Cluster Ligands Research Articles

In silico search for multi-target therapies for osteoarthritis based on 10 common Huoxue Huayu herbs and potential applications to other diseases

Huoxue Huayu (HXHY) has been widely used in traditional Chinese medicine (TCM) as a key therapeutic principle for osteoarthritis (OA), and related herbs have been widely prescribed to treat OA in the clinic. The aims of the present study were to explore a multi-target therapy for OA using 10 common HXHY herbs and to investigate their potential applications for treatment of other diseases. A novel computational simulation approach that integrates chemical structure, ligand clusters, chemical space and drug‑likeness evaluations, as well as docking and network analysis, was used to investigate the properties and effects of the herbs. The compounds contained in the studied HXHY herbs were divided into 10 clusters. Comparison of the chemical properties of these compounds to those of other compounds described in the DrugBank database indicated that the properties of the former are more diverse than those of the latter and that most of the HXHY-derived compounds do not violate the 'Lipinski's rule of five'. Docking analysis allowed for the identification of 39 potential bioactive compounds from HXHY herbs and 11 potential targets for these compounds. The identified targets were closely associated with 49 diseases, including neoplasms, musculoskeletal, nervous system and cardiovascular diseases. Ligand‑target (L‑T) and ligand‑target‑disease (L‑T‑D) networks were constructed in order to further elucidate the pharmacological effects of the herbs. Our findings suggest that a number of compounds from HXHY herbs are promising candidates for mult‑target therapeutic application in OA and may exert diverse pharmacological effects, affecting additional diseases besides OA.

Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach

Binding affinity prediction of potential drugs to target and off-target proteins is an essential asset in drug development. These predictions require the calculation of binding free energies. In such calculations, it is a major challenge to properly account for both the dynamic nature of the protein and the possible variety of ligand-binding orientations, while keeping computational costs tractable. Recently, an iterative Linear Interaction Energy (LIE) approach was introduced, in which results from multiple simulations of a protein-ligand complex are combined into a single binding free energy using a Boltzmann weighting-based scheme. This method was shown to reach experimental accuracy for flexible proteins while retaining the computational efficiency of the general LIE approach. Here, we show that the iterative LIE approach can be used to predict binding affinities in an automated way. A workflow was designed using preselected protein conformations, automated ligand docking and clustering, and a (semi-)automated molecular dynamics simulation setup. We show that using this workflow, binding affinities of aryloxypropanolamines to the malleable Cytochrome P450 2D6 enzyme can be predicted without a priori knowledge of dominant protein-ligand conformations. In addition, we provide an outlook for an approach to assess the quality of the LIE predictions, based on simulation outcomes only.

Structure versatility of coordination polymers constructed from a semirigid ligand and polynuclear metal clusters

Presented here are five coordination polymers based on semirigid polycarboxylate ligand and polynuclear metal clusters of particular interest is that the five compounds feature different topological networks.

Homoleptic and heteroleptic Au(I) complexes containing the new [Co5C(CO)12](-) cluster as ligand.

The new [{Co5C(CO)12}Au{Co(CO)4}](-), , cluster has been obtained from the reaction of [Co6C(CO)15](2-) with two equivalents of [AuCl4](-). reacts with an excess of HBF4 resulting in the formation of [{Co5C(CO)12}2Au](-), . The new derivatives [Co5C(CO)12(AuPPh3)], , and [Co5C(CO)11(AuPPh3)3], , have been obtained by reacting with two and four equivalents of [Au(PPh3)Cl], respectively. All the new species have been structurally characterised by means of X-ray crystallography as their [NEt4][], [NEt4][], [NMe3(CH2Ph)][], and thf·0.5C6H14 salts and solvates. may be viewed as a homoleptic Au(i) complex containing two [Co5C(CO)12](-) clusters as ligands. Similarly, and are heteroleptic Au(i) complexes containing one [Co5C(CO)12](-) cluster ligand as well as [Co(CO)4](-) or PPh3. Conversely, contains the [Co5C(CO)11](3-) cluster stabilized by three [AuPPh3](+) fragments. and have been investigated in solution by means of electrochemical and spectroelectrochemical methods, revealing a very rich redox propensity to form the closely related (n = 1-3) and (n = 0-3) species.

The first tyrosyl radical intermediate formed in the S2-S3 transition of photosystem II.

