A Label-free Sirtuin 1 Assay based on Droplet-Electrospray Ionization Mass Spectrometry

Rich analytic toolbox for the exploration, characterization, screening, and application studies of ω-transaminases

Omega-transaminases (ωTAs) constitute an important class of biocatalysts in the pharmaceutical, agrochemical, and fine chemical industries, because of their generally good performance in the efficient, enantiospecific, and environment-friendly synthesis of chiral amines that possess diverse chemical structures and biological activities. However, their practical applications are often hindered by unfavorable reaction equilibria, product inhibition, limited robustness, and relatively small accommodation for substrates. Many efforts, including the exploration of novel enzymes from various environments and the targeted engineering of identified enzymes, have been made to develop more specific and efficient ωTA catalysts. A simple, rapid, and accurate evaluation of enzyme activity is important. In addition to the classic chromatography-based methods, to date, at least 18 analytic methods, which are based on cell growth or colorimetry/spectrophotometry, pH, fluorescence and conductivity changes, have been developed and applied in both qualitative and quantitative analyses of ωTAs. These methods differ in terms of their principles, accuracy, throughput, simplicity, and cost-effectiveness. Here, we present a detailed examination of the advantages and drawbacks of these methods. Guidance for method selection from the perspective of practical applications is proposed to assist investigators in choosing appropriate methods according to different research purposes and existing conditions.

Droplet Microfluidics and Directed Evolution of Enzymes: An Intertwined Journey

Evolution is essential to the generation of complexity and ultimately life. It relies on the propagation of the properties, traits, and characteristics that allow an organism to survive in a challenging environment. It is evolution that shaped our world over about four billion years by slow and iterative adaptation. While natural evolution based on selection is slow and gradual, directed evolution allows the fast and streamlined optimization of a phenotype under selective conditions. The potential of directed evolution for the discovery and optimization of enzymes is mostly limited by the throughput of the tools and methods available for screening. Over the past twenty years, versatile tools based on droplet microfluidics have been developed to address the need for higher throughput. In this Review, we provide a chronological overview of the intertwined development of microfluidics droplet-based compartmentalization methods and in vivo directed evolution of enzymes.

Comparison of Design Approaches for Low-Cost Sampling Mechanisms in Open-Source Chemical Instrumentation

Robotic positioning systems are used in a variety of chemical instruments, primarily for liquid handling purposes, such as autosamplers from vials or well plates. Here, two approaches to the design of open-source autosampler positioning systems for use with 96-well plates are described and compared. The first system, a 3-axis design similar to many low-cost 3D printers that are available on the market, is constructed using an aluminum design and stepper motors. The other system relies upon a series of 3D printed parts to achieve movement with a series of linker arms based on Selective Compliance Assembly Robot Arm (SCARA) design principles. Full printer design files, assembly instructions, software, and user directions are included for both samplers. The positioning precision of the 3-axis system is better than the SCARA mechanism due to finer motor control, albeit with a slightly higher cost of materials. Based on the improved precision of this approach, the 3-axis autosampler system was used to demonstrate the generation of a segmented flow droplet stream from adjacent wells within a 96-well plate.

How electrospray potentials can disrupt droplet microfluidics and how to prevent this

A pressure-resistant microfluidic glass chip that integrates a packed-bed HPLC column, a droplet generator and a monolithic electrospray emitter is presented. This approach enables a seamless coupling of chip-HPLC and droplet microfluidics with ESI-MS detection. For the electrical contacting of the emitter, an electrode was integrated into the channel, which reaches up to the emitter tip. The incidental finding that under certain circumstances, the electrospray potential can strongly disturb the droplet microfluidics by electrowetting, was investigated in detail. Strategies to avoid this are evaluated and include electrical shielding and/or chip layouts, where the droplet generator is positioned at a long distance from the emitter.

