Implementing surface plasmon resonance biosensors in drug discovery

Advancing Sensitivity in Guided-Wave Surface Plasmon Resonance Sensor through Integration of 2D BlueP/MoS2 Hybrid Layers

The surface plasmon resonance (SPR) signal, generated from the Kretschmann configuration, has been developed as an effective detection technology in chemical and biological sensors. The sensitivity of SPR signals to changes in the surrounding media makes it a valuable tool, as even a slight variation in refractive index can cause a significant change in SPR signals, such as phase, intensity, and resonance angle. However, the detection of ultralow changes in refractive index, which occur in chemical reactions or biological actions, remains a challenge for conventional SPR sensors due to their limited sensitivity. To overcome this limitation, we theoretically propose a novel guided-wave SPR (GWSPR) configuration coated with a few-layer blue phosphorene (blueP)/MoS2 hybrid structure. This configuration aims to enhance the electric field and subsequently achieve a significant improvement in sensitivity. The results of our study demonstrate that the proposed blueP/MoS2-based GWSPR sensor exhibits a high sensitivity of 290°/RIU, which represents an impressive enhancement of approximately 82.4% compared to the conventional Au-based SPR sensor. This advancement addresses the challenge of detecting ultralow changes in refractive index and offers significant potential for enhancing the performance of chemical and biological sensors.

Design, Synthesis, and Pharmacological Evaluation of Second-Generation Soluble Adenylyl Cyclase (sAC, ADCY10) Inhibitors with Slow Dissociation Rates

Soluble adenylyl cyclase (sAC: ADCY10) is an enzyme involved in intracellular signaling. Inhibition of sAC has potential therapeutic utility in a number of areas. For example, sAC is integral to successful male fertility: sAC activation is required for sperm motility and ability to undergo the acrosome reaction, two processes central to oocyte fertilization. Pharmacologic evaluation of existing sAC inhibitors for utility as on-demand, nonhormonal male contraceptives suggested that both high intrinsic potency, fast on and slow dissociation rates are essential design elements for successful male contraceptive applications. During the course of the medicinal chemistry campaign described here, we identified sAC inhibitors that fulfill these criteria and are suitable for in vivo evaluation of diverse sAC pharmacology.

Exiting the tunnel of uncertainty: crystal soak to validated hit

Crystallographic fragment screens provide an efficient and effective way to identify small-molecule ligands of a crystallized protein. Due to their low molecular weight, such hits tend to have low, often unquantifiable, affinity for their target, complicating the twin challenges of validating the hits as authentic solution-phase ligands of the target and identifying the `best' hit(s) for further elaboration. In this article, approaches that address these challenges are assessed. Using retrospective analysis of a recent ATAD2 hit-identification campaign, alongside other examples of successful fragment-screening campaigns, it is suggested that hit validation and prioritization are best achieved by a `triangulation' approach in which the results of multiple available biochemical and biophysical techniques are correlated to develop qualitative structure-activity relationships (SARs). Such qualitative SARs may indeed be the only means by which to navigate a project through the tunnel of uncertainty that prevails before on-scale biophysical, biochemical and/or biological measurements become possible.

Review: Investigating the aggregation of amyloid beta with surface plasmon resonance: Do different approaches yield different results?

Aggregation of amyloid beta into amyloid plaques in the brain is a hallmark characteristic of Alzheimer's disease. Therapeutics aimed at preventing or retarding amyloid formation often rely on detailed characterization of the underlying mechanism and kinetics of protein aggregation. Surface plasmon resonance (SPR) spectroscopy is a robust technique used to determine binding affinity and kinetics of biomolecular interactions. This approach has been used to characterize the mechanism of aggregation of amyloid beta but there are multiple pitfalls that need to be addressed when working with this and other amyloidogenic proteins. The choice of method for analyte preparation and ligand immobilization to a sensor chip can lead to different theoretical and practical implications in terms of the mathematical modelling of binding data, different mechanisms of binding and the presence of different interacting species. This review examines preparation methods for SPR characterisation of the aggregation of amyloid beta and their influence on the findings derived from such studies.

Applications of Surface Plasmon Resonance and Biolayer Interferometry for Virus–Ligand Binding

Surface plasmon resonance and biolayer interferometry are two common real-time and label-free assays that quantify binding events by providing kinetic parameters. There is increased interest in using these techniques to characterize whole virus-ligand interactions, as the methods allow for more accurate characterization than that of a viral subunit-ligand interaction. This review aims to summarize and evaluate the uses of these technologies specifically in virus–ligand and virus-like particle–ligand binding cases to guide the field towards studies that apply these robust methods for whole virus-based studies.

