Looking towards label-free biomolecular interaction analysis in a high-throughput format: a review of new surface plasmon resonance technologies

A Comprehensive Exploration of Caspase Detection Methods: From Classical Approaches to Cutting-Edge Innovations

The activation of caspases is a crucial event and an indicator of programmed cell death, also known as apoptosis. These enzymes play a central role in cancer biology and are considered one promising target for current and future advancements in therapeutic interventions. Traditional methods of measuring caspase activity such as antibody-based methods provide fundamental insights into their biological functions, and are considered essential tools in the fields of cell and cancer biology, pharmacology and toxicology, and drug discovery. However, traditional methods, though extensively used, are now recognized as having various shortcomings. In addition, these methods fall short of providing solutions to and matching the needs of the rapid and expansive progress achieved in studying caspases. For these reasons, there has been a continuous improvement in detection methods for caspases and the network of pathways involved in their activation and downstream signaling. Over the past decade, newer methods based on cutting-edge state-of-the-art technologies have been introduced to the biomedical community. These methods enable both the temporal and spatial monitoring of the activity of caspases and their downstream substrates, and with enhanced accuracy and precision. These include fluorescent-labeled inhibitors (FLIs) for live imaging, single-cell live imaging, fluorescence resonance energy transfer (FRET) sensors, and activatable multifunctional probes for in vivo imaging. Recently, the recruitment of mass spectrometry (MS) techniques in the investigation of these enzymes expanded the repertoire of tools available for the identification and quantification of caspase substrates, cleavage products, and post-translational modifications in addition to unveiling the complex regulatory networks implicated. Collectively, these methods are enabling researchers to unravel much of the complex cellular processes involved in apoptosis, and are helping generate a clearer and comprehensive understanding of caspase-mediated proteolysis during apoptosis. Herein, we provide a comprehensive review of various assays and detection methods as they have evolved over the years, so to encourage further exploration of these enzymes, which should have direct implications for the advancement of therapeutics for cancer and other diseases.

Fluorescence-Based Protein Stability Monitoring-A Review

Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.

Distributed interferometric fiber tip biosensors for a multi-channel and label-free biomolecular interaction analysis

This paper describes fabrication and implementation of distributed optical fiber tip biosensor probes for simultaneously measuring label-free biomolecular interactions at multiple locations. Biosensor probes at the tip of a single-mode fiber are Fabry-Perot etalons that are functionalized with a capture layer for a specific biomolecule. A coherence multiplexing method is implemented to separate data collected from distributed biosensors in a single data stream. Multiplexing is achieved by using fiber tip biosensors of varying etalon lengths with the same or different capture layers for each biosensing channel. Experiments demonstrating simultaneous multi-channel recording of protein-to-protein interaction sensorgrams with fiber tip biosensor probes are presented.

Biophysical Approaches for the Characterization of Protein-Metabolite Interactions

With an estimate of hundred thousands of protein molecules per cell and the number of metabolites several orders of magnitude higher, protein-metabolite interactions are omnipresent. In vitro analyses are one of the main pillars on the way to establish a solid understanding of how these interactions contribute to maintaining cellular homeostasis. A repertoire of biophysical techniques is available by which protein-metabolite interactions can be quantitatively characterized in terms of affinity, specificity, and kinetics in a broad variety of solution environments. Several of those provide information on local or global conformational changes of the protein partner in response to ligand binding. This review chapter gives an overview of the state-of-the-art biophysical toolbox for the study of protein-metabolite interactions. It briefly introduces basic principles, highlights recent examples from the literature, and pinpoints promising future directions.

Recent Advances in Nanomaterial-Based Sensing for Food Safety Analysis

The increasing public attention on unceasing food safety incidents prompts the requirements of analytical techniques with high sensitivity, reliability, and reproducibility to timely prevent food safety incidents occurring. Food analysis is critically important for the health of both animals and human beings. Due to their unique physical and chemical properties, nanomaterials provide more opportunities for food quality and safety control. To date, nanomaterials have been widely used in the construction of sensors and biosensors to achieve more accurate, fast, and selective food safety detection. Here, various nanomaterial-based sensors for food analysis are outlined, including optical and electrochemical sensors. The discussion mainly involves the basic sensing principles, current strategies, and novel designs. Additionally, given the trend towards portable devices, various smartphone sensor-based point-of-care (POC) devices for home care testing are discussed.

Contemporary biophysical approaches for studying 14-3-3 protein-protein interactions

14-3-3 proteins are a family of regulatory hubs that function through a vast network of protein-protein interactions. Their dysfunction or dysregulation is implicated in a wide range of diseases, and thus they are attractive drug targets, especially for molecular glues that promote protein-protein interactions for therapeutic intervention. However, an incomplete understanding of the molecular mechanisms that underpin 14-3-3 function hampers progress in drug design and development. Biophysical methodologies are an essential element of the 14-3-3 analytical toolbox, but in many cases have not been fully exploited. Here, we present a contemporary review of the predominant biophysical techniques used to study 14-3-3 protein-protein interactions, with a focus on examples that address key questions and challenges in the 14-3-3 field.

