Ligand Template Research Articles

Spontaneous Galvanic Displacement Reactions: Effects of Template and Surface Ligand Interaction

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ReverseScreen3D: A Structure-Based Ligand Matching Method To Identify Protein Targets

Ligand promiscuity, which is now recognized as an extremely common phenomenon, is a major underlying cause of drug toxicity. We have developed a new reverse virtual screening (VS) method called ReverseScreen3D, which can be used to predict the potential protein targets of a query compound of interest. The method uses a 2D fingerprint-based method to select a ligand template from each unique binding site of each protein within a target database. The target database contains only the structurally determined bioactive conformations of known ligands. The 2D comparison is followed by a 3D structural comparison to the selected query ligand using a geometric matching method, in order to prioritize each target binding site in the database. We have evaluated the performance of the ReverseScreen2D and 3D methods using a diverse set of small molecule protein inhibitors known to have multiple targets, and have shown that they are able to provide a highly significant enrichment of true targets in the database. Furthermore, we have shown that the 3D structural comparison improves early enrichment when compared with the 2D method alone, and that the 3D method performs well even in the absence of 2D similarity to the template ligands. By carrying out further experimental screening on the prioritized list of targets, it may be possible to determine the potential targets of a new compound or determine the off-targets of an existing drug. The ReverseScreen3D method has been incorporated into a Web server, which is freely available at http://www.modelling.leeds.ac.uk/ReverseScreen3D .

Direct Evaluation of Ligand-Receptor Interaction by a Novel Imaging Model Based on Fluorescent Silica Nanoparticle as Ligand Probe and Molecular Imprinting Polymer as Artificial Receptor

A novel fluorescent imaging system was established to monitor ligand-receptor interactions. Fluorescent silica nanoparticles (FNPs) conjugated with ligand molecules were employed as ligands and molecular imprinting polymer (MIP) as artificial receptors in this work. Fluorescent silica nano-particles which have controllable and uniform size of 120 nm were synthesized and characterized by scanning electronic microscopy (SEM). The FNPs with excitation and emission peaks at 289 nm and 570 nm provide strong fluorescence intensity, excellent photostability, and easy surface modification. L-phenylalaninamide was employed as a test ligand and MIP template. By use of grafting initiator of 4,4′-azobis (4-cyanovaleric acid), a MIP receptor membrane was firmly grafted on the support layer by layer. Results showed that the specific affinity between artificial MIP receptor and ligand conjugated to the FNPs can be successfully monitored. It also suggests that the designed imaging system is suitable of studying molecular interactions and has a great potential for further application.

Double-Stranded Copper(II)meso-Helicates

Double-stranded oligonuclear copper(II) coordination complexes were prepared by self-assembly of copper(II) ions and oligo(2-methyl-1,3-phenyleneoxalamide) ligands. As a result of the ligand template effect, all the metal ions adopt a linear arrangement with the Cu˙˙˙Cu distances in the range of 7.20 to 7.40 Å. The copper(II) centers display alternating M or P helical chirality, resulting in achiral meso-helicates in the case of di- and ­tetranuclear complexes (2a and 2c) or a racemic mixture of M,P,M and P,M,P configurations for trinuclear 2b.

Thermoresponsive Copolymer Cryogel Possessing Molecular Memory: Synthesis, Energetics of Collapse and Interaction with Ligands

AbstractAn imprinted thermoresponsive cryogel of copolymer of N‐isopropylacrylamide and N‐[3‐(N,N′‐dimethylamino)propyl]acrylamide was synthesized in a frozen (−10 °C) aqueous medium in presence of a molecular template, the drug substance ibuprofen. A reversible volume phase transition upon heating (thermotropic collapse) of the swollen cryogel was studied by high‐sensitivity differential scanning calorimetry. In the absence of ligands, the transition temperature, enthalpy, and width were 82.5 °C, 9.8 J · g−1 and 32.2 °C, respectively. Significant changes in the transition parameters were observed in presence of the template ligand (ibuprofen): with increasing ligand concentration the transition temperature decreased down to 30 °C, the enthalpy passed through a minimum, and the transition width notably reduced. The binding constants of ibuprofen by the cryogel subchains in the collapsed and swollen states were 119 and 5 M−1, respectively. This implies a preferential binding of ibuprofen by the shrunken cryogel. The excess absorption of ibuprofen by the cryogel related to its collapse amounted to 0.327 mmol · g−1 while for all other ligands that were structural analogs of ibuprofen this parameter did not exceed 0.016 mmol · g−1. Consequently, the imprinted cryogel possessed a selective molecular memory toward the template ligand. magnified image

