超分子双膦配体的构筑及应用研究进展

超分子双膦配体是一类新兴起的基于非共价键作用构筑的双膦配体,近年来引起人们的重视.与传统的共价键连接的双膦配体相比,利用非共价相互作用的可逆性和选择性,超分子双膦配体具有合成简便,组合灵活,易于合成超分子配体库,并利用组合化学的方法对催化体系进行优化和筛选等优点.详细综述了近几年发展的基于氢键、配位键、主客体作用和静电作用等弱相互作用的超分子双膦配体,重点讨论了它们的构建方法以及在不对称催化反应中的应用,并对其发展前景进行了展望.     

High throughput screening (HTS) in identification new ligands and drugable targets of G protein-coupled receptors (GPCRs)

G protein-coupled receptors (GPCRs) which constitute one of the largest and most versatile families of cell surface receptors are involved in a wide spectrum of physiological functions, such as, neuronal transmission, chemotaxis, pacemaker activity and embryonic development. Therefore, in the past a few years GPCR families have become very important targets in pharmaceutical design. However, according to the human genome project, there are approximately 1000 genes encoding GPCRs, only about 200 of GPCRs have known ligands and functions. Searching for ligands of the unknown GPCRs and better modulators of known GPCRs are currently attracting lots of interest. High throughput screening (HTS), which is commonly defined as an automatic process of testing potential drug candidates efficiently, is widely used in drug discovery. In this review, the use of high throughput screening (HTS) in studying GPCRs and the choice of screening technology in different G-protein signaling pathways were summarized.     

New strategies in drug discovery for GPCRs: high throughput detection of cellular ERK phosphorylation

G-protein coupled receptors (GPCRs) are a large family of receptors for a wide range of stimulants, including hormones, neurotransmitters, and taste and olfactory chemicals. Due to their broad involvement in cellular responses, GPCRs affect many important body functions both in health and disease. Compared to other receptor families, the GPCRs have been a rich source of extracellularly-acting pharmaceuticals, due largely to the fact that many GPCR ligands are small molecules when compared with ligands for other receptors, such as the tyrosine kinase receptor family. This has allowed the development of small molecule modulators of receptor function that act on specific GPCRs, such as those involved in cardiovascular regulation. However, at several levels, current screening technologies of drug development for GPCRs are lacking. Firstly, responses from many GPCRs, such as the Gi-coupled GPCRs, are not easily measured in large screening programs by current techniques. Secondly, there are few options for detecting agonists of orphan GPCRs. Thirdly, it is now clear that the signaling from GPCRs is more complex than once thought, and the measurement of Ca(2+) and cAMP can account for only a fraction of the biological information emanating from an activated GPCR. Studies of the discrete and sometimes separable activation of the Ras/Raf/Mek/ERK cascade by many GPCRs is likely to offer development of new agonists and antagonists, contribute to new pharmacologies from receptors, and raise the potential for novel drug candidates in this important area of biology. Downstream activation of the ERK pathway, with or without transactivation of growth factor receptors, has not been measurable by high throughput methodologies. This article presents recent advances and associated applications for screening of GPCRs and other receptor species through the rapid measurement of protein phosphorylation events, such as ERK phosphorylation, as new readouts for drug discovery.     

Ligand-steered modeling and docking: A benchmarking study in class A G-protein-coupled receptors

Class A G-protein-coupled receptors (GPCRs) are among the most important targets for drug discovery. However, a large set of experimental structures, essential for a structure-based approach, will likely remain unavailable in the near future. Thus, there is an actual need for modeling tools to characterize satisfactorily at least the binding site of these receptors. Using experimentally solved GPCRs, we have enhanced and validated the ligand-steered homology method through cross-modeling and investigated the performance of the thus generated models in docking-based screening. The ligand-steered modeling method uses information about existing ligands to optimize the binding site by accounting for protein flexibility. We found that our method is able to generate quality models of GPCRs by using one structural template. These models perform better than templates, crude homology models, and random selection in small-scale high-throughput docking. Better quality models typically exhibit higher enrichment in docking exercises. Moreover, they were found to be reliable for selectivity prediction. Our results support the fact that the ligand-steered homology modeling method can successfully characterize pharmacologically relevant sites through a full flexible ligand-flexible receptor procedure.     

