Optical biosensors: where next and how soon?

Breast cancer detection based on cancer antigen 15-3; emphasis on optical and electrochemical methods: A review

Cancer antigen 15-3 (CA 15-3) is a crucial marker used in the diagnosis and monitoring of breast cancer (BC). The demand for early and precise cancer detection has grown, making the creation of biosensors that are highly sensitive and specific essential. This review paper provides a thorough examination of the progress made in optical and electrochemical biosensors for detecting the cancer biomarker CA 15-3. We focus on explaining their fundamental principles, sensitivity, specificity, and potential for point-of-care applications. The performance attributes of these biosensors are assessed by considering their limits of detection, reaction times, and operational stability, while also making comparisons to conventional methods of CA 15-3 detection. In addition, we explore the incorporation of nanomaterials and innovative transducer components to improve the performance of biosensors. This paper conducts a thorough examination of recent studies to identify the existing obstacles. It also suggests potential areas for future research in this fast progressing field.The paper provides insights into their advancement and utilization to enhance patient outcomes. Both categories of biosensors provide significant promise for the detection of CA 15-3 and offer distinct advantages compared to conventional analytical approaches.

Handheld Biosensor System Based on a Gradient Grating Period Guided-Mode Resonance Device

Handheld biosensors have attracted substantial attention for numerous applications, including disease diagnosis, drug dosage monitoring, and environmental sensing. This study presents a novel handheld biosensor based on a gradient grating period guided-mode resonance (GGP-GMR) sensor. Unlike conventional GMR sensors, the proposed sensor's grating period varies along the device length; hence, the resonant wavelength varies linearly along the device length. If a GGP-GMR sensor is illuminated with a narrow band of light at normal incidence, the light resonates and reflects at a specific period but transmits at other periods; this can be observed as a dark band by using a complementary metal oxide semiconductor (CMOS) underneath the sensor. The concentration of a target analyte can be determined by monitoring the shift of this dark band. We designed and fabricated a handheld device incorporating a light-emitting diode (LED) light source, the necessary optics, an optofluidic chip with an embedded GGP-GMR sensor, and a CMOS. LEDs with different beam angles and bandpass filters with different full width at half maximum values were investigated to optimize the dark band quality and improve the accuracy of the subsequent image analysis. Substrate materials with different refractive indices and waveguide thicknesses were also investigated to maximize the GGP-GMR sensor's figure of merit. Experiments were performed to validate the proposed handheld biosensor, which achieved a limit of detection (LOD) of 1.09 × 10-3 RIU for bulk solution measurement. The sensor's performance in the multiplexed detection of albumin and creatinine solutions at concentrations of 0-500 μg/mL and 0-10 mg/mL, respectively, was investigated; the corresponding LODs were 0.66 and 0.61 μg/mL.

Flexible Stacked Perovskite Photodetectors for High-Efficiency Multicolor Fluorescence Detection

A flexible, multicolor detector based on stacked perovskite layers with graded band gaps was presented. Different perovskite layers generate a series of photocurrents corresponding to light intensities at different wavelengths. Experimentally, the flexible detector demonstrated acceptable long-term stability and temperature stability in the bending state. To demonstrate the advantages of the flexible multicolor detector in biological applications, a tubular-shaped multicolor fluorescence detector that embraces the sample cell was constructed. As a result, the detection limits of three kinds of CdTe quantum dots (QDs) with central wavelengths of 545, 625, and 730 nm were 0.52, 0.85, and 0.43 nM, respectively, which was significantly improved by more than 10 times compared to those of planar detectors. Additionally, the detector was able to detect three kinds of QDs simultaneously in a mixed solution, and the relative deviation was smaller than 10% compared to the preset concentration. These results demonstrate that the flexible stacked perovskite detector and the tubular-shaped detection configuration hold promise for the simultaneous fluorescent detection of multiple biomolecules.

Using Bio-Layer Interferometry to Evaluate Anti-PEG Antibody-Mediated Complement Activation

The purpose of this study was to develop a Bio-layer interferometry (BLI) system that could be an alternative approach for the direct evaluation of anti-polyethylene glycol (PEG) immunoglobulin M (IgM)-mediated complement activation of the accelerated blood clearance (ABC) phenomenon. Complement activation is well known to play an important role in the clearance of PEGylated and non-PEGylated nanomedicines following intravenous injection. This complement system is also thought to be responsible for the ABC phenomenon wherein repeated injections of PEGylated products are bound by anti-PEG antibodies. This study used three different sources of anti-PEG antibodies: HIK-M09 monoclonal antibodies (mAbs); HIK-M11 mAbs; and antiserum containing polyclonal anti-PEG IgMs. 1,2-Distearoyl-sn-glycero-3-phosphoethanolamine-n-[methoxy (polyethylene glycol)-2000] (mPEG₂₀₀₀-DSPE) was immobilized as an antigen on aminopropyl silane biosensor chips of BLI. All anti-PEG IgMs in the sources increased the signals (thickness of the layer around the sensor tip) regarding binding of anti-PEG antibodies to PEG on the chips. In all anti-PEG IgM sources, further increases in the signals were observed when incubated in naïve mouse serum, which is a complement source, but not in heat inactivated (56 °C, 30 min) mouse serum, which abolishes complement activity. These findings show that the complement activation mediated via anti-PEG IgMs, which occurred on the sensor chips, was detected via BLI analysis. The complement activation induced by all anti-PEG IgM sources was confirmed via conventional enzyme-linked immunosorbent assay (ELISA), which is the conventional mode for detection of complement activation. Our study results show that BLI is a simple alternative method for the detection of complement activation.