The EPR "split signals" represent key intermediates of the S-state cycle where the redox active D1-Tyr161 (YZ) has been oxidized by the reaction center of the photosystem II enzyme to its tyrosyl radical form, but the successive oxidation of the Mn4CaO5 cluster has not yet occurred (SiYZ˙). Here we focus on the S2YZ˙ state, which is formed en route to the final metastable state of the catalyst, the S3 state, the state which immediately precedes O-O bond formation. Quantum chemical calculations demonstrate that both isomeric forms of the S2 state, the open and closed cubane isomers, can form states with an oxidized YZ˙ residue without prior deprotonation of the Mn4CaO5 cluster. The two forms are expected to lie close in energy and retain the electronic structure and magnetic topology of the corresponding S2 state of the inorganic core. As expected, tyrosine oxidation results in a proton shift towards His190. Analysis of the electronic rearrangements that occur upon formation of the tyrosyl radical suggests that a likely next step in the catalytic cycle is the deprotonation of a terminal water ligand (W1) of the Mn4CaO5 cluster. Diamagnetic metal ion substitution is used in our calculations to obtain the molecular g-tensor of YZ˙. It is known that the gx value is a sensitive probe not only of the extent of the proton shift between the tyrosine-histidine pair, but also of the polarization environment of the tyrosine, especially about the phenolic oxygen. It is shown for PSII that this environment is determined by the Ca(2+) ion, which locates two water molecules about the phenoxyl oxygen, indirectly modulating the oxidation potential of YZ.

Super-Resolution Methods to Understand Dynamics at Soft Interfaces

Super-resolution optical techniques make it possible to characterize biological structural detail with precision of tens of nanometers, approaching the size scale of single biomolecules. More recently, super-resolution methods have been used to monitor dynamics at soft interfaces with similar spatial resolution. We report direct measurement of super-resolved single α-lactalbumin adsorption/desorption dynamics at single ligands on a porous agarose support, allowing the first direct test of a molecular-scale statistical theory of protein adsorption that was developed over 50 years ago. Together with a molecular-scale comparison of engineered vs. accidentally clustered ligands, the resulting simulated chromatographic elution profiles demonstrate that engineered ligand clusters should be pursued for next-generation stationary phases for ion-exchange protein purification. More generally, this study illustrates the type of new information that can be acquired by applying super-resolution methods to study dynamics at soft interfaces.

Multivalent ligands control stem cell behaviour in vitro and in vivo

There is broad interest in designing nanostructured materials that can interact with cells and regulate key downstream functions1–7. In particular, materials with nanoscale features may enable control over multivalent interactions, which involve the simultaneous binding of multiple ligands on one entity to multiple receptors on another and are ubiquitous throughout biology8–10. Cellular signal transduction of growth factor and morphogen cues that play critical roles in regulating cell function and fate often begins with such multivalent binding of ligands, either secreted or cell-surface tethered, to target cell receptors, leading to receptor clustering11–18. Cellular mechanisms that orchestrate ligand-receptor oligomerisation are complex, however, and the capacity to control multivalent interactions and thereby modulate key signaling events within living systems is therefore currently very limited. Here we demonstrate the design of potent multivalent conjugates that can organise stem cell receptors into nanoscale clusters and control stem cell behaviour in vitro and in vivo. The ectodomain of ephrin-B2, normally an integral membrane protein ligand, was conjugated to a soluble biopolymer to yield multivalent nanoscale conjugates that potently induced signaling in neural stem cells and promoted their neuronal differentiation both in culture and within the brain. Super-resolution microscopy analysis yielded insights into the organisation of receptor-ligand clusters at the nanoscale. We also found that synthetic multivalent conjugates of ephrin-B1 strongly enhanced human embryonic and induced pluripotent stem cell differentiation into functional dopaminergic neurons. Multivalent bioconjugates thus represent powerful tools and potential nanoscale therapeutics for controlling the behaviour of target stem cells in vitro and in vivo.