Two-Dimensional Graphitic Carbon Nitride (g-C3N4) Nanosheets and Their Derivatives for Diagnosis and Detection Applications

The early diagnosis of certain fatal diseases is vital for preventing severe consequences and contributes to a more effective treatment. Despite numerous conventional methods to realize this goal, employing nanobiosensors is a novel approach that provides a fast and precise detection. Recently, nanomaterials have been widely applied as biosensors with distinctive features. Graphite phase carbon nitride (g-C₃N₄) is a two-dimensional (2D) carbon-based nanostructure that has received attention in biosensing. Biocompatibility, biodegradability, semiconductivity, high photoluminescence yield, low-cost synthesis, easy production process, antimicrobial activity, and high stability are prominent properties that have rendered g-C₃N₄ a promising candidate to be used in electrochemical, optical, and other kinds of biosensors. This review presents the g-C₃N₄ unique features, synthesis methods, and g-C₃N₄-based nanomaterials. In addition, recent relevant studies on using g-C₃N₄ in biosensors in regard to improving treatment pathways are reviewed.

Development of an intracellular quantitative assay to measure compound binding kinetics

Contemporary drug discovery typically quantifies the effect of a molecule on a biological target using the equilibrium-derived measurements of IC50, EC50, or KD. Kinetic descriptors of drug binding are frequently linked with the effectiveness of a molecule in modulating a disease phenotype; however, these parameters are yet to be fully adopted in early drug discovery. Nanoluciferase bioluminescence resonance energy transfer (NanoBRET) can be used to measure interactions between fluorophore-conjugated probes and luciferase fused target proteins. Here, we describe an intracellular NanoBRET competition assay that can be used to quantify cellular kinetic rates of compound binding to nanoluciferase-fused bromodomain and extra-terminal (BET) proteins. Comparative rates are generated using a cell-free NanoBRET assay and by utilizing orthogonal recombinant protein-based methodologies. A screen of known pan-BET inhibitors is used to demonstrate the value of this approach in the investigation of kinetic selectivity between closely related proteins.

Blood Group Testing

Red blood cell (RBC) transfusion is one of the most frequently performed clinical procedures and therapies to improve tissue oxygen delivery in hospitalized patients worldwide. Generally, the cross-match is the mandatory test in place to meet the clinical needs of RBC transfusion by examining donor-recipient compatibility with antigens and antibodies of blood groups. Blood groups are usually an individual's combination of antigens on the surface of RBCs, typically of the ABO blood group system and the RH blood group system. Accurate and reliable blood group typing is critical before blood transfusion. Serological testing is the routine method for blood group typing based on hemagglutination reactions with RBC antigens against specific antibodies. Nevertheless, emerging technologies for blood group testing may be alternative and supplemental approaches when serological methods cannot determine blood groups. Moreover, some new technologies, such as the evolving applications of blood group genotyping, can precisely identify variant antigens for clinical significance. Therefore, this review mainly presents a clinical overview and perspective of emerging technologies in blood group testing based on the literature. Collectively, this may highlight the most promising strategies and promote blood group typing development to ensure blood transfusion safety.

Flexible Microwave Biosensor for Skin Abnormality Detection Based on Spoof Surface Plasmon Polaritons

Point-of-care testing plays an important role in the detection of skin abnormalities. The detection of skin abnormalities requires sufficient depth and no harm. A flexible microwave biosensor based on spoof surface plasmon polaritons was designed to meet the requirements of skin abnormalities. The designed biosensor, which works at 11.3 GHz, is small and can be flexibly attached to the skin surface of any part of the human body for measurement. The health status of the skin can be evaluated by the resonant frequency and the magnitude of the reflection coefficient of the sensor. The sensor was tested on pork skin. The experiment results showed that the sensor can detect skin abnormalities such as skin burn, skin tumor, and others. Compared with other sensors, the sensor has sufficient penetration depth because of the strong penetration of microwave electromagnetic waves. It is the first flexible microwave biosensor used for skin, which involves point-of-care testing, and continuous monitoring of skin.

Discovery of novel ID2 antagonists from pharmacophore-based virtual screening as potential therapeutics for glioma

Glioma, especially the most aggressive type glioblastoma multiforme, is a malignant cancer of the central nervous system with a poor prognosis. Traditional treatments are mainly surgery combined with radiotherapy and chemotherapy, which is still far from satisfactory. Therefore, it is of great clinical significance to find new therapeutic agents. Serving as an inhibitor of differentiation, protein ID2 (inhibitor of DNA binding 2) plays an important role in neurogenesis, neovascularization and malignant development of gliomas. It has been shown that ID2 affects the malignant progression of gliomas through different mechanisms. In this study, a pharmacophore-based virtual screening was carried out and 16 hit compounds were purchased for pharmacological evaluations on their ID2 inhibitory activities. Based on the cytotoxicity of these small-molecule compounds, two compounds were shown to effectively inhibit the viability of glioma cells in the micromolar range. Among them, AK-778-XXMU was chosen for further study due to its better solubility in water. A SPR (Surface Plasma Resonance) assay proved the high affinity between AK-778-XXMU and ID2 protein with the K_D value as 129 nM. The plausible binding mode of ID2 was studied by molecular docking and it was found to match AGX51 very well in the same binding site. Subsequently, the cancer-suppressing potency of the compound was characterized both in vitro and in vivo. The data demonstrated that compound AK-778-XXMU is a potent ID2 antagonist which has the potential to be developed as a therapeutic agent against glioma.

