Literature

Feel free to peruse our literature, including brochures, posters, videos, and background info!

Brochures

Agile R100 Product Brochure

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Capture elusive binding data for all your key compounds with the ability to measure weak binders, tight binders, or unstable proteins like GPCRs, in complex samples including solvents and detergents.

Agile R100 Biosensor Selection Brochure

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For a quick overview on how to select the right Agile R100 biosensor for your experiment, see this 2-page flyer!

Agile R100 Kinetic Characterization Brochure

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What does the Agile R100 graphene biosensor do? How does the technology work? What are some examples of measurements from the tool? See this overview brochure for answers!

Feature Highlight: Precise Kinetic Characterization in Serum

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PAPER SUMMARY

  • In this application note, we show buffer and serum interactions for 3 target and small molecule binding pairs: a chemokine binding G-protein coupled receptor (CR GPCR) binding with small molecule Compound A, the cytokine tumor necrosis factor alpha (TNFα) protein binding with small molecule SPD304, and a DNA aptamer against colistin (i.e. colistin aptamer) binding with the antibiotic drug colistin. No assay adjustment is made in the transition from buffer to serum.
  • All kinetic constants between buffer and serum for the 3 binding interactions are within a factor of 1.9, displaying a high level of precision among multiple replicates and measurements.

Feature Highlight: Replicable Characterization of Functional GPCRs

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PAPER SUMMARY

  • GPCRs are crucial targets for therapeutic intervention in areas such as cancer, immune and inflammatory disorders, and neurological and metabolic diseases. However, this target class is notoriously difficult to characterize due to the instability of the solubilized protein. Prior kinetic binding techniques have substantial roadblocks in studying GPCRs, but in this application note, we present Agile R100’s success in analyzing these difficult targets.
  • Agile R100 advantages that enable successful GPCR characterization include: the ability to sense in complex samples containing solubilizing detergents, a non-microfluidic format that allows the target to be applied directly to the biosensor surface, reducing protein degradation, temperature versatility to keep GPCRs within their required stability range, and low target density requirements, enabling the study of even a tiny amount of purified GPCR.
  • We share 3 example experiments: The first 2 show that a single-concentration kinetics measurement performed with Agile R100 is highly consistent with kinetics found by running a full dose-response curve, letting you reduce the total number of measurements needed to gain accurate binding data, cutting material costs and experiment time.
  • The last example displays the temperature versatility of Agile R100. We place the system on a bed of ice to keep the temperature-sensitive GPCR target stable throughout the experiment. The temperature is monitored with built-in thermometers included in standard Agile biosensor chips, and displayed in real-time through Agile Plus software

Feature Highlight: Sense in Complex Samples: Solvents & Detergents

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PAPER SUMMARY

  • DMSO is often needed to keep high concentrations of small molecule compounds soluble during early stage drug discovery. This is a problem for common optical kinetic binding platforms, as DMSO negatively impacts optical properties.
  • Agile R100 leverages an orthogonal technology called Field Effect Biosensing (FEB), an electrical technique that is unaffected by changes in optical properties. The platform easily senses in optically challenging samples such as buffer containing 10% DMSO.
  • In this technical note, we share Agile R100 kinetic binding data (kon, koff, and KD) from the interaction of 3 small molecule compounds dissolved in 10% DMSO binding with their respective targets – 2 GPCRs solubilized in additional detergents and a cytokine protein.

Publication Highlight: Characterizing MYC Oncoprotein Interactions

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PAPER SUMMARY

  • Researchers from Dr. Kim Janda’s lab at the Scripps Research Institute developed a new series of compounds with the potential to down-regulate the transcriptional activities of MYC. Agile R100, described as a “field-effect transistor (Bio-FET) platform,” was used to characterize MYC oncoprotein and small molecule compound interactions.
  • In the study, Agile R100’s graphene surface was found to be significantly less prone to nonspecific interactions than surface plasmon resonance (SPR). The publication lists additional advantages of Agile R100: A much lower limit of detection than SPR or isothermal calorimetry (ITC), and a lower required target density, which reduced the amount of noise caused by aggregates on the chip surface.
  • Binding data from Agile R100 correlated well with cell-based assay data using chicken embryo fibroblasts (CEF), as opposed to SPR data, which did not.