Study of binding affinity and selectivity of perylene and coronene derivatives towards duplex and quadruplex DNA by ESI‐MS

In this paper, we report an extensive electrospray ionization mass spectrometry (ESI‐MS) study of the noncovalent interactions between different intermolecular and intramolecular G‐quadruplex structures and several perylene and coronene ligands. The selectivity of these compounds toward quadruplex structures with respect to duplex DNA, a fundamental topic for the biological evaluation and the pharmacological application of these ligands as potential chemotherapeutic agents, has also been investigated. After exploring this topic according to the classical approach based on the very simple duplex model of an autocomplementary dodecamer, we extended our analysis reporting for the first time a competition ESI‐MS experiment in the presence of genomic DNA fragments. Whereas those ligands showing a high level of selectivity between quadruplex and duplex oligonucleotides, in terms of binding constants and percentage of bound DNA, confirmed their selectivity in the competition experiment, the contrary was not always true: some ligands showing poor selectivity with the autocomplementary dodecamer resulted selective in the presence of genomic DNA fragments. This result suggests that physiologically nonrelevant interactions are possible with a short duplex oligonucleotide. This means that the dodecamer can fail in representing a biologically significant structural model, or, better, that it can be used to quickly screen potentially selective molecules, but bearing in mind the high probability of false negative results. Copyright © 2008 John Wiley & Sons, Ltd.     

An ontology for pharmaceutical ligands and its application for in silico screening and library design

Annotation efforts in biosciences have focused in past years mainly on the annotation of genomic sequences. Only very limited effort has been put into annotation schemes for pharmaceutical ligands. Here we propose annotation schemes for the ligands of four major target classes, enzymes, G protein-coupled receptors (GPCRs), nuclear receptors (NRs), and ligand-gated ion channels (LGICs), and outline their usage for in silico screening and combinatorial library design. The proposed schemes cover ligand functionality and hierarchical levels of target classification. The classification schemes are based on those established by the EC, GPCRDB, NuclearDB, and LGICDB. The ligands of the MDL Drug Data Report (MDDR) database serve as a reference data set of known pharmacologically active compounds. All ligands were annotated according to the schemes when attribution was possible based on the activity classification provided by the reference database. The purpose of the ligand-target classification schemes is to allow annotation-based searching of the ligand database. In addition, the biological sequence information of the target is directly linkable to the ligand, hereby allowing sequence similarity-based identification of ligands of next homologous receptors. Ligands of specified levels can easily be retrieved to serve as comprehensive reference sets for cheminformatics-based similarity searches and for design of target class focused compound libraries. Retrospective in silico screening experiments within the MDDR01.1 database, searching for structures binding to dopamine D2, all dopamine receptors and all amine-binding class A GPCRs using known dopamine D2 binding compounds as a reference set, have shown that such reference sets are in particular useful for the identification of ligands binding to receptors closely related to the reference system. The potential for ligand identification drops with increasing phylogenetic distance. The analysis of the focus of a tertiary amine based combinatorial library compared to known amine binding class A GPCRs, peptide binding class A GPCRs, and LGIC ligands constitutes a second application scenario which illustrates how the focus of a combinatorial library can be treated quantitatively. The provided annotation schemes, which bridge chem- and bioinformatics by linking ligands to sequences, are expected to be of key utility for further systematic chemogenomics exploration of previously well explored target families.     