Assays Used for Discovering Small Molecule Inhibitors of YAP Activity in Cancers

Simple Summary

Cancer is a disease in which cells grow in an uncontrolled manner. This can be due to excessive cell proliferation or reduced cell death or a combination of the two. The Hippo signaling pathway, when misregulated, promotes excessive growth and cancer development by inducing uncontrolled cell proliferation and inhibiting cell death. This is achieved due to unregulated activity of the oncogenic effector of this pathway, YAP/TAZ. Therefore, it is critical to develop inhibitors to disrupt YAP activity in cancers. This article reviews the different types of assays that are used in development of small molecule inhibitors for YAP activity in cancers.

Abstract

YAP/TAZ are transcriptional coactivators that function as the key downstream effectors of Hippo signaling. They are commonly misregulated in most human cancers, which exhibit a higher level of expression and nuclear localization of YAP/TAZ, and display addiction to YAP-dependent transcription. In the nucleus, these coactivators associate with TEA domain transcription factors (TEAD1-4) to regulate the expression of genes that promote cell proliferation and inhibit cell death. Together, this results in an excessive growth of the cancerous tissue. Further, YAP/TAZ play a critical role in tumor metastasis and chemotherapy resistance by promoting cancer stem cell fate. Furthermore, they affect tumor immunity by promoting the expression of PD-L1. Thus, YAP plays an important role in multiple aspects of cancer biology and thus, provides a critical target for cancer therapy. Here we discuss various assays that are used for conducting high-throughput screens of small molecule libraries for hit identification, and subsequent hit validation for successful discovery of potent inhibitors of YAP-transcriptional activity. Furthermore, we describe the advantages and limitations of these assays.

Prediction and Modeling of Protein–Protein Interactions Using “Spotted” Peptides with a Template-Based Approach

Protein–peptide interactions (PpIs) are a subset of the overall protein–protein interaction (PPI) network in the living cell and are pivotal for the majority of cell processes and functions. High-throughput methods to detect PpIs and PPIs usually require time and costs that are not always affordable. Therefore, reliable in silico predictions represent a valid and effective alternative. In this work, a new algorithm is described, implemented in a freely available tool, i.e., “PepThreader”, to carry out PPIs and PpIs prediction and analysis. PepThreader threads multiple fragments derived from a full-length protein sequence (or from a peptide library) onto a second template peptide, in complex with a protein target, “spotting” the potential binding peptides and ranking them according to a sequence-based and structure-based threading score. The threading algorithm first makes use of a scoring function that is based on peptides sequence similarity. Then, a rerank of the initial hits is performed, according to structure-based scoring functions. PepThreader has been benchmarked on a dataset of 292 protein–peptide complexes that were collected from existing databases of experimentally determined protein–peptide interactions. An accuracy of 80%, when considering the top predicted 25 hits, was achieved, which performs in a comparable way with the other state-of-art tools in PPIs and PpIs modeling. Nonetheless, PepThreader is unique in that it is able at the same time to spot a binding peptide within a full-length sequence involved in PPI and model its structure within the receptor. Therefore, PepThreader adds to the already-available tools supporting the experimental PPIs and PpIs identification and characterization.

Enhancing the Sensitivity of Surface Plasmon Resonance Measurements Utilizing Polymer Film/Au Assemblies

Surface plasmon resonance (SPR) is used to infer information about a sample that is in contact with an Au-coated glass slide coupled to the SPR prism. Shifts in the angle of the "SPR minimum reflection" can be related to changes in the refractive index (and/or thickness) of the sample that is in contact with the Au film, which can then be used to determine the concentration of an analyte in that sample. Here, we show that by depositing a layer of poly(N-isopropylacrylamide-co-acrylic acid) [p(NIPAm-co-AAc)] microgel on the SPR's Au film, with a subsequent layer of Au deposited on top of the microgels, the sensitivity of SPR to changes in solution properties can be enhanced. We investigated the sensitivity of the SPR to changes in the temperature of water in contact with the SPR's Au film as a function of the microgel immobilization density and the thickness of the Au layer deposited on the microgel layer. The data revealed that the SPR's Au film densely coated with microgels, with 5 nm of Au deposited, exhibited the maximal enhancement. The plasmon coupling effect between the additional Au film on the microgels and the SPR's Au film was further confirmed by 3D finite difference time domain simulations.

