DNA Programmed Affinity Labelling (DPAL)-based DEGL Screening
Overview of DPAL-based DEGL screening
DNA programmed affinity labeling (DPAL) based DNA-encoded glycan library (DEGL) screening is an innovative approach combining DPAL with DNA-encoded chemical libraries (DEL) for live-cell protein target identification. By using antibodies to guide labeling, this method overcomes the need for pre-known ligands and allows DEL selection directly on the surface of live cells. The approach enhances the effective target concentration, facilitating the discovery of ligands for challenging drug targets, such as GPCRs and ion channels, with high specificity and efficiency in a cellular context.
Unlocking the Power of Glycans with Precision Ligand Discovery
CD BioGlyco's DPAL-based DEGL screening service employs a sophisticated approach that merges DEL technology with affinity-based selection techniques. This standard workflow is crafted to pinpoint specific ligands that bind to targeted proteins, especially those that are typically difficult to isolate or examine using conventional methods.
Workflow
Target preparation
The workflow begins by preparing the glycan-related target, typically a glycoprotein or a glycan-binding protein, in a form that is optimal for selection.
DEGL construction
A comprehensive DEGL is synthesized, comprising millions to billions of diverse small molecules, each uniquely tagged with a DNA sequence that encodes its structure. These molecules are specifically designed to interact with glycan structures.
Affinity labeling and selection
The DEGL is incubated with the glycan-related target under conditions that allow selective interactions between the glycan sites and the library members. During this process, molecules that exhibit a strong affinity for the glycan structures bind and are tagged with DNA labels through photocrosslinking.
Hybridization and washing
Following incubation, the library undergoes washing steps to eliminate non-specific binders.
PCR amplification and next-generation sequencing (NGS)
The DNA tags attached to the bound molecules are amplified using PCR and sequenced with NGS. This process identifies the DNA sequences corresponding to the molecules that successfully interacted with the glycan target.
Data analysis and hit identification
The sequencing data are analyzed to pinpoint enriched DNA sequences, which correlate to molecules with the highest binding affinity to the glycan target.
Hit validation
The identified hits are resynthesized and subjected to additional assays to confirm their binding affinity and specificity to the glycan target.
Optimization and development
Validated hits undergo further optimization to enhance their binding properties, stability, and potential for therapeutic applications.
Applications
- The DPAL-based DEGL screening service is particularly effective for identifying small molecules that bind specifically to glycan structures on proteins.
- By identifying ligands that selectively bind to glycan structures, this screening service can be used to discover new biomarkers for various diseases.
- Our service can aid in the identification of molecules that interact with glycan epitopes on pathogens, which can be leveraged in the design of vaccines.
Advantages
- The integration of DEL technology with affinity-based selection processes ensures that the screening service can precisely target glycan structures, which are often challenging to study using conventional methods.
- The DPAL-based approach allows for rapid identification of ligands, significantly reducing the time required for drug discovery and development compared to traditional methods.
- Our workflow can be tailored to target specific glycan-related proteins or enzymes, making it highly adaptable to various research needs and therapeutic goals.
Publication
Technology: DEL synthesis and screening, Affinity labeling, PCR amplification, NGS
Journal: FEBS letters
IF: 3
Published: 2018
Results: The research highlights the maturation and widespread adoption of DEL technology as a powerful platform for small-molecule discovery. The study demonstrates how DEL technology has enabled the rapid identification and optimization of bioactive ligands for various therapeutically relevant targets, many of which are challenging to address with traditional screening methods. The key findings emphasize the efficiency, versatility, and cost-effectiveness of DELs compared to conventional approaches, showcasing their ability to screen vast chemical libraries in a pooled format, thereby significantly accelerating the drug discovery process.
Fig.1 Schematic representation of (A) a single-pharmacophore DEL and (B) a dual-pharmacophore DEL. (Favalli, et al., 2018)
Frequently Asked Questions
- How does the DPAL-based screening process work?
- The screening process involves preparing the glycan target, synthesizing a vast DNA-encoded library of potential ligands, and incubating this library with the target protein. Molecules that bind to the target are then identified through a process of DNA tagging, hybridization, washing, PCR amplification, and NGS. The hits are analyzed, validated, and optimized for potential therapeutic applications.
- What are the main applications of this screening service?
- Our DPAL-based DEGL screening service can be applied in drug discovery for glycan-targeted therapies, biomarker discovery, vaccine development, enzyme inhibitor screening, and the development of antibodies. It is particularly useful in identifying ligands for diseases where glycosylation is a key factor.
At CD BioGlyco, our DPAL-based DEGL screening service provides a comprehensive report that includes the identified hits, their corresponding DNA sequences, binding affinity data, and any additional validation results. Please feel free to contact us for more information and please do not hesitate to discover how we can support your research.
Reference
- Favalli, N.; et al. DNA-encoded chemical libraries-achievements and remaining challenges. FEBS letters. 2018, 592(12): 2168-2180.
For research use only. Not intended for any clinical use.
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