Origin and prediction of free-solution interaction studies performed label-free

Theoretical Basis for Refractive Index Changes Resulting from Solution Phase Molecular Interaction

Refractive index (RI) is a fundamental optical property widely used to investigate the physical and chemical characteristics of materials. Here, we build on our previous work to refine the framework for RI sensing in solution-phase chemical and biochemical interactions. Starting from the Clausius-Mossotti relation, we present a first-principles derivation of a relationship for the RI signal resulting from chemical binding. We then demonstrate how the binding-induced conformational and hydration changes of interacting species relate to their estimated change in dielectric and thus the solution-phase change in refractive index (ΔRI). By varying the model parameters, such as solvation shell size and polarizability, we investigate the RI changes for two interactions: Ca2+ with the protein Recoverin and benzenesulfonamide with carbonic anhydrase 2 (CAII). These examples show that our theory predicts that even for small changes in binding-induced polarizability (relative to previous literature values), a quantifiable RI change is produced within the detectable range of RI detectors operating at ca. 10-6 RIU. Empirical observations confirm our theoretical predictions. Surprisingly, theory and experiment yield a decrease in ΔRI for the benzenesulfonamide-CAII interaction. We attribute this observation to shielding of charged residues and water molecule displacement during the binding event. Our approach is generalized, enabling it to be extended to other binding systems, as well as those undergoing nonbinding conformational changes, and facilitates the exploration of diverse biological and chemical processes by solution-phase RI sensing.

Novel Multifunctional Meta-Surface Plasmon Resonance Chip Microplate for High-Throughput Molecular Screening

The utilization of surface plasmon resonance (SPR) sensors for real-time label-free molecular interaction analysis is already being employed in the fields of in vitro diagnostics and biomedicine. However, the widespread application of SPR technology is hindered by its limited detection throughput and high cost. To address this issue, this study introduces a novel multifunctional MetaSPR high-throughput microplate biosensor featuring 3D nanocups array structure, aiming to achieve high-throughput screening with a reduced cost and enhanced speed. Different types of MetaSPR sensors and analytical detection methods have been developed for accurate antibody subtype identification, epitope binding, affinity determination, antibody collocation, and quantitative detection， greatly promoting the screening and analysis of early-stage antibody drugs. The MetaSPR platform combined with nano-enhanced particles amplifies the detection signal and improves the detection sensitivity, making it more convenient, sensitive, and efficient than traditional ELISA. The findings demonstrate that the MetaSPR biosensor is a new practical technology detection platform that can improve the efficiency of biomolecular interaction studies with unlimited potential for new drug development.

Direct Binding Methods to Measure Receptor-Ligand Interactions

G-protein-coupled receptors (GPCRs) contribute to numerous physiological processes via complex network mechanisms. While indirect signaling assays (Ca2+ mobilization, cAMP production, and GTPγS binding) have been useful in identifying and characterizing downstream signaling mechanisms of GPCRs, these methods lack measurements of direct binding affinities, kinetics, binding specificity, and selectivity that are important parameters in GPCR drug discovery. In comparison to existing direct methods that use radio- or fluorescent labels, label-free techniques can closely emulate the native interactions around binding partners. Surface plasmon resonance (SPR) is a label-free technique that utilizes the refractive index (RI) property and is applied widely in quantitative GPCR-ligand binding kinetics measurement including small molecules screening. However, purified GPCRs are further embedded in a synthetic lipid environment which is immobilized through different tags to the SPR sensor surface, resulting in a non-native environment. Here, we introduced a methodology that also uses the RI property to measure binding interactions in a label-free, immobilization-free arrangement. The free-solution technique is successfully applied in quantifying the interaction of bioactive lipids to cognate lipid GPCRs, which is not purified but rather present in near-native conditions, i.e., in milieu of other cytoplasmic lipids and proteins. To further consider the wide applicability of these free-solution approaches in biomolecular interaction research, additional applications on a variety of receptor-ligand pairs are imperative.

Reducing uncertainty in cancer risk estimation for patients with indeterminate pulmonary nodules using an integrated deep learning model

OBJECTIVE

Patients with indeterminate pulmonary nodules (IPN) with an intermediate to a high probability of lung cancer generally undergo invasive diagnostic procedures. Chest computed tomography image and clinical data have been in estimating the pretest probability of lung cancer. In this study, we apply a deep learning network to integrate multi-modal data from CT images and clinical data (including blood-based biomarkers) to improve lung cancer diagnosis. Our goal is to reduce uncertainty and to avoid morbidity, mortality, over- and undertreatment of patients with IPNs.