Bond-valence model for metal cluster compounds. II. Matrix effect

The bond-valence model was commonly considered as inappropriate to metal cluster compounds, but recently it was shown that the model provides unique information on the lattice strains and stabilization mechanisms in (TM)6-chalcohalides, Mx(TM)6Ly (TM = transition metal, L = the chalcogen and/or halogen ligands; M = counter-cation). The previous study was mainly devoted to the non-uniform distribution of the anion valences (bond-valence sums) around clusters. This and the previous paper are focused on two additional phenomena: (i) a steric conflict between counter-cations and the cluster-ligand framework resulting in `common' lattice strains [previous paper: Levi et al. (2013). Acta Cryst. B69, 419-425], and (ii) steric conflict between the small (TM)6-cluster and the large coordination polyhedron around the cluster or so-called matrix effect (this paper). It was shown that both phenomena can be well described by changes in the bond-valence parameters. This paper demonstrates that the matrix effect results in high strains in the TM-L bonds in most of the (TM)6-chalcohalides (TM = Nb, Mo, W and Re). In spite of this, the violations for the total TM valence are minimal, because the cluster stretching is fully or partially compensated by compression of the TM-L bonds. As a result, the influence of the matrix effect on the material stability is rather positive: it decreases the volume of the structural units and in many cases ensures a more favorable distribution of the bond valences around TM atoms, stabilizing the cluster compound.

Bond-valence model for metal cluster compounds. I. Common lattice strains

The bond-valence model was commonly considered as inappropriate to metal cluster compounds, but recently it was shown that the model provides unique information on the lattice strains and stabilization mechanisms in (TM)6-chalcohalides (TM = transition metal in the cluster). The previous study was mainly devoted to the non-uniform distribution of the anion valences (bond-valence sums) around clusters. This and the following paper focuses on two additional phenomena: (i) a steric conflict between counter-cations and the cluster-ligand framework resulting in `common' lattice strains (this paper), and (ii) steric conflict between the small (TM)6-cluster and the large coordination polyhedron around the cluster or so-called matrix effect [the next paper; Levi et al. (2013), Acta Cryst. B69, 426-438]. It was shown that both phenomena can be well described by changes in the bond-valence parameters. The calculations were based on the structural data known to date for a variety of (TM)6-cluster compounds, Mx(TM)6Ly (TM = Nb, Mo, W and Re; M = various additional cations, L = the chalcogen and/or halogen ligands). The results were used to explain the structural peculiarities of these compounds with remarkable physical properties and the mechanisms of their stabilization.

Computational pharmacological comparison of Salvia miltiorrhiza and Panax notoginseng used in the therapy of cardiovascular diseases

The herb pair comprising Salvia miltiorrhiza (SM) and Panax notoginseng (PN) has been used as a classical formula for cardiovascular diseases (CVDs) in China and in western countries. However, the pharmacology of SM and PN in this herb pair has not been fully elucidated. The aim of this study was to compare the mechanisms of SM and PN at the molecular level for the treatment of CVDs. We used a systems pharmacology approach, integrating ligand clustering, chemical space, docking simulation and network analysis, to investigate these two herbal medicines. The compounds in SM were attached to clusters 2, 3, 5, 6, 8 and 9, while the compounds in PN were attached to clusters 1, 2, 4, 5, 6, 7, 8 and 10. The distributions of chemical space between the compounds from SM and PN were discrete, with the existence of small portions of overlap, and the majority of the compounds did not violate ‘Lipinski’s rule of five’. Docking indicated that the average number of targets correlated with each compound in SM and PN were 5.0 and 3.6, respectively. The minority nodes in the SM and PN drug-target networks possessed common values of betweenness centrality, closeness centrality, topological coefficients and shortest path length. Furthermore, network analyses revealed that SM and PN exerted different modes of action between compounds and targets. These results suggest that the method of computational pharmacology is able to intuitively trace out the similarities and differences of two herbs and their interaction with targets from the molecular level, and that the combination of two herbs may extend their activities in different potential multidrug combination therapies for CVDs.

FeoC from Klebsiella pneumoniae Contains a [4Fe-4S] Cluster

Iron is essential for pathogen survival, virulence, and colonization. Feo is suggested to function as the ferrous iron (Fe(2+)) transporter. The enterobacterial Feo system is composed of 3 proteins: FeoB is the indispensable component and is a large membrane protein likely to function as a permease; FeoA is a small Src homology 3 (SH3) domain protein that interacts with FeoB; FeoC is a winged-helix protein containing 4 conserved Cys residues in a sequence suitable for harboring a putative iron-sulfur (Fe-S) cluster. The presence of an iron-sulfur cluster on FeoC has never been shown experimentally. We report that under anaerobic conditions, the recombinant Klebsiella pneumoniae FeoC (KpFeoC) exhibited hyperfine-shifted nuclear magnetic resonance (NMR) and a UV-visible (UV-Vis) absorbance spectrum characteristic of a paramagnetic center. The electron paramagnetic resonance (EPR) and extended X-ray absorption fine structure (EXAFS) results were consistent only with the [4Fe-4S] clusters. Substituting the cysteinyl sulfur with oxygen resulted in significantly reduced cluster stability, establishing the roles of these cysteines as the ligands for the Fe-S cluster. When exposed to oxygen, the [4Fe-4S] cluster degraded to [3Fe-4S] and eventually disappeared. We propose that KpFeoC may regulate the function of the Feo transporter through the oxygen- or iron-sensitive coordination of the Fe-S cluster.