Molecular mechanism and thermodynamic study of Rosuvastatin interaction with human serum albumin using a surface plasmon resonance method combined with a multi-spectroscopic, and molecular modeling approach

Rosuvastatin (ROS) is an anti-cholesterol drug belonging to statin drugs. A multi-spectroscopic approach combined with a molecular modeling technique was used to assess ROS association with human serum albumin (HSA). Besides, an HSA immobilized surface plasmon resonance (SPR) chip was used to obtain kinetic parameters (ka, kd, and K_D). Fluorescence quenching titrations revealed that ROS interacts with HSA via a dynamic, exothermic, enthalpy-driven mechanism. Hydrogen bonds and van der Waals interactions as the most prevalent bonding forces contribute to ROS-HSA complex formation. ROS binding to HSA alters HSA conformation. The SPR results indicated that ROS and HSA have a strong interaction possessing an equilibrium constant (K_D) of 1.55 × 10^-8 M at 298 K. A competitive analysis of site markers showed that ROS has a higher tendency to bind to the warfarin binding site (site IIA), which may explain why warfarin has a higher anticoagulant effect in ROS users. FRET analysis indicated that non-radiation energy transfer occurred between ROS and HSA. According to molecular docking studies, ROS prefers binding sites IB and IIA while the ROS-HSA complex stabilizes due to the hydrogen bond and π-π interaction. The presence of hydrogen-bond donors and acceptors, as well as aromatic ROS moieties, facilitates such interactions.

Inhibitory Effects and Surface Plasmon Resonance-Based Binding Affinities of Dietary Hydrolyzable Tannins and Their Gut Microbial Metabolites on SARS-CoV-2 Main Protease

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) main protease (Mpro) inhibitors are considered as potential treatments for coronavirus disease 2019, and dietary polyphenols show promise in SARS-CoV-2 Mpro inhibition based on in silico studies. In the present study, we utilize a combination of biochemical-, surface plasmon resonance-, and docking-based assays to evaluate the inhibition and binding affinities of a series of tannins and their gut microbial metabolites on SARS-CoV-2 Mpro. The tested compounds (2-50 μM) were hydrolyzable tannins, including ellagitannins (punicalagin and ellagic acid) and gallotannins (tannic acid, pentagalloyl glucose, ginnalin A, and gallic acid), and their gut microbial metabolites, urolithins and pyrogallol, respectively. They inhibited SARS-CoV-2 Mpro (by 6.6-100.0% at 50 μM) and bound directly to the Mpro protein (with dissociation constants from 1.1 × 10-6 to 5.3 × 10-5 M). This study sheds light on the inhibitory effects of tannins and their metabolites on SARS-CoV-2 Mpro.

Nicotiana spp. for the Expression and Purification of Functional IgG3 Antibodies Directed Against the Staphylococcus aureus Alpha Toxin

Immunoglobulin subclass IgG1 is bound and neutralized effectively by Staphylococcus aureus protein A, allowing the bacterium to evade the host’s adaptive immune response. In contrast, the IgG3 subclass is not bound by protein A and can be used to treat S. aureus infections, including drug-resistant strains such as methicillin-resistant Staphylococcus aureus (MRSA). However, the yields of recombinant IgG3 are generally low because this subclass is prone to degradation, and recovery is hindered by the inability to use protein A as an affinity ligand for antibody purification. Here, we investigated plants (Nicotiana spp.) as an alternative to microbes and mammalian cell cultures for the production of an IgG3 antibody specific for the S. aureus alpha toxin. We targeted recombinant IgG3 to different subcellular compartments and tested different chromatography conditions to improve recovery and purification. Finally, we tested the antigen-binding capacity of the purified antibodies. The highest IgG3 levels in planta (>130 mg kg−1 wet biomass) were achieved by targeting the endoplasmic reticulum or apoplast. Although the purity of IgG3 exceeded 95% following protein G chromatography, product recovery requires further improvement. Importantly, the binding affinity of the purified antibodies was in the nanomolar range and thus comparable to previous studies using murine hybridoma cells as the production system.

eSPC: an online data-analysis platform for molecular biophysics

All biological processes rely on the formation of protein-ligand, protein-peptide and protein-protein complexes. Studying the affinity, kinetics and thermodynamics of binding between these pairs is critical for understanding basic cellular mechanisms. Many different technologies have been designed for probing interactions between biomolecules, each based on measuring different signals (fluorescence, heat, thermophoresis, scattering and interference, among others). Evaluation of the data from binding experiments and their fitting is an essential step towards the quantification of binding affinities. Here, user-friendly online tools to analyze biophysical data from steady-state fluorescence spectroscopy, microscale thermophoresis and differential scanning fluorimetry experiments are presented. The modules of the data-analysis platform (https://spc.embl-hamburg.de/) contain classical thermodynamic models and clear user guidelines for the determination of equilibrium dissociation constants (Kd) and thermal unfolding parameters such as melting temperatures (Tm).

