Core site-moiety maps reveal inhibitors and binding mechanisms of orthologous proteins by screening compound libraries

Members of protein families often share conserved structural subsites for interaction with chemically similar moieties despite low sequence identity. We propose a core site-moiety map of multiple proteins (called CoreSiMMap) to discover inhibitors and mechanisms by profiling subsite-moiety interactions of immense screening compounds. The consensus anchor, the subsite-moiety interactions with statistical significance, of a CoreSiMMap can be regarded as a "hot spot" that represents the conserved binding environments involved in biological functions. Here, we derive the CoreSiMMap with six consensus anchors and identify six inhibitors (IC(50)<8.0 μM) of shikimate kinases (SKs) of Mycobacterium tuberculosis and Helicobacter pylori from the NCI database (236,962 compounds). Studies of site-directed mutagenesis and analogues reveal that these conserved interacting residues and moieties contribute to pocket-moiety interaction spots and biological functions. These results reveal that our multi-target screening strategy and the CoreSiMMap can increase the accuracy of screening in the identification of novel inhibitors and subsite-moiety environments for elucidating the binding mechanisms of targets.     

Defining SH2 domain and PTP specificity by screening combinatorial peptide libraries

Src homology 2 (SH2) domains mediate protein-protein interactions by recognizing short phosphotyrosyl (pY) peptide motifs in their partner proteins. Protein tyrosine phosphatases (PTPs) catalyze the dephosphorylation of pY proteins, counteracting the protein tyrosine kinases. Both types of proteins exhibit primary sequence specificity, which plays at least a partial role in dictating their physiological interacting partners or substrates. A combinatorial peptide library method has been developed to systematically assess the sequence specificity of SH2 domains and PTPs. A "one-bead-one-compound" pY peptide library is synthesized on 90-microm TentaGel beads and screened against an SH2 domain or PTP of interest for binding or catalysis. The beads that carry the tightest binding sequences against the SH2 domain or the most efficient substrates of the PTP are selected by an enzyme-linked assay and individually sequenced by a partial Edman degradation/mass spectrometry technique. The combinatorial method has been applied to determine the sequence specificity of 8 SH2 domains from Src and Csk kinases, adaptor protein Grb2, and phosphatases SHP-1, SHP-2, and SHIP1 and a prototypical PTP, PTP1B.     

Chemiluminescence determination of pharmacologically active compounds by capillary electrophoresis.

A simple and rapid capillary electrophoresis with direct chemiluminescence method has been developed for the determination of five natural pharmacologically active compounds including rutin, protocatechuic aldehyde, chlorogenic acid, luteolin and protocatechuic acid. The luminol as a component of the separation electrolyte buffer was introduced at the head of the separation capillary. The separation of five compounds was carried out in a fused-silica capillary with 15.0 mmol/L tetraborate, 1.0 mmol/L SDS and 0.42 mmol/L luminol (pH 8.5). The analytes was determined by enhancing the chemiluminescence of luminol with 0.13 mmol/L K3Fe(CN)6 in 0.05 mol/L NaOH, which was introduced at the post-column stage. The voltage applied was 16 kV. Under the optimum conditions, the analytes were separated within 10 min. The excellent linearity was obtained over two to three orders of magnitude with a detection limit (signal:noise = 3) of 0.012-0.055 micromol/L for all five analytes. The method was successfully used in the analysis of pharmaceutical and biological samples, and the assay results were satisfactory.     

Synthesis of natural-product-based compound libraries

Natural products cover a diversity space not yet available from synthetic libraries, with an unrivalled success rate as drug leads. The combinatorial synthesis of non-oligomeric natural-product-based libraries, however, is still limited to few examples because access to easily modified units strongly depends on the availability of a core structure either from a natural source, or through a suitable synthetic route. Only a few resourceful groups have managed the latter approach for more demanding multifunctional natural drug leads, such as epothilones.     