Structure - Functionality of lentil protein-polyphenol conjugates

Lentil protein isolate (LPI) was conjugated with plant polyphenols (quercetin, rutin, ellagic acid), and the structural and functional characteristics of the conjugates were determined in comparison with the proteins and pure polyphenols. The interaction between polyphenols and protein was achieved by a grafting method at pH 9.0 in the presence of atmospheric oxygen. Surface plasmon resonance measurements showed polyphenols' direct interaction with LPI, with the order of binding strength quercetin > ellagic acid > rutin. The degree of conjugation also followed the same order. Structural analysis of the conjugates was performed using FTIR, intrinsic fluorescence, and surface hydrophobicity. A significant improvement in DPPḢ radical scavenging and ferric reducing antioxidant power of the conjugates was observed compared to the polyphenols. However, there was a decrease in the surface activity of the conjugates compared to LPI. Such conjugation provides a novel way to combine the advantages of using plant protein and polyphenols in developing a novel food ingredient.

Piceatannol protects against sepsis-induced myocardial dysfunction via direct inhibition of JAK2

Sepsis-induced myocardial dysfunction (SIMD) represents one of the serious complications secondary to sepsis, which is a leading cause of the high mortality rate among septic cases. Subsequent cardiomyocyte apoptosis, together with the uncontrolled inflammatory response, has been suggested to be closely related to SIMD. Piceatannol (PIC) is verified with potent anti-apoptotic and anti-inflammatory effects, but its function and molecular mechanism in SIMD remain unknown so far. This study aimed to explore the potential role and mechanism of action of PIC in resisting SIMD. The interaction of PIC with JAK2 proteins was evaluated by molecular docking, molecular dynamics (MD) simulation and surface plasmon resonance imaging (SPRi). The cecal ligation and puncture-induced septicemia mice and the LPS-stimulated H9C2 cardiomyocytes were prepared as the models in vivo and in vitro, separately. Molecular docking showed that JAK2-PIC complex had the -8.279 kcal/mol binding energy. MD simulations showed that JAK2-PIC binding was stable. SPRi analysis also showed that PIC has a strong binding affinity to JAK2. PIC treatment significantly ameliorated the cardiac function, attenuated the sepsis-induced myocardial loss, and suppressed the myocardial inflammatory responses both in vivo and in vitro. Further detection revealed that PIC inhibited the activation of the JAK2/STAT3 signaling, which was tightly associated with apoptosis and inflammation. Importantly, pre-incubation with a JAK2 inhibitor (AG490) partially blocked the cardioprotective effects of PIC. Collectively, the findings demonstrated that PIC restored the impaired cardiac function by attenuating the sepsis-induced apoptosis and inflammation via suppressing the JAK2/STAT3 pathway both in septic mice and H9C2 cardiomyocytes.

Kinetics of the multitasking high-affinity Win binding site of WDR5 in restricted and unrestricted conditions

Recent advances in quantitative proteomics show that WD40 proteins play a pivotal role in numerous cellular networks. Yet, they have been fairly unexplored and their physical associations with other proteins are ambiguous. A quantitative understanding of these interactions has wide-ranging significance. WD40 repeat protein 5 (WDR5) interacts with all members of human SET1/MLL methyltransferases, which regulate methylation of the histone 3 lysine 4 (H3K4). Here, using real-time binding measurements in a high-throughput setting, we identified the kinetic fingerprint of transient associations between WDR5 and 14-residue WDR5 interaction (Win) motif peptides of each SET1 protein (SET1Win). Our results reveal that the high-affinity WDR5-SET1Win interactions feature slow association kinetics. This finding is likely due to the requirement of SET1Win to insert into the narrow WDR5 cavity, also named the Win binding site. Furthermore, our explorations indicate fairly slow dissociation kinetics. This conclusion is in accordance with the primary role of WDR5 in maintaining the functional integrity of a large multisubunit complex, which regulates the histone methylation. Because the Win binding site is considered a key therapeutic target, the immediate outcomes of this study could form the basis for accelerated developments in medical biotechnology.

Can Antiviral Activity of Licorice Help Fight COVID-19 Infection?

