HTS technologies in biopharmaceutical discovery

Microfluidics in High-Throughput Drug Screening: Organ-on-a-Chip and C. elegans-Based Innovations

The development of therapeutic interventions for diseases necessitates a crucial step known as drug screening, wherein potential substances with medicinal properties are rigorously evaluated. This process has undergone a transformative evolution, driven by the imperative need for more efficient, rapid, and high-throughput screening platforms. Among these, microfluidic systems have emerged as the epitome of efficiency, enabling the screening of drug candidates with unprecedented speed and minimal sample consumption. This review paper explores the cutting-edge landscape of microfluidic-based drug screening platforms, with a specific emphasis on two pioneering approaches: organ-on-a-chip and C. elegans-based chips. Organ-on-a-chip technology harnesses human-derived cells to recreate the physiological functions of human organs, offering an invaluable tool for assessing drug efficacy and toxicity. In parallel, C. elegans-based chips, boasting up to 60% genetic homology with humans and a remarkable affinity for microfluidic systems, have proven to be robust models for drug screening. Our comprehensive review endeavors to provide readers with a profound understanding of the fundamental principles, advantages, and challenges associated with these innovative drug screening platforms. We delve into the latest breakthroughs and practical applications in this burgeoning field, illuminating the pivotal role these platforms play in expediting drug discovery and development. Furthermore, we engage in a forward-looking discussion to delineate the future directions and untapped potential inherent in these transformative technologies. Through this review, we aim to contribute to the collective knowledge base in the realm of drug screening, providing valuable insights to researchers, clinicians, and stakeholders alike. We invite readers to embark on a journey into the realm of microfluidic-based drug screening platforms, fostering a deeper appreciation for their significance and promising avenues yet to be explored.

High-Throughput Screening of Anti-cancer Drugs Using a Microfluidic Spheroid Culture Device with a Concentration Gradient Generator

Tumor spheroid models are widely used for drug screening as in vitro models of the tumor microenvironment. There are various ways in which tumor spheroid models can be prepared, including the self-assembly of cells using low-adherent plates, micro-patterned plates, or hanging-drop plates. Recently, drug high-throughput screening (HTS) approaches have incorporated the use of these culture systems. These HTS culture systems, however, require complicated equipment, such as robot arms, detectors, and software for handling solutions and data processing. Here, we describe protocols that allow tumor spheroids to be tested with different concentrations of a drug in a parallel fashion using a microfluidic device that generates a gradient of anti-cancer drugs. This microfluidic spheroid culture device with a concentration gradient generator (μFSCD-CGG) enables the formation of 50 tumor spheroids and the testing of drugs at five different concentrations. First, we provide a protocol for the fabrication of the μFSCD-CGG, which has both a culture array in which tumor cells are injected and aggregate to form spheroids and a concentration gradient generator for drug testing. Second, we provide a protocol for tumor spheroid formation and HTS of anti-cancer drugs using the device. Finally, we provide a protocol for assessing the response of tumor spheroids at different drug concentrations. To address the needs of the pharmaceutical industry, this protocol can be used for various cell types, including stem cells, and the number of tumor spheroids and drug concentration ranges that can be tested in the μFSCD-CGG can be increased. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Fabrication of a microfluidic spheroid culture device with a concentration gradient generator (μFSCD-CGG) Basic Protocol 2: Seeding cells and formation of spheroids in the μFSCD-CGG Basic Protocol 3: Drug treatment and assessment of cell viability in the μFSCD-CGG.

The impact of microfluidics in high-throughput drug-screening applications

Drug discovery is an expensive and lengthy process. Among the different phases, drug discovery and preclinical trials play an important role as only 5-10 of all drugs that begin preclinical tests proceed to clinical trials. Indeed, current high-throughput screening technologies are very expensive, as they are unable to dispense small liquid volumes in an accurate and quick way. Moreover, despite being simple and fast, drug screening assays are usually performed under static conditions, thus failing to recapitulate tissue-specific architecture and biomechanical cues present in vivo even in the case of 3D models. On the contrary, microfluidics might offer a more rapid and cost-effective alternative. Although considered incompatible with high-throughput systems for years, technological advancements have demonstrated how this gap is rapidly reducing. In this Review, we want to further outline the role of microfluidics in high-throughput drug screening applications by looking at the multiple strategies for cell seeding, compartmentalization, continuous flow, stimuli administration (e.g., drug gradients or shear stresses), and single-cell analyses.