Computerized Protein Modeling and Molecular Docking Analysis of Human Proto Oncogene Tyrosine Protein Kinase YES for Discovery of Novel Lead Molecules

AbstractHuman proto-oncogene tyrosine-protein kinase YES (YES) is a non receptor kinase belongs to Src family. This gene lies in close proximity to thymidylate synthase gene on chromosome 18, and a corresponding pseudogene has been found on chromosome 22. In hepatocellular carcinoma and colorectal carcinoma elevated human YES activity was observed. Inhibitors of human YES reported till date are in clinical trials and associated with several side effects. The present study was mainly aimed in homology modeling of human YES and discovery of novel lead molecules that inhibit YES kinase more efficiently with fewer side effects. Virtual screening and docking techniques were applied to identify novel lead molecule of YES kinase. As there was no reported human YES crystal structural data, the three dimensional structure of human YES was constructed based on template structure (PDB ID: 2H8H) obtained through homology search using MODELLER 9V7. The model was refined, energy minimized and assessed through PROCHECK. Active site residues of human YES were identified from the homology model in complex with template ligand AZD0530 and were further confirmed using CASTp. Five published inhibitors of YES family (Dasatinib, Bosutinib, SU6656, AZD0530 and CGP77675) were identified through literature search. High throughput virtual screening method at Ligand.Info was applied for these five inhibitors to establish a library of 1932 structural analogs. LigPrep was used to generate possible conformations of each ligand molecules from structural analog library. The ligand duplicates conformers, ligands having reactive functional group and poor ADME properties were rejected from the prepared dataset. Glide 5.5 was used to generate a grid box by picking the active site residues of human YES protein. Through sequential applications of stringent mode glide docking procedures from Glide HTVS to SP to XP respectively, 13 potential inhibitors were proposed. The docking complexes of each inhibitor with human YES protein were analyzed and lead ‘1’ molecule was identified to have higher binding affinity to human YES protein (XP Gscore: -12.07 Kcal/mol) compared to existing published inhibitors and other 12 lead molecules. The lead ‘1’ - human YES docking complex was highly stabilized through hydrogen bond network with amino acid residues Thr348, Asp358, Asp414 and Phe415. Moreover, from the results obtained we could decipher that lead ‘1’ molecule can be raised into potential inhibitors after binding assays, substantiated experimental investigations and passing several phases of clinical trials.

Homology-Modelling Protein–Ligand Interactions: Allowing for Ligand-Induced Conformational Change

Current homology-modelling methods do not consider small molecules in their automated processes. Therefore, the development of a reliable tool for protein–ligand homology modelling is an important next step in generating plausible models for molecular interactions. Two automated protein–ligand homology-modelling strategies, requiring no expert knowledge from the user, are investigated here. Both employ the “induced fit” concept with flexibility in side chains and ligand. The most successful strategy superimposes the new ligand over the original ligand before homology modelling, allowing the new ligand to be taken into consideration during protein modelling (rather than after), facilitating conformational change in the local backbone if necessary. We show that this approach results in successful modelling of the ligand and key binding-site residues of angiotensin-converting enzyme 2 (ACE2) from its homologue ACE, which is not possible via conventional homology modelling or by homology modelling followed by docking. Several other difficult target complexes are also successfully modelled, reproducing native protein–ligand contacts with significantly different biological substrates and different binding-site conformations. These include the modelling of Cdk5 (cyclin-dependent kinase 5) from Cdk2, thymidine phosphorylase from a bacterial homologue, and dihydrofolate reductase from a recombinant variant with a markedly different inhibitor. In terms of average modelling quality across 82 targets, the ligand RMSD with respect to the experimental structure is 1.4 Å (and 2.0 Å for the protein binding site) for “easy” cases and 2.9 Å for the ligand (and 2.7 Å for the protein binding site) in “hard” cases. This demonstrates the importance of selecting an optimal template. Ligand-modelling accuracy is strongly dependent on target–template ligand structural similarity, rather than target–template sequence identity. However, protein-modelling accuracy is dependent on both. Our automated protein–ligand homology-modelling strategy generates a higher degree of accuracy than homology modelling followed by docking, generating an average ligand RMSD that is 1–2 Å better than docking with homology models.