The phytotherapeutic properties of Glycyrrhiza glabra (licorice) extract are mainly attributed to glycyrrhizin (GR) and glycyrrhetinic acid (GA). Among their possible pharmacological actions, the ability to act against viruses belonging to different families, including SARS coronavirus, is particularly important. With the COVID-19 emergency and the urgent need for compounds to counteract the pandemic, the antiviral properties of GR and GA, as pure substances or as components of licorice extract, attracted attention in the last year and supported the launch of two clinical trials. In silico docking studies reported that GR and GA may directly interact with the key players in viral internalization and replication such as angiotensin-converting enzyme 2 (ACE2), spike protein, the host transmembrane serine protease 2, and 3-chymotrypsin-like cysteine protease. In vitro data indicated that GR can interfere with virus entry by directly interacting with ACE2 and spike, with a nonspecific effect on cell and viral membranes. Additional anti-inflammatory and antioxidant effects of GR cannot be excluded. These multiple activities of GR and licorice extract are critically re-assessed in this review, and their possible role against the spread of the SARS-CoV-2 and the features of COVID-19 disease is discussed.

Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)

The fundamentals of how protein-protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein-protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.

Reviewing the experimental and mathematical factors involved in tight binding inhibitors Ki values determination: The bi-functional protease inhibitor SmCI as a test model

Different methodologies for determining the dissociation equilibrium constant (K_i) of protein tight binding inhibitors are frequently found in the scientific literature. Taking into account that the K_i value is the main parameter characterizing the inhibition strength, its determination often represents the first step during the characterization of a potential drug. The purpose of this review is to summarize the current information related to tight binding inhibitors K_i values determination and discuss about the importance of different factors as the enzyme concentration, the inhibitor concentration dilution series, the enzyme-inhibitor incubation time and the dose-response data mathematical fitting. For this aim, the bi-functional SmCI protease inhibitor is used as a tool for exemplifying the experimental and mathematical steps performed during tight binding inhibitors K_i values determination. In addition, the natural and the different recombinant forms of SmCI were used to go deeply into the comparison of some mathematic approaches that are frequently used in the literature. Finally, other biochemical techniques that could be potentially used for tight binding inhibitors K_i values determination are also commented.

Biomedical analysis of exosomes using biosensing methods: recent progress

Exosomes are membrane-bound extracellular vesicles (EVs) that are produced in the endosomal compartments of most eukaryotic cells; they play important roles in intercellular communication in diverse cellular processes and transmit different types of biomolecules. Endocytic pathways release exosomes, which have diameters ranging from 50 to 200 nm. The unique functions of exosomes have been introduced as cancer bio-markers due to the cargo (protein, DNA and RNA) of external exosomes (tetraspanin) and internal exosomes (syntenin). The early detection of cancer by exosomes can be an excellent method for the treatment of cancer. Although detection methods based on exosomes are important, they require extensive sample purification, have high false-positive rates, and encounter labeling difficulties due to the small size of exosomes. Here, we have reviewed three major types of biosensors, namely, electrochemical biosensors, optical biosensors and electrochemiluminescence biosensors for the detection of exosomes released from breast, ovarian, pancreatic, lung, and cervical cancer cells. In addition, the importance of nanomaterials and their applications in the biomedical analysis of exosomes are discussed. Although exosomes can be used to identify various types of external and internal biomarkers by conjugating with recognition elements, most designed biosensors are based on CD9 and CD63. Therefore, the development of novel biosensors for the selective and sensitive detection of exosomes is a current challenge. We hope that this review will serve as a beneficial study for improving exosome detection in clinical samples.

SPR Biosensor Based on Polymer Multi-Mode Optical Waveguide and Nanoparticle Signal Enhancement

We present a surface plasmon resonance (SPR) biosensor that is based on a planar-optical multi-mode (MM) polymer waveguide structure applied for the detection of biomolecules in the lower nano-molar (nM) range. The basic sensor shows a sensitivity of 608.6 nm/RIU when exposed to refractive index changes with a measurement resolution of 4.3 × 10-3 RIU. By combining the SPR sensor with an aptamer-functionalized, gold-nanoparticle (AuNP)-enhanced sandwich assay, the detection of C-reactive protein (CRP) in a buffer solution was achieved with a response of 0.118 nm/nM. Due to the multi-mode polymer waveguide structure and the simple concept, the reported biosensor is well suited for low-cost disposable lab-on-a-chip applications and can be used with rather simple and economic devices. In particular, the sensor offers the potential for fast and multiplexed detection of several biomarkers on a single integrated platform.

Sensitive Readout for Microfluidic High-Throughput Applications using Scanning SQUID Microscopy

Microfluidic chips provide a powerful platform for high-throughput screening of diverse biophysical systems. The most prevalent detection methods are fluorescence based. Developing new readout techniques for microfluidics focusing on quantitative information in the low signal regime is desirable. In this work, we combine the well-established immunoassay approach, with magnetic nanoparticles, with a highly sensitive magnetic imaging technique. We offer to integrate a microfluidic array into a scanning superconducting quantum interference device (SQUID) microscope, to image nanoparticles that were moved through the microfluidic device. We demonstrate the technique on protein-protein interactions (PPI). We compare sensitivity to that of a conventional readout, quantify the amount of interactions, and demonstrate 0.1 atto-mole sensitivity. Our work serves as a proof of concept that will promote the development of a new set of eyes, a stable usable microfluidic-scanning SQUID microscopy.