Novel SERS-based process analysis for label-free segmented flow screenings

In microfluidic segmented flow processes label-free analytical techniques like surface enhanced Raman spectroscopy (SERS) can reveal the chemical composition of the individual droplet contents. The SERS system developed in this work enables a simple connection to micro segmented flow processes through miniaturization. The concept is based on the parallelization of silver/polyacrylamide composite SERS spots on a carrier plate on which the segments are deposited. The transfer of the segments allows an easy connection to existing flow processes and provides optimal conditions for Raman measurements using miniaturized spectrometers. The preparation of the SERS polymer composite was optimized in terms of the silver content in the polymer matrix to obtain a high SERS signal. The performance and long-term stability of the polymer have been successfully demonstrated. The deamination of adenine with sodium nitrite to hypoxanthine was chosen as a case study to demonstrate the capability of the novel SERS-based process analysis. A sequence of approximately one hundred segments in combination with a gradient of the nitrite concentration (0 to 0.4 mol L-1) was generated at two temperatures. The concentration of adenine and hypoxanthine were determined by using a multivariate calibration model, since the Raman spectra of both substances are overlapping. It was shown that the conversion of adenine is increased with higher nitrite concentration and temperature. A conversion of 35% was obtained at 50 °C and a conversion of 60% at 80 °C, respectively.

High-Throughput Nanoelectrospray Ionization-Mass Spectrometry Analysis of Microfluidic Droplet Samples

Droplet microfluidics enables high-throughput manipulation of fL-μL volume samples. Methods implemented for the chemical analysis of microfluidic droplets have been limited in scope, leaving some applications of droplet microfluidics difficult to perform or out of reach entirely. Nanoelectrospray ionization-mass spectrometry (nESI-MS) is an attractive approach for droplet analysis, because it allows rapid, label-free, information-rich analysis with high mass sensitivity and resistance to matrix effects. Previous proof-of-concept systems for the nESI-MS analysis of droplets have been limited by the microfluidics used so that stable, long-term operation needed for high-throughput applications has not been demonstrated. We describe a platform for the stable analysis of microfluidic droplet samples by nESI-MS. Continuous infusion of droplets to an nESI emitter was demonstrated for as long as 2.5 h, corresponding to analysis of over 20 000 samples. Stable signal was observed for droplets as small as 65 pL and for throughputs as high as 10 droplets/s. A linear-concentration-based response and sample-to-sample carryover of <3% were also shown. The system is demonstrated for measuring products of in-droplet enzymatic reactions.

Enabling Biocatalysis by High-Throughput Protein Engineering Using Droplet Microfluidics Coupled to Mass Spectrometry

Directed Evolution is a key technology driving the utility of biocatalysis in pharmaceutical synthesis. Conventional approaches to Directed Evolution are conducted using bacterial cells expressing enzymes in microplates, with catalyzed reactions measured by HPLC, high-performance liquid chromatography-mass spectrometry (HPLC-MS), or optical detectors, which require either long cycle times or tailor-made substrates. To better fit modern, fast-paced process chemistry development where solutions are rapidly needed for new substrates, droplet microfluidics interfaced with electrospray ionization (ESI)-MS provides a label-free high-throughput screening platform. To apply this method to industrial enzyme screening and to explore potential approaches that may further improve the overall throughput, we optimized the existing droplet-MS methods. Carryover between droplets, traditionally a significant issue, was reduced to undetectable level by replacing the stainless steel ESI needle with a Teflon needle within a capillary electrophoresis (CE)-MS source. Throughput was improved to 3 Hz with a wide range of droplet sizes (10-50 nL) by tuning the sheath flow within the CE-MS source. The optimized method was demonstrated by screening reactions using two different transaminase libraries. Good correlations (r² ∼ 0.95) were found between the droplet-MS and LC-MS methods, with 100% match on hit variants. We further explored the capability of the system by performing in vitro transcription-translation inside the droplets and directly analyzing the intact reaction mixture droplets by MS. The synthesized protein attained comparable activity to the protein standard, and the complex samples appeared well tolerated by the MS. The success of the above applications indicates that the MS analysis of the microfluidic droplets is an available option for considerably accelerating the screening of enzyme evolution libraries.

A Novel Flavonoid Glucoside from the Fruits of Lycium ruthenicun

A novel flavonoid glucoside, ruthenicunoid A (1), together with eight known substances, were isolated from the fruits of Lycium ruthenicun Murr. Their structures were elucidated by extensive spectroscopic data and chemical methods. Especially, the absolute configuration of glucose residue in 1 was assigned by acid hydrolysis followed by derivatization and GC analysis. Biological evaluation towards Sirtuin 1 (SIRT1) found that compounds 1 and 2 exhibit inhibitory activity against SIRT1 in a concentration-dependent manner, indicating its potential on SIRT1-associated disorders.

