Thermodynamic benchmark study using Biacore technology

Novel Approach for Obtaining Variable Domain of New Antigen Receptor with Different Physicochemical Properties from Japanese Topeshark (Hemitriakis japanica)

Diverse candidate antibodies are needed to successfully identify therapeutic and diagnostic applications. The variable domain of IgNAR (VNAR), a shark single-domain antibody, has attracted attention owing to its favorable physicochemical properties. The phage display method used to screen for optimal VNARs loses sequence diversity because of the bias caused by the differential ease of protein expression in Escherichia coli. Here, we investigated a VNAR selection method that combined panning with various selection pressures and next-generation sequencing (NGS) analyses to obtain additional candidates. Drawing inspiration from the physiological conditions of sharks and the physicochemical properties of VNARs, we examined the effects of NaCl and urea concentrations, low temperature, and preheating at the binding step of panning. VNAR phage libraries generated from Japanese topeshark (Hemitriakis japanica) were enriched under these conditions. We then performed NGS analysis and attempted to select clones that were specifically enriched under each panning condition. The identified VNARs exhibited higher reactivity than those obtained by panning without selection pressure. Additionally, they possess physicochemical properties that reflect their respective selection pressures. These results can greatly enhance our understanding of VNAR properties and offer guidance for the screening of high-quality VNAR clones that are present at low frequencies.

Grafting Strategies of Oxidation-Prone Coiled-Coil Peptides for Protein Capture in Bioassays: Impact of Orientation and the Oxidation State

Many biomedical and biosensing applications require functionalization of surfaces with proteins. To this end, the E/K coiled-coil peptide heterodimeric system has been shown to be advantageous. First, Kcoil peptides are covalently grafted onto a given surface. Ecoil-tagged proteins can then be non-covalently captured via a specific interaction with their Kcoil partners. Previously, oriented Kcoil grafting was achieved via thiol coupling, using a unique Kcoil with a terminal cysteine residue. However, cysteine-terminated Kcoil peptides are hard to produce, purify, and oxidize during storage. Indeed, they tend to homodimerize and form disulfide bonds via oxidation of their terminal thiol group, making it impossible to later graft them on thiol-reactive surfaces. Kcoil peptides also contain multiple free amine groups, available for covalent coupling through carbodiimide chemistry. Grafting Kcoil peptides on surfaces via amine coupling would thus guarantee their immobilization regardless of their terminal cysteine's oxidation state, at the expense of the control over their orientation. In this work, we compare Kcoil grafting strategies for the subsequent capture of Ecoil-tagged proteins, for applications such as surface plasmon resonance (SPR) biosensing and cell culture onto protein-decorated substrates. We compare the "classic" thiol coupling of cysteine-terminated Kcoil peptides to the amine coupling of (i) monomeric Kcoil and (ii) dimeric Kcoil-Kcoil linked by a disulfide bond. We have observed that SPR biosensing performances relying on captured Ecoil-tagged proteins were similar for amine-coupled dimeric Kcoil-Kcoil and thiol-coupled Kcoil peptides, at the expense of higher Ecoil-tagged protein consumption. For cell culture applications, Ecoil-tagged growth factors captured on amine-coupled monomeric Kcoil signaled through cell receptors similarly to those captured on thiol-coupled Kcoil peptides. Altogether, while oriented thiol coupling of cysteine-terminated Kcoil peptides remains the most reliable and versatile platform for Ecoil-tagged protein capture, amine coupling of Kcoil peptides, either monomeric or dimerized through a cysteine bond, can offer a good alternative when the challenges and costs associated with the production of monomeric cysteine-tagged Kcoil are too dissuasive for the application.

Recognizing the Less Explored "Active Solid"-"Moving Liquid" Interfaces in Bio/Chemical Sensors

Bio/chemical sensors possess a plethora of advantageous features that have proven to be invaluable tools in detecting and monitoring biomolecules, facilitating advancements in healthcare, environmental monitoring, food safety, and more. However, when it comes to their routine use in continuous fluid flow conditions, an intricate web of solid-liquid interfacial phenomena emerges, which requires a deep understanding of the sensor surface and fluid interations. These interfacial phenomena encompass a broad spectrum of physical, chemical, and biological processes, other than the actual detection, that influence the sensor's response. In this context, perhaps exploring a new theme "active solid"-"moving liquid" interface will unleash the full potential of bio/chemical sensors in any flow-based application.