Sensing Biomolecular Interactions by the Luminescence of a Planar Gold Film

We describe the operating principle and performance of a recently developed surface plasmon-enhanced optical sensor that utilizes two-photon excited luminescence of a planar gold film as the reporter signal. The sensor enables direct visualization of nanoscopic binding events near a sensing surface. Light is coupled to the Au/sample interface in an objective-based Kretschmann configuration to excite surface plasmon polariton (SPP) modes at a metal-dielectric interface. The gold luminescence induced by the confined optical field between the particle and the film is detected in the epi-direction by a far-field camera where individual binding events show up as diffraction limited bright spots against a dark background. We study the sensor's emission spectrum and the distance dependence between the target and substrate, which both suggest that the optical signal of the sensor originates from electron-hole pair excitations in the planar Au film. In addition, we show that the well-behaved pointspread function of the sensor enables a straightforward implementation of super-resolution techniques. Finally, we demonstrate the utility of the sensor for detecting DNA binding events, underlining the sensor's usefulness for label-free imaging of nanoscopic particles and biomolecular interactions.

Performance improvement of plasmonic sensors using a combination of AC electrokinetic effects for (bio)target capture

Analytes concentration techniques are being developed with the appealing expectation to boost the performance of biosensors. One promising method lies in the use of electrokinetic forces. We present hereafter a new design for a microstructured plasmonic sensor which is obtained by conventional microfabrication techniques, and which can easily be adapted on a classical surface plasmon resonance imaging (SPRI) system without further significant modification. Dielectrophoretic trapping and electro-osmotic displacement of the targets in the scanned fluid are performed through interdigitated 200 μm wide gold electrodes that also act as the SPR-sensing substrate. We demonstrate the efficiency of our device's collection capabilities for objects of different sizes (200 nm and 1 μm PS beads, as well as 5-10 μm yeast cells). SPRI is relevant for the spatial analysis of the mass accumulation at the electrode surface. We demonstrate that our device overcomes the diffusion limit encountered in classical SPR sensors thanks to rapid collection capabilities (<1 min) and we show a consequent improvement of the detection limit, by a factor >300. This study of an original device combining SPRI and electrokinetic forces paves the way to the development of fully integrated active plasmonic sensors with direct applications in life sciences, electrochemistry, environmental monitoring and agri-food industry.

Electrochemical Dithiothreitol Assay for Large-Scale Particulate Matter Studies

Particulate matter (PM) air pollution is associated with human morbidity and mortality. Measuring PM oxidative potential has been shown to provide a predictive measurement between PM exposure and adverse health impacts. The dithiothreitol (DTT) assay is commonly used to measure the oxidative potential of PM_2.5 (PM less than 2.5 μm aerodynamic diameter). In the common, kinetic form of this assay, the decay of DTT is quantified over time (indirectly) using 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB, Ellman's reagent) via UV/vis absorbance spectroscopy. The loss of DTT can also be quantified directly using electrochemical detection. The objectives of this work were (1) to evaluate the electrochemical assay, using commercially available equipment, relative to the UV/vis absorbance assay, and (2) to apply the electrochemical method to a large (>100) number of PM_2.5 aerosol filter samples. Also presented here is the comparison an end-point assay to the kinetic assay, in an attempt to reduce the time, labor, and materials neccssary to quantify PM oxidative potential. The end-point, electrochemical assay gave comparable results to the UV/vis absorbance assay for PM filter sample analysis. Finally, high filter mass loadings (higher than about 0.5 μg PM per mm² filter) lead to sub-optimal DTT assay performance, which suggests future studies should limit particle mass loadings on filters.

Discovery of novel elongator protein 2 inhibitors by compound library screening using surface plasmon resonance

Tumour necrosis factor-α (TNF-α) is a pleiotropic cytokine that becomes elevated in chronic inflammatory states, including slowing down osteogenic differentiation, which leads to bone dysplasia in long-term inflammatory microenvironments. The elongator complex plays a role in gene regulation and association with various cellular activities, including the downstream signal transduction of TNF-α in osteogenic cells. To find an inhibitor of Elongator Protein 2 (Elp2), we performed a compound library screen and verified the pharmaceutical effects of candidate compounds on the mouse myoblast cell (C2C12) and mouse osteoblastic cells (MC3T3-E1). The commercial FDA-approved drug (FD) library and the bioactive compound (BC) library were used as candidate libraries. After a label-free, high-throughput affinity measurement with surface plasmon resonance (SPRi), seven kinds of compounds showed binding affinity with mouse Elp2 protein. The seven candidates were then used to perform an inhibition test with TNF-α-induced C2C12 and MC3T3-E1 cell lines. One candidate compound reduced the differentiation suppression caused by TNF-α with resuscitated alkaline phosphatase (ALP) activity, mineralization intensity and expression of osteogenic differentiation marker genes. The results of our study provide a competitive candidate to mitigate the TNF-α-induced osteogenic differentia.