Two Novel Proline-Containing Catechin Glucoside from Water-Soluble Extract of Codonopsis pilosula

Choushenflavonoids A (1) and B (2), two unusual proline-containing catechin glucosides, were isolated from the roots of Codonopsis pilosula cultivated in a high-altitude location of Yunnan province. Their structures were determined by spectroscopic data and chemical methods. Specifically, the absolute configuration of glucose residue in 1 and 2 was assigned by acid hydrolysis followed by derivatization and gas chromatography (GC) analysis. In addition, biological evaluation of 1 and 2 against Sirtuin 1 (SIRT1) was carried out.

Chelatable trace zinc causes low, irreproducible KDAC8 activity

Acetylation is an important regulatory mechanism in cells, and emphasis is being placed on identifying substrates and small molecule modulators of this post-translational modification. However, the reported in vitro activity of the lysine deacetylase KDAC8 is inconsistent across experimental setups, even with the same substrate, complicating progress in the field. We detected trace levels of zinc, a known inhibitor of KDAC8 when present in excess, even in high-quality buffer reagents, at concentrations that are sufficient to significantly inhibit the enzyme under common reaction conditions. We hypothesized that trace zinc in solution could account for the observed variability in KDAC8 activity. We demonstrate that addition of chelators, including BSA, EDTA, and citrate, and/or the use of a phosphate-based buffer instead of the more common tris-based buffer, eliminates the inhibition from low levels of zinc as well as the dependence of specific activity on enzyme concentration. This results in high KDAC8 activity that is consistent across buffer systems, even using low concentrations of enzyme. We report conditions that are suitable for several assays to increase both enzyme activity and reproducibility. Our results have significant implications for approaches used to identify substrates and small molecule modulators of KDAC8 and interpretation of existing data.

Lysine Deacetylases Exhibit Distinct Changes in Activity Profiles Due to Fluorophore Conjugation of Substrates

Lysine deacetylases (KDACs) are enzymes that reverse the post-translational modification of lysine acetylation. Thousands of potential substrates, acetylated protein sequences, have been identified in mammalian cells. Properly regulated acetylation and deacetylation have been linked to many biological processes, while aberrant KDAC activity has also been linked to numerous diseases. Commercially available peptide substrates that are conjugated to fluorescent dye molecules, such as 7-amino-4-methylcoumarin (AMC), are commonly used to monitor deacetylation in studies addressing both substrate specificity and small molecule modulators of activity. Here, we have compared the activity of several KDACs, representing all major classes of KDACs, with substrates in the presence and absence of AMC as well as peptides for which tryptophan has been substituted for AMC. Our results unequivocally demonstrate that AMC has a significant effect on activity for all KDACs tested. Furthermore, in neither the nature of the effect nor the magnitude is consistent across KDACs, making it impossible to predict the effect of AMC on a particular enzyme-substrate pair. AMC did not affect acetyllysine preference in a multiply acetylated substrate. In contrast, AMC significantly enhanced KDAC6 substrate affinity, greatly reduced Sirt1 activity, eliminated the substrate sequence specificity of KDAC4, and had no consistent effect with KDAC8 substrates. These results indicate that profiling of KDAC activity with labeled peptides is unlikely to produce biologically relevant data.

Automated Microfluidic Droplet-Based Sample Chopper for Detection of Small Fluorescence Differences Using Lock-In Analysis