The GRID/CPCA approach in drug discovery

Importance of the field: Bimolecular recognition is the basis for almost all processes in biological systems. The geometrical and chemical complementarity of small molecule ligands and their macromolecular biological targets, matching paired interacting parts, can result in binding that will eventually yield a biological response.Areas covered in this review: The topics covered include the integration of molecular interaction fields and chemometrics, via the GRID/CPCA (consensus principal component analysis) method that is actively contributing to the optimization of potency and selectivity of ligands towards a chosen target. Key applications that hallmark the usefulness of the method are critically presented. By comparison of the GRID/CPCA and GRID/PCA, the breakthroughs and challenges are highlighted.What the reader will gain: Molecular recognition studies support the development of pharmacophore-based descriptors, which provide the means to identify new ligand templates (‘scaffold-hopping’). The GRID/CPCA approach can simultaneously reveal common trends in more than one block of data for more than two target proteins, with several three-dimensional structures per protein. It offers the benefit of improving the weighting between different interaction energy probes within the GRID parameterization. An important consequence is that hydrophobic interactions can be assessed for selectivity between proteins.Take home message: Molecular-field-based methods along with CPCA analysis are extremely powerful to understand bimolecular interactions. Because drug discovery and development is a costly, time consuming and high-risk activity and GRID/CPCA is at the forefront of the computer-aided design, it should be used as early as possible for discovering new drugs.

Hydrothermal preparation and characterization of based-alloy Bi 2Te 3 nanostructure with different morphology

In this paper, based-alloy Bi 2Te 3 nanostructure with different morphologies was synthesized by a hydrothermal process based on the reaction between Bi(NO 3) 3, TeCl 4, and KBH 4 in water at various conditions. The products were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), Fourier transform infrared spectrometry (FT-IR), X-ray photoelectron spectrum and inductively coupled plasma-atomic emission spectrometer and transmission electron microscopy (TEM). The result shows that the Bi 2Te 3 crystals have diameters ranging from 20 to 25 nm with high purity. Other factors, such as the reaction time, the different capping agent and the sort of reductant also have influence on the morphology of the final products to some extent. By variation of reductant, conversion rode-like to flower-like was obtained. Organic ligands play a manifold role in the formation of the chainlike nanostructures as both coordinate ligand and architecture template, and a possible formation mechanism is proposed.

LigMatch: A Multiple Structure-Based Ligand Matching Method for 3D Virtual Screening

We have developed a new virtual screening (VS) method called LigMatch and evaluated its performance on 13 protein targets using a filtered and clustered version of the directory of useful decoys (DUD). The method uses 3D structural comparison to a crystallographically determined ligand in a bioactive 'template' conformation, using a geometric hashing method, in order to prioritize each database compound. We show that LigMatch outperforms several other widely used VS methods on the 13 DUD targets. We go on to demonstrate that improved VS performance can be gained from using multiple, structurally diverse templates rather than a single template ligand for a particular protein target. In this case, a 2D fingerprint-based method is used to select a ligand template from a set of known bioactive conformations. Furthermore, we show that LigMatch performs well even in the absence of 2D similarity to the template ligands, thereby demonstrating its robustness with respect to purely 2D methods and its potential for scaffold hopping.

Alternate Arrangements of Two Different Metals at Chemically-Equivalent Binding Sites on a Circle

Two different metal ions, monovalent M(+) (M = Ag, Cu) and divalent Hg(2+), were alternately arranged on a circle with a diameter of 1.5 nm in such a way that six metal ions were put between two disk-shaped hexamonodentate template ligands (L), thereby forming the sandwich-shaped hexanuclear complexes [M(3)Hg(3)L(2)](9+). In spite of the fact that all six binding sites are completely equivalent, the arrangement of the two kinds of monovalent and divalent metal ions is precisely controlled to minimize electrostatic interactions between the adjacent metal ions.

Liquid phase deposition of titania onto nanostructured poly-p-xylylene thin films

We describe a simple, solution-based, two-step process for the fabrication of titania–parylene composite films as a prerequisite for their evaluation as materials for bioimplant applications. In the first step, a ligand capable of binding titania, such as phenylphosphonic acid, is physisorbed onto a nanostructured poly-p-xylylene thin film previously prepared via surface-promoted oblique angle polymerization of radicals formed during vapor-phase pyrolysis of [2.2]-p-cyclophanes. The adsorbed ligand templates conformal growth of titania on the polymer surface in the second step via a liquid phase deposition process involving the controlled hydrolysis of (NH4)2TiF6 in the presence of H3BO3 in pH 2.88 aqueous solution at ∼50 °C. SEM and AFM analyses support a deposition mechanism that includes direct growth of titania on the ligand-impregnated parylene surface, as well as incorporation of titania nanoparticles nucleated in solution into the growing film. XPS and XRD results show that the as-deposited titania contains both amorphous and nanocrystalline anatase phases, with the latter readily consolidated by annealing at ∼200 °C without destruction of the underlying parylene polymer. Titania adhesion can be tuned by proper choice of the ligand, with ligands such as phenylphosphonic acid that strongly bind to titanium dioxide leading to deposition of titania films that pass the Scotch® tape adhesion test.