Tailored Biosensors for Drug Screening, Efficacy Assessment, and Toxicity Evaluation

Biosensors have been flourishing in the field of drug discovery with pronounced developments in the past few years. They facilitate the screening and discovery of innovative drugs. However, there is still a lack of critical reviews that compare the merits and shortcomings of these biosensors from a pharmaceutical point of view. This contribution presents a critical and up-to-date overview on the recent progress of tailored biosensors, including surface plasmon resonance, fluorescent, photoelectrochemical, and electrochemical systems with emphasis on their mechanisms and applications in drug screening, efficacy assessment, and toxicity evaluation. Multiple functional nanomaterials have also been incorporated into the biosensors. Representative examples of each type of biosensors are discussed in terms of design strategy, response mechanism, and potential applications. In the end, we also compare the results and summarize the major insights gained from the works, demonstrating the challenges and prospects of biosensors-assisted drug discovery.

Identifying and Validating MYC:Protein Interactors in Pursuit of Novel Anti-MYC Therapies

By identifying MYC protein-protein interactors, we aim to gain a deeper mechanistic understanding of MYC as a regulator of gene transcription and potent oncoprotein. This information can then be used to devise strategies for disrupting critical MYC protein-protein interactions to inhibit MYC-driven tumorigenesis. In this chapter, we discuss four techniques to identify and validate MYC-interacting partners. First, we highlight BioID, a powerful discovery method used to identify high-confidence proximal interactors in living cells. We also discuss bioinformatic prioritization strategies for the BioID-derived MYC-proximal complexes. Next, we discuss how protein interactions can be validated using techniques such as in vivo-in vitro pull-down assays and the proximity ligation assay (PLA). We conclude with an overview of biolayer interferometry (BLI), a quantitative method used to characterize direct interactions between two proteins in vitro. Overall, we highlight the principles of each assay and provide methodology necessary to conduct these experiments and adapt them to the study of interactors of additional proteins of interest.

Quantifying misfolded protein oligomers as drug targets and biomarkers in Alzheimer and Parkinson diseases

Protein misfolding and aggregation are characteristic of a wide range of neurodegenerative disorders, including Alzheimer and Parkinson diseases. A hallmark of these diseases is the aggregation of otherwise soluble and functional proteins into amyloid aggregates. Although for many decades such amyloid deposits have been thought to be responsible for disease progression, it is now increasingly recognized that the misfolded protein oligomers formed during aggregation are, instead, the main agents causing pathological processes. These oligomers are transient and heterogeneous, which makes it difficult to detect and quantify them, generating confusion about their exact role in disease. The lack of suitable methods to address these challenges has hampered efforts to investigate the molecular mechanisms of oligomer toxicity and to develop oligomer-based diagnostic and therapeutic tools to combat protein misfolding diseases. In this Review, we describe methods to quantify misfolded protein oligomers, with particular emphasis on diagnostic applications as disease biomarkers and on therapeutic applications as target biomarkers. The development of these methods is ongoing, and we discuss the challenges that remain to be addressed to establish measurement tools capable of overcoming existing limitations and to meet present needs.

Gradient Waveguide Thickness Guided-Mode Resonance Biosensor

Portable systems for detecting biomolecules have attracted considerable attention, owing to the demand for point-of-care testing applications. This has led to the development of lab-on-a-chip (LOC) devices. However, most LOCs are developed with a focus on automation and preprocessing of samples; fluorescence measurement, which requires additional off-chip detection instruments, remains the main detection method in conventional assays. By incorporating optical biosensors into LOCs, the biosensing system can be simplified and miniaturized. However, many optical sensors require an additional coupling device, such as a grating or prism, which complicates the optical path design of the system. In this study, we propose a new type of biosensor based on gradient waveguide thickness guided-mode resonance (GWT-GMR), which allows for the conversion of spectral information into spatial information such that the output signal can be recorded on a charge-coupled device for further analysis without any additional dispersive elements. A two-channel microfluidic chip with embedded GWT-GMRs was developed to detect two model assays in a buffer solution: albumin and creatinine. The results indicated that the limit of detection for albumin was 2.92 μg/mL for the concentration range of 0.8–500 μg/mL investigated in this study, and that for creatinine it was 12.05 μg/mL for the concentration range of 1–10,000 μg/mL. These results indicated that the proposed GWT-GMR sensor is suitable for use in clinical applications. Owing to its simple readout and optical path design, the GWT-GMR is considered ideal for integration with smartphones or as miniaturized displays in handheld devices, which could prove beneficial for future point-of-care applications.

