Two-dimensional turbulent flow chromatography coupled on-line to liquid chromatography–mass spectrometry for solution-based ligand screening against multiple proteins

We present herein a novel bioseparation/chemical analysis strategy for protein–ligand screening and affinity ranking in compound mixtures, designed to increase screening rates and improve sensitivity and ruggedness in performance. The strategy is carried out by combining on-line two-dimensional turbulent flow chromatography (2D-TFC) with liquid chromatography–mass spectrometry (LC–MS), and accomplished through the following steps: (1) a reversed-phase TFC stage to separate the protein/ligand complex from the unbound free molecules, (2) an on-line dissociation process to release the bound ligands from the complexes, and (3) a second mixed-mode cation-exchange/reversed-phase TFC stage to trap the bound ligands and to remove the proteins and salts, followed by LC–MS analysis for identification and determination of the binding affinities. The technique can implement an ultra-fast isolation of protein/ligand complex with the retention time of a complex peak in about 5 s, and on-line prepare the “clean” sample to be directly compatible with the LC–MS analysis. The improvement in performance of this 2D-TFC/LC–MS approach over the conventional approach has been demonstrated by determining affinity-selected ligands of the target proteins acetylcholinesterase and butyrylcholinesterase from a small library with known binding affinities and a steroidal alkaloid library composed of structurally similar compounds. Our results show that 2D-TFC/LC–MS is a generic and efficient tool for high-throughput screening of ligands with low-to-high binding affinities, and structure-activity relationship evaluation.     

Lessons for fragment library design: analysis of output from multiple screening campaigns

Over the past 8 years, we have developed, refined and applied a fragment based discovery approach to a range of protein targets. Here we report computational analyses of various aspects of our fragment library and the results obtained for fragment screening. We reinforce the finding of others that the experimentally observed hit rate for screening fragments can be related to a computationally defined druggability index for the target. In general, the physicochemical properties of the fragment hits display the same profile as the library, as is expected for a truly diverse library which probes the relevant chemical space. An analysis of the fragment hits against various protein classes has shown that the physicochemical properties of the fragments are complementary to the properties of the target binding site. The effectiveness of some fragments appears to be achieved by an appropriate mix of pharmacophore features and enhanced aromaticity, with hydrophobic interactions playing an important role. The analysis emphasizes that it is possible to identify small fragments that are specific for different binding sites. To conclude, we discuss how the results could inform further development and improvement of our fragment library. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification of novel target sites and an inhibitor of the dengue virus E protein

Dengue and related flaviviruses represent a significant global health threat. The envelope glycoprotein E mediates virus attachment to a host cell and the subsequent fusion of viral and host cell membranes. The fusion process is driven by conformational changes in the E protein and is an essential step in the virus life cycle. In this study, we analyzed the pre-fusion and post-fusion structures of the dengue virus E protein to identify potential novel sites that could bind small molecules, which could interfere with the conformational transitions that mediate the fusion process. We used an in silico virtual screening approach combining three different docking algorithms (DOCK, GOLD and FlexX) to identify compounds that are likely to bind to these sites. Seven structurally diverse molecules were selected to test experimentally for inhibition of dengue virus propagation. The best compound showed an IC₅₀ in the micromolar range against dengue virus type 2. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Robust optimization of scoring functions for a target class

Target-specific optimization of scoring functions for protein–ligand docking is an effective method for significantly improving the discrimination of active and inactive molecules in virtual screening applications. Its applicability, however, is limited due to the narrow focus on, e.g., single protein structures. Using an ensemble of protein kinase structures, the publically available directory of useful decoys ligand dataset, and a novel multi-factorial optimization procedure, it is shown here that scoring functions can be tuned to multiple targets of a target class simultaneously. This leads to an improved robustness of the resulting scoring function parameters. Extensive validation experiments clearly demonstrate that (1) virtual screening performance for kinases improves significantly; (2) variations in database content affect this kind of machine-learning strategy to a lesser extent than binary QSAR models, and (3) the reweighting of interaction types is of particular importance for improved screening performance. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Analysis and use of fragment-occurrence data in similarity-based virtual screening