The interdependence between screening methods and screening libraries

The most common methods for discovery of chemical compounds capable of manipulating biological function involves some form of screening. The success of such screens is highly dependent on the chemical materials - commonly referred to as libraries - that are assayed. Classic methods for the design of screening libraries have depended on knowledge of target structure and relevant pharmacophores for target focus, and on simple count-based measures to assess other properties. The recent proliferation of two novel screening paradigms, structure-based screening and high-content screening, prompts a profound rethink about the ideal composition of small-molecule screening libraries. We suggest that currently utilized libraries are not optimal for addressing new targets by high-throughput screening, or complex phenotypes by high-content screening.     

Chromatographic and electrophoretic methods for Lingzhi pharmacologically active components

Lingzhi is the Chinese name given to the Ganoderma family of mushrooms, which was considered the most valuable medicine in ancient China and was believed to bring longevity, due to its mysterious power of healing the body and calming the mind. Today, Lingzhi is still widely revered as a valuable health supplement and herbal medicine worldwide, as studies (mostly conducted in China, Korea, Japan and the United States) into the medicinal and nutritional values of Lingzhi revealed that it does indeed contain certain bioactive ingredients (such as triterpenes and polysaccharides) that might be beneficial for the prevention and treatment of a variety of ailments, including important diseases such as hypertension, diabetes, hepatitis, cancers, and AIDS. As research into the biological activities of Lingzhi, as well as the quality assurance and quality control of Lingzhi products, require the isolation/purification of active ingredients from Lingzhi, followed by subsequent analytical and/or preparative separations, the present review summarizes the various chromatographic and electrophoretic methods (as well as sample pretreatment methods) typically employed to achieve such extraction/separation procedures.     

Differential screening of phage-ab libraries by oligonucleotide microarray technology

A novel and efficient tagArray technology was developed that allows rapid identification of antibodies which bind to receptors with a specific expression profile, in the absence of biological information. This method is based on the cloning of a specific, short nucleotide sequence (tag) in the phagemid coding for each phage-displayed antibody fragment (phage-Ab) present in a library. In order to set up and validate the method we identified about 10,000 different phage-Abs binding to receptors expressed in their native form on the cell surface (10 k Membranome collection) and tagged each individual phage-Ab. The frequency of each phage-Ab in a given population can at this point be inferred by measuring the frequency of its associated tag sequence through standard DNA hybridization methods. Using tiny amounts of biological samples we identified phage-Abs binding to receptors preferentially expressed on primary tumor cells rather than on cells obtained from matched normal tissues. These antibodies inhibited cell proliferation in vitro and tumor development in vivo, thus representing therapeutic lead candidates.     

High-throughput screening of enzyme libraries

Directed evolution is becoming a widely used technique for modifying or enhancing protein performance. Ultimately, the success of directed protein evolution experiments hinges on the efficiency of the methods used to screen libraries for mutants with properties of interest. Although there is still a paucity of general methods for enzyme library screening, in recent years a number of promising strategies have emerged and are increasingly being used to explore challenging issues in protein engineering.     

Structure-based tailoring of compound libraries for high-throughput screening: discovery of novel EphB4 kinase inhibitors

High-throughput docking is a computational tool frequently used to discover small-molecule inhibitors of enzymes or receptors of known three-dimensional structure. Because of the large number of molecules in chemical libraries, automatic procedures to prune multimillion compound collections are useful for high-throughput docking and necessary for in vitro screening. Here, we propose an anchor-based library tailoring approach (termed ALTA) to focus a chemical library by docking and prioritizing molecular fragments according to their binding energy which includes continuum electrostatics solvation. In principle, ALTA does not require prior knowledge of known inhibitors, but receptor-based pharmacophore information (hydrogen bonds with the hinge region) is additionally used here to identify molecules with optimal anchor fragments for the ATP-binding site of the EphB4 receptor tyrosine kinase. The 21,418 molecules of the focused library (from an initial collection of about 730,000) are docked into EphB4 and ranked by force-field-based energy including electrostatic solvation. Among the 43 compounds tested in vitro, eight molecules originating from two different anchors show low-micromolar activity in a fluorescence-based enzymatic assay. Four of them are active in a cell-based assay and are potential anti-angiogenic compounds.     