Multi-temperature experiments to ease analysis of heterogeneous binder solutions by surface plasmon resonance biosensing

Surface Plasmon Resonance (SPR) biosensing is a well-established tool for the investigation of binding kinetics between a soluble species and an immobilized (bio)molecule. While robust and accurate data analysis techniques are readily available for single species, methods to exploit data collected with a solution containing multiple interactants are scarce. In a previous study, our group proposed two data analysis algorithms for (1) the precise and reliable identification of the kinetic parameters of N interactants present at different ratios in N mixtures and (2) the estimation of the composition of a given mixture, assuming that the kinetic parameters and the total concentration of all interactants are known. Here, we extend the first algorithm by reducing the number of necessary mixtures. This is achieved by conducting experiments at different temperatures. Through the Van't Hoff and Eyring equations, identifying the kinetic and thermodynamic parameters of N binders becomes possible with M mixtures with M comprised between 2 and N and at least N/M temperatures. The second algorithm is improved by adding the total analyte concentration as a supplementary variable to be identified in an optimization routine. We validated our analysis framework experimentally with a system consisting of mixtures of low molecular weight drugs, each competing to bind to an immobilized protein. We believe that the analysis of mixtures and composition estimation could pave the way for SPR biosensing to become a bioprocess monitoring tool, on top of expanding its already substantial role in drug discovery and development.

The feasibility of determining kinetic constants from isothermal titration calorimetry data

Isothermal titration calorimetry (ITC) has long been established as an excellent means to determine the thermodynamic parameters of biomolecular interactions. More recently, efforts have focused on exploiting the power/time trace (the "thermogram") resulting from ITC experiments to glean kinetic association and dissociation rates for these interactions. The ability to do so rests on the ability of algorithms to simulate with high accuracy the output of the calorimeter. Thus, several critical factors must be taken into account: the injection protocol, the kinetics of the interaction, accurate discovery of the instrumental response to heat signals, and the addition of unrelated signals. All of these aspects of extracting kinetic constants from thermograms have been considered and addressed in the current work. To validate the resultant methods, we performed several ITC experiments, titrating small-molecule inhibitors into solutions of bovine carbonic anhydrase II or titrating lysozyme into solutions of anti-lysozyme nanobodies. We found that our methods could arrive at kinetic constants that were close to the known values for these interactions taken from other methods. Finally, the effort to improve ITC kinetic characterizations uncovered a set of best practices for both the calorimetric experiment and the subsequent analyses (termed "kinetically optimized ITC" or "KO-ITC") that is detailed in this work.

Determination of the composition of heterogeneous binder solutions by surface plasmon resonance biosensing

Surface plasmon resonance-based biosensors have been extensively applied to the characterization of the binding kinetics between purified (bio)molecules, thanks to robust data analysis techniques. However, data analysis for solutions containing multiple interactants is still at its infancy. We here present two algorithms for (1) the reliable and accurate determination of the kinetic parameters of N interactants present at different ratios in N mixtures and (2) the estimation of the ratios of each interactant in a given mixture, assuming that their kinetic parameters are known. Both algorithms assume that the interactants compete to bind to an immobilized ligand in a 1:1 fashion and necessitate prior knowledge of the total concentration of all interactants combined. The effectiveness of these two algorithms was experimentally validated with a model system corresponding to mixtures of four small molecular weight drugs binding to an immobilized protein. This approach enables the in-depth characterization of mixtures using SPR, which may be of considerable interest for many drug discovery or development applications, notably for protein glycovariant analysis.

Simultaneous determination of thermodynamic and kinetic data by isothermal titration calorimetry

BACKGROUND

Thermodynamic and binding kinetic data increasingly support and guide the drug optimization process.

METHODS

Because ITC thermograms contain binding thermodynamic and kinetic information, an efficient protocol for the simultaneous extraction of thermodynamic and kinetic data for 1:1 protein ligand reactions from AFFINImeter kinITC in one single experiment are presented.

RESULTS

The effort to apply this protocol requires the same time as for the standard protocol but increases the precision of both thermodynamic and kinetic data.

CONCLUSIONS

The protocol enables reliable extraction of both thermodynamic and kinetic data for 1:1 protein-ligand binding reactions with improved precision compared to the 'standard protocol'.

GENERAL SIGNIFICANCE

Thermodynamic and kinetic data are recorded under exactly the same conditions in solution without any labeling or immobilization from a protein sample that is not 100% active and would otherwise render the extraction of kinetic parameters impossible.

Direct Comparison of Label-Free Biosensor Binding Kinetics Obtained on the Biacore 8K and the Carterra LSA

Funding pressure on the pharmaceutical industry to deliver new medicines to the market under aggressive timelines has led to a demand for analytical tools with higher detection sensitivity, increased throughput, and automation to speed up research and discovery efforts and converge upon clinically fit leads faster. In the quest for therapeutic antibodies, the early adoption of interaction analysis platforms utilizing surface plasmon resonance (SPR) detection provides insightful molecular-level information about the binding properties of antibody libraries that are key to understanding an antibody's mechanism of action and can guide the library-to-leads triage. Here, we sought to compare the binding kinetics obtained on two state-of-the-art high-throughput SPR platforms in an independent study conducted by unrelated groups located on different continents. We show that when experiments were performed by skilled users adhering to SPR best practices and allowed freedom in their assay design, the two platforms yielded near-identical results, establishing them both as reliable tools in accelerating the characterization of antibody libraries in providing critical information needed to advance leads to the clinic.