Multi-Organs-on-Chips for Testing Small-Molecule Drugs: Challenges and Perspectives

Organ-on-a-chip technology has been used in testing small-molecule drugs for screening potential therapeutics and regulatory protocols. The technology is expected to boost the development of novel therapies and accelerate the discovery of drug combinations in the coming years. This has led to the development of multi-organ-on-a-chip (MOC) for recapitulating various organs involved in the drug-body interactions. In this review, we discuss the current MOCs used in screening small-molecule drugs and then focus on the dynamic process of drug absorption, distribution, metabolism, and excretion. We also address appropriate materials used for MOCs at low cost and scale-up capacity suitable for high-performance analysis of drugs and commercial high-throughput screening platforms.

Nanocosm: a well plate photobioreactor for environmental and biotechnological studies

Phytoplankton are key primary producers at the bottom of the aquatic food chain. They are a highly diverse group of organisms essential for the functioning of our ecosystems and because of their characteristics, their biomass is considered for various commercial applications. A full appreciation of their abundance, diversity and potential is only feasible by using systems that enable simultaneous testing of strains and/or variables in a fast and easy way. A major bottleneck is the lack of a cost-effective method with the capacity for complex experimental set-ups that enable fast and reproducible screening and analysis. In this study, we present nanocosm, a versatile LED-based micro-scale photobioreactor (PBR) that allows simultaneous testing of multiple variables such as temperature and light within the same plate. Every well can be independently controlled for intensity, temporal variation and light type (RGB, white, UV). We show that our systems guarantee homogeneous conditions because of controlled temperature and evaporation and adjustments for light crosstalk. By ensuring controlled environmental conditions the nanocosm is suitable for running factorial experimental designs where each well can be used as an independent micro-PBR. To validate culture performances, we assess well-to-well reproducibility and our results show minimal well-to-well variability for all the conditions tested. Possible modes of operation and application are discussed together with future development of the system.

Accelerating organic solar cell material's discovery: high-throughput screening and big data

The discovery of novel high-performing materials such as non-fullerene acceptors and low band gap donor polymers underlines the steady increase of record efficiencies in organic solar cells witnessed during the past years. Nowadays, the resulting catalogue of organic photovoltaic materials is becoming unaffordably vast to be evaluated following classical experimentation methodologies: their requirements in terms of human workforce time and resources are prohibitively high, which slows momentum to the evolution of the organic photovoltaic technology. As a result, high-throughput experimental and computational methodologies are fostered to leverage their inherently high exploratory paces and accelerate novel materials discovery. In this review, we present some of the computational (pre)screening approaches performed prior to experimentation to select the most promising molecular candidates from the available materials libraries or, alternatively, generate molecules beyond human intuition. Then, we outline the main high-throuhgput experimental screening and characterization approaches with application in organic solar cells, namely those based on lateral parametric gradients (measuring-intensive) and on automated device prototyping (fabrication-intensive). In both cases, experimental datasets are generated at unbeatable paces, which notably enhance big data readiness. Herein, machine-learning algorithms find a rewarding application niche to retrieve quantitative structure-activity relationships and extract molecular design rationale, which are expected to keep the material's discovery pace up in organic photovoltaics.

Intein mediated high throughput screening for bispecific antibodies

Bispecific antibodies comprise extremely diverse architectures enabling complex modes of action, such as effector cell recruitment or conditional target modulation via dual targeting, not conveyed by monospecific antibodies. In recent years, research on bispecific therapeutics has substantially grown. However, evaluation of binding moiety combinations often leads to undesired prolonged development times. While high throughput screening for small molecules and classical antibodies has evolved into a mature discipline in the pharmaceutical industry, dual-targeting antibody screening methodologies lack the ability to fully evaluate the tremendous number of possible combinations and cover only a limited portion of the combinatorial screening space. Here, we propose a novel combinatorial screening approach for bispecific IgG-like antibodies to extenuate screening limitations in industrial scale, expanding the limiting screening space. Harnessing the ability of a protein trans-splicing reaction by the split intein Npu DnaE, antibody fragments were reconstituted within the hinge region in vitro. This method allows for fully automated, rapid one-pot antibody reconstitution, providing biological activity in several biochemical and functional assays. The technology presented here is suitable for automated functional and combinatorial high throughput screening of bispecific antibodies.

