the other hand, liposomes containing (R)8 PPQ, (R)8 RGD, or (R)8 GDV were internalized by activated platelets, and the extent of internalization was inversely related to ligand affinity to the target.

Reactions of 2,4-hexadiyne-1,6-diol with [H2Os3(CO)9(PR3)] clusters. Cyclization of the diyne and reversible exchange of the phosphine ligands between different positions of the "Os3C3" framework.

Reactions between unsaturated [H(2)Os(3)(CO)(9)(PR(3))] clusters (PR(3)= PPh(3), P(4-CF(3)-C(6)H(4))(3), PEt(3)) and 2,4-hexadiyne-1,6-diol have been studied. It was found that the diyne ligand easily reacts with all these complexes to give [HOs(3)(CO)8(PR3)-[mu3, eta1:eta3:eta1)-(CH(3)-C-C=CH-CH=C-O)]] complexes (V, VI and VII, respectively) containing the "Os3C3" pentagonal pyramid cluster framework. This structural pattern is formed through the diyne cyclization, dissociation of a CO ligand and eventual coordination of the cyclized organic moiety to the osmium triangle in the [mu3, eta1:eta3:eta1) manner. In the case of the PEt(3) substituted cluster the second hydride transfer onto the organic fragment occurs to afford the nonhydride [Os(3)(CO)(8)(PR3)[mu3), eta1:eta2:eta1)-(CH(3)-CH-C=CH-CH=C-O)]] cluster, VIII, containing distorted pentagonal pyramid framework with a broken Os-C bond. Heating V, VI of VII and in hexane solutions results in formation of the regioisomers (Va, VIa and VIIa) with the phosphine ligand located at adjacent osmium atoms across the Os-Os bond bridged by the coordinated organic fragment. The most probable mechanism of the isomerization includes reversible phosphine migration between these metal centres. Solid-state structure of V, Va, VI, VIIa and VIII have been established by single crystal X-ray diffraction. A general mechanistic scheme for the diyne ligand cyclization and cluster framework transformations is suggested and discussed.

Molecular characterization and substrate preference of a polycyclic aromatic hydrocarbon dioxygenase from Cycloclasticus sp. strain A5.

Cycloclasticus sp. strain A5 is able to grow with petroleum polycyclic aromatic hydrocarbons (PAHs), including unsubstituted and substituted naphthalenes, dibenzothiophenes, phenanthrenes, and fluorenes. A set of genes responsible for the degradation of petroleum PAHs was isolated by using the ability of the organism to oxidize indole to indigo. This 10.5-kb DNA fragment was sequenced and found to contain 10 open reading frames (ORFs). Seven ORFs showed homology to previously characterized genes for PAH degradation and were designated phn genes, although the sequence and order of these phn genes were significantly different from the sequence and order of the known PAH-degrading genes. The phnA1, phnA2, phnA3, and phnA4 genes, which encode the alpha and beta subunits of an iron-sulfur protein, a ferredoxin, and a ferredoxin reductase, respectively, were identified as the genes coding for PAH dioxygenase. The phnA4A3 gene cluster was located 3.7 kb downstream of the phnA2 gene. PhnA1 and PhnA2 exhibited moderate (less than 62%) sequence identity to the alpha and beta subunits of other aromatic ring-hydroxylating dioxygenases, but motifs such as the Fe(II)-binding site and the [2Fe-2S] cluster ligands were conserved. Escherichia coli cells possessing the phnA1A2A3A4 genes were able to convert phenanthrene, naphthalene, and methylnaphthalene in addition to the tricyclic heterocycles dibenzofuran and dibenzothiophene to their hydroxylated forms. Significantly, the E. coli cells also transformed biphenyl and diphenylmethane, which are ordinarily the substrates of biphenyl dioxygenases.