METHOD

We use a retrospective study design with cross-validation and external-validation from four different sites. We introduce a deep learning framework with a two-path structure to learn from CT images and clinical data. The proposed model can learn and predict with single modality if the multi-modal data is not complete. We use 1284 patients in the learning cohort for model development. Three external sites (with 155, 136 and 96 patients, respectively) provided patient data for external validation. We compare our model to widely applied clinical prediction models (Mayo and Brock models) and image-only methods (e.g., Liao et al. model).

RESULTS

Our co-learning model improves upon the performance of clinical-factor-only (Mayo and Brock models) and image-only (Liao et al.) models in both cross-validation of learning cohort (e.g.

, AUC

0.787 (ours) vs. 0.707-0.719 (baselines), results reported in validation fold and external-validation using three datasets from University of Pittsburgh Medical Center (e.g., 0.918 (ours) vs. 0.828-0.886 (baselines)), Detection of Early Cancer Among Military Personnel (e.g., 0.712 (ours) vs. 0.576-0.709 (baselines)), and University of Colorado Denver (e.g., 0.847 (ours) vs. 0.679-0.746 (baselines)). In addition, our model achieves better re-classification performance (cNRI 0.04 to 0.20) in all cross- and external-validation sets compared to the Mayo model.

CONCLUSIONS

Lung cancer risk estimation in patients with IPNs can benefit from the co-learning of CT image and clinical data. Learning from more subjects, even though those only have a single modality, can improve the prediction accuracy. An integrated deep learning model can achieve reasonable discrimination and re-classification performance.

Assay Performance of a Label-Free, Solution-Phase CYFRA 21-1 Determination

CYFRA 21.1, a cytokeratin fragment of epithelial origin, has long been a valuable blood-based biomarker. As with most biomarkers, the clinical diagnostic value of CYFRA 21.1 is dependent on the quantitative performance of the assay. Looking toward translation, it is shown here that a free-solution assay (FSA) coupled with a compensated interferometric reader (CIR) can be used to provide excellent analytical performance in quantifying CYFRA 21.1 in patient serum samples. This report focuses on the analytical performance of the high-sensitivity (hs)-CYFRA 21.1 assay in the context of quantifying the biomarker in two indeterminate pulmonary nodule (IPN) patient cohorts totaling 179 patients. Each of the ten assay calibrations consisted of 6 concentrations, each run as 7 replicates (e.g., 10 × 6 × 7 data points) and were performed on two different instruments by two different operators. Coefficients of variation (CVs) for the hs-CYFRA 21.1 analytical figures of merit, limit of quantification (LOQ) of ca. 60 pg/mL, B _max, initial slope, probe-target binding affinity, and reproducibility of quantifying an unknown were found to range from 2.5 to 8.3%. Our results demonstrate the excellent performance of our FSA-CIR hs-CYFRA 21-1 assay and a proof of concept for potentially redefining the performance characteristics of this existing important candidate biomarker.

Novel Antagonist of the Type 2 Lysophosphatidic Acid Receptor (LPA2), UCM-14216, Ameliorates Spinal Cord Injury in Mice

Spinal cord injuries (SCIs) irreversibly disrupt spinal connectivity, leading to permanent neurological disabilities. Current medical treatments for reducing the secondary damage that follows the initial injury are limited to surgical decompression and anti-inflammatory drugs, so there is a pressing need for new therapeutic strategies. Inhibition of the type 2 lysophosphatidic acid receptor (LPA₂) has recently emerged as a new potential pharmacological approach to decrease SCI-associated damage. Toward validating this receptor as a target in SCI, we have developed a new series of LPA₂ antagonists, among which compound 54 (UCM-14216) stands out as a potent and selective LPA₂ receptor antagonist (E_max = 90%, IC₅₀ = 1.9 μM, K_D = 1.3 nM; inactive at LPA_1,3–6 receptors). This compound shows efficacy in an in vivo mouse model of SCI in an LPA₂-dependent manner, confirming the potential of LPA₂ inhibition for providing a new alternative for treating SCI.

