A mathematical model of measurement uncertainty of single substrate enzyme assays

Clinical laboratory tests provide critical information at every stage of the medical decision‐making process, and measurement of the activity levels of enzymes such as alkaline phosphatase, lactate dehydrogenase, etc. provide information regarding various body functions such as the liver and gastrointestinal tract. The uncertainty associated with these enzyme measurement processes describes the quality of the measurement process, and therefore methods to improve the quality of the measurement process require minimizing the measurement uncertainty of the enzyme assay. In this study, we develop a mathematical model of the lactate dehydrogenase measurement process, with uncertainty introduced into its parameters that represent the sources of variation in the different components and stages of the measurement process. The Monte Carlo method is then utilized to estimate the uncertainty associated with the model, and therefore the measurement process. An empirical function used to generate estimates of uncertainty for patient samples with unknown activity levels is constructed using the model. The model is then used to quantify the contributions of the individual sources of uncertainty to the net measurement uncertainty and also quantify the effect of uncertainty within the calibration process on the distribution of the measurement result. Copyright © 2014 John Wiley & Sons, Ltd.     

Synthesis of stereochemical probes for new fluorogenic assays for yeast transketolase variants

For the screening of yeast transketolase (TK) variants with improved or new properties acquired by random mutagenesis, we report on the stereoselective synthesis of fluorogenic substrates as probes for measuring TK activity. Compound 1 (7-(2′,3′,5′-trihydroxy-4′-oxo-pentyl)oxycoumarine), prepared as previously described, [Tetrahedron Lett.2003, 44, 827-830] enabled us to evaluate wild type TK velocity in a simple, specific and reproducible way. To select TK mutants able to produce d-threo aldoses, we prepared compound 2 (dihydroxy-4-O-(2′-oxo-benzopyran-7′-yl-D-threose) from dimethyl tartrate. Starting from d-ribose, we successfully obtained compound 3 (7′-(2,3,5-trihydroxy-4-oxo-pentyl)oxycoumarine) as a probe for TK mutants able to produce l-erythro ketoses.     

Gold Nanoparticle–Fluorophore Complexes: Sensitive and Discerning “Noses” for Biosystems Sensing

Gold nanoparticles (NPs) efficiently quench adsorbed fluorophores. Upon disruption of such complexes by an analyte, fluorescence turn‐on is observed. By judicious choice of the functionalized NP and the fluorophore, these complexes display different responses to analytes, thus leading to versatile yet simple array‐based sensor platforms. Using this strategy, we can identify proteins in buffer and serum, distinguish between both different species and different strains of bacteria, and differentiate between healthy, cancerous, and metastatic human and murine cells.     

A miniaturized arrayed assay format for detecting small molecule-protein interactions in cells

Background: Two complementary approaches to studying the cellular function of proteins involve alteration of function either by mutating protein-encoding genes or by binding a small molecule to the protein. A mutagen can generate millions of genetic mutations; correspondingly, split-pool synthesis can generate millions of unique ligands attached to individual beads. Genetic screening of mutations is relatively straightforward but, in contrast, split-pool synthesis presents a challenge to current methods of screening for compounds that alter protein function. The methods used to screen natural products are not feasible for large libraries composed of covalently immobilized compounds on synthesis beads. The sheer number of compounds synthesized by split-pool synthesis, and the small quantity of individual compound attached to each bead require assay miniaturization for efficient screening.Results: We present a miniaturized cell-based technique for the screening of ligands prepared by split-pool synthesis. Spatially defined droplets with uniform volumes of approximately 50–150 nanoliters (depending on well dimensions) are arrayed on plastic devices prepared using a combination of photolithography and polymer molding. Using this microtechnology, approximately 6,500 assays using either yeast cells or mammalian tissue culture can be performed within the dimensions of a standard 10 cm petri dish. We demonstrate that the biological effect of a small molecule prepared by split-pool synthesis can be detected in this format following its photorelease from a bead.Conclusions: The miniaturized format described here allows uniformly sized nanodroplets to be arrayed on plastic devices. The design is amenable to a large number of biological assays and the spatially arrayed format ensures uniform and controlled ligand concentrations and should facilitate automation of assays. The screening method presented here provides an efficient means of rapidly screening large numbers of ligands made by split-pool synthesis in both yeast and mammalian cells.     