Spectroscopic characterization of a novel 2×[4Fe–4S] ferredoxin isolated from Desulfovibrio desulfuricans ATCC 27774

A novel iron–sulfur containing protein, a ferredoxin (Fd), was purified to homogeneity from the extract of Desulfovibrio desulfuricans American type culture collection (ATCC) 27774. The purified protein is a 13.4 kDa homodimer with a polypeptide chain of 60 amino acids residues, containing eight cysteines that coordinate two [4Fe–4S] clusters. The protein is shown to be air sensitive and cluster conversions take place. We structurally characterize a redox state that contains two [4Fe–4S] cores. 1D and 2D 1H NMR studies are reported on form containing the clusters in the oxidized state. Based on the nuclear Overhauser effect (NOE), relaxation measurements and comparison of the present data with the available spectra of the analogous 8Fe Fds, the cluster ligands were specifically assigned to the eight-cysteinyl residues.

Reactions of Diphosphine-Stabilized Tetracobalt Carbonyl Clusters with −Si(OR)3-Functionalized Alkynes

Short-bite ligand cluster stabilization is achieved in the tetrahedral clusters [Co4(μ-CO)3 (CO)7(μ-dppy)] (1a−c), obtained in high yields by reactions of [Co4(CO)12] with 1 equiv of the diphosphine ligands dppy, Ph2PCH2PPh2 (dppm), Ph2PNHPPh2 (dppa), or (Ph2P)2N(CH2)3Si(OEt)3 (dppaSi), respectively. The structure of 1a has been determined by X-ray diffraction, and the P atoms occupy axial positions on the basal face, transoid to a Co−Co bond. Clusters 1a−c were reacted with phenylacetylene to afford the corresponding butterfly clusters [Co4(μ-CO)2(CO)6(μ-dppy)(μ4-η2-PhC2H)] (2a−c) by insertion of the alkyne into a Co−Co bond of the precursor. This was established by an X-ray diffraction study of [Co4(μ-CO)2(CO)6(μ-dppm)(μ4-η2-PhC2H)] (2a). In an alternative synthetic procedure, the alkyne cluster [Co4(CO)10(μ4-η2-PhC2H)] (3), prepared from [Co4(CO)12] and phenylacetylene, was reacted with the diphosphines dppy. This led in good yields to butterfly clusters, isomeric with 2a−c in terms of the position of ...

Endogenously Produced Endothelial Lipase Enhances Binding and Cellular Processing of Plasma Lipoproteins via Heparan Sulfate Proteoglycan-mediated Pathway

Endothelial lipase (EL) is a new member of the triglyceride lipase gene family, which includes lipoprotein lipase (LpL) and hepatic lipase (HL). Enzymatic activity of EL has been studied before. Here we characterized the ability of EL to bridge lipoproteins to the cell surface. Expression of EL in wild-type Chinese hamster ovary (CHO)-K1 but not in heparan sulfate proteoglycan (HSPG)-deficient CHO-677 cells resulted in 3-4.4-fold increases of 125I-low density lipoprotein (LDL) and 125I-high density lipoprotein 3 binding (HDL3). Inhibition of proteoglycan sulfation by sodium chlorate or incubation of cells with labeled lipoproteins in the presence of heparin (100 microg/ml) abolished bridging effects of EL. An enzymatically inactive EL, EL-S149A, was equally effective in facilitating lipoprotein bridging as native EL. Processing of LDL and HDL differed notably after initial binding via EL to the cell surface. More than 90% of the surface-bound 125I-LDL was destined for internalization and degradation, whereas about 70% of the surface-bound 125I-HDL3 was released back into the medium. These differences were significantly attenuated after HDL clustering was promoted using antibody against apolipoprotein A-I. At equal protein concentration of added lipoproteins the ratio of HDL3 to VLDL bridging via EL was 0.092 compared with 0.174 via HL and 0.002 via LpL. In summary, EL mediates binding and uptake of plasma lipoproteins via a process that is independent of its enzymatic activity, requires cellular heparan sulfate proteoglycans, and is regulated by ligand clustering.

