Literature

Application Notes

Screen with the Biodesy Delta

Protein structure defines function. Modern efforts to develop selective and potent therapies seek to improve human health by perturbing protein conformation. Thus, measuring ligand-induced conformational change earlier in the screening process holds promise to finding better drugs faster. He we present the typical drug discovery workflow involved when using the Biodesy Delta as a screening tool.

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Brochures

1536 well plate

Biodesy’s new 1536-well plate delivers the highest degree of sample efficiency on the Delta System, through significantly increased throughput (>100,000 drug can- didates/week) and lower sample consumption.

These enhanced capabilities allow researchers to dis- cover functionally qualified hits earlier in the screening pipeline. With the addition of our new 1536-well plate, customers can now choose the plate format (384-well or 1536-well) that best suits their screening needs.

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Biodesy Delta Brochure

The Biodesy Delta is an easy-to-use, high-throughput system that automates measurement of protein conformational change. It is being used to study a wide range of proteins, regardless of mass or structure, and a wide range of interactions, including fragments, small molecules, antibodies and protein complexes.

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Biodesy Summary Sheet

Many potent and selective drugs induce or stabilize distinct target conformations that improve human health. Novel, innovative and higher throughput technologies that reveal this valuable structural information are needed to enable better decisions earlier in the drug discovery process, accelerating discovery-to-market timelines.

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Detecting molecular interactions by measuring conformational changes in real-time and at high-throughput

Biodesy develops technology and tools to deliver highly sensitive detection of conformational changes. Our flagship product, the Delta™ System is an integrated hardware/software platform that utilizes a phenomenon called second-harmonic generation (SHG) to monitor conformational changes of biomolecules in real-time and at high-throughput. This approach enables more immediate understanding of the functional outcome of analyte binding, revealing conformational signatures that distinguish activators from inhibitors and allosteric from orthosteric interactions. Importantly, the Delta System is not limited by the type or size of the target of interest, and our strong scientific expertise has enabled assay development for traditionally challenging targets. Thus, we anticipate that our SHG-based, commercially-available research platform will have significant impact on drug discovery and design broadly across a variety of biomolecular targets.

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Hit Your Target Conformation

The Biodesy Delta employs second harmonic generation (SHG) technology to measure conformational change at high throughput, enabling a more immediate understanding of the mechanistic and functional consequences of ligand binding. The conformational signatures revealed by the Delta enable discrimination of activators from inhibitors and allosteric from orthosteric interactions, even for the most challenging targets.

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Structural Insights in Seconds

Posters

CHARACTERIZING CONFORMATIONAL CHANGES BY SECOND HARMONIC GENERATION (SHG) - A NOVEL TECHNOLOGY FOR MEMBRANE PROTEIN ON-TARGET BINDING AND MECHANISM OF ACTION DIFFERENTIATION

Here, we describe SHG characterization of membrane protein conformational changes upon binding of tool compounds.  We demonstrate how SHG enables the discovery of new chemical matter through screening in a 384- or 1536-well format. In addition, we demonstrate how SHG can distinguish different mechanisms of action through ligand binding (e.g. agonist vs. antagonist).

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Detection of Ligand-Induced Conformational Changes in Oligonucleotides by Second-Harmonic Generation

This work demonstrates the broad potential of SHG for studying oligonucleotides and their conformational changes upon interaction with ligands. As SHG offers a powerful, high-throughput screening approach, our results here also open an important new avenue for identifying novel chemical probes or sequence-targeted drugs that disrupt or modulate DNA or RNA structure and function.

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Determination Of Inhibitor Binding Site (Allosteric vs. Active Site) By Protein Phosphatase Conformational Signatures Detected By Second-Harmonic Generation

Proteins are dynamic molecules that perform specialized functions through unique conformational changes accessible in physiological environments. An ability to specifically and selectively control protein function via conformational modulation is an important goal for development of novel therapeutics and studies of protein mechanism in biological networks and disease. This is exemplified in the SH2 domaincontaining phosphatase 2 (Shp2), a bona fide proto-oncogene member of the protein tyrosine phosphatases (PTP) superfamily. Shp2 exists in equilibrium between multiple conformations, simplified herein as “open” and “closed” states. It consists of two Src Homology domain 2 (SH2) domains and a Protein Tyrosine Phosphatase (PTP) domain. Crystal structures revealed an autoinhibited state where the N-terminal SH2 domain (N-SH2) blocks access to the phosphatase active site. A gain of function mutation, E76K, results in constitutive activation by destabilizing the autoinhibited closed state. Shp2 inhibitors have been reported and they can be generally classified as PTP site binders or allosteric binders. Development of those PTP competitive inhibitors has proven challenging in part due to selectivity issues. One approach to overcome those challenges is to target non-conserved regions outside the active site via development of allosteric inhibitors. Therefore, it is desirable to have assays that can readily identify the binding mode for potential inhibitors.