Critical assessment of relevant methods in the field of biosensors with direct optical detection based on fibers and waveguides using plasmonic, resonance, and interference effects

Direct optical detection has proven to be a highly interesting tool in biomolecular interaction analysis to be used in drug discovery, ligand/receptor interactions, environmental analysis, clinical diagnostics, screening of large data volumes in immunology, cancer therapy, or personalized medicine. In this review, the fundamental optical principles and applications are reviewed. Devices are based on concepts such as refractometry, evanescent field, waveguides modes, reflectometry, resonance and/or interference. They are realized in ring resonators; prism couplers; surface plasmon resonance; resonant mirror; Bragg grating; grating couplers; photonic crystals, Mach-Zehnder, Young, Hartman interferometers; backscattering; ellipsometry; or reflectance interferometry. The physical theories of various optical principles have already been reviewed in detail elsewhere and are therefore only cited. This review provides an overall survey on the application of these methods in direct optical biosensing. The "historical" development of the main principles is given to understand the various, and sometimes only slightly modified variations published as "new" methods or the use of a new acronym and commercialization by different companies. Improvement of optics is only one way to increase the quality of biosensors. Additional essential aspects are the surface modification of transducers, immobilization strategies, selection of recognition elements, the influence of non-specific interaction, selectivity, and sensitivity. Furthermore, papers use for reporting minimal amounts of detectable analyte terms such as value of mass, moles, grams, or mol/L which are difficult to compare. Both these essential aspects (i.e., biochemistry and the presentation of LOD values) can be discussed only in brief (but references are provided) in order to prevent the paper from becoming too long. The review will concentrate on a comparison of the optical methods, their application, and the resulting bioanalytical quality.

Exopolysaccharide from Streptococcus thermophilus as stabilizer in fermented dairy: Binding kinetics and interactions with casein of milk

Exopolysaccharides (EPSs) from lactic acid bacteria have great effect on the quality of fermented milk products. However, the mechanism for the quality improvement has not been well described. This study aimed to investigate the molecular binding kinetics and interactions between EPS obtained from Streptococcus thermophilus AR333 (EPS333) and casein of milk (CM) in a simulated acidifying process. The results indicated that EPS333 had a significant effect on the stability of casein micelles at acidic pH (6.0-4.5) according to the turbidity, ζ-potential, particle size and distribution analysis. The adsorption-desorption study by bio-layer interferometry identified the direct affinity binding between EPS333 and CM, the interactive moiety of casein was α-casein, rather than β- or κ-casein. Fluorescence quenching analysis revealed that the force types of interaction between EPS333 and CM were dynamically changeable during the acidifying process, mainly from electrostatic interaction at pH 7.0-6.5, to hydrophobic or hydrogen bonding at pH 6.5-5.5, and then transferred to electrostatic interaction again at pH 5.5-5.0. Conclusively, EPS333 could bind with CM directly via different binding forces during acidifying process to stabilize the properties of casein micelles.

On the Measurement of Energy Dissipation of Adhered Cells with the Quartz Microbalance with Dissipation Monitoring

We previously reported the finding of a linear correlation between the change of energy dissipation (Δ D) of adhered cells measured with the quartz crystal microbalance with dissipation monitoring (QCM-D) and the level of focal adhesions of the cells. To account for this correlation, we have developed a theoretical framework for assessing the Δ D-response of adhered cells. We rationalized that the mechanical energy of an oscillating QCM-D sensor coupled with a cell monolayer is dissipated through three main processes: the interfacial friction through the dynamic restructuring (formation and rupture) of cell-extracellular matrix (ECM) bonds, the interfacial viscous damping by the liquid trapped between the QCM-D sensor and the basal membrane of the cell layer, and the intracellular viscous damping through the viscous slip between the cytoplasm and stress fibers as well as among stress fibers themselves. Our modeling study shows that the interfacial viscous damping by the trapped liquid is the primary process for energy dissipation during the early stage of the cell adhesion, whereas the dynamic restructuring of cell-ECM bonds becomes more prevalent during the later stage of the cell adhesion. Our modeling study also establishes a positive linear correlation between the Δ D-response and the level of cell adhesion quantified with the number of cell-ECM bonds, which corroborates our previous experimental finding. This correlation with a wide well-defined linear dynamic range provides a much needed theoretical validation of the dissipation monitoring function of the QCM-D as a powerful quantitative analytical tool for cell study.

Thermotropic Liquid Crystal-Assisted Chemical and Biological Sensors

In this review article, we analyze recent progress in the application of liquid crystal-assisted advanced functional materials for sensing biological and chemical analytes. Multiple research groups demonstrate substantial interest in liquid crystal (LC) sensing platforms, generating an increasing number of scientific articles. We review trends in implementing LC sensing techniques and identify common problems related to the stability and reliability of the sensing materials as well as to experimental set-ups. Finally, we suggest possible means of bridging scientific findings to viable and attractive LC sensor platforms.