Stable and selective permeable hydrogel microcapsules for high-throughput cell cultivation and enzymatic analysis

BACKGROUND

Miniaturization of biochemical reaction volumes within artificial microcompartments has been the key driver for directed evolution of several catalysts in the past two decades. Typically, single cells are co-compartmentalized within water-in-oil emulsion droplets with a fluorogenic substrate whose conversion allows identification of catalysts with improved performance. However, emulsion droplet-based technologies prevent cell proliferation to high density and preclude the feasibility of biochemical reactions that require the exchange of small molecule substrates. Here, we report on the development of a high-throughput screening method that addresses these shortcomings and that relies on a novel selective permeable polymer hydrogel microcapsule.

RESULTS

Hollow-core polyelectrolyte-coated chitosan alginate microcapsules (HC-PCAMs) with selective permeability were successfully constructed by jet break-up and layer-by-layer (LBL) technology. We showed that HC-PCAMs serve as miniaturized vessels for single cell encapsulation, enabling cell growth to high density and cell lysis to generate monoclonal cell lysate compartments suitable for high-throughput analysis using a large particle sorter (COPAS). The feasibility of using HC-PCAMs as reaction compartments which exchange small molecule substrates was demonstrated using the transpeptidation reaction catalyzed by the bond-forming enzyme sortase F from P. acnes. The polyelectrolyte shell surrounding microcapsules allowed a fluorescently labelled peptide substrate to enter the microcapsule and take part in the transpeptidation reaction catalyzed by the intracellularly expressed sortase enzyme retained within the capsule upon cell lysis. The specific retention of fluorescent transpeptidation products inside microcapsules enabled the sortase activity to be linked with a fluorescent readout and allowed clear separation of microcapsules expressing the wild type SrtF from those expressing the inactive variant.

CONCLUSION

A novel polymer hydrogel microcapsule-based method, which allows for high-throughput analysis based on encapsulation of single cells has been developed. The method has been validated for the transpeptidation activity of sortase enzymes and represents a powerful tool for screening of libraries of sortases, other bond-forming enzymes, as well as of binding affinities in directed evolution experiments. Moreover, selective permeable microcapsules encapsulating microcolonies provide a new and efficient means for preparing novel caged biocatalyst and biosensor agents.

FACS-Based Functional Protein Screening via Microfluidic Co-encapsulation of Yeast Secretor and Mammalian Reporter Cells

In this study, we present a straightforward approach for functional cell-based screening by co-encapsulation of secretor yeast cells and reporter mammalian cells in millions of individual agarose-containing microdroplets. Our system is compatible with ultra-high-throughput selection utilizing standard fluorescence-activated cell sorters (FACS) without need of extensive adaptation and optimization. In a model study we co-encapsulated murine interleukin 3 (mIL-3)-secreting S. cerevisiae cells with murine Ba/F3 reporter cells, which express green fluorescent protein (GFP) upon stimulation with mIL-3, and could observe specific and robust induction of fluorescence signal compared to a control with yeast cells secreting a non-functional mIL-3 mutant. We demonstrate the successful enrichment of activating mIL-3 wt-secreting yeast cells from a 1:10,000 dilution in cells expressing the inactive cytokine variant by two consecutive cycles of co-encapsulation and FACS. This indicates the suitability of the presented strategy for functional screening of high-diversity yeast-based libraries and demonstrates its potential for the efficient isolation of clones secreting bioactive recombinant proteins.