Capturing intercellular sugar-mediated ligand-receptor recognitions via a simple yet highly biospecific interfacial system

Intercellular ligand-receptor recognitions are crucial natural interactions that initiate a number of biological and pathological events. We present here the simple construction of a unique class of biomimetic interfaces based on a graphene-mediated self-assembly of glycosyl anthraquinones to a screen-printed electrode for the detection of transmembrane glycoprotein receptors expressed on a hepatoma cell line. We show that an electroactive interface confined with densely clustered galactosyl ligands is able to ingeniously recognize the asialoglycoprotein receptors on live Hep-G2 cells employing simple electrochemical techniques. The only facility used is a personal laptop in connection with a cheap and portable electrochemical workstation.

A Structural Snapshot of CYP2B4 in Complex with Paroxetine Provides Insights into Ligand Binding and Clusters of Conformational States

An X-ray crystal structure of CYP2B4 in complex with the drug paroxetine [(3S,4R)-3-[(2H-1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine] was solved at 2.14 Å resolution. The structure revealed a conformation intermediate to that of the recently solved complex with amlodipine and that of the more compact complex with 4-(4-chlorophenyl)imidazole in terms of the placement of the F-G cassette. Moreover, comparison of the new structure with 15 previously solved structures of CYP2B4 revealed some new insights into the determinants of active-site size and shape. The 2B4-paroxetine structure is nearly superimposable on a previously solved closed structure in a ligand-free state. Despite the overall conformational similarity among multiple closed structures, the active-site cavity volume of the paroxetine complex is enlarged. Further analysis of the accessible space and binding pocket near the heme reveals a new subchamber that resulted from the movement of secondary structural elements and rearrangements of active-site side chains. Overall, the results from the comparison of all 16 structures of CYP2B4 demonstrate a cluster of protein conformations that were observed in the presence or absence of various ligands.

X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe 4 S 4 clusters

Fe4S4 clusters are very common versatile prosthetic groups in proteins. Their redox property of being sensitive to O2-induced oxidative damage is, for instance, used by the cell to sense oxygen levels and switch between aerobic and anaerobic metabolisms, as exemplified by the fumarate, nitrate reduction regulator (FNR). Using the hydrogenase maturase HydE from Thermotoga maritima as a template, we obtained several unusual forms of FeS clusters, some of which are associated with important structural changes. These structures represent intermediate states relevant to both FeS cluster assembly and degradation. We observe one Fe2S2 cluster bound by two cysteine persulfide residues. This observation lends structural support to a very recent Raman study, which reported that Fe4S4-to-Fe2S2 cluster conversion upon oxygen exposure in FNR resulted in concomitant production of cysteine persulfide as cluster ligands. Similar persulfide ligands have been observed in vitro for several other Fe4S4 cluster-containing proteins. We have also monitored FeS cluster conversion directly in our protein crystals. Our structures indicate that the Fe4S4-to-Fe2S2 change requires large structural modifications, which are most likely responsible for the dimer-monomer transition in FNR.

Computational approaches for exploring the potential synergy and polypharmacology of Duhuo Jisheng Decoction in the therapy of osteoarthritis

The Duhuo Jisheng Decoction (DHJSD), a traditional Chinese medicine (TCM), has been widely used to treat osteoarthritis (OA). However, the mechanisms of action of the DHJSD have not been clearly elucidated. In the present study, the compounds in the DHJSD were characterized by three computational methods; the ligand clustering, chemical space distribution and network construction and analysis methods. The compounds that formed the medical composition of the DHJSD were divided into 10 clusters and possessed a broad diversity in chemical space distribution. The compounds also had the same coverage of chemical space as the OA drug/drug‑like compounds from DrugBank. In addition, multiple active compounds were identified as able to target multiple proteins in the drug‑target association networks (D‑T networks). A certain number of key compounds in the D‑T networks have been previously reported in the literature. The present study also constructed drug‑drug association networks (D‑D networks) and classified the DHJSD compounds into five clusters. The clusters represented multiple diverse combinations binding to the OA targets. These results suggested that the DHJSD had drug‑ and lead‑like compounds with potential synergy and polypharmacology against OA.