SPR platform based on image acquisition for HER2 antigen detection

HER2 antigen is a marker used for breast cancer diagnosis and prevention. Its determination has great importance since breast cancer is one of the most insidious types of cancer in women. HER2 antigen assessment in human serum is traditionally achieved by enzyme-linked immunosorbent assay (ELISA method), but it has some disadvantages, such as suppressing the thermodynamic-kinetic studies regarding the antibody-antigen interaction, and the use of labeled molecules that can promote false positive responses. Biosensors based on surface plasmon resonance (SPR) are sensitive optical techniques widely applied on bioassays. The plasmonic devices do not operate with labeled molecules, overcoming conventional immunoassay limitations, and enabling a direct detection of target analytes. In this way, a new SPR biosensor to assess HER2 antigen has been proposed, using nanohole arrays on a gold thin film by signal transduction of transmitted light measurements from array image acquisitions. These metallic nanostructures may couple the light directly on surface plasmons using a simple collinear arrangement. The proposed device reached an average sensitivity for refractive index (RI) variation on a metal surface of 4146 intensity units/RIU (RIU = RI units). The device feasibility on biomolecular assessment was evaluated. For this, 3 ng ml^-1 known HER2 antigen concentration was efficiently flowed (using a microfluidic system) and detected from aqueous solutions. This outcome shows that the device may be a powerful apparatus for bioassays, particularly toward breast cancer diagnosis and prognosis.

Retroreflective Janus Microparticle as a Nonspectroscopic Optical Immunosensing Probe

We developed retroreflective Janus microparticles (RJPs) as a novel optical immunosensing probe for use in a nonspectroscopic retroreflection-based immunoassay. By coating the metals on the hemispherical surface of silica particles, highly reflective RJPs were fabricated. On the basis of the retroreflection principle, the RJPs responded to polychromatic white light sources, in contrast to conventional optical probes, which require specific monochromatic light. The retroreflection signals from RJPs were distinctively recognized as shining dots, which can be intuitively counted using a digital camera setup. Using the developed retroreflective immunosensing system, cardiac troponin I, a specific biomarker of acute myocardial infarction, was detected with high sensitivity. On the basis of the demonstrated features of the retroreflective immunosensing platform, we expect that our approach may be applied for various point-of-care-testing applications.

Point-of-Need bioanalytics based on planar optical interferometry

This review brings about a comprehensive presentation of the research on interferometric transducers, which have emerged as extremely promising candidates for viable, truly-marketable solutions for PoN applications due to the attested performance that has reached down to 10(-8) in term of effective refractive index changes. The review explores the operation of the various interferometric architectures along with their design, fabrication, and analytical performance aspects. The issues of biosensor functionalization and immobilization of receptors are also addressed. As a conclusion, the comparison among them is attempted in order to delve into and acknowledge their current limitations, and define the future trends.

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.

Total internal reflection fluorescence quantification of receptor pharmacology

Total internal reflection fluorescence (TIRF) microscopy has been widely used as a single molecule imaging technique to study various fundamental aspects of cell biology, owing to its ability to selectively excite a very thin fluorescent volume immediately above the substrate on which the cells are grown. However, TIRF microscopy has found little use in high content screening due to its complexity in instrumental setup and experimental procedures. Inspired by the recent demonstration of label-free evanescent wave biosensors for cell phenotypic profiling and drug screening with high throughput, we had hypothesized and demonstrated that TIRF imaging is also amenable to receptor pharmacology profiling. This paper reviews key considerations and recent applications of TIRF imaging for pharmacology profiling.

Label-free kinetic analysis of an antibody-antigen interaction using biolayer interferometry

Biolayer Interferometry (BLI) is a powerful technique that enables direct measurement of biomolecular interactions in real time without the need for labeled reagents. Here we describe the analysis of a high-affinity binding interaction between a monoclonal antibody and purified antigen using BLI. A simple Dip-and-Read™ format in which biosensors are dipped into microplate wells containing purified or complex samples provides a highly parallel, user-friendly technique to study molecular interactions. A rapid rise in publications citing the use of BLI technology in a wide range of applications, from biopharmaceutical discovery to infectious diseases monitoring, suggests broad utility of this technology in the life sciences.

Live cell optical sensing for high throughput applications

Live cell optical sensing employs label-free optical biosensors to non-invasively measure stimulus-induced dynamic mass redistribution (DMR) in live cells within the sensing volume of the biosensor. The resultant DMR signal is an integrated cellular response, and reflects cell signaling mediated through the cellular target(s) with which the stimulus intervenes. This article describes the uses of live cell optical sensing for probing cell biology and ligand pharmacology, with an emphasis of resonant waveguide grating biosensor cellular assays for high throughput applications.