Effect of Methadone and Tramadol Opioids on Stem Cells Based on Integrated Plasmonic-Ellipsometry Technique

Introduction: Plasmonic biosensors provide high sensitivity in detecting the low amount of biomarkers and pharmaceutical drugs. We studied the mesenchyme cell activity under the treatment of common sedative drugs of methadone and tramadol using the integrated plasmonic-ellipsometry technique. Methods: Mesenchymal stem cells were cultured on patterned plasmonic chips under the treatment of methadone and tramadol drugs. Three cultured chips were kept non-treated as the control ones. The plasmonic-ellipsometry technique was applied to study the signaling characteristic of the cells affected by these two drugs. In this technique, optical information regarding the amplitude ratio and phase change between p- and s-polarized light was recorded. Results: This drug treatment could affect the spectral plasmonic resonance and subsequently the phase shift (Δ) and the amplitude ratio (Ψ) values under p- and s-polarized impinging light. A more significant Δ value for tramadol treatment meant that the phase split was larger between p- and s-polarized light. Tramadol also had more prominent absolute Δ eff and Ψ eff values in comparison with methadone. Conclusion: We showed that tramadol caused more contrast in phase shift (Δ) and amplitude ratio (Ψ) between p- and s-polarized impinging light for cultured stem cells in comparison with methadone. It means that tramadol differentiated more the optical responses for p- and s-polarized lights compared to methadone. Our proposed technique possesses the potential of quantitative and qualitative analysis of drugs on humans even on a cell scale.

A review on plasmonic and metamaterial based biosensing platforms for virus detection

Due to changes in our climate and constant loss of habitat for animals, new pathogens for humans are constantly erupting. SARS-CoV-2 virus, become so infectious and deadly that they put new challenge to the whole technological advancement of healthcare. Within this very decade, several other deadly virus outbreaks were witnessed by humans such as Zika virus, Ebola virus, MERS-coronavirus etc. and there might be even more infectious and deadlier diseases in the horizon. Though conventional techniques have succeeded in detecting these viruses to some extent, these techniques are time-consuming, costly, and require trained human-resources. Plasmonic metamaterial based biosensors might pave the way to low-cost rapid virus detection. So this review discusses in details, the latest development in plasmonics and metamaterial based biosensors for virus, viral particles and antigen detection and the future direction of research in this field.

Fluorescent detection of target proteins via a molecularly imprinted hydrogel

Proteins are typically separated by an immune reaction, such as an enzyme-linked immunosorbent assay, and are detected by selective fluorescent labeling. This has potential for complicated procedures and the denaturation of proteins by labeling, and is cost consuming. In this study, we propose a technique for the selective separation and detection of a target protein using a molecularly imprinted hydrogel (PI gel) with fluorescent monomers. We focused on 8-anilino-1-naphthalenesulfonic acid (ANS), where the fluorescence intensity is easily changed by the interaction with proteins, and successfully synthesized the ANS monomer and a poly(ethylene glycol) (PEG) conjugated ANS monomer. The PI gel with the ANS monomers using bovine serum albumin (BSA) as a template showed the selective adsorption of BSA and the fluorescence intensity increased due to the adsorption of BSA.

Kinetic Microscale Thermophoresis for Simultaneous Measurement of Binding Affinity and Kinetics

Microscale thermophoresis (MST) is a versatile technique to measure binding affinities of binder-ligand systems, based on the directional movement of molecules in a temperature gradient. We extended MST to measure binding kinetics as well as binding affinity in a single experiment by increasing the thermal dissipation of the sample. The kinetic relaxation fingerprints were derived from the fluorescence changes during thermodynamic re-equilibration of the sample after local heating. Using this method, we measured DNA hybridization on-rates and off-rates in the range 10⁴ -10⁶  m^-1  s^-1 and 10^-4 -10^-1  s^-1 , respectively. We observed the expected exponential dependence of the DNA hybridization off-rates on salt concentration, strand length and inverse temperature. The measured on-rates showed a linear dependence on salt concentration and weak dependence on strand length and temperature. For biomolecular interactions with large enthalpic contributions, the kinetic MST technique offers a robust, cost-effective and immobilization-free determination of kinetic rates and binding affinity simultaneously, even in crowded solutions.