Structure of the Yeast Cytochrome bc1 Complex with a Hydroxyquinone Anion Qo Site Inhibitor Bound

Bifurcated electron transfer during ubiquinol oxidation is the key reaction of cytochrome bc1 complex catalysis. Binding of the competitive inhibitor 5-n-heptyl-6-hydroxy-4,7-dioxobenzothiazole to the Qo site of the cytochrome bc1 complex from Saccharomyces cerevisiae was analyzed by x-ray crystallography. This alkylhydroxydioxobenzothiazole is bound in its ionized form as evident from the crystal structure and confirmed by spectroscopic analysis, consistent with a measured pKa = 6.1 of the hydroxy group in detergent micelles. Stabilizing forces for the hydroxyquinone anion inhibitor include a polarized hydrogen bond to the iron-sulfur cluster ligand His181 and on-edge interactions via weak hydrogen bonds with cytochrome b residue Tyr279. The hydroxy group of the latter contributes to stabilization of the Rieske protein in the b-position by donating a hydrogen bond. The reported pH dependence of inhibition with lower efficacy at alkaline pH is attributed to the protonation state of His181 with a pKa of 7.5. Glu272, a proposed primary ligand and proton acceptor of ubiquinol, is not bound to the carbonyl group of the hydroxydioxobenzothiazole ring but is rotated out of the binding pocket toward the heme bL propionate A, to which it is hydrogen-bonded via a single water molecule. The observed hydrogen bonding pattern provides experimental evidence for the previously proposed proton exit pathway involving the heme propionate and a chain of water molecules. Binding of the alkyl-6-hydroxy-4,7-dioxobenzothiazole is discussed as resembling an intermediate step of ubiquinol oxidation, supporting a single occupancy model at the Qo site.

A novel mode for integrin-mediated signaling: tethering is required for phosphorylation of FAK Y397.

The common model for integrin mediated signaling is based on integrin clustering and the potential for that clustering to recruit signaling molecules including FAK and src. The clustering model for transmembrane signaling originated with the analysis of the EGF receptor signaling and remains the predominant model. The roles for substrate-bound ligand and ligand occupancy in integrin-mediated signaling are less clear. A kinetic model was established using HT1080 cells in which there was a linear relationship between the strength of adhesion, the proportion of alpha5beta1 integrin that could be chemically cross-linked, and the number of receptor-ligand bonds. This graded signal produced a similarly graded response measured by the level of specific phosphorylation of FAK Y397. FAK Y397 phosphorylation could also be induced by antibody bound to the substrate. In contrast, clustering of alpha5beta1 on suspended cells with either antibody to beta1 or by clustering of soluble ligand bound to alpha5beta1 induced the phosphorylation of FAK Y861 but not Y397. There were no differences in signaling when activating antibodies were compared with blocking antibodies, presence or absence of ligand. Only tethering of alpha5beta1 to the substrate was required for induction of FAK Y397 phosphorylation.

Aromatic ring destruction in complexes of dipositive metal cations

Singly charged metal cations do not normally activate the π-ring in monoaromatic ligands. Here pyridine complexes of six dipositive metal cations (Ca, Mg, Mn, Fe, Co, and Cu) are probed using collisional dissociation. Except for Cu, species with one–three ligands (depending on the metal) exhibit two significant aromaticity-destroying ligand cleavage processes. One proceeds with charge reduction yielding singly charged bare or ligated metal cyanide cations and C 4H 5 +, and the other retains the double charge eliminating one or two small neutrals such as NH 2 or CH 3. The previously reported cluster-to-metal charge transfer producing charged ligand clusters is shown to not occur.