Nonlinear Dose-Response Modeling of High-Throughput Screening Data Using an Evolutionary Algorithm

Nonlinear dose-response relationships exist extensively in the cellular, biochemical, and physiologic processes that are affected by varying levels of biological, chemical, or radiation stress. Modeling such responses is a crucial component of toxicity testing and chemical screening. Traditional model fitting methods such as nonlinear least squares (NLS) are very sensitive to initial parameter values and often had convergence failure. The use of evolutionary algorithms (EAs) has been proposed to address many of the limitations of traditional approaches, but previous methods have been limited in the types of models they can fit. Therefore, we propose the use of an EA for dose-response modeling for a range of potential response model functional forms. This new method can not only fit the most commonly used nonlinear dose-response models (eg, exponential models and 3-, 4-, and 5-parameter logistic models) but also select the best model if no model assumption is made, which is especially useful in the case of high-throughput curve fitting. Compared with NLS, the new method provides stable and robust solutions without sensitivity to initial values.

A Microfluidic Spheroid Culture Device with a Concentration Gradient Generator for High-Throughput Screening of Drug Efficacy

Three-dimensional (3D) cell culture is considered more clinically relevant in mimicking the structural and physiological conditions of tumors in vivo compared to two-dimensional cell cultures. In recent years, high-throughput screening (HTS) in 3D cell arrays has been extensively used for drug discovery because of its usability and applicability. Herein, we developed a microfluidic spheroid culture device (μFSCD) with a concentration gradient generator (CGG) that enabled cells to form spheroids and grow in the presence of cancer drug gradients. The device is composed of concave microwells with several serpentine micro-channels which generate a concentration gradient. Once the colon cancer cells (HCT116) formed a single spheroid (approximately 120 μm in diameter) in each microwell, spheroids were perfused in the presence of the cancer drug gradient irinotecan for three days. The number of spheroids, roundness, and cell viability, were inversely proportional to the drug concentration. These results suggest that the μFSCD with a CGG has the potential to become an HTS platform for screening the efficacy of cancer drugs.

Construction of a versatile expression library for all human single-pass transmembrane proteins for receptor pairings by high throughput screening

Interactions between protein ligands and receptors play crucial roles in cell-cell signalling. Most of the human cell surface receptors have been identified in the post-Human Genome Project era but many of their corresponding ligands remain unknown. To facilitate the pairing of orphan receptors, 2762 sequences encoding all human single-pass transmembrane proteins were selected for inclusion into a mammalian-cell expression library. This expression library, consisting of all the individual extracellular domains (ECDs), was constructed as a Fab fusion for each protein. In this format, individual ECD can be produced as a soluble protein or displayed on cell surface, depending on the applied heavy-chain Fab configuration. The unique design of the Fab fusion concept used in the library led to not only superior success rate of protein production, but also versatile applications in various high-throughput screening paradigms including protein-protein binding assays as well as cell binding assays, which were not possible for any other existing expression libraries. The protein library was screened against human coagulation factor VIIa (FVIIa), an approved therapeutic for the treatment of hemophilia, for binding partners by AlphaScreen and ForteBio assays. Two previously known physiological ligands of FVIIa, tissue factor (TF) and endothelial protein C receptor (EPCR) were identified by both assays. The cell surface displayed library was screened against V-domain Ig suppressor of T-cell activation (VISTA), an important immune-checkpoint regulator. Immunoglobulin superfamily member 11 (IgSF11), a potential target for cancer immunotherapy, was identified as a new and previously undescribed binding partner for VISTA. The specificity of the binding was confirmed and validated by both fluorescence-activated cell sorting (FACS) and surface plasmon resonance (SPR) assays in different experimental setups.

Crossed flow microfluidics for high throughput screening of bioactive chemical-cell interactions

This paper describes the use of crossed laminar flow microfluidics for the selective capture of multiple cell types on-chip aiming for high throughput screening of various cell treatment compounds. Parallel laminar streams containing different cell types were perfused and captured on a cell adhesion protein-functionalized reaction area. Thereafter, parallel streams containing cell treatment solutions were delivered orthogonally over the captured cells. Multiple cell types and a range of cell treatment conditions could therefore be assessed in a single experiment. We were also able to sort mixed cell populations via antibody array clusters, and to further deliver treatments to subpopulations of cells. Moreover, using solutions with different tonicities, we successfully demonstrated the incorporation of a live/dead cell viability assessment on-chip for a direct read out assay following the treatments. This crossed laminar flow microfluidics for generation of a cell-based assay could therefore offer an interesting platform for high throughput screening of potential drug candidates, nanoparticle toxicity testing, or other cellular and molecular interventions.