Label-free Quantification of Direct Protein-protein Interactions with Backscattering Interferometry

The functional performance of a cell depends on how macromolecules, in particular proteins, come together in a precise orientation, how they assemble into protein complexes and interact with each other. In order to study protein-protein interactions at a molecular level, a variety of methods to investigate these binding processes yield affinity constants and/or the identification of binding regions. There are several well-established biophysical techniques for biomolecular interaction studies, such as fluorescence spectroscopy and surface plasmon resonance. Although these techniques have been proven to be efficient, they either need labeling or immobilization of one interaction partner. Backscattering interferometry (BSI) is a label-free detection method, which allows label- and immobilization-free interaction analysis under physiologically relevant conditions with high sensitivity and in small volumes. We used BSI to measure the interaction of the neuronal calcium sensor recoverin with its target G protein-coupled receptor kinase 1 (GRK1) as a model system. Increasing concentrations of purified recoverin were mixed with a specific concentration of a GRK1 fusion protein. In this protocol, we provide a full description of the instrumental setup, data acquisition, and evaluation. Equilibrium dissociation constants of recoverin-GRK1 interaction determined by the BSI instrumental setup are in full agreement with affinity constants obtained by different methods as described in the literature.

Integrated Biomarkers for the Management of Indeterminate Pulmonary Nodules

Rationale: Patients with indeterminate pulmonary nodules (IPNs) at risk of cancer undergo high rates of invasive, costly, and morbid procedures. Objectives: To train and externally validate a risk prediction model that combined clinical, blood, and imaging biomarkers to improve the noninvasive management of IPNs. Methods: In this prospectively collected, retrospective blinded evaluation study, probability of cancer was calculated for 456 patient nodules using the Mayo Clinic model, and patients were categorized into low-, intermediate-, and high-risk groups. A combined biomarker model (CBM) including clinical variables, serum high sensitivity CYFRA 21-1 level, and a radiomic signature was trained in cohort 1 (n = 170) and validated in cohorts 2-4 (total n = 286). All patients were pooled to recalibrate the model for clinical implementation. The clinical utility of the CBM compared with current clinical care was evaluated in 2 cohorts. Measurements and Main Results: The CBM provided improved diagnostic accuracy over the Mayo Clinic model with an improvement in area under the curve of 0.124 (95% bootstrap confidence interval, 0.091-0.156; P < 2 × 10-16). Applying 10% and 70% risk thresholds resulted in a bias-corrected clinical reclassification index for cases and control subjects of 0.15 and 0.12, respectively. A clinical utility analysis of patient medical records estimated that a CBM-guided strategy would have reduced invasive procedures from 62.9% to 50.6% in the intermediate-risk benign population and shortened the median time to diagnosis of cancer from 60 to 21 days in intermediate-risk cancers. Conclusions: Integration of clinical, blood, and image biomarkers improves noninvasive diagnosis of patients with IPNs, potentially reducing the rate of unnecessary invasive procedures while shortening the time to diagnosis.

Negative SPR Signals during Low Molecular Weight Analyte Recognition

Surface plasmon resonance (SPR) is a powerful technique for studying biomolecular interactions mainly due to its sensitivity and real-time and label free advantages. While SPR signals are usually positive, only a few studies have reported sensorgrams with negative signals. The aim of the present work is to investigate and to explain the observation of negative SPR signals with the hypothesis that it reflects major changes in ligand conformation resulting from target binding. We demonstrated that these negative unconventional signals were due to the negative complex (ligand/analyte) refractive index increment (RII) deviation from the sum of the RII of the individual entities which counterbalanced the theoretical increase of the signal triggered by the target recognition and the ligand folding. We also found that the conformation change of biomolecules can induce a negative or a positive complex RII deviation depending on its sequence and immobilization mode.

Heptameric Peptide Interferes with Amyloid-β Aggregation by Structural Reorganization of the Toxic Oligomers

