Droplets as microreactors for high-throughput biology

Inspired by the principles of biological evolution, biologists--and others--have in recent decades harnessed the power of "natural" selection to sift through huge libraries of genes and find those with desirable properties. At the same time, the demand for high-throughput biochemical and genetic assays and screens has driven the development of increasingly miniaturised assay systems. An exciting synergy is now emerging between these two fields, whereby the tools of ultrahigh-throughput screening promise to open up new directions in molecular engineering.     

An adaptable luminescence resonance energy transfer assay for measuring and screening protein-protein interactions and their inhibition

Protein-protein interactions (PPIs) are central to biological processes and represent an important class of therapeutic targets. Here we show that the interaction between FK506-binding protein 12 fused to green fluorescent protein (GFP-FKBP) and the rapamycin-binding domain of mTor fused to Escherichia coli dihydrofolate reductase (FRB-eDHFR) can be sensitively detected (signal-to-background ratio (S/B)>100) and accurately quantified within an impure cell lysate matrix using a luminescence resonance energy transfer (LRET) assay. Ascomycin-mediated inhibition of GFP-FKBP-rapamycin-FRB-eDHFR complex formation was also detected at high S/B ratio (>80) and Z'-factor (0.89). The method leverages the selective, stable binding of trimethoprim (TMP)-terbium complex conjugates to eDHFR, and time-resolved, background-free detection of the long-lifetime (～ms) terbium-to-GFP LRET signal that indicates target binding. TMP-eDHFR labeling can be adapted to develop high-throughput screening assays and complementary, quantitative counter-screens for a wide variety of PPI targets with a broad range of affinities that may not be amenable to purification.     

Substrate Selection Influences Molecular Recognition in a Screen for Lymphoid Tyrosine Phosphatase Inhibitors

Assay design is an important variable that influences the outcome of an inhibitor screen. Here, we have investigated the hypothesis that protein tyrosine phosphatase inhibitors with improved biological activity could be identified from a screen by using a biologically relevant peptide substrate, rather than traditional phosphotyrosine mimetic substrates. A 2000‐member library of drugs and drug‐like compounds was screened for inhibitors of lymphoid tyrosine phosphatase (LYP) by using both a peptide substrate (Ac‐ARLIEDNE‐pCAP‐TAREG‐NH₂, peptide 1) and a small‐molecule phosphotyrosine mimetic substrate (difluoromethyl umbelliferyl phosphate, DiFMUP). The results demonstrate that compounds that inhibited enzyme activity on the peptide substrate had greater biological activity than compounds that only inhibited enzyme activity on DiFMUP. Finally, epigallocatechin‐3,5‐digallate was identified as the most potent inhibitor of lymphoid tyrosine phosphatase activity to date, with an IC₅₀ of 50 nM and significant activity in T‐cells. Molecular docking simulations provided a first model for binding of this potent inhibitor to LYP; this will constitute the platform for ongoing lead optimization efforts.     

Activity‐Fed Translation (AFT) Assay: A New High‐Throughput Screening Strategy for Enzymes in Droplets

There is an increasing demand for the development of sensitive enzymatic assays compatible with droplet‐based microfluidics. Here we describe an original strategy, activity‐fed translation (AFT), based on the coupling of enzymatic activity to in vitro translation of a fluorescent protein. We show that methionine release upon the hydrolysis of phenylacetylmethionine by penicillin acylase enabled in vitro expression of green fluorescent protein. An autocatalytic setup where both proteins are expressed makes the assay highly sensitive, as fluorescence was detected in droplets containing single PAC genes. Adding a PCR step in the droplets prior to the assay increased the sensitivity further. The strategy is potentially applicable for any activity that can be coupled to the production of an amino acid, and as the microdroplet volume is small the use of costly reagents such as in vitro expression mixtures is not limiting for high‐throughput screening projects.     

Experimental problems in the application of UV/visible based methods as the quantification tool for the entrapped/released insulin from PLGA carriers

BACKGROUND: Controlled release of medicaments from biodegradable polymers remains the most convenient way for their sustained release. Although a number of articles have been published, experimental work involving the preparation of polymer‐based carriers and release procedures are not described with sufficient level of detail to allow other researchers to reproduce the experiments and to compare published results with their own. In this contribution the experimental background of the entrapment and release of insulin from PLGA carriers is described and the problems found at each step related to UV/Visible method used to quantify them are addressed in detail. RESULTS: The quantification of entrapped insulin by UV/visible methods was affected by aggregation. The design of the release experiment influenced the results regarding the entrapment efficiency (EE) and the maximum percentage of released insulin. It was also found that the presence of colloidal polymeric particles, insufficient centrifugation times and the kind of solvent used in the release test might lead to mistakes in the percentage of liberated insulin when UV/visible based methods are employed. CONCLUSIONS: This contribution demonstrates that serious discrepancies in the EE and percentage of released protein may arise if some key experimental factors are not taken into account. Therefore, the analysis presented here tries to point out important aspects of this topic currently not reported, unnoticed or not properly analyzed in the open literature. The results are useful for the entrapment of any protein on any polymeric device using UV/visible based methods to quantify them. Copyright © 2009 Society of Chemical Industry