Delivery of minimally dispersed liquid interfaces for sequential surface chemistry

We present a method for sequential delivery of reagents to a reaction site with minimal dispersion of their interfaces. Using segmented flow to encapsulate the reagents as droplets, the dispersion between reagent plugs remains confined in a limited volume, while being transmitted to the reaction surface. In close proximity to the target surface, we use a passive array of microstructures for removal of the oil phase such that the original reagent sequence is reconstructed, and only the aqueous phase reaches the reaction surface. We provide a detailed analysis of the conditions under which the method can be applied and demonstrate maintaining a transition time of 560 ms between reagents transported to a reaction site over a distance of 60 cm. We implemented the method using a vertical microfluidic probe on an open surface, allowing contact-free interaction with biological samples, and demonstrated two examples of assays implemented using the method: measurements of receptor-ligand reaction kinetics and of the fluorescence response of immobilized GFP to local variations in pH. We believe that the method can be useful for studying the dynamic response of cells and proteins to various stimuli, as well as for highly automated multi-step assays.

Advances in the Study of Heart Development and Disease Using Zebrafish

Animal models of cardiovascular disease are key players in the translational medicine pipeline used to define the conserved genetic and molecular basis of disease. Congenital heart diseases (CHDs) are the most common type of human birth defect and feature structural abnormalities that arise during cardiac development and maturation. The zebrafish, Danio rerio, is a valuable vertebrate model organism, offering advantages over traditional mammalian models. These advantages include the rapid, stereotyped and external development of transparent embryos produced in large numbers from inexpensively housed adults, vast capacity for genetic manipulation, and amenability to high-throughput screening. With the help of modern genetics and a sequenced genome, zebrafish have led to insights in cardiovascular diseases ranging from CHDs to arrhythmia and cardiomyopathy. Here, we discuss the utility of zebrafish as a model system and summarize zebrafish cardiac morphogenesis with emphasis on parallels to human heart diseases. Additionally, we discuss the specific tools and experimental platforms utilized in the zebrafish model including forward screens, functional characterization of candidate genes, and high throughput applications.

Type IV traffic ATPase TrwD as molecular target to inhibit bacterial conjugation

Bacterial conjugation is the main mechanism responsible for the dissemination of antibiotic resistance genes. Hence, the search for specific conjugation inhibitors is paramount in the fight against the spread of these genes. In this pursuit, unsaturated fatty acids have been found to specifically inhibit bacterial conjugation. Despite the growing interest on these compounds, their mode of action and their specific target remain unknown. Here, we identified TrwD, a Type IV secretion traffic ATPase, as the molecular target for fatty acid-mediated inhibition of conjugation. Moreover, 2-alkynoic fatty acids, which are also potent inhibitors of bacterial conjugation, are also powerful inhibitors of the ATPase activity of TrwD. Characterization of the kinetic parameters of ATPase inhibition has led us to identify the catalytic mechanism by which fatty acids exert their activity. These results open a new avenue for the rational design of inhibitors of bacterial conjugation in the fight against the dissemination of antibiotic resistance genes.

Microfluidics for cell-based high throughput screening platforms - A review

In the last decades, the basic techniques of microfluidics for the study of cells such as cell culture, cell separation, and cell lysis, have been well developed. Based on cell handling techniques, microfluidics has been widely applied in the field of PCR (Polymerase Chain Reaction), immunoassays, organ-on-chip, stem cell research, and analysis and identification of circulating tumor cells. As a major step in drug discovery, high-throughput screening allows rapid analysis of thousands of chemical, biochemical, genetic or pharmacological tests in parallel. In this review, we summarize the application of microfluidics in cell-based high throughput screening. The screening methods mentioned in this paper include approaches using the perfusion flow mode, the droplet mode, and the microarray mode. We also discuss the future development of microfluidic based high throughput screening platform for drug discovery.