Pathogenesis of Alzheimer's disease (AD), the most common type of dementia, involves misfolding and aggregation of the extracellular amyloid-β (Aβ) protein where the intermediate oligomers, formed during the aggregation progression cascade, are considered the prime toxic species. Here, we identify an active peptide fragment from a medicinal plant-derived (Aristolochia indica) fibrinolytic enzyme having anti-amyloidogenic effects against Aβ fibrillation and toxicity. Liquid chromatography with tandem mass spectrometry (LC-MS/MS), followed by computational analysis of the peptide pool generated by proteolytic digestion of the enzyme, identifies two peptide sequences with predictive high-propensity binding to Aβ₄₂. Microscopic visualizations in conjunction with biochemical and biophysical assessments suggest that the synthetic version of one of the peptides (termed here P_active, GFLLHQK) arrests Aβ molecules in off-pathway oligomers that can no longer participate in the cytotoxic fibrillation pathway. In contrast, the other peptide (termed P₁) aggravates the fibrillation process. Further investigations confirm the strong binding affinity of P_active with both Aβ₄₂ monomers and toxic oligomers by biolayer interferometric assays. We have also shown that, mechanistically, P_active binding induces conformational alterations in the Aβ molecule along with modification of Aβ hydrophobicity, one of the key players in aggregation. Importantly, the biostability of P_active in human blood serum and its nontoxic nature make it a promising therapeutic candidate against Alzheimer's, for which no disease-modifying treatments are available to date.

Noninvasive biomarkers for lung cancer diagnosis, where do we stand?

The 2010's saw demonstration of the power of lung cancer screening to reduce mortality. However, with implementation of lung cancer screening comes the challenge of diagnosing millions of lung nodules every year. When compared to other cancers with widespread screening strategies (breast, colorectal, cervical, prostate, and skin), obtaining a lung nodule tissue biopsy to confirm a positive screening test remains associated with higher morbidity and cost. Therefore, non-invasive diagnostic biomarkers may have a unique opportunity in lung cancer to greatly improve the management of patients at risk. This review covers recent advances in the field of liquid biomarkers and computed tomographic imaging features, with special attention to new methods for combination of biomarkers as well as the use of artificial intelligence for the discrimination of benign from malignant nodules.

Free Solution Assay Signal Modulation in Variable-Stem-Length Hairpin Aptamers

Interferometric measurements of free solution assays (FSAs) quantify changes in molecular conformation and hydration upon binding. Here, we demonstrate that aptamer probes designed to undergo varying levels of conformational change upon binding produce corresponding variations in FSA signals. A series of hairpin aptamers were synthesized for the small molecule (tenofovir) with identical loop regions that contain the binding pocket, with between 2 and 10 self-associating base pairings in the stem region. Aptamers selected for tenofovir showed a decrease in the FSA signal and binding affinity (increase in K _D) with increasing stem length. Thermodynamic calculations of the Gibbs free energy (ΔG) reported a decrease in ΔG with respect to a corresponding increase in the aptamer stem length. Collectively, these observations provide an expanded understanding of FSA and demonstrate the potential for the rational design of label-free aptamer beacons using FSA as readout.

Quantification of Opioids in Urine Using an Aptamer-Based Free-Solution Assay

The opioid epidemic continues in the United States. Many have been impacted by this epidemic, including neonates who exhibit Neonatal Abstinence Syndrome (NAS). Opioid diagnosis and NAS can be negatively impacted by limited testing options outside the hospital, due to poor assay performance, false-negatives, rapid drug clearance rates, and difficulty in obtaining enough specimen for testing. Here we report a small volume urine assay for oxycodone, hydrocodone, fentanyl, noroxycodone, norhydrocodone, and norfentanyl with excellent LODs and LOQs. The free-solution assay (FSA), coupled with high affinity DNA aptamer probes and a compensated interferometric reader (CIR), represents a potential solution for quantifying opioids rapidly, at high sensitivity, and noninvasively on small sample volumes. The mix-and-read test is 5- to 275-fold and 50- to 1250-fold more sensitive than LC-MS/MS and immunoassays, respectively. Using FSA, oxycodone, hydrocodone, fentanyl, and their urinary metabolites were quantified using 10 μL of urine at 28-81 pg/mL, with >95% specificity and excellent accuracy in ∼1 h. The assay sensitivity, small sample size requirement, and speed could enable opioid screening, particularly for neonates, and points to the potential for pharmacokinetic tracking.