Label-free monitoring of μ-opioid receptor-mediated signaling

In this study, we used a combination of traditional signaling investigation approaches, bioluminescence resonance energy transfer (BRET) biosensors, and the label-free approach surface plasmon resonance (SPR) spectroscopy to monitor the signaling cascades of the μ-opioid receptor (MOP). In human embryonic kidney cells stably expressing a Flag-tagged version of human MOP, we compared the signals triggered by the noninternalizing and internalizing MOP agonists morphine and DAMGO (Tyr-D-Ala-Gly-N-methyl-Phe-Gly-ol), respectively. We studied three major and well described components of MOP signaling: receptor internalization, G protein coupling, and activation of extracellular signal-regulated kinase ERK1/ERK2. Our results show that morphine and DAMGO display different profiles of receptor internalization and a similar ability to trigger the phosphorylation of ERK1/ERK2. Our SPR analyses revealed that morphine and DAMGO evoke similar SPR signatures and that Gαi, cAMP-dependent pathways, and ERK1/ERK2 have key roles in morphine- and DAMGO-mediated signaling. Most interestingly, we found that the so-called MOP neutral antagonists CTOP (D-Phe-Cys-Tyr-D-Trp-Orn-Thr-Pen-Thr-NH(2)), naloxone, and naltrexone behave like partial agonists. Even more intriguing, BRET experiments indicate that CTAP (D-Phe-Cys-Tyr-D-Trp-Arg-Thr-Pen-Thr-NH(2)) induces similar conformational changes as naltrexone at the Gαi-βγ interface, whereas it appears as an inverse agonist based on its SPR response thus indicating distinct signaling mechanisms for the two ligands. Taken together, our results support the usefulness of label-free methods such as SPR to study whole-cell responses and signaling cascades triggered by G protein-coupled receptors and complement the conventional approaches by revealing cellular responses that would have been otherwise undetectable.

New LIC vectors for production of proteins from genes containing rare codons

In the effort to produce proteins coded by diverse genomes, structural genomics projects often must express genes containing codons that are rare in the production strain. To address this problem, genes expressing tRNAs corresponding to those codons are typically coexpressed from a second plasmid in the host strain, or from genes incorporated into production plasmids. Here we describe the modification of a series of LIC pMCSG vectors currently used in the high-throughput (HTP) production of proteins to include crucial tRNA genes covering rare codons for Arg (AGG/AGA) and Ile (AUA). We also present variants of these new vectors that allow analysis of ligand binding or co-expression of multiple proteins introduced through two independent LIC steps. Additionally, to accommodate the cloning of multiple large proteins, the size of the plasmids was reduced by approximately one kilobase through the removal of non-essential DNA from the base vector. Production of proteins from core vectors of this series validated the desired enhanced capabilities: higher yields of proteins expressed from genes with rare codons occurred in most cases, biotinylated derivatives enabled detailed automated ligand binding analysis, and multiple proteins introduced by dual LIC cloning were expressed successfully and in near balanced stoichiometry, allowing tandem purification of interacting proteins.

Comparison of surface plasmon resonance, resonant waveguide grating biosensing and enzyme linked immunosorbent assay (ELISA) in the evaluation of a dengue virus immunoassay

Two label-free biosensor platforms, Resonance Waveguide Grating (RWG) and Surface Plasmon Resonance (SPR), were used to rank a large panel of anti-dengue virus NS1 antibodies. Dengue non-structural 1 (NS1) protein is an established serological marker for the early detection of dengue infection. A variety of commercial dengue NS1 antigen capture immunoassays are available in both ELISA and lateral flow format. However, there is a significant scope to improve both the sensitivity and the specificity of those tests. The interactions of antibody (Ab)-antigen (Ag) were profiled, with weak interactions (K_D= 1–0.1 μM) able to be detected under static equilibrium conditions by RWG, but not observed to under more rigorous flow conditions using SPR. There were significant differences in the absolute affinities determined by the two technologies, and there was a poor correlation between antibodies best ranked by RWG and the lower limit of detection (LLOD) found by ELISA. Hence, whilst high-throughput RWG can be useful as preliminary screening for higher affinity antibodies, care should be exercised in the assignation of quantitative values for affinity between different assay formats.

Affinity capture of biotinylated proteins at acidic conditions to facilitate hydrogen/deuterium exchange mass spectrometry analysis of multimeric protein complexes

Characterization of conformational and dynamic changes associated with protein interactions can be done by hydrogen/deuterium exchange mass spectrometry (HDX-MS) by comparing the deuterium uptake in the bound and unbound state of the proteins. Investigation of local hydrogen/deuterium exchange in heteromultimeric protein complexes poses a challenge for the method due to the increased complexity of the mixture of peptides originating from all interaction partners in the complex. Previously, interference of peptides from one interaction partner has been removed by immobilizing the intact protein on beads prior to the HDX-MS experiment. However, when studying protein complexes of more than two proteins, immobilization can possibly introduce steric limitations to the interactions. Here, we present a method based on the high affinity biotin-streptavidin interaction that allows selective capture of biotinylated proteins even under the extreme conditions for hydrogen/deuterium exchange quenching i.e. pH 2.5 and 0 °C. This biotin-streptavidin capture strategy allows hydrogen/deuterium exchange to occur in proteins in solution and enables characterization of specific proteins in heteromultimeric protein complexes without interference of peptides originating from other interaction partners in the complex. The biotin-streptavidin strategy has been successfully implemented in a model system with two recombinant monoclonal antibodies that target nonoverlapping epitopes on the human epidermal growth factor receptor (EGFR). We present a workflow for biotinylation and characterization of recombinant antibodies and demonstrate affinity capture of biotinylated antibodies under hydrogen/deuterium exchange quench conditions by the biotin-streptavidin strategy.