Role of Hydrophobicity and Charge of Amyloid-Beta Oligomer Eliminating d-Peptides in the Interaction with Amyloid-Beta Monomers

Inhibition of the self-assembly process of amyloid-beta and even more the removal of already existing toxic amyloid-beta assemblies represent promising therapeutic strategies against Alzheimer's disease. To approach this aim, we selected a d-enantiomeric peptide by phage-display based on the interaction with amyloid-beta monomers. This lead compound was successfully optimized by peptide microarrays with respect to its affinity and specificity to the target resulting in d-peptides with both increased hydrophobicity and net charge. Here, we present a detailed biophysical characterization of the interactions between these optimized d-peptides and amyloid-beta monomers in comparison to the original lead compound in order to obtain a more thorough understanding of the physicochemical determinants of the interactions. Kinetics and apparent stoichiometry of complex formation were studied using surface plasmon resonance. Potential modes of binding to amyloid-beta were identified, and the influences of ionic strength on complex stability, as well as on the inhibitory effect on amyloid-beta aggregation were investigated. The results reveal a very different mode of interaction of the optimized d-peptides based on a combination of electrostatic and hydrophobic interactions as compared to the mostly electrostatically driven interaction of the lead compound. These conclusions were supported by the thermodynamic profiles of the interaction between optimized d-peptides and Aβ monomers, which indicate an increase in binding entropy with respect to the lead compound.

Applications of NMR and ITC for the Study of the Kinetics of Carbohydrate Binding by AMPK β-Subunit Carbohydrate-Binding Modules

Understanding the kinetics of proteins interacting with their ligands is important for characterizing molecular mechanism. However, it can be difficult to determine the extent and nature of these interactions for weakly formed protein-ligand complexes that have lifetimes of micro- to milliseconds. Nuclear magnetic resonance (NMR) spectroscopy is a powerful solution-based method for the atomic-level analysis of molecular interactions on a wide range of timescales, including micro- to milliseconds. Recently the combination of thermodynamic experiments using isothermal titration calorimetry (ITC) with kinetic measurements using ZZ-exchange and CPMG relaxation dispersion NMR spectroscopy have been used to determine the kinetics of weakly interacting protein systems. This chapter describes the application of ITC and NMR to understand the differences in the kinetics of carbohydrate binding by the β1- and β2-carbohydrate-binding modules of AMP-activated protein kinase.

Rapid screening of IgG quality attributes - effects on Fc receptor binding

The interactions of therapeutic antibodies with fragment crystallizable γ (Fcγ) receptors and neonatal Fc receptors (FcRn) are measured in vitro as indicators of antibody functional performance. Antibodies are anchored to immune cells through the Fc tail, and these interactions are important for the efficacy and safety of therapeutic antibodies. High‐throughput binding studies on each of the human Fcγ receptor classes (FcγRI, FcγRIIa, FcγRIIb, FcγRIIIa, and FcγRIIIb) as well as FcRn have been developed and performed with human IgG after stress‐induced modifications to identify potential impact in vivo. Interestingly, we found that asparagine deamidation (D‐N) reduced the binding of IgG to the low‐affinity Fcγ receptors (FcγRIIa, FcγRIIb, FcγRIIIa, and FcγRIIIb), while FcγRI and FcRn binding was not impacted. Deglycosylation completely inhibited binding to all Fcγ receptors, but showed no impact on binding to FcRn. On the other hand, afucosylation only impacted binding to FcγRIIIa and FcγRIIIb. Methionine oxidation at levels below 7%, multiple freeze/thaw cycles and short‐term thermal/shake stress did not influence binding to any of the Fc receptors. The presence of high molecular weight species, or aggregates, disturbed measurements in these binding assays; up to 5% of aggregates in IgG samples changed the binding and kinetics to each of the Fc receptors. Overall, the screening assays described in this manuscript prove that rapid and multiplexed binding assays may be a valuable tool for lead optimization, process development, in‐process controls, and biosimilarity assessment of IgGs during development and manufacturing of therapeutic IgGs.

Measuring Rapid Time-Scale Reaction Kinetics Using Isothermal Titration Calorimetry

Isothermal titration calorimetry (ITC) is a powerful tool for acquiring both thermodynamic and kinetic data for biological interactions including molecular recognition and enzymatic catalysis. ITC-based kinetics measurements typically focus on reactions taking place over long time scales (tens of minutes or hours) in order to avoid complications due to the finite length of time needed detect heat flow in the calorimeter cell. While progress has been made toward analyzing more rapid reaction kinetics by ITC, the capabilities and limitations of this approach have not been thoroughly tested to date. Here, we report that the time resolution of commercial instruments is on the order of 0.2 s or less. We successfully performed rapid ITC kinetics assays with durations of just tens of seconds using the enzyme trypsin. This is substantially shorter than previous ITC enzyme measurements. However, we noticed that for short reaction durations, standard assumptions regarding the ITC instrument response led to significant deviations between calculated and measured ITC peak shapes. To address this issue, we developed an ITC empirical response model (ITC-ERM) that quantitatively reproduces ITC peak shapes for all reaction durations. Applying the ITC-ERM approach to another enzyme (prolyl oligopeptidase), we unexpectedly discovered non-Michaelis-Menten kinetics in short time-scale measurements that are absent in more typical long time-scale experiments and are obscured in short time-scale experiments when standard assumptions regarding the instrument response are made. This highlights the potential of ITC measurements of rapid time scale kinetics in conjunction with the ITC-ERM approach to shed new light on biological dynamics.

Thermo-kinetic analysis space expansion for cyclophilin-ligand interactions - identification of a new nonpeptide inhibitor using Biacore™ T200

We have established a refined methodology for generating surface plasmon resonance sensor surfaces of recombinant his‐tagged human cyclophilin‐A. Our orientation‐specific stabilisation approach captures his‐tagged protein under ‘physiological conditions’ (150 mm NaCl, pH 7.5) and covalently stabilises it on Ni²⁺‐nitrilotriacetic acid surfaces, very briefly activated for primary amine‐coupling reactions, producing very stable and active surfaces (≥ 95% specific activity) of cyclophilin‐A. Variation in protein concentration with the same contact time allows straightforward generation of variable density surfaces, with essentially no loss of activity, making the protocol easily adaptable for studying numerous interactions; from very small fragments, ~ 100 Da, to large protein ligands. This new method results in an increased stability and activity of the immobilised protein and allowed us to expand the thermo‐kinetic analysis space, and to determine accurate and robust thermodynamic parameters for the cyclophilin‐A–cyclosporin‐A interaction. Furthermore, the increased sensitivity of the surface allowed identification of a new nonpeptide inhibitor of cyclophilin‐A, from a screen of a fragment library. This fragment, 2,3‐diaminopyridine, bound specifically with a mean affinity of 248 ± 60 μm. The X‐ray structure of this 109‐Da fragment bound in the active site of cyclophilin‐A was solved to a resolution of 1.25 Å (PDB: 5LUD), providing new insight into the molecular details for a potential new series of nonpeptide cyclophilin‐A inhibitors.

Measuring Protein-Protein Interactions Using Biacore

The use of optical biosensors for studying macromolecular interactions is gaining increasing popularity. In one study, 1514 papers that involved the application of biosensor data were identified for the year 2009 alone (Rich and Myszka, J Mol Recognit 24:892-914, 2011), the sheer volume and variety of which present a daunting task for the burgeoning biosensor user to accumulate and decipher. This chapter is designed to provide the reader with the tools necessary to prepare, design, and efficiently execute a kinetic experiment on Biacore. It is written to guide the Biacore user through basic theory, system maintenance, and assay setup while also offering some practical tips that we find useful for Biacore-based studies. Many kinetic-based screening assays require rigorous sample preparation and purification prior to analysis. To highlight these procedures, this protocol describes the kinetic characterization of single chain Fv (scFv) antibody fragments from crude bacterial lysates using an antibody affinity capture approach. Even though we specifically describe the capture of HA-tagged scFv antibody fragments to an anti-HA tag monoclonal antibody-immobilized surface prior to kinetic analysis, the same methodologies are universally applicable and can be used for practically any affinity pair and most Biacore systems.

A Perspective on the Kinetics of Covalent and Irreversible Inhibition

The clinical and commercial success of covalent drugs has prompted a renewed and more deliberate pursuit of covalent and irreversible mechanisms within drug discovery. A covalent mechanism can produce potent inhibition in a biochemical, cellular, or in vivo setting. In many cases, teams choose to focus on the consequences of the covalent event, defined by an IC₅₀ value. In a biochemical assay, the IC₅₀ may simply reflect the target protein concentration in the assay. What has received less attention is the importance of the rate of covalent modification, defined by k_inact/K_I. The k_inact/K_I is a rate constant describing the efficiency of covalent bond formation resulting from the potency (K_I) of the first reversible binding event and the maximum potential rate (k_inact) of inactivation. In this perspective, it is proposed that the k_inact/K_I should be employed as a critical parameter to identify covalent inhibitors, interpret structure-activity relationships (SARs), translate activity from biochemical assays to the cell, and more accurately define selectivity. It is also proposed that a physiologically relevant k_inact/K_I and an (unbound) AUC generated from a pharmacokinetic profile reflecting direct exposure of the inhibitor to the target protein are two critical determinants of in vivo covalent occupancy. A simple equation is presented to define this relationship and improve the interpretation of covalent and irreversible kinetics.

Enthalpy screen of drug candidates

The enthalpic and entropic contributions to the binding affinity of drug candidates have been acknowledged to be important determinants of the quality of a drug molecule. These quantities, usually summarized in the thermodynamic signature, provide a rapid assessment of the forces that drive the binding of a ligand. Having access to the thermodynamic signature in the early stages of the drug discovery process will provide critical information towards the selection of the best drug candidates for development. In this paper, the Enthalpy Screen technique is presented. The enthalpy screen allows fast and accurate determination of the binding enthalpy for hundreds of ligands. As such, it appears to be ideally suited to aid in the ranking of the hundreds of hits that are usually identified after standard high throughput screening.

Optimizing Multiple Analyte Injections in Surface Plasmon Resonance Biosensors with Analytes having Different Refractive Index Increments

Surface plasmon resonance-based biosensors have been successfully applied to the study of the interactions between macromolecules and small molecular weight compounds. In an effort to increase the throughput of these SPR-based experiments, we have already proposed to inject multiple compounds simultaneously over the same surface. When specifically applied to small molecular weight compounds, such a strategy would however require prior knowledge of the refractive index increment of each compound in order to correctly interpret the recorded signal. An additional experiment is typically required to obtain this information. In this manuscript, we show that through the introduction of an additional global parameter corresponding to the ratio of the saturating signals associated with each molecule, the kinetic parameters could be identified with similar confidence intervals without any other experimentation.

Compact multi-channel surface plasmon resonance sensor for real-time multi-analyte biosensing

A compact multi-channel surface plasmon resonance (SPR) biosensor is demonstrated based on a tablet as the measurement platform. The SPR biosensor employs a bundle of fiber-optic SPR sensors as the multiplexed sensing elements that are illuminated by a light-emitting diode (LED) plane light source and detected by a cordless camera. The multi-channel SPR biosensor was based on optical fiber components for precise, label-free and high-throughput detection without the use of complex, specialized or fragile instrumentation that would require optical calibration. The reference and control channels compensated for the fluctuation of the LED light source and the bulk refractive index, increasing the accuracy and reliability of the biosensor. The multi-channel SPR biosensor was applied for multi-analyte biosensing of immunoglobulin G (IgG) and concanavalin A (Con A). The channels functionalized with staphylococcal protein A (SPA) and ribonuclease B (RNase B) only showed relative intensity responses to their corresponding analytes. Moreover, the multi-channel SPR sensors responded to the specific detection of IgG and Con A with an approximately linear relative intensity response to the analyte concentration. Hence, multiple analytes were simultaneously and quantitatively detected with the multi-channel SPR biosensor. This compact, cost-effective multi-channel SPR biosensor is adapted for point-of-care tests, which are important in healthcare and environmental monitoring and for biomolecular interaction analysis.

Identification of two-step chemical mechanisms using small temperature oscillations and a single tagged species

In order to identify two-step chemical mechanisms, we propose a method based on a small temperature modulation and on the analysis of the concentration oscillations of a single tagged species involved in the first step. The thermokinetic parameters of the first reaction step are first determined. Then, we build test functions that are constant only if the chemical system actually possesses some assumed two-step mechanism. Next, if the test functions plotted using experimental data are actually even, the mechanism is attributed and the obtained constant values provide the rate constants and enthalpy of reaction of the second step. The advantage of the protocol is to use the first step as a probe reaction to reveal the dynamics of the second step, which can hence be relieved of any tagging. The protocol is anticipated to apply to many mechanisms of biological relevance. As far as ligand binding is considered, our approach can address receptor conformational changes or dimerization as well as competition with or modulation by a second partner. The method can also be used to screen libraries of untagged compounds, relying on a tracer whose concentration can be spectroscopically monitored.

Computational prediction and experimental validation of low-affinity target of triptolide and its analogues

ERα as a novel low affinity target for triptolide and its analogues triptonide and triptriolide.

On-line kinetic model discrimination for optimized surface plasmon resonance experiments

In order to improve the throughput of surface plasmon resonance-based biosensors, an on-line iterative optimization algorithm has been presented aiming at reducing experimental time and material consumption without any loss of confidence on kinetic parameters [De Crescenzo (2008) J. Mol Recognit., 21, 256-66.]. This algorithm was based on a simple Langmuirian model to compute the confidence and predict optimal injections. However, this kinetic model is not suitable for all interactions, as it does not include mass transfer limitation that may occur for fast interaction kinetics. If a simple model was to be used when this phenomenon influenced the interactions, kinetic parameters would be biased. On the other hand, we show in this paper that data analysis with a kinetic model including a mass transfer limitation step would lead to longer experiments and poorer confidence if the interactions were simple. So, in this manuscript, we present an on-line model discrimination and optimization approach to increase the throughput of surface plasmon resonance biosensors.

Fragment screening by SPR and advanced application to GPCRs

Surface plasmon resonance (SPR) is one of the primary biophysical methods for the screening of low molecular weight 'fragment' libraries, due to its low protein consumption and 'label-free' methodology. SPR biosensor interaction analysis is employed to both screen and confirm the binding of compounds in fragment screening experiments, as it provides accurate information on the affinity and kinetics of molecular interactions. The most advanced application of the use of SPR for fragment screening is against membrane protein drug targets, such G-protein coupled receptors (GPCRs). Biophysical GPCR assays using SPR have been validated with pharmacological measurements approximate to cell-based methods, yet provide the advantage of biophysical methods in their ability to measure the weak affinities of low molecular weight fragments. A number of SPR fragment screens against GPCRs have now been disclosed in the literature. SPR fragment screening is proving versatile to screen both thermostabilised GPCRs and solubilised wild type receptors. In this chapter, we discuss the state-of-the-art in GPCR fragment screening by SPR and the technical considerations in performing such experiments.

Label-free characterization of carbonic anhydrase-novel inhibitor interactions using surface plasmon resonance, isothermal titration calorimetry and fluorescence-based thermal shift assays

This work describes the development of biophysical unbiased methods to study the interactions between new designed compounds and carbonic anhydrase II (CAII) enzyme. These methods have to permit both a screening of a series of sulfonamide derivatives and the identification of a lead compound after a thorough study of the most promising molecules. Interactions data were collected using surface plasmon resonance (SPR) and thermal shift assay (TSA). In the first step, experiments were performed with bovine CAII isoform and were extended to human CAII. Isothermal titration calorimetry (ITC) experiments were also conducted to obtain thermodynamics parameters necessary for the processing of the TSA data. Results obtained with this reference methodology demonstrate the effectiveness of SPR and TSA. KD values obtained from SPR data were in perfect accordance with ITC. For TSA, despite the fact that the absolute values of KD were quite different, the same affinity scale was obtained for all compounds. The binding affinities of the analytes studied vary by more than 50 orders of magnitude; for example, the KD value determined by SPR were 6 ± 4 and 299 ± 25 nM for compounds 1 and 3, respectively. This paper discusses some of the theoretical and experimental aspects of the affinity-based methods and evaluates the protein consumption to develop methods for the screening of further new compounds. The double interest of SPR, that is, for screening and for the quick thorough study of the interactions parameters (ka , kd , and KD ), leads us to choose this methodology for the study of new potential inhibitors.

Applications of SPR for the characterization of molecules important in the pathogenesis and treatment of neurodegenerative diseases

Characterization of binding kinetics and affinity between a potential drug and its receptor are key steps in the development of new drugs. Among the techniques available to determine binding affinities, surface plasmon resonance has emerged as the gold standard because it can measure binding and dissociation rates in real-time in a label-free fashion. Surface plasmon resonance is now finding applications in the characterization of molecules for treatment of neurodegenerative diseases, characterization of molecules associated with pathogenesis of neurodegenerative diseases and detection of neurodegenerative disease biomarkers. In addition it has been used in the characterization of a new class of natural autoantibodies that have therapeutic potential in a number of neurologic diseases. In this review we will introduce surface plasmon resonance and describe some applications of the technique that pertain to neurodegenerative disorders and their treatment.

Surface plasmon resonance using the catalytic domain of soluble guanylate cyclase allows the detection of enzyme activators

Soluble Guanylate Cyclase (sGC) is the receptor for the signalling agent nitric oxide (NO) and catalyses the production of the second messenger cyclic guanosine monophosphate (cGMP) from guanosine triphosphate (GTP). The enzyme is an attractive drug target for small molecules that act in the cardiovascular and pulmonary systems, and has also shown to be a potential target in neurological disorders. We have discovered that 5-(indazol-3-yl)-1,2,4-oxadiazoles activate the enzyme in the absence of added NO and shown they bind to the catalytic domain of the enzyme after development of a surface plasmon resonance assay that allows the biophysical detection of intrinsic binding of ligands to the full length sGC and to a construct of the catalytic domain.

Bridging the past and the future of virology: surface plasmon resonance as a powerful tool to investigate virus/host interactions

Despite decades of antiviral drug research and development, viruses still remain a top global healthcare problem. Compared to eukaryotic cells, viruses are composed by a limited numbers of proteins that, nevertheless, set up multiple interactions with cellular components, allowing the virus to take control of the infected cell. Each virus/host interaction can be considered as a therapeutical target for new antiviral drugs but, unfortunately, the systematic study of a so huge number of interactions is time-consuming and expensive, calling for models overcoming these drawbacks. Surface plasmon resonance (SPR) is a label-free optical technique to study biomolecular interactions in real time by detecting reflected light from a prism-gold film interface. Launched 20 years ago, SPR has become a nearly irreplaceable technology for the study of biomolecular interactions. Accordingly, SPR is increasingly used in the field of virology, spanning from the study of biological interactions to the identification of putative antiviral drugs. From the literature available, SPR emerges as an ideal link between conventional biological experimentation and system biology studies functional to the identification of highly connected viral or host proteins that act as nodal points in virus life cycle and thus considerable as therapeutical targets for the development of innovative antiviral strategies.

Real-time Recognition of Mycobacterium tuberculosis and Lipoarabinomannan using the Quartz Crystal Microbalance

A quartz crystal microbalance (QCM) immunosensor has been successfully employed to screen for both whole Mycobacteria tuberculosis (Mtb) bacilli and a Mtb surface antigen, lipoarabinomannan (LAM). One of the most abundant components of the Mtb cell surface, LAM, may be detected without the presence of the entire bacterium. Using available antibodies with proven utility in enzyme-linked immunoassays (ELISAs), a sensor was designed to measure Mtb bacilli and LAM. Equilibrium association constants (K(a)) were determined for the interaction of Mtb with immobilized α-LAM and anti-H37Rv antibodies, where avidity was seen to strengthen this interaction and provide for greater binding than might have otherwise been achieved. The binding of LAM to immobilized α-LAM had a high associate rate constant (k(a)) allowing for rapid detection. Evaluating these binding constants helped the compare the sensitivity of these immunosensors to conventional ELISAs. The use of these assays with the better antibodies may allow for immunosensor use in determining LAM as a point-of-care (POC) diagnostic for Mtb.

Increasing throughput of surface plasmon resonance-based biosensors by multiple analyte injections

Surface plasmon resonance-based biosensors are now acknowledged as robust and reliable instruments to determine the kinetic parameters related to the interactions between biomolecules. These kinetic parameters are used in screening campaigns: there is a considerable interest in reducing the experimental time, thus improving the throughput of the surface plasmon resonance assays. Kinetic parameters are typically obtained by analyzing data from several injections of a given analyte at different concentrations over a surface where its binding partner has been immobilized. It has been already proven that an iterative optimization approach aiming at determining optimal analyte injections to be performed online can significantly reduce the experimentation time devoted to kinetic parameter determination, without any detrimental effect on their standard errors. In this study, we explore the potential of this iterative optimization approach to further reduce experiment duration by combining it with the simultaneous injection of two analytes.

Overcoming antibody expression and screening limitations by smart design: applications to PSA immunoassay development

Improving the functional and structural properties of target proteins can often be a challenge for researchers. This paper highlights the importance of antibody construct on screening performance, and ultimately, the clone that is selected. We report the reformatting of phage-selected single chain antibody variable region fragments (scFvs) into single chain antibody fragments (scAbs) for improved screening and binding studies. The generation of a scAb, which had a fused human kappa light chain constant domain (C(k)), was shown to significantly improve expression levels in Escherichia coli. Antibody expression levels were compared between the two antibody constructs (scFv and scAb) by ELISA and a 100-fold improvement was observed. The C(k) domain in the expressed scAb also facilitated high throughput analysis by a Biacore capture assay approach. Individual functional scAbs were ranked on the basis of their remaining binding percentage after 5 min dissociation. Selected antibodies were further characterised by kinetic analysis and a sandwich-based immunoassay developed. The scAb construct enhanced expression levels significantly, facilitating antibody screening and immunoassay development for prostate-specific antigen (PSA), a marker for prostate cancer.

Emerging role of surface plasmon resonance in fragment-based drug discovery

Surface plasmon resonance (SPR) offers a method of biophysical fragment screening that is fast, efficient, cost effective and accurate. SPR is increasingly being adopted as a secondary assay to validate fragment hits. Recently, technical advances have resulted in the emergence of SPR as a primary screening methodology for fragment-based drug discovery. Moreover, SPR biosensor assays can be developed for a wide range of proteins, including membrane proteins, such as G-protein-coupled receptors. In this review, we discuss the advantages and limitations of SPR fragment screening including experimental consideration of reducing false positive and false negative rates to a minimum. We discuss how ligand efficiency can be used both as a method to eliminate false positives and to understand which fragments in a library may be a source of false negatives.

Label-free detection of protein binding with multisine SPR microchips

Label-free techniques such as surface plasmon resonance (SPR) have used a step-response excitation method to characterize the binding of two biochemical entities. A major drawback of the step response technique is its high susceptibility to thermal drifts and noise which directly determine the minimum detectable binding mass. In this paper we present a new frequency-domain method based on the use of multisine chemical excitation that is much less sensitive to these disturbances. The multisine method was implemented in a PDMS microfluidic chip using a dual channel, dual multiplug chemical signal generator connected to functionalized and reference SPR binding spots. Kinetic constants for the reaction are extracted from the characteristics of the sense spot response versus frequency. The feasibility of the technique was tested using a model system of Carbonic Anhydrase-II analyte and amino-benzenesulfonamide ligand. The experimental signal to noise ratio (SNR) for the multisine measurement is about 32 dB; 7 dB higher than that observed with the single step-response method, while the overall measurement time is twice as long as the step method.

Estimation of analyte concentration by surface plasmon resonance-based biosensing using parameter identification techniques

Surface plasmon resonance-based biosensors have been applied to the determination of macromolecule concentration. Up to now, the proposed experimental approaches have relied either on the generation of a calibration curve that exploits only a few data points from each sensorgram or on multiple injections of the unknown sample at various flow rates. In this article, we show that prior knowledge of the kinetic parameters related to the interaction of the species with a given partner could advantageously reduce the number of injections required by both aforementioned methods, thereby reducing experimental time while maintaining a good level of confidence on the determined concentrations.

Biosensor-Based Approach to the Identification of Protein Kinase Ligands with Dual-Site Modes of Action

The authors have used a surface plasmon resonance (SPR)–based biosensor approach to identify and characterize compounds with a unique binding mode to protein kinases. Biacore was used to characterize hits from an enzymatic high-throughput screen of the Tec family tyrosine kinase, IL2-inducible T cell kinase (ITK). Complex binding kinetics was observed for some compounds, which led to identification of compounds that bound simultaneously at both the adenosine triphosphate (ATP) binding site and a second, allosteric site on ITK. The presence of the second binding site was confirmed by X-ray crystallography. The second site is located in the N-terminal lobe of the protein kinase catalytic domain, adjacent to but distinct from the ATP site. To enable rapid optimization of binding properties, a competition-based Biacore assay has been developed to successfully identify second site noncompetitive binders that have been confirmed by X-ray crystallographic studies. The authors have found that SPR technology is a key method for rapid identification of compounds with dual-site modes of action.

Measuring protein-protein interactions using Biacore

The use of optical biosensors for studying macromolecular interactions is gaining increasing popularity. In one study, 1,179 papers that involved the application of biosensor data were identified for the year 2007 alone (Rich and Myszka, J Mol Recognit 21:355-400, 2008), the sheer volume and variety of which present a daunting task for the burgeoning biosensor user to accumulate and decipher. This chapter is designed to provide the reader with the tools necessary to prepare, design, and efficiently execute a kinetic experiment on Biacore. It is written to guide the Biacore user through basic theory, system maintenance, and assay set-up while also offering some practical tips that we find useful for Biacore-based studies. Many kinetic-based screening assays require rigorous sample preparation and purification prior to analysis. To highlight these procedures, this protocol describes the kinetic characterisation of single chain Fv (scFv) antibody fragments from crude bacterial lysates using an antibody affinity capture approach. Even though we specifically describe the capture of HA-tagged scFv antibody fragments to an anti-HA tag monoclonal antibody-immobilised surface prior to kinetic analysis, the same methodologies are universally applicable and can be used for practically any affinity pair and most Biacore systems.

HTS reporter displacement assay for fragment screening and fragment evolution toward leads with optimized binding kinetics, binding selectivity, and thermodynamic signature

Parameters such as residence time, kinetic selectivity, and thermodynamic signature are more and more under debate as optimization objectives within fragment-based lead discovery. However, broad implementation of these parameters is hampered by the lack of technologies that give rapid access to binding kinetics and thermodynamic information for large amounts of compound-target interactions. Here, the authors describe a technology--the reporter displacement assay--that is capable of opening this bottleneck and of supporting data-driven design of lead compounds with tailor-made residence time, kinetic selectivity, and thermodynamic signature.

Low noise detection of biomolecular interactions with signal-locking surface plasmon resonance

Surface plasmon resonance (SPR) is a popular technique for label-free detection of biomolecular interactions at a surface. SPR yields quantitative kinetic association and dissociation constants of surface interactions such as the binding of two molecular species, one present in the liquid phase and the other immobilized at the surface. Current state-of-the-art SPR systems extract kinetic constants from measurements of the step response of the interaction versus time. The step response measurement is subject to the influence of noise and drift disturbances that limit its minimum-detectable mass changes. This paper presents a new SPR technique that measures the biomolecular interaction not in time but over a very narrow frequency range under periodic excitation. The measured response is, thus, locked to a very specific narrow band signal. This narrow band spectral sensing scheme has a very high degree of rejection to uncorrelated spurious signals. The signal-locked SPR technique was implemented using a chemical modulator chip connected to a set of functionalized Au sensing sites downstream. Binding experiments for a model system of carbonic anhydrase-II (CA-II) analyte and immobilized 4-(2-aminoethyl)benzenesulfonamide (ABS) ligand display a 100-fold (20 dB) improvement in the measured signal-to-noise ratio (SNR) when using the new technique compared to the SNR achieved using the conventional step response method.

Biophysical characterization of recombinant proteins: a key to higher structural genomics success

Hundreds of genomes have been successfully sequenced to date, and the data are publicly available. At the same time, the advances in large-scale expression and purification of recombinant proteins have paved the way for structural genomics efforts. Frequently, however, little is known about newly expressed proteins calling for large-scale protein characterization to better understand their biochemical roles and to enable structure-function relationship studies. In the Structural Genomics Consortium (SGC), we have established a platform to characterize large numbers of purified proteins. This includes screening for ligands, enzyme assays, peptide arrays and peptide displacement in a 384-well format. In this review, we describe this platform in more detail and report on how our approach significantly increases the success rate for structure determination. Coupled with high-resolution X-ray crystallography and structure-guided methods, this platform can also be used toward the development of chemical probes through screening families of proteins against a variety of chemical series and focused chemical libraries.