Compensated Interferometry Measures of CYFRA 21-1 Improve Diagnosis of Lung Cancer

Diagnosis of lung cancer patients with indeterminate pulmonary nodules (IPNs) presents a significant clinical challenge, with morbidity and management costs of $28 billion/year. We show that a quantitative free-solution assay (FSA), coupled with a compensated interferometric reader (CIR), improves the diagnostic performance of CYFRA 21-1 as a lung cancer biomarker. FSA-CIR is a rapid, mix-and-read, isothermal, label- and enzyme-free, matrix-insensitive, and target and probe-agnostic assay. Operating FSA-CIR at ∼40, 0.75 μL samples/day delivered a serum CYFRA 21-1 limit of quantification (LOQ) of 81 pg/mL with intra-assay and interassay CVs of 4.9% and 9.6% for four-day replicate determinations. Blinded analysis of a 225 patient cohort, consisting of 75 nonmalignant nodules, 45 adenocarcinomas, 44 squamous cell carcinomas, and 61 small cell lung cancers, gave a clear separation of cases and controls, not observed in the Cobas ECL analysis. The area under the curve (AUC) for the Mayo model increased from 0.595 to 0.923 when combined with the FSA-CIR CYFRA 21-1 measurements. In a population with nodules between 6 and 30 mm, the AUC increased from 0.567 to 0.943. In this subgroup, the positive predictive value (PPV) for all tumors by the CYFRA 21-1 assay was 98.7%. Our results demonstrate increased performance of the CYFRA 21-1 assay using FSA-CIR and represents a proof of concept for redefining the performance characteristics of this important candidate biomarker.

Rapid quantification of two chemical nerve agent metabolites in serum

Organophosphorus compounds (OPs) continue to represent a significant chemical threat to humans due to exposures from their use as weapons, their potential storage hazards, and from their continued use agriculturally. Existing methods for detection include ELISA and mass spectrometry. The new approach presented here provides an innovative first step toward a portable OP quantification method that surmounts conventional limitations involving sensitivity, selectivity, complexity, and portability. DNA affinity probes, or aptamers, represent an emerging technology that, when combined with a mix-and-read, free-solution assay (FSA) and a compensated interferometer (CI) can provide a novel alternative to existing OP nerve agent (OPNA) quantification methods. Here it is shown that FSA can be used to rapidly screen prospective aptamers in the biological matrix of interest, allowing the identification of a 'best-in-class' probe. It is also shown that combining aptamers with FSA-CI enables quantification of the OPNA metabolites, Sarin (NATO designation "G-series, B", or GB) and Venomous Agent X (VX) acids, rapidly with high selectivity at detection limits of sub-10 pg/mL in 25% serum (by volume in PBS). These results suggest there is potential to directly impact diagnostic specificity and sensitivity of emergency response testing methods by both simplifying sample preparation procedures and making a benchtop reader available for OPNA metabolite quantification.

Real-Time Interferometric Refractive Index Change Measurement for the Direct Detection of Enzymatic Reactions and the Determination of Enzyme Kinetics

Back scatter interferometry (BSI) is a sensitive method for detecting changes in the bulk refractive index of a solution in a microfluidic system. Here we demonstrate that BSI can be used to directly detect enzymatic reactions and, for the first time, derive kinetic parameters. While many methods in biomedical assays rely on detectable biproducts to produce a signal, direct detection is possible if the substrate or the product exert distinct differences in their specific refractive index so that the total refractive index changes during the enzymatic reaction. In this study, both the conversion of glucose to glucose-6-phosphate, catalyzed by hexokinase, and the conversion of adenosine-triphosphate to adenosine di-phosphate and mono-phosphate, catalyzed by apyrase, were monitored by BSI. When adding hexokinase to glucose solutions containing adenosine-triphosphate, the conversion can be directly followed by BSI, which shows the increasing refractive index and a final plateau corresponding to the particular concentration. From the initial reaction velocities, K_M was found to be 0.33 mM using Michaelis–Menten kinetics. The experiments with apyrase indicate that the refractive index also depends on the presence of various ions that must be taken into account when using this technique. This study clearly demonstrates that measuring changes in the refractive index can be used for the direct determination of substrate concentrations and enzyme kinetics.