Are multivalent cluster glycosides a means of controlling ligand density of glycoarrays?

Bacterial adhesion to the glycocalyx of human host cells is of biological and medicinal importance. This process is often initiated by the interaction of bacterial lectins and specific carbohydrate ligands. Thus, adhesion of bacterial cells to glycosylated surfaces is a suitable model system to study various parameters of lectin-mediated carbohydrate recognition. Glycoarrays have become important tools to study such lectin-mediated carbohydrate recognition. However, it is difficult to adjust the characteristics of a specific glycoarray regarding its carbohydrate density or the clustering of sugar ligands, respectively. Thus, we have made an attempt to use synthetic cluster glycosides of different valencies to vary carbohydrate density on a polystyrene surface. A series of mono-, di- and trivalent mannosides were synthesised for immobilisation on pre-functionalised polystyrene microtiter plates and the resulting glycoarrays were tested as adhesive surfaces in mannose-specific adhesion of Escherichia coli. Our measurements give first promising hints about the potential of this approach to alter ligand density of glycoarrays in a systematic way.

Synthesis, characterization and optical properties of low nuclearity liganded silver clusters: Ag31(SG)19 and Ag15(SG)11

We report a simple synthesis of silver:glutathione (Ag:SG) clusters using a cyclic reduction under oxidative conditions. Two syntheses are described which lead to solutions containing well-defined Ag31(SG)19 and Ag15(SG)11 clusters that have been characterized by mass spectrometry. The optical properties of silver:glutathione (Ag:SG) cluster solutions have been investigated experimentally. In particular, the solution containing Ag15(SG)11 clusters shows a bright and photostable emission. For Ag31(SG)19 and Ag15(SG)11 clusters, the comparison of experimental findings with DFT and TDDFT calculations allowed us to reveal the structural and electronic properties of such low nuclearity liganded silver clusters.

Integrin and matrix metalloprotease dual-targeting with an MMP substrate–RGD conjugate

A fluorescent clustered RGD-containing ligand encompassing an MMP substrate was designed and successfully used in vivo for the dual-targeting of α(V)β(3) integrin receptors and MMP-9 extracellular proteases in the tumor region.

The fate of Au25(SR)18 clusters upon ligand exchange with binaphthyl-dithiol: interstaple binding vs. decomposition

The ligand exchange reaction between monodisperse Au25(2-PET)18 (2-PET: 2-phenylethylthiolate) clusters and 1,1'-binaphthyl-2,2'-dithiol (BINAS) was long thought to induce decomposition of the cluster (Si et al., J. Phys. Chem. C, 2009). We repeated the experiment and analyzed the reaction products using MALDI-TOF mass spectrometry. The spectra clearly indicate successful ligand exchange, bidentate binding of the BINAS ligand and intact Au25 clusters. The reaction products are identified as Au25(2-PET)18-2x(BINAS)x (x = 1-4) for a 24 h reaction with a 50-fold molar excess of BINAS. Two likely binding motifs are discussed. Analysis of atomic distances in both the cluster and the free ligand indicates interstaple binding connecting the central sulfur atom of the protecting (SRAu)2SR with the outer sulfur atom of a second unit. The results presented have implications on the binding position of BINAS in Au38(SR)24-2x(BINAS)x clusters.

A simple competition assay to probe pentacopper(I)-thiolato cluster ligand exchange

Two pentanuclear copper(I) thiolato clusters of the formula [Cu5(L)3]− (L = pyridine-2,6-dimethanethiolate (L1), (1); 4-methylpyridine-2,6-dimethanethiolate (L2), (2)) were synthesized utilizing a single-step procedure, and their structures were characterized by X-ray crystallography. The aforementioned pentanuclear complexes possess an interesting propeller-like Cu5S6 core where all Cu centers are three-coordinate. Electrospray ionization mass spectrometry (ESI-MS) investigation of the pentanuclear copper(I) thiolato clusters with added hetero-ligands demonstrated interesting ligand exchange behavior. The product distribution resulting from ligand exchange not only depended on the quantity of added ligand, but also was sensitive to the coordination ability of the ligand. The ESI-MS method used in this study can serve as a useful tool for probing exchange behavior in coordination metal complexes that cannot otherwise be determined by NMR.