Publication Highlight: 10x More Sensitive than BLI or ELISA

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PAPER SUMMARY

  • Zika viral antigen is measured using an Octet RED96, a Bio-layer Interferometry (BLI) platform, and Agile R100, an FEB platform, both of which provide kinetic binding data. Agile R100 shows detection at a concentration 10 times lower than on the Octet, while providing kinetic analysis in line with the BLI instrument.
  • Inflammatory protein IL-6 is measured with an Invitrogen ELISA kit and with Agile R100. Agile R100 lowered the limit of detection (LLOD) for IL-6 by a factor of 60 over the ELISA.
  • Agile R100 is an easy-to-use assay system that increases signal-to-noise (SNR) at ultra-low concentrations by 10 times over BLI, a typical kinetic characterization platform, and ELISA, a conventional tool for clinical diagnostics. With FEB, you have an affordable label-free technology that can be used throughout drug discovery and disease research to reduce data and assay translations across phases.

Publication Highlight: High Sensitivity and Detection in Serum

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PAPER SUMMARY

  • Agile R100 detected Zika viral antigen in buffer using monoclonal antibodies developed by the CDC at 18 ng/mL, an exceptional level of sensitivity unmatched by any portable device.
  • Additional measurements showed detection of Zika viral antigen in simulated human serum at a CV% in line with specs set by the Clinical Laboratory Standards Institute (CLSI). At 500 ng/mL, this represents the ability to detect clinically-relevant levels of antigen in serum.
  • Agile R100 is the only graphene-based portable biosensor of its kind. Its affordability, small size, high sensitivity, and ability to detect in serum make it an ideal on-site platform for PK/PD studies, and a candidate for development as an early-stage medical diagnostic test that can be run by the healthcare provider.

Posters

Novel Graphene-based Biosensor for Early Detection of Zika Virus Infection

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Presented at the CDC in Atlanta in 2017.

This poster shows measurements of Zika protein at 18 ng/mL sensitivity and additional measurements in serum at a clinically relevant level of sensitivity. It also shows specificity versus the Japanese Encephalitis virus, a potentially co-founding infection.

Agile R100: An Orthogonal Biosensing Tool for Affinity Ranking During Drug Discovery Hit Validation

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Presented at the Drug Discovery Chemistry Conference in San Diego in 2017.
This poster displays a simple SAR study performed with Agile R100 using TNFα as the immobilized target and three inhibitor compounds as analyte. The activity and affinity of the inhibitor compounds are quantified with dose-response curves and kinetic binding data.

Direct Detection of Borrelia Burgdorferi Antigen Using Field Effect Biosensing (FEB) Technology

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Presented at the Centers for Disease Control and Prevention (CDC) in Atlanta in 2016.
This poster depicts the detection of various concentrations of lysed Borrelia burgdorferi cells with AGILE R100.

Novel Protein Binding Kinetics Measurements in Complex Biological Samples Using Agile

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Presented at the Experimental Biology Conference in San Diego in 2016.

This poster shows results from measurements directly from cell lysate, protein extract, growth media, tissue lysate, and undiluted plasma.

Agile Sensors Quantify Interactions in Challenging Samples for Drug Discovery

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Presented at the Drug Discovery Chemistry Conference in San Diego in 2016.
This poster shows results from measurements with quantity-limited samples (50 µg of total protein) and at fM concentration.

Videos

Introducing Agile R100, a personal assay system for sensitive label-free kinetic binding data (2:05)

Welcome to Agile R100, the first personal assay system for label-free kinetic binding analysis of small molecules and proteins at your bench. Agile R100 is the perfect platform for drug discovery researchers who want to save time, cost, and resources. Designed specifically to validate hits, its single-sample format makes assays easy to run, with no complicated processes or systems to learn. If your goal is to get reliable, sensitive kinetic binding data early in the drug discovery process, see this video for an introduction to Agile R100.