Interferometric Reflectance Imaging Sensor (IRIS) for Molecular Kinetics with a Low-Cost, Disposable Fluidic Cartridge

The determination of kinetic information and appropriate binding pairs is fundamental to the proper optimization and selection of ligands used in immunoassays, diagnostics, and therapeutics. However, the ability to estimate such parameters in a multiplexed and inexpensive format remains difficult and modification of the ligand is often necessary. Here, we detail the methods and materials necessary to evaluate hundreds of unlabeled ligands simultaneously using the interferometric reflectance imaging sensor (IRIS). The incorporation of a low-cost fluidic cartridge that integrates on the top of the sensor simplifies reagent handling considerably.

Molecular architecture for DNA wiring

Detection of the hybridisation events is of great importance in many different biotechnology applications such as diagnosis, computing, molecular bioelectronics, and among others. However, one important drawback is the low current of some redox reporters that limits their application. This paper demonstrates the powerful features of molecular wires, in particular the case of S-[4-[2-[4-(2-Phenylethynyl)phenyl]ethynyl]phenyl] thiol molecule and the key role that play the nanometric design of the capture probe linkers to achieve an efficient couple of the DNA complementary ferrocene label with the molecular wire for an effective electron transfer in co-immobilised self-assembled monolayers (SAMs) for DNA hybridisation detection. In this article, the length of the linker capture probe was studied for electron transfer enhancement from the ferrocene-motifs of immobilised molecules towards the electrode surface to obtain higher kinetics in the presence of thiolated molecular wires. The use of the right couple of capture probe linker and molecular wire has found to be beneficial as it helps to amplify eightfold the signal obtained.

Ultra-sensitive detection by metal nanoparticles-mediated enhanced SPR biosensors

Surface plasmon resonance (SPR), as an optical technique, has widely been used for the detection of biomarkers. Various investigations have been conducted to address the impacts of SPR on the kinetics of biological interactions between the ligand and its cognate bio-element. Up until now, different biofunctionalized metal nanoparticles (NPs) have been used for the ultrasensitive detection of biomarkers in the enhanced SPR. The enhancement of plasmonic properties and refractive index by means of metal NPs in SPR-based biosensors have significantly improved the diagnosis and monitoring of molecular markers in different disesaes including malignancies. In all the enhanced SPR systems utilized for the direct/sandwich assay, each NP is covalently modified with the analyte molecules like antibody (Ab) or a nucleic acid such as DNA/RNA aptamer (Ap) capable of interaction with the related biomarker(s). The increasing of density near the gold surface and plasmonic coupling of gold film and NPs can provide a large shift in the refractive index enhancing the plasmonic resonance because the SPR response unit is sensitive to alteration of the refractive index and the mass shifting onto the chip surface. In this study, we review the potential applications of two major NPs for enhancing the SPR signals for the detection of molecular biomarkers, including gold and magnetic NPs.

Label-free, spatially multiplexed SPR detection of immunoassays on a highly integrated centrifugal Lab-on-a-Disc platform

As a direct, label-free method, Surface Plasmon Resonance (SPR) detection significantly reduces the needs for liquid handling and reagent storage compared to common enzyme-linked immunosorbent assays (ELISAs), thus enabling comprehensive multiplexing of bioassays on microfluidic sample-to-answer systems. This paper describes a highly integrated centrifugal Lab-on-a-Disc (LoaD) platform for automating the full process chain extending between plasma extraction and subsequent aliquoting to five parallelized reaction channels for quantitative SPR detection by an inexpensive smartphone camera. The entire, multi-step / multi-reagent operation completes within less than 1 h. While the emphasis of this work is on the fluidic automation and parallelization by previously introduced, very robust event-triggered valving and buoyancy-driven centripetal pumping schemes, we successfully implement an immunoglobulin G (IgG) assay; by specific functionalization of the detection surfaces, the same disc layout can readily be customised for immunoassays panels from whole blood.

Particle sensing with confined optical field enhanced fluorescence emission (Cofefe)

We describe the development and performance of a new type of optical sensor suitable for registering the binding/dissociation of nanoscopic particles near a gold sensing surface. The method shares similarities with surface plasmon resonance microscopy but uses a completely different optical signature for reading out binding events. This new optical read-out mechanism, which we call confined optical field enhanced fluorescence emission (Cofefe), uses pulsed surface plasmon polariton fields at the gold/liquid interface that give rise to confined optical fields upon binding of the target particle to the gold surface. The confined near-fields are sufficient to induce two-photon absorption in the gold sensor surface near the binding site. Subsequent radiative recombination of the electron-hole pairs in the gold produces fluorescence emission, which can be captured by a camera in the far-field. Bound nanoparticles show up as bright confined spots against a dark background on the camera. We show that the Cofefe sensor is capable of detecting gold and silicon nanoparticles, as well as polymer nanospheres and sub-μm lipid droplets in a label-free manner with average illumination powers of less than 10 μW/μm2.