Selecting and screening recombinant antibody libraries

During the past decade several display methods and other library screening techniques have been developed for isolating monoclonal antibodies (mAbs) from large collections of recombinant antibody fragments. These technologies are now widely exploited to build human antibodies with high affinity and specificity. Clever antibody library designs and selection concepts are now able to identify mAb leads with virtually any specificity. Innovative strategies enable directed evolution of binding sites with ultra-high affinity, high stability and increased potency, sometimes to a level that cannot be achieved by immunization. Automation of the technology is making it possible to identify hundreds of different antibody leads to a single therapeutic target. With the first antibody of this new generation, adalimumab (Humira, a human IgG1 specific for human tumor necrosis factor (TNF)), already approved for therapy and with many more in clinical trials, these recombinant antibody technologies will provide a solid basis for the discovery of antibody-based biopharmaceuticals, diagnostics and research reagents for decades to come.     

Separation procedures for the pharmacologically active components of rhubarb

Rhubarb, as an important Chinese medicine, has many functions owing to containing anthraquinone derivatives. The analysis of anthraquinone derivatives in Chinese rhubarb is reviewed. The analytical techniques include high performance liquid chromatography, capillary electrophoresis, thin-layer chromatography and so on. The main operation parameters in every technique were given. The structures of anthraquinone derivatives and the classification of Chinese rhubarb were summarized too.     

The displacement of calcium ions from phospholipid monolayers by pharmacologically active and other organic bases

1. The binding of (45)Ca(2+) to a monolayer of phosphatidylinositol at the air-water interface was maximal when the separation of the phospholipid head groups approximated to the diameter of a hydrated Ca(2+) ion. 2. The displacement of Ca(2+) adsorbed on monomolecular films of phosphatidylinositol by a series of drugs (both narcotic and excitatory) and other organic bases was related to the ability of the bases to penetrate into the film. 3. With films of phosphatidylinositol at constant area, and at an initial surface pressure of 10dynes/cm., the displacement of Ca(2+) by increasing concentrations of the local anaesthetic, tetracaine, was linearly related to the change in surface pressure (Deltapi) caused by the penetration of the drug. 4. Deltapi and the displacement of Ca(2+) showed a related fall when the initial surface pressure of the phosphatidylinositol film was increased from 4 to 40dynes/cm. both at a constant bulk tetracaine concentration and when this latter concentration was adjusted to keep it at a constant ratio to the surface density of phosphatidylinositol molecules. 5. The displacement of Ca(2+) from phosphatidylinositol films by cetyltri-methylammonium ions was directly compared with the surface concentration of the base in the film, measured by using labelled base and a surface-radioactivity technique. 6. The ability of a series of straight-chain aliphatic amines to displace Ca(2+) from phosphatidylinositol films increased with the number of carbon atoms up to C(12). However, there was a marked jump in the displacing activity after hexylamine, and this could probably be correlated with the carbon chain's being of sufficient length to just reach the hydrophobic fatty acid chains of the orientated phospholipid molecules with the charges on both substances in juxtaposition.     

Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules

Culture-independent studies on environmental samples indicate that most bacteria are not readily cultured in the laboratory. The small fraction of bacteria that have been successfully cultured from environmental samples have been a very rewarding source of novel biologically active natural products. The introduction of DNA extracted directly from environmental samples into easily cultured bacteria and the screening of these large libraries for clones that produce biologically active small molecules is one means to access natural products encoded by the genomes of previously uncultured bacteria. This protocol provides detailed procedures for cloning DNA directly from environmental samples and screening these clones for the production of antibacterially active natural products. The entire protocol, from soil sample to the identification of antibacterially active environmental DNA clones, will take approximately 2 weeks.