A few key Agile R100 benefits you’ll see in this video:
– Sense in complex samples including detergents, solvents, cell fractions, tissue lysate
– Use just a 10 µL drop of sample
– 11-log dynamic range
– Easy to use
– Breakthrough, orthogonal technique for label-free kinetic binding data

Overview of Field Effect Biosensing (FEB), used in Agile R100 (1:30)

Field Effect Biosensing (FEB) is a breakthrough label-free technique for measuring biomolecular interactions in real-time. It provides valuable kinetic binding data and kinetic characterization of drug molecules, and it’s increasing the speed of drug discovery in R&D labs everywhere. Here’s how it works!

FEB is a unique orthogonal technology that detects when optical methods fail, and it can only be found with innovative personal benchtop assay Agile R100.

How to Use the Agile R100 Label-free Kinetic Binding Assay (7:30)

Welcome to Agile R100, the first personal assay system for label-free kinetic characterization of small molecules and proteins at your bench, and under your control. With an unprecedented 11-log dynamic range, Agile R100 is all you need to develop weakly-binding fragments into high-affinity compounds with accuracy and reliability.

Agile R100 has a microfluidic-free design that is easy to learn and use. Your 10 µL drop of sample is applied directly to the biosensor surface via a pipettor. In contrast to most label-free platforms, if you can run an ELISA, you can have the Agile R100 running in a matter of minutes.

This video provides an overview of how to run a kinetic binding measurement on the Agile R100 system, the analysis that Agile Plus software provides, and the principles of Field Effect Biosensing (FEB) on which Agile R100 is based.

Background Info

Solvent Correction versus In-line Reference Measurement

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▪ Optical systems such as SPR and BLI often have difficulty with nonspecific noise when measuring low molecular weight analyte in organic solvents.
▪ Solvent correction is a type of reference measurement that can subtract this noise but requires carefully-prepared reference samples, a dedicated reference cell, and supplementary measurements, costing time and resources.
▪ FEB does not require additional solvent correction measurements because it is an electrical technique, not an optical one. The biosensor responds minimally to organic solvents, which are neutral particles. FEB uses an in-line reference measurement that reduces time to data and conserves sample.

Assay Development Tips for COOH Agile Biosensors

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The sensitivity and specificity of a biosensor are directly related to the availability and functionality of immobilized capture molecules, but ambient compounds may also nonspecifically contribute to the sensor response, thereby decreasing the signal-to-noise ratio (SNR). Blocking and quenching steps are used in biosensors to reduce the contributions from background compounds that interfere with the measurement signal. Several aspects of biosensor functionalization can be optimized to drive down the effects of nonspecific interactions and increase the SNR for targeted detection, critical to sensing low concentrations of target analyte with low signal. This technical note demonstrates possible blocking and quenching techniques useful for assay development with the COOH Agile R100 biosensor.

User Manuals

Agile R100 User Manual

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Background detail about Field Effect Biosensing (FEB) technology and the Agile R100 system, experimental design, software setup, data acquisition, and data analysis.


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Application Notes

Reproducible Kinetic Characterization of Small Molecule Compounds in Serum with Agile R100

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  • In this application note, we show that Agile R100 provides reproducible kinetic binding data for small molecules with no assay adjustment when transitioning from buffer to serum. We examine 3 low molecular weight compounds interacting with their targets – a CR GPCR, a cytokine, and an aptamer in both buffer and serum. All kinetic constants between buffer and serum are within a factor of 1.9.
  • Agile R100 leverages breakthrough FEB technology to easily sense in complex matrices, providing earlier information about the behavior of a drug in serum without extensive assay development and optimization.