A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

The detection of ligand-binding sites is often the starting point for protein function identification and drug discovery. Because of inaccuracies in predicted protein structures, extant binding pocket-detection methods are limited to experimentally solved structures. Here, FINDSITE, a method for ligand-binding site prediction and functional annotation based on binding-site similarity across groups of weakly homologous template structures identified from threading, is described. For crystal structures, considering a cutoff distance of 4 A as the hit criterion, the success rate is 70.9% for identifying the best of top five predicted ligand-binding sites with a ranking accuracy of 76.0%. Both high prediction accuracy and ability to correctly rank identified binding sites are sustained when approximate protein models (<35% sequence identity to the closest template structure) are used, showing a 67.3% success rate with 75.5% ranking accuracy. In practice, FINDSITE tolerates structural inaccuracies in protein models up to a rmsd from the crystal structure of 8-10 A. This is because analysis of weakly homologous protein models reveals that about half have a rmsd from the native binding site <2 A. Furthermore, the chemical properties of template-bound ligands can be used to select ligand templates associated with the binding site. In most cases, FINDSITE can accurately assign a molecular function to the protein model.

Electrostatically Controlled Hierarchical Arrangement of Monocationic Silver(I) and Dicationic Mercury(II) Ions between Disk-Shaped Template Ligands

This paper describes hierarchical arrangement of three Ag+ and three Hg2+ ions using two disk-shaped hexa-monodentate template ligands in which three oxazolyl rings are arranged each on the two concentric circles. The hierarchical manner of ligand arrangement allows the selective binding of monocationic Ag+ and dicationic Hg2+ ions to the inner first and the outer second generation coordination sites, respectively. This hierarchically well-balanced metal assembly should arise primarily from a minimized electrostatic repulsion between positively charged six metal ions arranged within the heteronuclear complex.

Geometric Accuracy of Three-Dimensional Molecular Overlays

This study examines the dependence of molecular alignment accuracy on a variety of factors including the choice of molecular template, alignment method, conformational flexibility, and type of protein target. We used eight test systems for which X-ray data on 145 ligand-protein complexes were available. The use of X-ray structures allowed an unambiguous assignment of bioactive overlays for each compound set. The alignment accuracy depended on multiple factors and ranged from 6% for flexible overlays to 73% for X-ray rigid overlays, when the conformation of the template ligand came from X-ray structures. The dependence of the overlay accuracy on the choice of templates and molecules to be aligned was found to be the most significant factor in six and seven of the eight ligand-protein complex data sets, respectively. While finding little preference for the overlay method, we observed that the introduction of molecule flexibility resulted in a decrease of overlay accuracy in 50% of the cases. We derived rules to maximize the accuracy of alignment, leading to a more than 2-fold improvement in accuracy (from 19% to 48%). The rules also allowed the identification of compounds with a low (<5%) chance to be correctly aligned. Last, the accuracy of the alignment derived without any utilization of X-ray conformers varied from <1% for the human immunodeficiency virus data set to 53% for the trypsin data set. We found that the accuracy was directly proportional to the product of the overlay accuracy from the templates in their bioactive conformations and the chance of obtaining the correct bioactive conformation of the templates. This study generates a much needed benchmark for the expectations of molecular alignment accuracy and shows appropriate usages and best practices to maximize hypothesis generation success.

Cover Picture: Ligand‐Template Directed Assembly: An Efficient Approach for the Supramolecular Encapsulation of Transition‐Metal Catalysts (Chem. Eur. J. 16/2006)

Encapsulated catalysts are discussed in the Concept article by J. N. H. Reek and A. W. Kleij on p. 4218 ff. The authors show how template ligands can be used to form assemblies in which transition‐metal catalysts are encapsulated. These novel supramolecular catalysts are not only aesthetically attractive but show improved activity and selectivities compared with their non‐encapsulated analogues.