A one-bead, one-stock solution approach to chemical genetics: part 2

BACKGROUND: Chemical genetics provides a systematic means to study biology using small molecules to effect spatial and temporal control over protein function. As complementary approaches, phenotypic and proteomic screens of structurally diverse and complex small molecules may yield not only interesting individual probes of biological function, but also global information about small molecule collections and the interactions of their members with biological systems. RESULTS: We report a general high-throughput method for converting high-capacity beads into arrayed stock solutions amenable to both phenotypic and proteomic assays. Polystyrene beads from diversity-oriented syntheses were arrayed individually into wells. Bound compounds were cleaved, eluted, and resuspended to generate 'mother plates' of stock solutions. The second phase of development of our technology platform includes optimized cleavage and elution conditions, a novel bead arraying method, and robotic distribution of stock solutions of small molecules into 'daughter plates' for direct use in chemical genetic assays. This library formatting strategy enables what we refer to as annotation screening, in which every member of a library is annotated with biological assay data. This phase was validated by arraying and screening 708 members of an encoded 4320-member library of structurally diverse and complex dihydropyrancarboxamides. CONCLUSIONS: Our 'one-bead, multiple-stock solution' library formatting strategy is a central element of a technology platform aimed at advancing chemical genetics. Annotation screening provides a means for biology to inform chemistry, complementary to the way that chemistry can inform biology in conventional ('investigator-initiated') small molecule screens.     

Homogeneous Phosphodiesterase and Hybridization Assays Using Europium Cryptate: Oligonucleotide Conjugates

Upon conjugation to single-stranded oligonucleotides, a europium cryptate (Eu³⁺ tris-bipyridine) showed a marked increase in its fluorescence lifetime and was much less sensitive to fluorescence quenching by uric acid. This behavior was shown to be moderately dependent on the length and sequence of the oligonucleotide and all the single-stranded oligonucleotides studied displayed similar behavior. In contrast, a cryptate moiety attached to a double-stranded oligonucleotide did not display such an increase in its fluorescence lifetime and was quenched in presence of uric acid. Taking advantage of this unique behavior characterizing single-stranded K-ODN conjugates, a new concept of dosage based on the modulation of the cryptate fluorescence by a quencher was set up. This fluorescence quenching assay involving a single fluorescent label was applied to the monitoring of hybridization reactions and detection of a phosphodiesterase activity.     

Design and Synthesis of Hsp90 Inhibitors with B-Raf and PDHK1 Multi-Target Activity

The design of multi-target ligands has become an innovative approach for the identification of effective therapeutic treatments against complex diseases, such as cancer. Recent studies have demonstrated that the combined inhibition of Hsp90 and B-Raf provides synergistic effects against several types of cancers. Moreover, it has been reported that PDHK1, which presents an ATP-binding pocket similar to that of Hsp90, plays an important role in tumor initiation, maintenance and progression, participating also to the senescence process induced by B-Raf oncogenic proteins. Based on these premises, the simultaneous inhibition of these targets may provide several benefits for the treatment of cancer. In this work, we set up a design strategy including the assembly and integration of molecular fragments known to be important for binding to the Hsp90, PDHK1 and B-Raf targets, aided by molecular docking for the selection of a set of compounds potentially able to exert Hsp90-B-Raf-PDHK1 multi-target activities. The designed compounds were synthesized and experimentally validated in vitro. According to the in vitro assays, compounds 4 a , 4 d and 4 e potently inhibited Hsp90 and moderately inhibited the PDHK1 kinase. Finally, molecular dynamics simulations were performed to provide further insights into the structural basis of their multi-target activity.