A new molecular imprinted PEDOT glassy carbon electrode for carbamazepine detection

An electrochemical sensor for the detection of carbamazepine was fabricated by the electropolymerization of PEDOT on glassy carbon electrodes. Molecular imprinted polymer sites were synthesized by cyclic voltammetry on the electrodes' surfaces providing high selectivity and sensitivity towards carbamazepine molecules. Scanning electron microscopy validated the formation of the polymer. Extraction of carbamazepine from the polymer was performed by immersion in acetonitrile and validated by ultraviolet-visible spectroscopy along with cyclic voltammetry experiments comparing pre- and post-template extraction data. Further cyclic voltammetry and square-wave voltammetry tests aided in characterizing the electrodes' response to carbamazepine concentration in PBS solution with [Fe(CN)₆]^3-/4- as a redox pair/mediator. The limits of detection and quantification were found to be 0.98 x 10^-3 M and 2.97 x 10^-3 M respectively. The biosensor was highly sensitive to carbamazepine molecules in comparison to non-imprinted electrodes, simple to construct and easy to operate.

Characterization of drug binding with alpha1-acid glycoprotein in clinical samples using ultrafast affinity extraction

Many drugs bind to serum transport proteins, which can affect both drug distribution and activity in the body. α₁-Acid glycoprotein (AGP) is a key transport protein for basic and neutral drugs. Both elevated levels and altered glycosylation patterns of AGP have been seen in clinical conditions such as systemic lupus erythematosus (SLE). This study developed, optimized, and used the method of ultrafast affinity extraction (UAE) to examine whether these changes in AGP are associated with changes in the binding by some drugs to this transport protein. This approach used affinity microcolumns to capture and measure, in serum, the free fractions of several drugs known to bind AGP. These measurements were made with pooled normal control serum and serum samples from individuals with SLE. Immunoaffinity chromatography was used to obtain the content of AGP and HSA in these samples, and CE was used to examine the glycoform pattern for AGP in each serum sample. The free drug fractions measured for normal control serum ranged from 3.5 to 29.1%, in agreement with the results of ultrafiltration, and provided binding constants of ~10⁵-10⁶ M^-1 for the given drugs with AGP at 37⁰C. Analysis of a screening set of SLE serum samples by UAE gave decreased free fractions (relative change, 12-55%) vs normal serum when spiked with the same types and amounts of drugs. These changes were related in some cases to AGP content, with some SLE samples having AGP levels 1.3- to 2.1-fold above the upper end of the normal range. In other cases, the changes in free fractions appeared to be linked to alterations in the glycoforms and binding constants of AGP, with some affinities differing by 1.2- to 1.5-fold vs normal AGP. This approach can be employed with other solute-protein systems and to investigate binding by other drugs or transport proteins directly in clinical samples.

Uncertainty in protein-ligand binding constants: asymmetric confidence intervals versus standard errors

Equilibrium binding constants (K_b) between chemical compounds and target proteins or between interacting proteins provide a quantitative understanding of biological interaction mechanisms. Reported uncertainties of measured experimental parameters are critical for decision-making in many scientific areas, e.g., in lead compound discovery processes and in comparing computational predictions with experimental results. Uncertainties in measured K_b values are commonly represented by a symmetric normal distribution, often quoted in terms of the experimental value plus-minus the standard deviation. However, in general, the distributions of measured K_b (and equivalent K_d) values and the corresponding free energy change ΔG_b are all asymmetric to varying degree. Here, using a simulation approach, we illustrate the effect of asymmetric K_b distributions within the realm of isothermal titration calorimetry (ITC) experiments. Further we illustrate the known, but perhaps not widely appreciated, fact that when distributions of any of K_b, K_d and ΔG_b are transformed into each other, their degree of asymmetry is changed. Consequently, we recommend that a more accurate way of expressing the uncertainties of K_b, K_d, and ΔG_b values is to consistently report 95% confidence intervals, in line with other authors' suggestions. The ways to obtain such error ranges are discussed in detail and exemplified for a binding reaction obtained by ITC.

Systematic Screening of Viral Entry Inhibitors Using Surface Plasmon Resonance

Surface plasmon resonance (SPR) analytical method was initially used as biosensor for analyzing diverse biomolecular interactions and recently gained important place in the drug discovery. Here, I describe the procedures for screening of inhibitors against the viral proteins using the SPR. Using the described procedures, in the past, we were able to identify several antiviral products that interfere viral-host receptor proteins interactions.