Here we applied a second-harmonic generation (SHG) based technique for determining the conformational signatures of full-length wild-type Shp2 (FL-Shp2(WT)) as well as full-length Shp2(E76K) (FL-Shp2(E76K)) mutant protein. Using the Biodesy Delta System and a set of previously characterized inhibitors, we confirmed two distinct phosphatase conformations depending on the inhibitor binding mode to the allosteric or PTP catalytic site. This assay was then utilized to bin 62 test compounds into allosteric or PTP site binders.

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Discrimination of kinase conformational states upon inhibitor binding by second harmonic generation

Here, we use SHG to discriminate between conformational states of two full-length kinases and a pseudokinase upon binding to well-characterized tool compounds. Our data demonstrate that SHG provides a quick and easy means to differentiate between inhibitor classes, such as type I and type II kinase inhibitors, and that these SHG results correlate with structural features revealed by X-ray crystallography. As our data highlight, SHG conformational change assays can be easily developed for full-length kinases and proteins lacking enzymatic or biochemical activity, both of which can be difficult to work with in traditional screening assays. SHG measurements can be done in a high-throughput format (384- or 1536-well) with minimal protein consumption. Thus, SHG enables structural screening early in the drug discovery process and will be an invaluable tool for the identification of non-classical kinase inhibitors.

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IDENTIFICATION OF ALLOSTERIC MODULATORS OF KRAS USING BIODESY’S SECOND HARMONIC GENERATION TECHNOLOGY

To screen for conformational modulators of oncogenic K-Ras (G12D), we built and optimized, unbiased SHG assay, which we validated using antibody controls. From an initial ~2700 fragment library screen, we identified several KRas conformational modulators. We believe these fragments will reveal novel allosteric binding pockets for drug targeting and lead compounds to interrogate the relationship between KRas conformation and its biological functions.

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Small Molecules Detected by SHG Modulate the Conformation of alpha-Synuclein

Proteins are structurally dynamic molecules that perform specialized functions through unique conformational changes accessible in physiological environments. An ability to specifically and selectively control protein function via conformational modulation is an important goal for development of novel therapeutics and studies of protein mechanism in biological networks and disease. Here we applied a second-harmonic generation-based technique for studying protein conformation in solution and in real time to the intrinsically disordered, Parkinson disease related protein α-synuclein. 

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Protein Conformational Changes Are Detected and Resolved Site Specifically by Second-Harmonic Generation

Proteins are dynamic molecules that perform specialized functions through unique conformational changes accessible in physiological environments.  An ability to specifically and selectively control protein function via conformational modulation is an important goal for development of novel therapeutics and studies of protein functions in biological networks.  Current structural techniques are limited in their ability to probe conformational changes in many proteins and in solution.  To bridge this gap, we developed an SHG-based technique and applied it to three different protein models: calmodulin, maltose-binding protein, and dihydrofolate reductase. 

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Services

Biodesy CUSTOMIZED Services

  • Development of complex assays for a variety of targets: undruggables, oligonucleotides, kinases, phosphatases, nuclear hormone receptors, and protein-protein interactions
  • High-throughput screening with >100,000 drug candidates/week
  • Identification of conformational signatures to distinguish activators from inhibitors and allosteric from orthosteric interactions
  • Please contact us for a scientific consultation

 

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RNA Drug Discovery Services

The Delta System is a highly sensitive, robust, mass-independent platform amenable to use with the intrinsically dynamic RNA structures. The Delta generates conformational insights that are routinely used to distinguish between structural mechanisms of action and between specific and promiscuous ligands, such as intercalators.

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White Papers

Detecting Conformational Change in Peripheral Membrane Proteins

Peripheral membrane proteins are key regulators of signal transduction pathways at cell membranes. These signaling pathways are activated by conformational changes that occur in peripheral membrane proteins upon ligand binding. Currently, the ability to measure ligand induced conformational change in peripheral membrane proteins under physi- ological conditions is difficult. Here, we discuss a novel approach for detecting and measuring conformational change in peripheral membrane proteins when attached directly to physiologically relevant supported lipid bilayers.

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