A comprehensive high-throughput FTIR spectroscopy-based method for evaluating the transfection event: estimating the transfection efficiency and extracting associated metabolic responses

Reporter genes are routinely used in every laboratory for molecular and cellular biology for studying heterologous gene expression and general cellular biological mechanisms, such as transfection processes. Although well characterized and broadly implemented, reporter genes present serious limitations, either by involving time-consuming procedures or by presenting possible side effects on the expression of the heterologous gene or even in the general cellular metabolism. Fourier transform mid-infrared (FT-MIR) spectroscopy was evaluated to simultaneously analyze in a rapid (minutes) and high-throughput mode (using 96-wells microplates), the transfection efficiency, and the effect of the transfection process on the host cell biochemical composition and metabolism. Semi-adherent HEK and adherent AGS cell lines, transfected with the plasmid pVAX-GFP using Lipofectamine, were used as model systems. Good partial least squares (PLS) models were built to estimate the transfection efficiency, either considering each cell line independently (R (2) ≥ 0.92; RMSECV ≤ 2 %) or simultaneously considering both cell lines (R (2) = 0.90; RMSECV = 2 %). Additionally, the effect of the transfection process on the HEK cell biochemical and metabolic features could be evaluated directly from the FT-IR spectra. Due to the high sensitivity of the technique, it was also possible to discriminate the effect of the transfection process from the transfection reagent on KEK cells, e.g., by the analysis of spectral biomarkers and biochemical and metabolic features. The present results are far beyond what any reporter gene assay or other specific probe can offer for these purposes.

Screening technologies for small molecule discovery: the state of the art

Screening, high-throughput screening, and ultra-high-throughput screening are all really just points on a spectrum that represent differing applications of the same process: the creation of biologically relevant assays that are relevant, reproducible, reliable, and robust. Whether the discovery program is developing a pharmaceutical, an academic probe, cosmetics, pesticides, or a toxicity monitoring assay, the development of a screen focuses on generating a method that will reliably deliver reproducible results over a period of weeks, months, or years and that will generate consistent results for every test along the way. This review provides both historical perspective on how this unique scientific discipline evolved and commentary on the current state of the art technologies and techniques.

Fluorescence anisotropy: from single molecules to live cells

The polarization of light emitted by fluorescent probes is an easily accessible physical quantity that is related to a multitude of molecular parameters including conformation, orientation, size and the nanoscale environment conditions, such as dynamic viscosity and temperature. In analytical biochemistry and analytical chemistry applied to biological problems, fluorescence anisotropy is widely used for measuring the folding state of proteins and nucleic acids, and the affinity constant of ligands through titration experiments. The emphasis of this review is on new multi-parameter single-molecule detection schemes and their bioanalytical applications, and on the use of ensemble polarization assays to study binding and conformational dynamics of proteins and aptamers and for high-throughput discovery of small-molecule drugs.

Automation of the SomaLogic Proteomics Assay: A Platform for Biomarker Discovery

At SomaLogic, we have embarked on an ambitious program of clinical studies using a novel aptamerbased proteomics technology to discover biomarkers and develop new tools to diagnose, understand, and treat human disease. As part of this program, we designed and implemented an automated assay for its highly multiplexed proteomics discovery platform. The performance of the automated assay was validated in a study that compared the automated assay to the specifications of an established manual method. Results showed that the automated method performed to the required specifications, and that the automation system improved the efficiency, productivity, and economics of our biomarker discovery program.

The stability of the circulating human proteome to variations in sample collection and handling procedures measured with an aptamer-based proteomics array

Blood-based protein biomarkers hold great promise to advance medicine with applications that detect and diagnose diseases and aid in their treatment. We are developing such applications with our proteomics technology that combines high-content with low limits of detection. Biomarker discovery relies heavily on archived blood sample collections. Blood is dynamic and changes with different sampling procedures potentially confounding biomarker studies. In order to better understand the effects of sampling procedures on the circulating proteome, we studied three sample collection variables commonly encountered in archived sample sets. These variables included (1) three different sample tube types, PPT plasma, SST serum, and Red Top serum, (2) the time from venipuncture to centrifugation, and (3) the time from centrifugation to freezing. We profiled 498 proteins for each of 240 samples and compared the results by ANOVA. The results found no significant variation in the measurements for most proteins (approximately 99%) when the two sample processing times tested were 2h or less, regardless of sample tube type. Even at the longest timepoints, 20 h, approximately 82% of the proteins, on average for the three collection tube types, showed no significant change. These results are encouraging for proteomic biomarker discovery.