Differential Peptidoglycan Recognition Assay Using Varied Surface Presentations

Bacterial peptidoglycan (PG) is recognized by the human innate immune system to generate an appropriate response. To gain an appreciation of how this essential polymer is sensed, a surface plasmon resonance (SPR) assay using varied PG surface presentation was developed. PG derivatives were synthesized and immobilized on the surface at different positions on the molecule to assess effects of ligand orientation on the binding affinities of NOD-like receptors (NLRs). NLRP1 and NOD2 are cytosolic innate immune proteins known to generate an immune response to PG. Both possess conserved leucine rich repeat domains (LRR) as proposed sites of molecular recognition, though limited biochemical evidence exists regarding the mechanisms of PG recognition. Here direct biochemical evidence for the association of PG fragments to NOD2 and NLRP1 with nanomolar affinity is shown. The orientations in which the fragments were presented on the SPR surface influenced the strength of PG recognition by both NLRs. This assay displays fundamental differences in binding preferences for PG by innate immune receptors and reveals unique recognition mechanisms between the LRRs. Each receptor uses specific ligand structural features to achieve optimal binding, which will be critical information to manipulate these responses and combat diseases.

Applied Biophysical Methods in Fragment-Based Drug Discovery

Fragment-based drug discovery (FBDD) has come of age in the last decade with the FDA approval of four fragment-derived drugs. Biophysical methods are at the heart of hit discovery and validation in FBDD campaigns. The three most commonly used methods, thermal shift, surface plasmon resonance, and nuclear magnetic resonance, can be daunting for the novice user. We aim here to provide the nonexpert user of these methods with a summary of problems and challenges that might be faced, but also highlight the potential gains that each method can contribute to an FBDD project. While our view on FBDD is slightly biased toward enabling structure-guided drug discovery, most of the points we address in this review are also valid for non-structure-focused FBDD.

Kinetic Analysis by Affinity Chromatography

Important information on chemical processes in living systems can be obtained by the rates at which these biological interactions occur. This review will discuss several techniques based on traditional and high-performance affinity chromatography that may be used to examine the kinetics of biological reactions. These methods include band-broadening measurements, techniques for peak fitting, split-peak analysis, peak decay studies, and ultrafast affinity extraction. The general principles and theory of each method, as applied to the determination of rate constants, will be discussed. The applications of each approach, along with its advantages and limitations, will also be considered.

Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design

The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.

Characterization of solution-phase drug-protein interactions by ultrafast affinity extraction

A number of tools based on high-performance affinity separations have been developed for studying drug-protein interactions. An example of one recent approach is ultrafast affinity extraction. This method has been employed to examine the free (or non-bound) fractions of drugs and other solutes in simple or complex samples that contain soluble binding agents. These free fractions have also been used to determine the binding constants and rate constants for the interactions of drugs with these soluble agents. This report describes the general principles of ultrafast affinity extraction and the experimental conditions under which it can be used to characterize such interactions. This method will be illustrated by utilizing data that have been obtained when using this approach to measure the binding and dissociation of various drugs with the serum transport proteins human serum albumin and alpha₁-acid glycoprotein. A number of practical factors will be discussed that should be considered in the design and optimization of this approach for use with single-column or multi-column systems. Techniques will also be described for analyzing the resulting data for the determination of free fractions, rate constants and binding constants. In addition, the extension of this method to complex samples, such as clinical specimens, will be considered.

Systematic screening of viral entry inhibitors using surface plasmon resonance

Viral binding and entry into host cells for various viruses have been studied extensively, yielding a detailed understanding of the overall viral entry process. As cell entry is an essential and requisite process by which a virus initiates infection, it is an attractive target for therapeutic intervention. The advantages of targeting viral entry are an extracellular target site, relatively easy access for biological interventions, and lower toxicity. Several cell-based strategies and biophysical techniques have been used to screen compounds that block viral entry. These studies led to the discovery of inhibitors against HIV, HCV, influenza, Ebola, and RSV. In recent years, several compounds screened by fragment-based drug discovery have been approved as drugs or are in the final stages of clinical trials. Among fragment screening technologies, surface plasmon resonance has been widely used because it provides accurate information on binding kinetics, allows real-time monitoring of ligand-drug interactions, requires very small sample amounts to perform analyses, and requires no modifications to or labeling of ligands. This review focuses on surface plasmon resonance-based schemes for screening viral entry inhibitors.