Reproducible Characterization of GPCR and Small Molecule Compound Interactions Using Agile R100

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GPCRs are primary drug targets for therapeutic intervention in multiple disease models, but they are notoriously difficult to characterize due to their inherent instability upon purification. Prior kinetic binding techniques have substantial roadblocks in studying GPCRs, but in this application note, we present Agile R100’s success in quantifying these difficult compounds. Features of Agile R100 that enable successful detection GPCR interactions include: the ability to sense in complex samples containing detergents and solvents, a non-microfluidic format that allows the sample to be applied directly to the surface of the biosensor chip, temperature versatility, and low target concentration and small sample volume requirements.

Kinetic Characterization of Small Molecules in 10% DMSO Interacting with GPCR and TNFα Targets

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In this application note, we present Agile R100 kinetic binding data (kon, koff, and KD) from the interaction of 3 small molecule compounds dissolved in 10% DMSO binding with their respective targets – 2 GPCRs solubilized in additional detergents and a cytokine protein.

Affinity Ranking of SPD304, Evans Blue, and Trypan Blue to TNFα Using Agile R100

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Affinity ranking is critical to optimizing the relationship between a target protein and a potential drug compound during the hit-to-lead optimization phase of drug discovery. In this application note, Agile R100 characterizes the activity of the target protein TNFα interacting with the small molecule drug compounds, SPD304, Evans Blue, and Trypan Blue in order to rank order by affinity.

Technical Notes

Calculating Dissociation Rates of Tight Binders Using kobs

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  • In the later stages of drug discovery, candidates often have high affinities that make it difficult to accurately quantify dissociation rates (koff). The longer an experiment is run, the more likely slight deviations lead to large inaccuracies. With some tight binders, it may not be feasible to run the interaction for the length of time required to directly measure k
  • The kobs plot methodology is an alternative way to gather kinetic data including kon, koff, and KD, that requires only the association binding interaction as an input. This method can be used when direct measurements of koff are inaccurate or impractical.
  • In this technical note, we provide precise kon, koff, and KD values for the interaction of TNFα and SPD304 using the kobs plot methodology. Our KD values from the kobs plot are in the same range as the reported literature values

Kinetic Binding Analysis on Agile R100

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Biosensors are used in a variety of fields to characterize biomolecular interactions in real-time. The results of these interaction studies inform the development of the next generation of diagnostics and therapeutics and provide insights into the mechanisms by which pathogens evolve and infect. Label-free assays are particularly useful in these endeavors because they eliminate both the chance of the added label interfering with the native binding chemistry and the additional chemistry steps to attach the label to the molecule under investigation. This technical note provides an overview of the kinetic binding data collected by Agile R100.

Comparison Studies

Agile R100 versus MicroCal iTC200 Kinetic Binding Data

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Agile R100 is a graphene biosensor with unprecedented functionality, providing label-free, real-time kinetic binding data. As a novel technology, Agile R100 is compared to MicroCal iTC200 to demonstrate its benefits compared to a standard kinetic binding analysis tool, isothermal titration calorimetry (ITC). In this study, kinetic binding data between the two instruments is compared by measuring Rho guanosine triphosphate hydrolase enzyme (GTPase) interacting with GTPase activating protein (GAP). The association and dissociation binding rate (ka and kd, respectively) and dissociation constants (KD) are reported. Agile R100 has a precise binding affinity measurement (KD = 1.35 ± 0.06 µM), comparable to MicroCal iTC200 (KD = 2.7 ± 0.3 µM), while also obtaining ka and kd values. Additionally, Agile R100 uses up to 30 million times less sample material and up to 30 times less sample volume and can perform 2.5 times more measurements in a given workday compared to MicroCal iTC200.

Guides

Agile R100 Sensor Response Optimization Guide

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Fun infographic that shares 3 main things that affect Agile R100 biosensor response and ways to increase binding signal on the platform.

Intro to Kinetic Binding Data Guide

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Need a quick refresher on kinetics? Our Intro to Kinetic Binding Data Guide is a short primer on kinetic and affinity data.