Human Thyroid Receptor Forms Tetramers in Solution, Which Dissociate Into Dimers Upon Ligand Binding

Thyroid hormone nuclear receptors (TRs) bind to DNA and activate transcription as heterodimers with the retinoid X receptor (RXR) or as homodimers or monomers. RXR also binds to DNA and activates transcription as homodimers but can, in addition, self-associate into homotetramers in the absence of ligand and DNA templates. It is thought that homotetramer formation serves to sequester excess RXRs into an inactive pool within the cell. Here, we report systematic studies of the multimeric state of a recombinant human TRbeta1 truncation (hTRbeta1deltaAB) that encompasses the complete DNA binding domain and ligand binding domain in solution. Native gel electrophoresis, chemical crosslinking, gel filtration, and dynamic light scattering experiments reveal that hTRbeta1deltaAB forms a mixture of monomers, dimers, and tetramers. Like RXR, increasing protein concentration shifts the equilibrium between TR multimers toward tetramer formation, whereas binding of cognate thyroid hormone leads to dissociation of tetramers and increased formation of dimers. This work represents the first evidence that apo-hTRbeta1 forms homotetramers. The findings raise the possibility that tetramer formation provides an additional, and previously unsuspected, level of control of TR activity and that the capacity for homotetramer formation may be more widespread in the nuclear receptor family than previously thought.

Template Refolding by Use of an Antibody‐Coupled Affinity Column

AbstractTo improve the efficiency and throughput, the biointeraction between an antigen and antibody was used for refolding in a packed column, in which an antibody against carbonic anhydrase coupled on a gel support was used as a template ligand. A denatured solution of CAB was mixed with a refolding buffer in a mixing chamber, and was supplied to the antibody‐coupled column for refolding. Higher refolding efficiencies were obtained in the column than by the batch dilution method at relatively low concentrations of denaturant. By increasing the adsorption capacity of the column, the efficiency of refolding, as well as the throughput, could be increased.

Improved FlexX Docking Using FlexS-Determined Base Fragment Placement

We report on a novel hybrid FlexX/FlexS docking approach, whereby the base fragment of the test ligand is chosen by FlexS superposition onto a cocrystallized template ligand and then fed into FlexX for the incremental construction of the final solution. The new approach is tested on the diverse 200 protein-ligand complex dataset that has been previously described for FlexX validation. In total, 62.9% of the complexes can be reproduced at rank 1 by our approach, which compares favorably with 46.9% when using FlexX alone. In addition, we report "cross-docking" experiments in which several receptor structures of complexes with identical proteins have been used for docking all cocrystallized ligands of these complexes. The results show that, in almost all cases, the hybrid approach can acceptably dock a ligand into a foreign receptor structure using a different ligand template, can give solutions where FlexX alone fails, and tends to give solutions that are more accurately positioned.

Design of a Novel Molecular-Imprinted Rh−Amine Complex on SiO2and Its Shape-Selective Catalysis for α-Methylstyrene Hydrogenation

A new molecular-imprinted Rh−amine complex with a template-shaped cavity acting as a shape-selective reaction space was prepared by metal-complex attaching and molecular imprinting techniques on a SiO2 surface. Rh(η3-C3H5)3 reacted with SiO2, and the precursor was attached on the surface to form a bidentate structure Rh(C3H5)(OSi)2. α-Methylbenzylamine with a shape similar to that of a half-hydrogenated alkyl intermediate of α-methylstyrene coordinated to the attached Rh as a template ligand. Then SiO2−matrix overlayers were stacked on the surface by the hydrolysis−polymerization of Si(OCH3)4 surrounding the attached Rh complexes with the amine template. Final evacuation at 373 K promoted the removal of the template ligand from the Rh complex embedded in the surface pore of the SiO2−matrix overlayers. All the structures of the attached Rh complexes were characterized by the means of ICP, XPS, ESR, FT-IR, solid-state MAS NMR, EXAFS, DFT, GC, and H2 adsorption. The imprinted Rh complex has an unsaturated structure Rh(amine)(OSi)(HOSi) and exhibits high catalytic activity for α-methylstyrene hydrogenation. On the contrary, the other supported Rh complexes before imprinting are inactive for the hydrogenation. Furthermore, the active Rh complex is durable under the reaction condition despite the unsaturated conformation which usually tends to gather each other. The imprinted cavity locating on the active Rh center acts as a shape-selective reaction space for α-methylstyrene. The inhibition of the hydrogenation by the use of seven amines with different shapes demonstrates the shape-selective behavior of the imprinted Rh complex discriminating one methyl group and the position of the phenyl ring.