Lysophospholipid G protein-coupled receptor binding parameters as determined by backscattering interferometry

Lysophosphatidic acid (LPA) activates cognate G protein-coupled receptors (GPCRs) to initiate biological signaling cascades. Lysophospholipid (LP) receptor binding properties remain incompletely assessed because of difficulties with ligand lipophilicity and lipid "stickiness." These inherent attributes produce high levels of nonspecific binding within cell-membrane preparations used to assess GPCRs, as has been shown in classical binding assays using radiolabeled ligands, making accurate measurements of lipid binding kinetics difficult to achieve. Backscattering interferometry (BSI) is an optical technology that measures molecular binding interactions by reporting changes in the refractive index of a solution after binding events. Here, we report the use of BSI to assess LPA1 for its ability to bind to naturally occurring lipids and a synthetic LPA1 antagonist (ONO-9780307), under both primary- and competition-binding conditions. Assessment of 12 different lipids demonstrated that the known LP ligand, 1-oleoyl-LPA, as well as an endocannabinoid metabolite, anandamide phosphate, are specific ligands for LPA1, whereas other LPs tested were not. Newly determined dissociation constants (Kd values) for orthosteric lipid ligands approximated 10-9 M, substantially lower (i.e., with higher affinity) than measured Kd values in classical binding or cell-based assays. These results demonstrate that BSI may have particular utility in assessing binding interactions between lipid receptors and their lipid ligands and could provide new screening approaches for lipid receptor identification and drug discovery.

A Highly Compensated Interferometer for Biochemical Analysis

Here we report an improved interferometric sensing approach that facilitates high sensitivity nanovolume refractive index (RI) measurements and molecular interaction assays without a temperature controller. The compensated backscattering interferometer (CBSI) is based on a helium-neon (He-Ne) laser, a microfluidic chip, and a CCD array. The CBSI enables simultaneous differential RI measurements within nanoliter volumes, at a compensation level of ca. 5 × 10^-8 RIU in the presence of large thermal perturbations (8 °C). This level of d n/d T compensation is enabled by elongating the laser beam along the central axis of the microfluidic channel and measuring the difference in positional shift of interference patterns from two adjacent regions of the channel. By separating two solutions by an air gap or oil droplet, CBSI can discriminate the difference in RI for the sample and reference at a detection limit of 7 × 10^-7 RIU in the absence of electronic filtering. At this level of ΔRI sensitivity, it is possible to perform label-free, free-solution biochemical assays at the 10s of nM level without the typical high-resolution temperature control needed in conventional interferometers. Here we illustrate the effective use of CBSI by quantifying the binding affinities for mannose-concanavalin A and Ca²⁺-recoverin interactions.

Control of the Nucleotide Cycle in Photoreceptor Cell Extracts by Retinal Degeneration Protein 3

Retinal degeneration protein 3 (RD3) is crucial for photoreceptor cell survival and linked to Leber Congenital Amaurosis type 12 (LCA12), a hereditary retinal disease in humans. RD3 inhibits photoreceptor guanylate cyclases GC-E and GC-F and is involved in transport of GCs from the inner to the outer segments. Otherwise, its role in photoreceptor physiology is poorly understood. Here, we describe a new function of RD3. Purified RD3 evoked an increase in guanylate kinase activity, an enzyme that is involved in the nucleotide cycle in photoreceptors. We demonstrate a direct interaction between guanylate kinase and RD3 using back-scattering interferometry and show by immunohistochemistry of mouse retina sections that RD3 and guanylate kinase co-localize in photoreceptor inner segments and to a lesser extent in the outer plexiform layer. Our findings point toward a more complex function of RD3 in photoreceptors. The RD3 – guanylate kinase interaction may also play a role in other cellular systems, while the GC – RD3 interaction is exclusive to photoreceptors.

Longitudinal pixel averaging for improved compensation in backscattering interferometry

Longitudinal averaging of the interference pattern in a compensated backscattering interferometer provides improved compensation for temperature induced refractive index perturbations. Fringe pattern likeness between two discrete detection regions of an off-the-shelf microfluidic chip illuminated by an inexpensive diode laser scales with interrogation length. Averaging the intensity distribution along a 2.75 mm length of the channel results in a 750-fold reduction in sensitivity to temperature and a baseline noise level of 3×10^-8 refractive index units (RIU). These observations enable nanoliter-volume interferometric measurements at a level of 10^-7  RIU in the presence of a 2°C temperature variation without the need for temperature control.

Aptamers in Bordeaux 2017: An exceptional "millésime"

About 150 participants attended the symposium organised at the Palais de la Bourse in Bordeaux, France on September 22-23, 2017. Thirty speakers from all over the world delivered lectures covering selection processes, aptamer chemistry and innovative applications of these powerful tools that display major advantages over antibodies. Beyond the remarkable science presented, lively discussion and fruitful exchange between participants made this meeting a great success. A series of lectures were focused on synthetic biology (riboswitches, new synthetic base pairs, mutated polymerases). Innovative selection procedures including functional screening of oligonucleotide pools were described. Examples of aptasensors for the detection of pathogens were reported. The potential of aptamers for the diagnostic and the treatment of diseases was also presented. Brief summaries of the lectures presented during the symposium are given in this report. The third edition of this symposium will take place in Boulder, Colorado in Summer 2018 (information available at http://www.aptamers-in-bordeaux.com/).