Current systems for similarity-based virtual screening use similarity measures in which all the fragments in a fingerprint contribute equally to the calculation of structural similarity. This paper discusses the weighting of fragments on the basis of their frequencies of occurrence in molecules. Extensive experiments with sets of active molecules from the MDL Drug Data Report and the World of Molecular Bioactivity databases, using fingerprints encoding Tripos holograms, Pipeline Pilot ECFC_4 circular substructures and Sunset Molecular keys, demonstrate clearly that frequency-based screening is generally more effective than conventional, unweighted screening. The results suggest that standardising the raw occurrence frequencies by taking the square root of the frequencies will maximise the effectiveness of virtual screening. An upper-bound analysis shows the complex interactions that can take place between representations, weighting schemes and similarity coefficients when similarity measures are computed, and provides a rationalisation of the relative performance of the various weighting schemes.     

A Highly Sensitive Fluorescence Probe for Fast Thiol‐Quantification Assay of Glutathione Reductase

Fast detection of cellular thiols in aqueous medium was achieved using a newly developed fluorescence probe (see picture). Based on this probe, a high‐throughput fluorescence assay for glutathione reductase was developed.

     

Coupling Microdroplet Microreactors with Mass Spectrometry: Reading the Contents of Single Droplets Online

Fully integrated : Mass spectrometry has been integrated into a detection scheme for microdroplets that are created within microfluidic channels (see picture, scale bar 200 μm). This technique allows droplets to be identified based on the compounds they contain, and combines fluorescence screening with MS analysis. These experiments indicate how similar approaches can be applied to the ambitious goals of on‐chip protein evolution and chemical synthesis.

     

Design of a Full‐Profile‐Matching Solution for High‐Throughput Analysis of Multiphase Samples Through Powder X‐ray Diffraction

Finding a clear route to new structures : The design of an adaptable time warping (ATW) methodology (see figure) for automatically, quickly, and reliably deciphering X‐ray diffraction patterns is described.

     

药物配体与生物大分子受体相互作用核磁共振的研究进展

药物与生物体内目标大分子之间的相互作用,是决定药物药理活性和代谢稳定性的主要因素。如何快速高效地识别出能与靶分子相互作用且能抑制其体外活性的药物分子,是制药工业普遍关注的问题。核磁共振已经成为研究小分子配体和生物大分子相互作用的一种非常重要的手段。检测小分子配体信号在作用过程中的变化以识别药物分子,是核磁共振进行药物筛选的主要方法之一。本文介绍了近年来这方面的研究进展。     

Potential of atmospheric pressure chemical ionization source in GC‐QTOF MS for pesticide residue analysis

The potential applications of a new atmospheric pressure source for GC‐MS analysis have been investigated in this work. A list of around 100 GC‐amenable pesticides, which includes organochlorine, organophosphorus and organonitrogenated compounds, has been used to evaluate their behavior in the new source. Favoring the major formation of the molecular ion in the source has been the main goal due to the wide‐scope screening possibilities that this fact brings in comparison with the traditional, highly fragmented electron ionization spectra. Thus, the addition of water as modifier has been tested as a way to promote the generation of protonated molecules. Pesticides investigated have been classified into six groups according to their ionization/fragmentation behavior. Four of them are characterized by the abundant formation of the protonated molecule in the atmospheric pressure source, mostly being the base peak of the spectrum. These results show that wide‐scope screening could be easily performed with this source by investigating the presence of the protonated molecule ion, MH+. The developed procedure has been applied to pesticide screening in different food samples (nectarine, orange and spinach) and it has allowed the presence of several pesticides to be confirmed such as chlorpyriphos ethyl, deltamethrin and endosulfan sulfate. The availability of a quadrupole time‐of‐flight instrument made it feasible to perform additional MS/MS experiments for both standards and samples to go further in the confirmation of the identity of the detected compounds. Results shown in this paper have been obtained using a prototype source which exhibits promising features that could be applied to other analytical problems apart from those illustrated in this work. Copyright © 2010 John Wiley & Sons, Ltd.