Cell-Free Approaches in Synthetic Biology Utilizing Microfluidics

Synthetic biology is a rapidly growing multidisciplinary branch of science which aims to mimic complex biological systems by creating similar forms. Constructing an artificial system requires optimization at the gene and protein levels to allow the formation of entire biological pathways. Advances in cell-free synthetic biology have helped in discovering new genes, proteins, and pathways bypassing the complexity of the complex pathway interactions in living cells. Furthermore, this method is cost- and time-effective with access to the cellular protein factory without the membrane boundaries. The freedom of design, full automation, and mimicking of in vivo systems reveal advantages of synthetic biology that can improve the molecular understanding of processes, relevant for life science applications. In parallel, in vitro approaches have enhanced our understanding of the living system. This review highlights the recent evolution of cell-free gene design, proteins, and cells integrated with microfluidic platforms as a promising technology, which has allowed for the transformation of the concept of bioprocesses. Although several challenges remain, the manipulation of biological synthetic machinery in microfluidic devices as suitable 'homes' for in vitro protein synthesis has been proposed as a pioneering approach for the development of new platforms, relevant in biomedical and diagnostic contexts towards even the sensing and monitoring of environmental issues.

Fast Focal Point Correction in Prism-Coupled Total Internal Reflection Scanning Imager Using an Electronically Tunable Lens

Total internal reflection (TIR) is useful for interrogating physical and chemical processes that occur at the interface between two transparent media. Yet prism-coupled TIR imaging microscopes suffer from limited sensing areas due to the fact that the interface (the object plane) is not perpendicular to the optical axis of the microscope. In this paper, we show that an electrically tunable lens can be used to rapidly and reproducibly correct the focal length of an oblique-incidence scanning microscope (OI-RD) in a prism-coupled TIR geometry. We demonstrate the performance of such a correction by acquiring an image of a protein microarray over a scan area of 4 cm² with an effective resolution of less than 20 microns. The electronic focal length tuning eliminates the mechanical movement of the illumination lens in the scanning microscope and in turn the noise and background drift associated with the motion.

Nanoplasmonic sensors for detecting circulating cancer biomarkers

The detection of cancer biomarkers represents an important aspect of cancer diagnosis and prognosis. Recently, the concept of liquid biopsy has been introduced whereby diagnosis and prognosis are performed by means of analyzing biological fluids obtained from patients to detect and quantify circulating cancer biomarkers. Unlike conventional biopsy whereby primary tumor cells are analyzed, liquid biopsy enables the detection of a wide variety of circulating cancer biomarkers, including microRNA (miRNA), circulating tumor DNA (ctDNA), proteins, exosomes and circulating tumor cells (CTCs). Among the various techniques that have been developed to detect circulating cancer biomarkers, nanoplasmonic sensors represent a promising measurement approach due to high sensitivity and specificity as well as ease of instrumentation and operation. In this review, we discuss the relevance and applicability of three different categories of nanoplasmonic sensing techniques, namely surface plasmon resonance (SPR), localized surface plasmon resonance (LSPR) and surface-enhanced Raman scattering (SERS), for the detection of different classes of circulating cancer biomarkers.

Quantitative investigation of the direct interaction between Hemagglutinin and fusion proteins of Peste des petits ruminant virus using surface Plasmon resonance

Background

The specific and dynamic interaction between the hemagglutinin (H) and fusion (F) proteins of morbilliviruses is a prerequisite for the conformational rearrangements and membrane fusion during infection process. The two heptad repeat regions (HRA and HRB) of F protein are both important for the triggering of F protein.

Methods

In this study, the direct interactions of Peste des petits ruminants virus (PPRV) H with F, HRA and HRB were quantitatively evaluated using biosensor surface plasmon resonance (SPR).

Results

The binding affinities of immobilized pCMV-HA-H (HA-H) interacted with proteins pCMV-HA-F (HA-F) and pCMV-HA-HRB (HA-HRB) (K_D = 1.91 × 10^− 8 M and 2.60 × 10^− 7 M, respectively) reacted an order of magnitude more strongly than that of pCMV-HA-HRA (HA-HRA) and pCMV-HA-Tp IGFR-LD (HA) (K_D = 1.08 × 10^− 4 M and 1.43 × 10^− 4 M, respectively).

Conclusions

The differences of the binding affinities suggested that HRB is involved in functionally important intermolecular interaction in the fusion process.

Phase-Sensitive Surface Plasmon Resonance Sensors: Recent Progress and Future Prospects

Surface plasmon resonance (SPR) is an optical sensing technique that is capable of performing real-time, label-free and high-sensitivity monitoring of molecular interactions. SPR biosensors can be divided according to their operating principles into angle-, wavelength-, intensity- and phase-interrogated devices. With their complex optical configurations, phase-interrogated SPR sensors generally provide higher sensitivity and throughput, and have thus recently emerged as prominent biosensing devices. To date, several methods have been developed for SPR phase interrogation, including heterodyne detection, polarimetry, shear interferometry, spatial phase modulation interferometry and temporal phase modulation interferometry. This paper summarizes the fundamentals of phase-sensitive SPR sensing, reviews the available methods for phase interrogation of these sensors, and discusses the future prospects for and trends in the development of this technology.

