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

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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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

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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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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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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