Spin-state effects on the outer core-level multiplet structures for high-spin Mn molecular clusters

Oxo-bridged manganese polynuclear complexes have applications in a variety of technologies, such as single-molecule nanomagnets, catalysis, and photosynthetic redox chemistry. X-ray photoemission spectroscopy was used to study the Mn 3p, 3s, and valence band electronic behavior as a function of Mn cluster structural properties, where the cluster size and nuclearity are systematically varied. Results show a chemical shift of the Mn 3p3/2,1/2 spin–orbit pair related to the cluster size and nuclearity. In addition, the Mn 3s S7 and S5 final state multiplet components shift since they involve the binding energy of a ligand valence electron. In addition, the branching ratio of the S7:S5 states is related to the 3s–3d electron correlation. Specifically, in the S7 state, the remaining 3s electron is well correlated with 3d electrons of parallel spin, while in the S5 state, the two spins are antiparallel. Changes in this electron correlation are clearly observed in the S7:S5 branching ratio as a function of cluster size and ligand electronegativity.

The Role of Guest Molecules in the Self‐Assembly of Metal—Ligand Clusters

AbstractFor Abstract see ChemInform Abstract in Full Text.

Visualization and Characterization of Receptor Clusters by Transmission Electron Microscopy

Publisher Summary Multivalent ligands often bind avidly to their target receptors. In addition, they can simultaneously bind multiple receptors and cause them to become clustered. Receptor clustering by multivalent ligands modulates the cell adhesion and signaling functions of many carbohydratebinding proteins, including galectins and selectins. Not all clusters, however, are equivalent in signaling potency or adhesion properties. Clusters that contain multiple copies of a receptor often elicit greater responses; therefore, the stoichiometry of receptor–ligand clusters can be an important determinant of activity. The prevalence of multivalency in protein–carbohydrate interactions mandates that new methods to characterize multivalent binding should be developed. Although many assays focus on assessing the apparent affinity of a multivalent carbohydrate–lectin interaction, many multivalent ligands promote lectin clustering. Because the clustering of a lectin can interfere with or augment its function, methods to characterize lectin–ligand assemblies are needed. The TEM method described in this chapter facilitates the visualization and characterization of such clusters. In addition, using this technique, the effects of ligand valency on cluster size can be investigated. Another potential use of this TEM method is in exploring heterogeneous multireceptor clusters.

Adaptor protein Ruk1 forms protein-protein complexes with endonuclease activity in HEK293 cells.

The structural and functional organization of the adaptor protein Ruk(1) is characterized by the presence of three SH3-domains at the N-terminus followed by Pro- and Ser-rich sequences and a C-terminal coiled-coil region. Multiple modules in the Ruk(1) structure involved in protein-protein interactions can provide for formation of ligand clusters with varied properties and subcellular location. To study the nature and biological role of such complexes, the recombinant protein Ruk(1) with a Glu-epitope at the C-terminus (Ruk(1) Glu-tagged) was purified from transfected HEK293 cells by affinity chromatography on protein G-Sepharose with covalently conjugated anti-Glu-tag antibodies. By SDS polyacrylamide gel electrophoresis with subsequent staining with silver, a set of minor bands in addition to the 85-kD Ruk(1) Glu-tagged was detected in the purified preparation of the recombinant protein. Proteins with affinity for nucleic acids were also revealed in the Ruk(1) Glu-tagged preparation by retardation of electrophoretic mobility of 32P-labeled oligodeoxyribonucleotides in gel. The Ruk(1) Glu-tagged preparation was also shown to hydrolyze both deoxyribonucleotides and plasmid DNA. ZnCl2 and heparin inhibited the DNAse activity. These findings suggest the presence of DNases associated with the Ruk(1) protein in HEK293 cells. Such complexes were isolated from lysates of HEK293 cells by chromatography on heparin-Sepharose. By elution with 0.5 and 1.0 M NaCl, two fractions with DNase activity and containing proteins with molecular weights of 83, 80, and 72 kD were obtained. The reaction was inhibited by ZnCl2 and heparin, and previous precipitation of Ruk-related proteins with anti-Ruk antibodies resulted in the exhaustion of nuclease activity. By immunoblotting with anti-Ruk antibodies, 83-kD protein immunologically related to the Ruk(1) protein was identified in the fractions. It was concluded that the adaptor protein Ruk(1) forms complexes with endonucleases in HEK293 cells.