Metallo-β-lactamase Domain-Containing Protein 1 (MBLAC1) Is a Specific, High-Affinity Target for the Glutamate Transporter Inducer Ceftriaxone

Ceftriaxone, a β-lactam antibiotic, has been reported to act independently of its antimicrobial actions to normalize perturbed central nervous system glutamate levels, principally by elevating expression of glial glutamate transporters. Identification of a specific, high-affinity target for ceftriaxone could significantly impact therapeutic development for multiple brain disorders, ranging from neurodegenerative disorders to addiction. Recently, we identified a glial-expressed Caenorhabditis elegans gene, swip-10, that encodes a metallo-β-lactamase domain-containing protein, and limits glutamate-dependent changes in dopamine neuron excitability. Bioinformatic analyses identified MBLAC1 as the likely mammalian orthologue of swip-10. Using cyanogen bromide immobilized ceftriaxone for affinity capture experiments and backscattering interferometry to monitor MBLAC1 binding of unmodified ceftriaxone, we obtained evidence for specific, high affinity (K_D = 2.2 μM) binding of ceftriaxone to MBLAC1. We discuss our findings with respect to MBLAC1 as a potentially exclusive, high-affinity binding partner of ceftriaxone in the CNS, and the path forward in the development of novel, MBLAC1-based therapeutics.

An experimental check of backscattering interferometry

Backscattering interferometry (BSI) was used to determine the association constants for four well-known biomolecular interactions: protein A + IgG, trypsin + antitrypsin, trypsin + p-aminobenzamidine, and antithrombin + heparin. Each gave well-defined binding curves and K_d values in close agreement with published findings obtained using other techniques. These results stand in direct contrast to the claims in a 2015 publication in this journal (Discussion of "Back Scattering Interferometry revisited-a theoretical and experimental investigation" Jørgensen, T.M.; Jepsen, S.T.; Sørensen, H.S.; di Gennaro, A.K.; Kristensen, S.R. Sensors and Actuators B 2015, 220, 1328-1337, doi: 10.1016/j.snb.2015.06.121), thus invalidating the claim that BSI is unable to make measurements of this kind. The experimental details are discussed, and several potential sources of error in the previous publication are identified. No comments are made here on the discussion of the theoretical aspects of the BSI technique.

Label-free quantification of calcium-sensor targeting to photoreceptor guanylate cyclase and rhodopsin kinase by backscattering interferometry

Quantification of protein binding to membrane proteins is challenging and a limited set of methods is available to study such systems. Here we employed backscattering interferometry (BSI), a free-solution label-free method with high sensitivity, to quantify the interaction of neuronal Ca²⁺-Sensor proteins with their targets operating in phototransduction. We tested direct binding of guanylate cyclase–activating proteins (GCAP1 and GCAP2) to their membrane target guanylate cyclase 1. The regulatory mechanism of GCAPs including their binding interface in the target is unresolved. Here we used a label-free, free-solution assay method based on BSI to determine binding constants of GCAP1 and GCAP2 to the full-length membrane-bound guanylate cyclase type 1. GCAP1 and GCAP2 bound to different regions on the target guanylate cyclase with submicromolar affinity (apparent K_D-values of 663 ± 121 nM and 231 ± 63 nM for Ca²⁺-free GCAP1 and GCAP2, respectively). A guanylate cyclase construct containing the juxta-membrane and kinase homology domain harbored an exclusive binding site for GCAP1 with similar affinities as the full-length protein, whereas GCAP2 did not bind to this region. We provide a model in which GCAP1 and GCAP2 do not share a single binding site to the target, thus cannot exchange upon fluctuating Ca²⁺ levels.