Nanoengineered glycan sensors enabling native glycoprofiling for medicinal applications: towards profiling glycoproteins without labeling or liberation steps

Nanoengineered glycan sensors may help realize the long-held goal of accurate and rapid glycoprotein profiling without labeling or glycan liberation steps. Current methods of profiling oligosaccharides displayed on protein surfaces, such as liquid chromatography, mass spectrometry, capillary electrophoresis, and microarray methods, are limited by sample pretreatment and quantitative accuracy. Microarrayed platforms can be improved with methods that better estimate kinetic parameters rather than simply reporting relative binding information. These quantitative glycan sensors are enabled by an emerging class of nanoengineered materials that differ in their mode of signal transduction from traditional methods. Platforms that respond to mass changes include a quartz crystal microbalance and cantilever sensors. Electronic response can be detected from electrochemical, field effect transistor, and pore impedance sensors. Optical methods include fluorescent frontal affinity chromatography, surface plasmon resonance methods, and fluorescent carbon nanotubes. After a very brief primer on glycobiology and its connection to medicine, these emerging systems are critically reviewed for their potential use as core sensors in future glycoprofiling tools.

Evaluating Inhibition of the Epidermal Growth Factor (EGF)-Induced Response of Mutant MCF10A Cells with an Acoustic Sensor

Many cancer treatments rely on inhibition of epidermal growth factor (EGF)-induced cellular responses. Evaluating drug effects on such responses becomes critical to the development of new cancer therapeutics. In this report, we have employed a label-free acoustic sensor, the quartz crystal microbalance with dissipation monitoring (QCM-D), to track the EGF-induced response of mutant MCF10A cells under various inhibitory conditions. We have identified a complex cell de-adhesion process, which can be distinctly altered by inhibitors of signaling pathways and cytoskeleton formation in a dose-dependent manner. The dose dependencies of the inhibitors provide IC₅₀ values which are in strong agreement with the values reported in the literature, demonstrating the sensitivity and reliability of the QCM-D as a screening tool. Using immunofluorescence imaging, we have also verified the quantitative relationship between the ΔD-response (change in energy dissipation factor) and the level of focal adhesions quantified with the areal density of immunostained vinculin under those inhibitory conditions. Such a correlation suggests that the dynamic restructuring of focal adhesions can be assessed based on the time-dependent change in ΔD-response. Overall, this report has shown that the QCM-D has the potential to become an effective sensing platform for screening therapeutic agents that target signaling and cytoskeletal proteins.

Cellular cofactors of lentiviral integrase: from target validation to drug discovery

To accomplish their life cycle, lentiviruses make use of host proteins, the so-called cellular cofactors. Interactions between host cell and viral proteins during early stages of lentiviral infection provide attractive new antiviral targets. The insertion of lentiviral cDNA in a host cell chromosome is a step of no return in the replication cycle, after which the host cell becomes a permanent carrier of the viral genome and a producer of lentiviral progeny. Integration is carried out by integrase (IN), an enzyme playing also an important role during nuclear import. Plenty of cellular cofactors of HIV-1 IN have been proposed. To date, the lens epithelium-derived growth factor (LEDGF/p75) is the best studied cofactor of HIV-1 IN. Moreover, small molecules that block the LEDGF/p75-IN interaction have recently been developed for the treatment of HIV infection. The nuclear import factor transportin-SR2 (TRN-SR2) has been proposed as another interactor of HIV IN-mediating nuclear import of the virus. Using both proteins as examples, we will describe approaches to be taken to identify and validate novel cofactors as new antiviral targets. Finally, we will highlight recent advances in the design and the development of small-molecule inhibitors binding to the LEDGF/p75-binding pocket in IN (LEDGINs).

A Comparative Study of Impedance versus Optical Label-Free Systems Relative to Labelled Assays in a Predominantly Gi Coupled GPCR (C5aR) Signalling

Profiling ligand function on G-protein coupled receptors (GPCRs) typically involves using transfected cells over-expressing a target of interest, a labelled ligand, and intracellular secondary messenger reporters. In contrast, label-free assays are sensitive enough to allow detection in native cells, which may provide a more physiologically relevant readout. Here, we compare four agonists (native agonists, a peptide full agonist and a peptide partial agonist) that stimulate the human inflammatory GPCR C5aR. The receptor was challenged when present in human monocyte-derived macrophages (HMDM) versus stably transfected human C5aR-CHO cells. Receptor activation was compared on label-free optical and impedance biosensors and contrasted with results from two traditional reporter assays. The rank order of potencies observed across label-free and pathway specific assays was similar. However, label-free read outs gave consistently lower potency values in both native and transfected cells. Relative to pathway-specific assays, these technologies measure whole-cell responses that may encompass multiple signalling events, including down-regulatory events, which may explain the potency discrepancies observed. These observations have important implications for screening compound libraries against GPCR targets and for selecting drug candidates for in vivo assays.