Subtype selectivity of dopamine receptor ligands: insights from structure and ligand-based methods

Subtype selective dopamine receptor ligands have long been sought after as therapeutic and/or imaging agents for the treatment and monitoring of neurologic disorders. We report herein on a combined structure- and ligand-based approach to explore the molecular mechanism of the subtype selectivity for a large class of D?-like dopamine receptor ligands (163 ligands in total). Homology models were built for both human D(?L) and D? receptors in complex with haloperidol. Other ligands, which included multiple examples of substituted phenylpiperazines, were aligned against the binding conformations of haloperidol, and three-dimensional quantitative structure activity relationship (3D-QSAR) analyses were carried out. The receptor models show that although D? and D? share highly similar folds and 3D conformations, the slight sequence differences at their extracellular loop regions result in the binding cavity in D? being comparably shallower than in D?, which may explain why some larger ligands bind with greater affinity at D? compared to D? receptors. The QSAR models show excellent correlation and high predictive power even when evaluated by the most stringent criteria. They confirm that the origins of subtype selectivity for the ligands arise primarily due to differences in the contours of the two binding sites. The predictive models suggest that while both steric and electrostatic interactions contribute to the compounds' binding affinity, the major contribution arises from hydrophobic interactions, with hydrogen bonding conferring binding specificity. The current work provides clues for the development of more subtype selective dopamine receptor ligands. Furthermore, it demonstrates the possibility of being able to apply similar modeling methods to other subtypes or classes of receptors to study GPCR receptor-ligand interactions at a molecular level.     

High throughput screening of G-protein coupled receptors via flow cytometry

The molecular assemblies of signal transduction components, for example kinases and their target proteins or receptor-ligand complexes and intracellular signaling molecules, are critical for biological functions in cells. To better understand the interactions of these molecular assemblies and to screen for new pharmaceutics that could control and modulate these types of interactions, we have focused on developing high throughput approaches for the analysis of G-protein coupled receptors via flow cytometry. Flow cytometry offers a number of advantages including real-time collection of multicomponent data, and together with improvements in sample handling, the high throughput sampling rate is up to 100 samples per minute. For our targets, assemblies of solubilized GPCRs, a screening platform of a dextran bead has proven to be flexible, allowing different surface chemistries on the beads. The bead can be either ligand-labeled or have epitope-linked proteins attached to the bead surface, enabling several molecular assemblies to be constructed and analyzed. A major improvement with this system is that for screening ligands for GPCRs the underlying mechanism of action for these compounds can be investigated and incorporated into the definition of a 'hit'. Our current screening system is capable of simultaneously distinguishing GPCR agonists and antagonists.     

Latest development in drug discovery on G protein-coupled receptors

G protein-coupled receptors (GPCRs) represent the family of proteins with the highest impact from social, therapeutic and economic point of view. Today, more than 50% of drug targets are based on GPCRs and the annual worldwide sales exceeds 50 billion dollars. GPCRs are involved in all major disease areas such as cardiovascular, metabolic, neurodegenerative, psychiatric, cancer and infectious diseases. The classical drug discovery process has relied on screening compounds, which interact favorably with the GPCR of interest followed by further chemical engineering as a mean of improving efficacy and selectivity. In this review, methods for sophisticated chemical library screening procedures will be presented. Furthermore, development of cell-based assays for functional coupling of GPCRs to G proteins will be discussed. Finally, the possibility of applying structure-based drug design will be summarized. This includes the application of bioinformatics knowledge and molecular modeling approaches in drug development programs. The major efforts established through large networks of structural genomics on GPCRs, where recombinantly expressed GPCRs are subjected to purification and crystallization attempts with the intention of obtaining high-resolution structures, are presented as a promising future approach for tailor-made drug development.     

A virtual screen for diverse ligands: discovery of selective G protein-coupled receptor antagonists

Virtual screening has become a major focus of bioactive small molecule lead identification, and reports of agonists and antagonists discovered via virtual methods are becoming more frequent. G protein-coupled receptors (GPCRs) are the one class of protein targets for which success with this approach has been limited. This is likely due to the paucity of detailed experimental information describing GPCR structure and the intrinsic function-associated structural flexibility of GPCRs which present major challenges in the application of receptor-based virtual screening. Here we describe an in silico methodology that diminishes the effects of structural uncertainty, allowing for more inclusive representation of a potential docking interaction with exogenous ligands. Using this approach, we screened one million compounds from a virtual database, and a diverse subgroup of 100 compounds was selected, leading to experimental identification of five structurally diverse antagonists of the thyrotropin-releasing hormone receptors (TRH-R1 and TRH-R2). The chirality of the most potent chemotype was demonstrated to be important in its binding affinity to TRH receptors; the most potent stereoisomer was noted to have a 13-fold selectivity for TRH-R1 over TRH-R2. A comprehensive mutational analysis of key amino acid residues that form the putative binding pocket of TRH receptors further verified the binding modality of these small molecule antagonists. The described virtual screening approach may prove applicable in the search for novel small molecule agonists and antagonists of other GPCRs.     

Selective detection of catecholamines by synthetic receptors embedded in chromatic polydiacetylene vesicles

A new detection scheme for catecholamines was constructed through embedding synthetic receptors within vesicles comprising phospholipids and polydiacetylene. Fluorescence emission of the polydiacetylene was induced through specific interactions between the soluble ligands and the vesicle-incorporated hosts. The system demonstrated remarkable selectivity among structurally similar ligands and achieved much lower detection thresholds compared to that of other reported catecholamine sensors. The chromatic assembly provides a generic route for high sensitivity detection of ligand-receptor interactions.     

Engineering Gram Selectivity of Mixed‐Charge Gold Nanoparticles by Tuning the Balance of Surface Charges

Nanoparticles covered with ligand shells comprising both positively and negatively charged ligands exhibit Gram‐selective antibacterial action controlled by a single experimental parameter, namely the proportion of [+] and [?] ligands tethered onto these particles. Gram selectivity is attributed to the interplay between polyvalent electrostatic and non‐covalent interactions that work in unison to disrupt the bacterial cell wall. The [+/?] nanoparticles are effective in low doses, are non‐toxic to mammalian cells, and are tolerated well in mice. These results constitute the first example of rational engineering of Gram selectivity at the (macro)molecular level.     

A systematic evaluation of molecular recognition phenomena. 2. Interaction between phosphates and nucleotides with hexaazamacrocyclic ligands containing diethylic ether spacers

The host-guest interactions between ortho- (Ph), pyro- (Pp), and tripolyphosphate (Tr) anions together with ATP (At), ADP (Ad), and AMP (Am) nucleotides and the two hexaazamacrocyclic ligands 1,15-dioxa-4,8,12,18,22,26-hexaazacyclooctacosane (Pn) and 1,13-dioxa-4,7,10,16,20,24-hexaazacyclohexacosane (Op) have been investigated by potentiometric equilibrium methods. Ternary complexes are formed in aqueous solution as a result of hydrogen bond formation and Coulombic attraction between the host and the guest. Formation constants for all the species obtained are reported. The selectivity of the Pn and Op ligands with regard to the different phosphate and nucleotide substrates is discussed and illustrated with total species distribution diagrams. A comparison is also carried out, with the results obtained in this work and those obtained previously with three other closely related hexaazamacrocyclic ligands. This comparison manifests the importance of ligand basicity, rigidity, and pi-stacking capability in order to understand their binding and selectivity.     

Biological applications of the receptor mimetic peptide mastoparan

The receptor mimetic and mast cell degranulating peptide mastoparan (MP) translocates cell membranes as an amphipathic alpha-helix, a feature that is undoubtedly a major determinant of bioactivity through the activation of heterotrimeric G proteins. Chimeric combinations of MP with G protein-coupled receptor (GPCR) ligands has produced peptides that exhibit biological activities distinct from their composite components. Thus, chimeric peptides such as galparan and M391 differentially modulate GTPase activity, display altered binding affinities for appropriate GPCRs and possess disparate secretory properties. MP and MP-containing chimerae also bind and modulate the activities of various other intracellular protein targets and are valuable tools to manipulate and study enzymatic activity, calcium homeostasis and apoptotic signalling pathways. In addition, charge delocalisation within the hydrophilic face of MP has produced analogues, including [Lys5, Lys8,Aib10]MP, that differentially regulate mast cell secretion and/or cytotoxicity. Finally, the identification of cell penetrant variants of MP chimerae has enabled the effective intracellular delivery of non-permeable biomolecules and presents an opportunity to target novel intracellular therapeutic loci.     