Direct Measurement of Trafficking of the Cystic Fibrosis Transmembrane Conductance Regulator to the Cell Surface and Binding to a Chemical Chaperone

Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) result in the disease cystic fibrosis. Deletion of Phe508, the most prevalent mutation associated with this disease, disrupts trafficking of the protein. Small molecule correctors yield moderate improvements in the trafficking of ΔF508-CFTR to the plasma membrane. It is currently not known if correctors increase the level of trafficking through improved cargo loading of transport vesicles or through direct binding to CFTR. Real-time measurements of trafficking were utilized to identify the mechanistic details of chemical, biochemical, and thermal factors that impact CFTR correction, using the corrector molecule VX-809, a secondary mutation (I539T), and low-temperature conditions. Each individually improved trafficking of ΔF508-CFTR to approximately 10% of wild-type levels. The combination of VX-809 with either low temperature or the I539T mutation increased the amount of CFTR on the plasma membrane to nearly 40%, indicating synergistic activity. The number of vesicles reaching the surface was significantly altered; however, the amount of channel in each vesicle remained the same. Direct binding measurements of VX-809 in native membranes using backscattering interferometry indicate tight binding to CFTR, which occurred in a manner independent of mutation. The similar values obtained for all forms of the channel indicate that the binding site is not compromised or enhanced by these mutations.

Physiologically relevant binding affinity quantification of monoclonal antibody PF-00547659 to mucosal addressin cell adhesion molecule for in vitro in vivo correlation

Background and Purpose

A monoclonal antibody (PF‐00547659) against mucosal addressin cell adhesion molecule (MAdCAM), expressed as both soluble (sMAdCAM) and trans‐membrane (mMAdCAM) target forms, showed over 30‐fold difference in antibody‐target K_D between in vitro (Biacore) and clinically derived (K_D,in‐vivo) values. Back‐scattering interferometry (BSI) was applied to acquire physiologically relevant K_D values which were used to establish in vitro and in vivo correlation (IVIVC).

Experimental Approach

BSI was applied to obtain K_D values between PF‐00547659 and recombinant human MAdCAM in buffer or CHO cells and endogenous MAdCAM in human serum or colon tissue. CHO cells and tissue were minimally processed to yield homogenate containing membrane vesicles and soluble proteins. A series of binding affinities in serum with various dilution factors was used to estimate both K_D,in‐vivo and target concentrations; MAdCAM concentrations were also measured using LC–MS/MS.

Key Results

BSI measurements revealed low K_D values (higher affinity) for sMAdCAM in buffer and serum, yet a 20‐fold higher K_D value (lower affinity) for mMAdCAM in CHO, mMAdCAM and sMAdCAM in tissue. BSI predicted K_D,in‐vivo in serum was similar to clinically derived K_D,in‐vivo, and the BSI‐estimated serum sMAdCAM concentration also matched the measured concentration by LC–MS/MS.

Conclusions and Implications

Our results successfully demonstrated that BSI measurements of physiologically relevant K_D values can be used to establish IVIVC, for PF‐00547659 to MAdCAM despite the lack of correlation when using Biacore measured K_D and accurately estimates endogenous target concentrations. The application of BSI would greatly enhance successful basic pharmacological research and drug development.

Fingerprints of Calcium-Binding Protein Conformational Dynamics Monitored by Surface Plasmon Resonance

Surface plasmon resonance (SPR) spectroscopy is widely used to probe interactions involving biological macromolecules by detecting changes in the refractive index in a metal/dielectric interface following the dynamic formation of a molecular complex. In past years, SPR-based experimental approaches were developed to monitor conformational changes induced by the binding of small analytes to proteins coupled to the surface of commercially available sensor chips. A significant contribution to our understanding of the phenomenon came from the study of several Ca(2+)-sensor proteins operating in diverse cellular scenarios, in which the conformational switch is triggered by specific Ca(2+) signals. Structural and physicochemical analyses demonstrated that the SPR signal not only depends on the change in protein size upon Ca(2+)-binding but likely originates from variations in the hydration shell structure. The resulting changes in the dielectric properties of water or of the protein-water interface eventually reflect different crowding conditions on the SPR sensor chip, which mimic the cellular environment. SPR could hence be used to monitor conformational transitions in proteins, especially when a significant variation in the hydrophobicity of the solvent-exposed protein surface occurs, thus leading to changes in the dielectric milieu of the whole sensor chip surface. We review recent work in which SPR has been successfully employed to provide a fingerprint of the conformational change dynamics in proteins under native and altered conditions, which include post-translational modifications, copresence of competing analytes, and point mutations of single amino acids associated with genetic diseases.