Bacillus anthracis inosine 5'-monophosphate dehydrogenase in action: the first bacterial series of structures of phosphate ion-, substrate-, and product-bound complexes

Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the first unique step of the GMP branch of the purine nucleotide biosynthetic pathway. This enzyme is found in organisms of all three kingdoms. IMPDH inhibitors have broad clinical applications in cancer treatment, as antiviral drugs and as immunosuppressants, and have also displayed antibiotic activity. We have determined three crystal structures of Bacillus anthracis IMPDH, in a phosphate ion-bound (termed "apo") form and in complex with its substrate, inosine 5'-monophosphate (IMP), and product, xanthosine 5'-monophosphate (XMP). This is the first example of a bacterial IMPDH in more than one state from the same organism. Furthermore, for the first time for a prokaryotic enzyme, the entire active site flap, containing the conserved Arg-Tyr dyad, is clearly visible in the structure of the apoenzyme. Kinetic parameters for the enzymatic reaction were also determined, and the inhibitory effect of XMP and mycophenolic acid (MPA) has been studied. In addition, the inhibitory potential of two known Cryptosporidium parvum IMPDH inhibitors was examined for the B. anthracis enzyme and compared with those of three bacterial IMPDHs from Campylobacter jejuni, Clostridium perfringens, and Vibrio cholerae. The structures contribute to the characterization of the active site and design of inhibitors that specifically target B. anthracis and other microbial IMPDH enzymes.

Label-free detection of G protein-SNARE interactions and screening for small molecule modulators

G(i/o)-coupled presynaptic GPCRs are major targets in neuropsychiatric diseases. For example, presynaptic auto- or heteroreceptors include the D(2) dopamine receptor, H(3) histamine receptor, 5HT(1) serotonin receptors, M(4) acetylcholine receptors, GABA(B) receptors, Class II and III metabotropic glutamate receptors, opioid receptors, as well as many other receptors. These GPCRs exert their influence by decreasing exocytosis of synaptic vesicles. One mechanism by which they act is through direct interaction of the Gβγ subunit with members of the SNARE complex downstream of voltage-dependent calcium channels, and specifically with the C-terminus of SNAP25 and the H3 domain of syntaxin1A(1-3). Small molecule inhibitors of the Gβγ-SNARE interaction would allow the study of the relative importance of this mechanism in more detail. We have utilized novel, label-free technology to detect this protein-protein interaction and screen for several small molecule compounds that perturb the interaction, demonstrating the viability of this approach. Interestingly, the screen also produced enhancers of the Gβγ-SNARE interaction.

The Peroxisomal Targeting Signal 1 in sterol carrier protein 2 is autonomous and essential for receptor recognition

Background

The majority of peroxisomal matrix proteins destined for translocation into the peroxisomal lumen are recognised via a C-terminal Peroxisomal Target Signal type 1 by the cycling receptor Pex5p. The only structure to date of Pex5p in complex with a cargo protein is that of the C-terminal cargo-binding domain of the receptor with sterol carrier protein 2, a small, model peroxisomal protein. In this study, we have tested the contribution of a second, ancillary receptor-cargo binding site, which was found in addition to the characterised Peroxisomal Target Signal type 1.

Results

To investigate the function of this secondary interface we have mutated two key residues from the ancillary binding site and analyzed the level of binding first by a yeast-two-hybrid assay, followed by quantitative measurement of the binding affinity and kinetics of purified protein components and finally, by in vivo measurements, to determine translocation capability. While a moderate but significant reduction of the interaction was found in binding assays, we were not able to measure any significant defects in vivo.

Conclusions

Our data therefore suggest that at least in the case of sterol carrier protein 2 the contribution of the second binding site is not essential for peroxisomal import. At this stage, however, we cannot rule out that other cargo proteins may require this ancillary binding site.

Free-solution interaction assay of carbonic anhydrase to its inhibitors using back-scattering interferometry

Back-scattering interferometry (BSI) is a label-free, free-solution, small-volume technique used for characterizing binding interactions, which is also relevant to a growing number of biosensing applications including drug discovery. Here, we use BSI to characterize the interaction of carbonic anhydrase enzyme II with five well-known carbonic anhydrase enzyme II inhibitors (± sulpiride, sulfanilamide, benzene sulfonamide, dansylamide, and acetazolamide) in the presence of DMSO. Dissociation constants calculated for each interaction were consistent with literature values previously obtained using surface plasmon resonance and fluorescence-based competition assays. Results demonstrate the potential of BSI as a drug-screening tool which is fully compatible with DMSO and does not require immobilization or labeling, therefore allowing binding interactions to be characterized in the native state. BSI has the potential for reducing labor costs, sample consumption, and assay time while providing enhanced reliability over existing techniques.