Surface Plasmon Resonance Sensors on Raman and Fluorescence Spectroscopy

The performance of chemical reactions has been enhanced immensely with surface plasmon resonance (SPR)-based sensors. In this review, the principle and application of SPR sensors are introduced and summarized thoroughly. We introduce the mechanism of the SPR sensors and present a thorough summary about the optical design, including the substrate and excitation modes of the surface plasmons. Additionally, the applications based on SPR sensors are described by the Raman and fluorescence spectroscopy in plasmon-driven surface catalytic reactions and the measurement of refractive index sensing, especially.

Current Trends in Ligand Binding Real-Time Measurement Technologies

Numerous advances in ligand binding assay (LBA) real-time measurement technologies have been made within the last several years, ranging from the development of novel platforms to drive technology expansion to the adaptation of existing platforms to optimize performance and throughput. In this review, we have chosen to focus on technologies that provide increased value to two distinct segments of the LBA community. First, experimentally, by measuring real-time binding events, these technologies provide data that can be used to interrogate receptor/ligand binding interactions. While overall the platforms are not new, they have made significant advances in throughput, multiplexing, and/or sensitivity. Second, clinically, these point-of-care (POC) technologies provide instantaneous information which facilitates rapid treatment decisions.

Label-Free Sensing on Microarrays

Microarrays of biological molecules such as DNAs, proteins, carbohydrates, and small molecules provide a high-throughput platform for screening tens of thousands of biomolecular interactions simultaneously, facilitating the functional characterization of these biomolecules in areas of genomics, proteomics, glycomics, and cytomics. Routinely, analysis of binding reactions between solution-phased probes and surface-immobilized targets involves some kinds of fluorescence-based detection methods. Even though these methods have advantages of high sensitivity and wide dynamic range, labeling probes and/or targets inevitably changes their innate properties and in turn affects probe-target interactions in often uncharacterized ways. Therefore, in recent years, various label-free sensing technologies have been developed for characterizing biomolecular interactions in microarray format. These biosensors, to a certain extent, take the place of fluorescent methods by providing a comparable sensitivity as well as retaining the conformational and functional integrality of biomolecules to be investigated. More importantly, some of these biosensors are capable of real-time monitoring probe-target interactions, providing the binding affinities of these reactions. Using label-free biosensors in microarrays has become a current trend in developing high-throughput screening platforms for drug discoveries and applications in all areas of "-omics." This article is aimed to provide principles and recent developments in label-free sensing technologies applicable to microarrays, with special attentions being paid to surface plasmon resonance microscopy and oblique-incidence reflectivity difference microscopy.

Design and mechanisms of antifouling materials for surface plasmon resonance sensors

Surface plasmon resonance (SPR) biosensors have many possible applications, but are limited by sensor chip surface fouling, which blocks immobilization and specific binding by the recognizer elements. Therefore, there is a pressing need for the development of antifouling surfaces. In this paper, the mechanisms of antifouling materials were firstly discussed, including both theories (hydration and steric hindrance) and factors influencing antifouling effects (molecular structures and self-assembled monolayer (SAM) architectures, surface charges, molecular hydrophilicity, and grafting thickness and density). Then, the most recent advances in antifouling materials applied on SPR biosensors were systematically reviewed, together with the grafting strategies, antifouling capacity, as well as their merits and demerits. These materials included, but not limited to, zwitterionic compounds, polyethylene glycol-based, and polysaccharide-based materials. Finally, the prospective research directions in the development of SPR antifouling materials were discussed.

STATEMENT OF SIGNIFICANCE

Surface plasmon resonance (SPR) is a powerful tool in monitoring biomolecular interactions. The principle of SPR biosensors is the conversion of refractive index change caused by molecular binding into resonant spectral shifts. However, the fouling on the surface of SPR gold chips is ubiquitous and troublesome. It limits the application of SPR biosensors by blocking recognition element immobilization and specific binding. Hence, we write this paper to review the antifouling mechanisms and the recent advances of the design of antifouling materials that can improve the accuracy and sensitivity of SPR biosensors. To our knowledge, this is the first review focusing on the antifouling materials that were applied or had potential to be applied on SPR biosensors.

Microfluidic Surface Plasmon Resonance Sensors: From Principles to Point-of-Care Applications

Surface plasmon resonance (SPR) is a label-free, highly-sensitive, and real-time sensing technique. Conventional SPR sensors, which involve a planar thin gold film, have been widely exploited in biosensing; various miniaturized formats have been devised for portability purposes. Another type of SPR sensor which utilizes localized SPR (LSPR), is based on metal nanostructures with surface plasmon modes at the structural interface. The resonance condition is sensitive to the refractive index change of the local medium. The principles of these two types of SPR sensors are reviewed and their integration with microfluidic platforms is described. Further applications of microfluidic SPR sensors to point-of-care (POC) diagnostics are discussed.

Current Experimental Methods for Characterizing Protein-Protein Interactions

Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.

Current Experimental Methods for Characterizing Protein-Protein Interactions

Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.