π-Stacking interactions at the service of [Cu]-bis(oxazoline) recycling

Anthracene- and pyrene-tagged bis(oxazoline) ligands have been prepared and immobilized on charcoal, fullerene, and single-walled carbon nanotubes through π–π interactions. The corresponding copper complexes have been evaluated for their propensity to promote heterogeneous asymmetric Henry and ene reactions. The best results, in terms of activity, selectivity, and stability toward the recycling procedure have been obtained with the pyrene/SWCNT system, as the first example demonstrating the usefulness of such reversible interactions for the asymmetric formation of new C–C bonds.     

Tetranuclear Dicationic Aurophilic Gold(I) Catalysts in Enyne Cycloisomerization: Cooperativity for a Dramatic Shift in Selectivity

In comparison to mononuclear gold Lewis acid catalysts, digold complexes and dual-gold catalysis have illustrated a distinct and powerful potential for the activation of carbon-carbon multiple bonds. Herein, this concept is pushed further by designing novel tetranuclear gold(I) dicationic complexes structurally supported by strongly stabilizing constraint diphosphinoferrocenyl ligands and attractive closed-shell Au⋅⋅⋅Au aurophilic interactions. The use of a molecularly-defined tetranuclear dicationic aurophilic gold(I) precatalyst for the selectivity-challenging cycloisomerization of low-substituted 1,6-enynes favors the formation with high selectivity of strained azabicyclo[4.1.0]hept-4-enes – even in the complete absence of activating/orienting substituents on alkyne and olefin reactive functions. This selectivity is not achieved by the reported phosphine- and carbene-stabilized mono- and dinuclear cationic gold(I) complexes, including the ones formed from the same ligands. More importantly this selectivity differs also from nanoparticles and heterogeneous gold catalysts reported to date. DFT studies correlated to experimental mechanistic investigations support an unprecedented “cluster-like” reactivity from polynuclear cooperation at the origin of this peculiar selectivity where the aurophilic interactions preexist, and pre-organize, gold cluster reactive intermediates.     

Designing Multivalent Ligands to Control Biological Interactions: From Vaccines and Cellular Effectors to Targeted Drug Delivery

Multivalent interactions in which multiple ligands on one object bind to multiple receptors on another are commonly found in natural biological systems. In addition, these interactions can lead to increased strength and selectivity when compared to the corresponding monovalent interaction. These attributes have also guided the design of synthetic multivalent ligands to control biological interactions. This review will highlight the recent literature describing the use of multivalent ligand display in the design of vaccines, immunomodulators, cell signaling effectors, and vehicles for targeted drug delivery.     

Estimation of alkali and alkaline earth ion selectivity of electrically neutral carrier-antibiotics and model compounds

Using model calculations, the influence of coordination number, properties of ligand groups, dimension of the ligand, steric interactions, and solvent on the complexation of alkali- and alkaline earth metal cations by electrically neutral ligands (carrier antibiotics, model compounds) is discussed. Information is given on the molecular parameters needed to achieve a given ion selectivity in view of the use of such ligands as carriers in ion selective membranes.     

Using silico methods predicting ligands for orphan GPCRs

The G-protein coupled receptor (GPCR) superfamily is one of the most important drug target classes for the pharmaceutical industry. The completion of the human genome project has revealed that there are more than 300 potential GPCR targets of interest. The identification of their natural ligands can gain significant insights into regulatory mechanisms of cellular signaling networks and provide unprecedented opportunities for drug discovery. Much effort has been directed towards the GPCR ligand discovery study by both academic institutions and pharmaceutical industries. However, the endogenous ligands still remain unknown for about 150 GPCRs in the human genome. It is necessary to develop new strategies to predict candidate ligands for these so-called orphan receptors. Computational techniques are playing an increasingly important role in finding and validating novel ligands for orphan GPCRs (oGPCRs). In this paper, we focus on recent development in applying bioinformatics approaches for the discovery of GPCR ligands. In addition, some of the data resources for ligand identification are also provided.