Biosensors for diagnostic applications

Biosensors combine a transducer with a biorecognition element and thus are able to transform a biochemical event on the transducer surface directly into a measurable signal. By this they have the potential to provide rapid, real-time, and accurate results in a comparatively easy way, which makes them promising analytical devices. Since the first biosensor was introduced in 1962 as an "enzyme electrode" for monitoring glucose in blood, medical applications have been the main driving force for further biosensor development. In this chapter we outline potential biosensor setups, focusing on transduction principles, biorecognition layers, and biosensor test formats, with regard to potential applications. A summary of relevant aspects concerning biosensor integration in efficient analytical setups is included. We describe the latest applications of biosensors in diagnostic applications focusing on detection of molecular biomarkers in real samples. An overview of the current state and future trends of biosensors in this field is given.

Label-Free Biosensors for Cell Biology

Label-free biosensors for studying cell biology have finally come of age. Recent developments have advanced the biosensors from low throughput and high maintenance research tools to high throughput and low maintenance screening platforms. In parallel, the biosensors have evolved from an analytical tool solely for molecular interaction analysis to powerful platforms for studying cell biology at the whole cell level. This paper presents historical development, detection principles, and applications in cell biology of label-free biosensors. Future perspectives are also discussed.

Label-free imaging and temporal signature in phenotypic cellular assays: a new approach to high-content screening

Some drug targets are not amenable to screening because of the lack of a practical or validated biological assay. Likewise, some screening assays may not be predictive of compound activity in a more disease-relevant scenario, or assay development may demand excessive allocation of resources (i.e., time, money or personnel) with limited knowledge of the actual tractability of the target. Label-free methodologies, implemented in microtiter plate format, may help address these issues and complement, simplify, or facilitate assays. Label-free biosensors, based on grating resonance or electrical impedance, are versatile platforms for detecting phenotypic changes in both engineered and native cells. Their non-invasive nature allows for the kinetic monitoring of multiple real-time cellular responses to external stimuli, as well as for the use of successive pharmacological challenges. The temporal signature recorded for a particular stimulus is characteristic of the cell type and the signaling pathway activated upon binding of a ligand to its receptor. Cellular label-free technology is an important technical advance in the study of functional pharmacological selectivity. Described in this overview are some of the hurdles encountered in modern drug discovery and the ways in which label-free technologies can be used to overcome these obstacles.

Therapeutic antibodies: Discovery and development using the ProteOn XPR36 biosensor interaction array system

Therapeutic monoclonal antibodies are becoming a significant and rapidly growing class of therapeutic pharmaceuticals. Their discovery and development requires fast and high-throughput methodologies for screening and selecting appropriate candidate antibodies having high affinity for the target as well as high specificity and low cross-reactivity. This study demonstrates the use of the ProteOn XPR36 protein interaction array system and its novel approach, termed One-Shot Kinetics, for the rapid screening and selection of high-affinity antibodies. This approach allows multiple quantitative protein binding analyses in parallel, providing association, dissociation, and affinity constants for several antibodies or supernatants simultaneously in one experiment. We show that the ProteOn XPR36 system is a valuable tool for use across multiple stages of the therapeutic antibody discovery and development process, enabling efficient and rapid screening after panning, affinity maturation, assay validation, and clone selection.

A stable, label-free optical interferometric biosensor based on TiO2 nanotube arrays

Optical interferometry of a thin film array of titanium dioxide (TiO2) nanotubes allows the label-free sensing of rabbit immunoglobulin G (IgG). A protein A capture probe is used, which is immobilized on the inner pore walls of the nanotubes by electrostatic adsorption. Control experiments using IgG from chicken (which does not bind to protein A) confirms the specificity of the protein A-modified TiO2 nanotube array sensor. The aqueous stability of the TiO2 nanotube array was examined and compared with porous silica (SiO2), a more extensively studied thin film optical biosensor. The TiO2 nanotube array is stable in the pH range 2 to 12, whereas the porous SiO2 sensor displays significant degradation at pH > 8.

Binding Rate Screen - a high-throughput assay in soluble lysate for prioritizing protein expression constructs

Identification of constructs suitable for the recombinant protein production pipeline is a bottleneck for structural genomics efforts, as most methods require purified proteins and/or are labor-intensive. Here, we present a novel high-throughput approach, Binding Rate Screen, that can alleviate this bottleneck by screening expression constructs in crude soluble lysate. This functional screen utilizes the frequently employed hexahistidine (His(6)) tag as a reporter, and measures its binding rate to an affinity matrix as a metric to reflect aggregation, concentration, and purifiability of the target protein. The constructs with the highest binding rates also exhibit high expression of soluble monomeric protein as judged by analytical size-exclusion chromatography. Constructs expressing variations of the target protein can be prioritized on a time scale of minutes, which is at least 10-100 times faster than any other technologies currently available.