Computational multiscale modeling in protein--ligand docking

In biological systems, the binding of small molecule ligands to proteins is a crucial process for almost every aspect of biochemistry and molecular biology. Enzymes are proteins that function by catalyzing specific biochemical reactions that convert reactants into products. Complex organisms are typically composed of cells in which thousands of enzymes participate in complex and interconnected biochemical pathways. Some enzymes serve as sequential steps in specific pathways (such as energy metabolism), while others function to regulate entire pathways and cellular functions [1]. Small molecule ligands can be designed to bind to a specific enzyme and inhibit the biochemical reaction. Inhibiting the activity of key enzymes may result in the entire biochemical pathways being turned on or off [2], [3]. Many small molecule drugs marketed today function in this generic way as enzyme inhibitors. If research identifies a specific enzyme as being crucial to the progress of disease, then this enzyme may be targeted with an inhibitor, which may slow down or reverse the progress of disease. In this way, enzymes are targeted from specific pathogens (e.g., virus, bacteria, fungi) for infectious diseases [4], [5], and human enzymes are targeted for noninfectious diseases such as cardiovascular disease, cancer, diabetes, and neurodegenerative diseases [6].

Generation of arbitrary monotonic concentration profiles by a serial dilution microfluidic network composed of microchannels with a high fluidic-resistance ratio

This paper reports a serial dilution microfluidic network composed of microchannels with a high fluidic-resistance ratio for generating linear concentration profiles as well as logarithmic concentration profiles spanning 3 and 6 orders of magnitude. The microfluidic networks were composed of thin fluidic-resistance microchannels with 160 to 730 microm(2) cross-sectional areas and thick diffusion-mixing microchannels with 3,600 to 17,000 microm(2) cross-sectional areas, and were fabricated from polydimethylsiloxane by multilayer photolithography and replica molding. We proposed a design algorithm of the microfluidic network for an arbitrary monotonic concentration profile by means of a hydrodynamic calculation. Because of the high fluidic-resistance ratio of the fluidic-resistance microchannels to the diffusion-mixing microchannels, appropriate geometry and dimensions of the fluidic-resistance microchannels allowed us to obtain desired concentration profiles. The fabricated microfluidic network was compact, occupying a 8 x 18 to 21.0 x 13.5 mm(2) area on the microchip. Both the linear and the logarithmic concentration profiles were successfully generated with the error less than 15% for the linear concentration profile, 22% and 35% for the logarithmic concentration profiles of 3 and 6 orders of magnitude, respectively. The generated linear concentration profiles of the small molecule, calcein, were independent of the flow rate within the range of 0.009 to 0.23 microL/min. The concentration profiles of the large molecules, dextrans, depended on the flow rate and molecular weight. The required residence time of large molecules in the diffusion-mixing microchannel was correlated with dimensionless diffusion time, Fick number, and was discussed based on the scaling law. These compact, stable serial dilution microfluidic networks are expected to be applied to various integrated on-chip analyses.

Micro- and nanofluidic systems for high-throughput biological screening

High-throughput screening (HTS) is a method of scientific experimentation widely used in drug discovery and relevant to the fields of biology. The development of micro- and nanofluidic systems for use in the biological sciences has been driven by a range of fundamental attributes that accompany miniaturization and massively parallel experimentation. We review recent advances in both arraying strategies based on nano/microfluidics and novel nano/microfluidic devices with high analytical throughput rates.

The current status of cDNA cloning

The cloning of cDNAs, copies of cellular RNA, is one of the classical technologies in molecular biology. Over the past 30 years cDNA cloning technologies have been improved to enable the cloning of large cDNA collections, which are fundamental to today's understanding of the utilization of genetic information. With the discovery of noncoding RNAs, additional new approaches to the cloning of short RNAs have been developed. However, with the realization that much larger portions of genomes are transcribed than anticipated from genome annotations, cDNA cloning faces new challenges to uncover rare transcripts and to make the corresponding cDNAs available for functional studies. This review provides an overview on the current status of cDNA cloning and possibilities for the discovery and characterization of new RNA families.