Fluorescence is widely used for small-volume analysis and is a primary tool for on-chip detection in microfluidic devices, yet additional expertise, more elaborate optics, and phase-locked detectors are needed for ultrasensitive measurements. Recently, we designed a microfluidic analog to an optical beam chopper (μChopper) that alternated formation of picoliter volume sample and reference droplets. Without complex optics, the device negated large signal drifts (1/f noise), allowing absorbance detection in a mere 27 μm optical path. Here, we extend the μChopper concept to fluorescence detection with standard wide-field microscope optics. Precision of droplet control in the μChopper was improved by automation with pneumatic valves, allowing fluorescence measurements to be strictly phase locked at 0.04 Hz bandwidth to droplets generated at 3.50 Hz. A detection limit of 12 pM fluorescein was achieved when sampling 20 droplets, and as few as 310 zeptomoles (3.1 × 10-19 mol) were detectable in single droplets (8.8 nL). When applied to free fatty acid (FFA) uptake in 3T3-L1 adipocytes, this μChopper permitted single-cell FFA uptake rates to be quantified at 3.5 ± 0.2 × 10-15 mol cell-1 for the first time. Additionally, homogeneous immunoassays in droplets exhibited insulin detection limits of 9.3 nM or 190 amol (1.9 × 10-16 mol). The combination of this novel, automated μChopper with lock-in detection provides a high-performance platform for detecting small differences with standard fluorescence optics, particularly in situations where sample volume is limited. The technique should be simple to implement into a variety of other droplet fluidics devices.

A droplet-chip/mass spectrometry approach to study organic synthesis at nanoliter scale

A droplet-based microfluidic device with seamless hyphenation to electrospray mass spectrometry was developed to rapidly investigate organic reactions in segmented flow providing a versatile tool for drug development. A chip-MS interface with an integrated counterelectrode allowed for a flexible positioning of the chip-emitter in front of the MS orifice as well as an independent adjustment of the electrospray potentials. This was necessary to avoid contamination of the mass spectrometer as well as sample overloading due to the high analyte concentrations. The device was exemplarily applied to study the scope of an amino-catalyzed domino reaction with low picomole amount of catalyst in individual nanoliter sized droplets.

Epigenetic assays for chemical biology and drug discovery

The implication of epigenetic abnormalities in many diseases and the approval of a number of compounds that modulate specific epigenetic targets in a therapeutically relevant manner in cancer specifically confirms that some of these targets are druggable by small molecules. Furthermore, a number of compounds are currently in clinical trials for other diseases including cardiovascular, neurological and metabolic disorders. Despite these advances, the approved treatments for cancer only extend progression-free survival for a relatively short time and being associated with significant side effects. The current clinical trials involving the next generation of epigenetic drugs may address the disadvantages of the currently approved epigenetic drugs.

The identification of chemical starting points of many drugs often makes use of screening in vitro assays against libraries of synthetic or natural products. These assays can be biochemical (using purified protein) or cell-based (using for example, genetically modified, cancer cell lines or primary cells) and performed in microtiter plates, thus enabling a large number of samples to be tested. A considerable number of such assays are available to monitor epigenetic target activity, and this review provides an overview of drug discovery and chemical biology and describes assays that monitor activities of histone deacetylase, lysine-specific demethylase, histone methyltransferase, histone acetyltransferase and bromodomain. It is of critical importance that an appropriate assay is developed and comprehensively validated for a given drug target prior to screening in order to improve the probability of the compound progressing in the drug discovery value chain.

Are fluorine-rich pharmaceuticals lost by partition into fluorous phases?

The recently developed technology of droplet microfluidics has demonstrated great potential for many applications such as biochemical assay, high throughput screening, cell culture, directed evolution, and chemical synthesis. Intrigued by its capabilities for miniaturization, flexible manipulation, rapid reagent mixing and high throughput experimentation and analysis, the pharmaceutical industry has begun to investigate droplet microfluidic implementation in medicinal and process chemistry. Segmented by an immiscible secondary phase, usually perfluorinated oil, aqueous or organic droplets serve as individual micro-reactors without suffering cross-contamination. As many drug molecules contain fluorines, it is necessary to investigate whether such compounds will be preferentially extracted into the fluorous phase via fluorophilic solvation, which could lead to erroneous analytical results. In this work, we chose drugs with up to 10 fluorines to probe their partition into perfluorodecalin (PFD) from a variety of organic solvents. A fast and straightforward MISER (Multiple Injections in a Single Experimental Run) LC-MS method was applied to measure the loss of drug after mixing with PFD. We found that no significant partition occurred, with the concentration of drugs in the 'experimental' group measured as ±10% of the 'control' group. The RSD% of multiple injections is <5%. The finding was further validated by the conventional LC-MS approach.