Methods of probing the interactions between small molecules and disordered proteins

It is generally recognized that a large fraction of the human proteome is made up of proteins that remain disordered in their native states. Despite the fact that such proteins play key biological roles and are involved in many major human diseases, they still represent challenging targets for drug discovery. A major bottleneck for the identification of compounds capable of interacting with these proteins and modulating their disease-promoting behaviour is the development of effective techniques to probe such interactions. The difficulties in carrying out binding measurements have resulted in a poor understanding of the mechanisms underlying these interactions. In order to facilitate further methodological advances, here we review the most commonly used techniques to probe three types of interactions involving small molecules: (1) those that disrupt functional interactions between disordered proteins; (2) those that inhibit the aberrant aggregation of disordered proteins, and (3) those that lead to binding disordered proteins in their monomeric states. In discussing these techniques, we also point out directions for future developments.

Kinetic and thermodynamic study of bovine serum albumin interaction with rifampicin using surface plasmon resonance and molecular docking methods

The interaction of bovine serum albumin (BSA) with various drugs, such as antibiotics, due to the importance of BSA in drug delivery has attracted increasing research attention at present. Therefore, the aim of this study was investigation of BSA interaction with rifampicin using surface plasmon resonance (SPR) and molecular docking methods under the imitated physiological conditions ( pH = 7.4 ). BSA immobilization on carboxymethyl dextran hydrogel chip has been carried out after activation with N-hydroxysuccinimide/N-ethyl-N-(3-diethylaminopropyl) carbodiimide. The dose-response sensorgrams of BSA upon increasing concentration of refampicin were attained in SPR analysis. The high affinity of rifampicin to BSA was demonstrated by a low equilibrium constants ( K D ) value ( 3.46 × 10 ? 5 at 40°C). The process of kinetic values changing shows that affinity of BSA to rifampicin decreased with rising temperature. The positive value of both enthalpy change ( ? H ) and entropy change ( ? S ) showed that hydrophobic force plays major role in the BSA interaction with rifampicin. The positive value of ? G was indicative of nonspontaneous and enthalpy-driven binding process. In addition, according to the molecular docking study, hydrogen binding has some contributions in the interaction of rifampicin with BSA.

Harnessing the Versatility of Optical Biosensors for Target-Based Small-Molecule Drug Discovery

Optical biosensors entered target-based small-molecule drug discovery more than two decades ago and have since transformed into a value-adding component in the decision-making process. Here, we briefly highlight the major application areas of optical biosensors and focus on desirable profiles of such platforms in order to ensure their effective use in small molecule drug discovery. Furthermore, we will emphasize current technology-based constraints and discuss experimental strategies to address these limitations as well as provide a view of necessary technology improvements for next generation platforms.

SPR-based assays enable the full functional analysis of bispecific molecules

The increasing complexity of novel biotherapeutics such as bispecific antibodies or fusion proteins raises new challenges for functional characterization. When compared to standard antibodies, two individual interactions and the inter-dependency of binding events need to be considered for bispecific antibodies. We have previously described an SPR-based assay setup, which enables us to assess the binding activity of a bivalent-bispecific molecule to both targets simultaneously and - in addition to one individual target - in a single setup. However, there might be some pitfalls when applying the bridging assay, e.g. change of antigen activity upon immobilization. Therefore, we have developed an alternative SPR-based assay principle, which allows the individual assessment of both targets in solution. Comparison of data between the assays showed that simultaneous binding can be calculated based on both individual readouts, and revealed a good correlation. Hence, both SPR-based assay principles allow a "full" functional analysis of a bispecific CrossMab in only one assay. The assay principles can be qualified and enable an efficient drug development.

Differentiating between drugs with short and long residence times

The kinetic aspects of the ligand–receptor interaction, characterising the residence time of a ligand in its binding site, play an important role in drug effectiveness.

Characterizing nerve growth factor-p75(NTR) interactions and small molecule inhibition using surface plasmon resonance spectroscopy

Nerve growth factor (NGF) is critical for the proliferation, differentiation, and survival of neurons through its binding to the p75(NTR) and TrkA receptors. Dysregulation of NGF has been implicated in several pathologies, including neurodegeneration (i.e., Parkinson's and Alzheimer's diseases) and both inflammatory and neuropathic pain states. Therefore, small molecule inhibitors that block NGF-receptor interactions have significant therapeutic potential. Small molecule antagonists ALE-0540, PD90780, Ro 08-2750, and PQC 083 have all been reported to inhibit NGF from binding the TrkA receptor. Interestingly, the characterization of the ability of these molecules to block NGF-p75(NTR) interactions has not been performed. In addition, the inhibitory action of these molecules has never been evaluated using surface plasmon resonance (SPR) spectroscopy, which has been proven to be highly useful in drug discovery applications. In the current study, we used SPR biosensors to characterize the binding of NGF to the p75(NTR) receptor in addition to characterizing the inhibitory potential of the known NGF antagonists. The results of this study provide the first evaluation of the ability of these compounds to block NGF binding to p75(NTR) receptor. In addition, only PD90780 was effective at inhibiting the interaction of NGF with p75(NTR), suggesting receptor selectivity between known NGF inhibitors.

