Small molecule-dependent genetic selection in stochastic nanodroplets as a means of detecting protein-ligand interactions on a large scale

Background: Understanding the cellular role of a protein often requires a means of altering its function, most commonly by mutating the gene encoding the protein. Alternatively, protein function can be altered directly using a small molecule that binds to the protein, but no general method exists for the systematic discovery of small molecule ligands. Split-pool synthesis provides a means of synthesizing vast numbers of small molecules. Synthetic chemists will soon be able to synthesize natural product-like substances by this method, so compatible screening methods that detect the activity of minute quantities of molecules among many inactive ones will be in demand.Results: We describe two advances towards achieving the above goals. First, a technique is described that uses a simple spray gun to create 5000–8000 droplets randomly, each having a volume of 50–200 nanoliters. The individual ‘nanodroplets’ contain a controlled number of cells and many also contain individual synthesis beads. As small molecules can be photochemically released from the beads in a time-dependent manner, the concentration of ligands that the cells are exposed to can be controlled. The spatial segregation of nanodroplets prevents the mixing of compounds from other beads so the effects of each molecule can be assayed individually. Second, a small molecule-dependent genetic selection involving engineered budding yeast cells was used to detect intracellular protein-ligand interactions in nanodroplets.Conclusions: The technique described here should facilitate the discovery of new cell-permeable ligands, especially when combined with a positive selection assay that detects intracellular binding of small molecules to proteins. Using ‘anchored combinatorial libraries’, it may be possible to screen entire libraries of natural product-like molecules against the entire collection of proteins encoded within cDNA libraries in a single experiment.     

MASPIT: three-hybrid trap for quantitative proteome fingerprinting of small molecule-protein interactions in mammalian cells

Organic small molecules generally act by perturbing the function of one or more cellular target proteins, the identification of which is essential to an understanding of the molecular basis of drug action. Here we describe the application of methotrexate-linked small molecule ligands to a mammalian three-hybrid interaction trap for proteome-wide identification of small molecule targets, quantification of the targeting potency of unmodified small molecules for such targets in intact cells, and screening for inhibitors of small molecule-protein interactions. During the course of this study we also identified the pyrido[2,3-d]pyrimidine PD173955, a known SRC kinase inhibitor, as a potent inhibitor of several ephrin receptor tyrosine kinases. This finding could perhaps be exploited in the design of inhibitors for this kinase subfamily, members of which have been implicated in the pathogenesis of various diseases, including cancer.     

利用化学指示剂在多相催化反应中进行高通量筛选

 介绍了一种简单的组合化学技术,该技术利用催化反应中产物或反应物导致的化学指示剂的颜色变化快速地指示反应进程. 选用甲基橙为指示剂,分子筛为催化剂,考察了不同反应条件下羧酸的酯化反应,并用气相色谱和高效液相色谱分析方法对实验结果进行验证. 结果表明,利用化学指示剂进行的高通量颜色筛选结果与色谱检测结果很好地吻合,该方法具有简单和高效的特点,可应用于对化学指示剂敏感的反应.     

动态组合化学最新进展

动态组合化学是组合化学的一个新兴分支,在药物先导化合物的发现中有广阔的应用前景。在动态组合化学库中,利用靶标分子的诱导结合作用,通过可逆共价反应,能够选择性的筛选到与靶标分子存在强相互作用的优势化合物。本文按照动态组合化学方法简介、动态组合化学中的可逆共价化学、动态组合化学库的分类、动态组合化学库筛选方法的研究进展及动态组合化学在药物先导化合物发现过程中的应用等5个方面对动态组合化学进行了概述。     

A practical high-throughput screening system for enantioselectivity by using FTIR spectroscopy

For the first time FTIR spectroscopy has been applied to the measurement of enantiomeric purity. The underlying concept is based on the use of pseudo-enantiomers that are (13)C-labeled at appropriate positions. Upon applying Lambert-Beer's law in the determination of the concentrations of both enantiomers, the ee values are accessible, accuracy to within +/-5 % of the true values being possible. The application of a commercially available high-throughput FTIR system results in a slightly decreased accuracy (+/-7% for the ee values), but this allows a throughput of up to 10000 samples per day. The method is of interest in the area of combinatorial symmetric catalysis and directed evolution of enantioselective enzymes.     

A simple visual assay based on small molecule hydrogels for detecting inhibitors of enzymes

Here we report a simple approach to develop assays based on the hydrogelation of small molecules for quick detecting inhibitors of enzymes.     

化学多样性空间探索与组合药物设计

本文综述组合化学的最新进展, 内容涵盖组合化学的基本概念、原理、技术, 在药物发现中的应用, 以及组合化学和其他科学技术分枝的关系。最后, 提出了组合化学工程中亟须研究的一些项目, 介绍了开展这些研究所必需的条件, 并给出了解决方案。     

Electrospray ionization tandem mass spectrometry in high-throughput screening of homogeneous catalysts

The frontispiece shows an illustration by John Tenniel and an excerpt from the 1865 edition of Lewis Carroll's "Alice in Wonderland". Because everything in Wonderland runs counter to logic, the Queen of Hearts declares in Alice's trial "Sentence first-verdict afterwards". High-throughput screening of catalysts, as it is conventionally practiced, does "Synthesis first-screening afterwards" which, as is argued in this review, also backwards. Given the particular constraints present in organometallic complexes, it is more efficient to develop a selective synthesis only when it has already been determined that a structure is likely to be better. The consequence is that screening methods must be able to handle ill-defined mixtures. Electrospray ionization tandem mass spectrometry is presented as a technical solution to this problem.     

A small molecule promotes mitochondrial fusion in Mammalian cells

Mitochondrial dynamics: An image-based screen identified a small molecule, M1, that specifically promotes the fusion of fragmented mitochondria and protects cells from mitochondrial-fragmentation-associated cell death. Mechanistic studies revealed that M1 shifts the mitochondrial dynamic balance towards fusion.     

A homogeneous assay for protein analysis in droplets by fluorescence polarization

We present a novel homogeneous (“mix‐incubate‐read”) droplet microfluidic assay for specific protein detection in picoliter volumes by fluorescence polarization (FP), for the first time demonstrating the use of FP in a droplet microfluidic assay. Using an FP‐based assay we detect streptavidin concentrations as low as 500 nM and demonstrate that an FP assay allows us to distinguish droplets containing 5 μM rabbit IgG from droplets without IgG with an accuracy of 95%, levels relevant for hybridoma screening. This adds to the repertoire of droplet assay techniques a direct protein detection method which can be performed entirely inside droplets without the need for labeling of the analyte molecules.     

The first fluorogenic assay for detecting a Baeyer-Villigerase activity in microbial cells

The first fluorogenic assay allowing for detection of microbial enzymes able to perform Baeyer-Villiger oxidation is described. This is based on the use of 4-oxopentyl umbelliferyl ether 1 as a fluorogenic substrate. When Baeyer-Villigerases active against this test ketone are present in the selected whole cells, 1 is transformed into 3-hydroxypropyl umbelliferyl ether 3, which, in a subsequent step, releases the fluorescent product umbelliferone. Different microorganisms, known to be endowed with Baeyer-Villigerase activity, were assayed.