Analytical methods for kinetic studies of biological interactions: A review

The rates at which biological interactions occur can provide important information concerning the mechanism and behavior of these processes in living systems. This review discusses several analytical methods that can be used to examine the kinetics of biological interactions. These techniques include common or traditional methods such as stopped-flow analysis and surface plasmon resonance spectroscopy, as well as alternative methods based on affinity chromatography and capillary electrophoresis. The general principles and theory behind these approaches are examined, and it is shown how each technique can be utilized to provide information on the kinetics of biological interactions. Examples of applications are also given for each method. In addition, a discussion is provided on the relative advantages or potential limitations of each technique regarding its use in kinetic studies.

A [(32)P]NAD(+)-based method to identify and quantitate long residence time enoyl-acyl carrier protein reductase inhibitors

The classical methods for quantifying drug-target residence time (tR) use loss or regain of enzyme activity in progress curve kinetic assays. However, such methods become imprecise at very long residence times, mitigating the use of alternative strategies. Using the NAD(P)H-dependent FabI enoyl-acyl carrier protein (enoyl-ACP) reductase as a model system, we developed a Penefsky column-based method for direct measurement of tR, where the off-rate of the drug was determined with radiolabeled [adenylate-(32)P]NAD(P(+)) cofactor. In total, 23 FabI inhibitors were analyzed, and a mathematical model was used to estimate limits to the tR values of each inhibitor based on percentage drug-target complex recovery following gel filtration. In general, this method showed good agreement with the classical steady-state kinetic methods for compounds with tR values of 10 to 100 min. In addition, we were able to identify seven long tR inhibitors (100-1500 min) and to accurately determine their tR values. The method was then used to measure tR as a function of temperature, an analysis not previously possible using the standard kinetic approach due to decreased NAD(P)H stability at elevated temperatures. In general, a 4-fold difference in tR was observed when the temperature was increased from 25 to 37 °C.

Plasmonic biosensors

The unique optical properties of plasmon resonant nanostructures enable exploration of nanoscale environments using relatively simple optical characterization techniques. For this reason, the field of plasmonics continues to garner the attention of the biosensing community. Biosensors based on propagating surface plasmon resonances (SPRs) in films are the most well-recognized plasmonic biosensors, but there is great potential for the new, developing technologies to surpass the robustness and popularity of film-based SPR sensing. This review surveys the current plasmonic biosensor landscape with emphasis on the basic operating principles of each plasmonic sensing technique and the practical considerations when developing a sensing platform with the various techniques. The 'gold standard' film SPR technique is reviewed briefly, but special emphasis is devoted to the up-and-coming localized surface plasmon resonance and plasmonically coupled sensor technology.

Trends in protein-based biosensor assemblies for drug screening and pharmaceutical kinetic studies

The selection of natural and chemical compounds for potential applications in new pharmaceutical formulations constitutes a time-consuming procedure in drug screening. To overcome this issue, new devices called biosensors, have already demonstrated their versatility and capacity for routine clinical diagnosis. Designed to perform analytical analysis for the detection of a particular analyte, biosensors based on the coupling of proteins to amperometric and optical devices have shown the appropriate selectivity, sensibility and accuracy. During the last years, the exponential demand for pharmacokinetic studies in the early phases of drug development, along with the need of lower molecular weight detection, have led to new biosensor structure materials with innovative immobilization strategies. The result has been the development of smaller, more reproducible biosensors with lower detection limits, and with a drastic reduction in the required sample volumes. Therefore in order to describe the main achievements in biosensor fields, the present review has the main aim of summarizing the essential strategies used to generate these specific devices, that can provide, under physiological conditions, a credible molecule profile and assess specific pharmacokinetic parameters.

Why you should be using more SPR biosensor technology

There are three ways of looking at surface plasmon resonance biosensor technology: bewilderment (I can not believe this sort of technology actually exists), love (without this technology I would cry), or hate (this technology does not work). Whether you love them or hate them, or just have never heard of them, it is time to take a fresh look at how SPR biosensors can help you get from point A to point B in your drug discovery efforts.: