Scaffold-based DNA-encoded Glycan Library (DEGL)

Overview of Scaffold-based DNA-encoded Glycan Library (DEGL)

DEGL technology has transformed the way we approach the synthesis and screening of glycan libraries by combining the principles of DNA tagging with glycan synthesis.

At CD BioGlyco, our scaffold-based DEGL construction service uses client-specified molecules (such as lead compounds or molecules synthesized by clients) as the scaffold, and efficiently combines glycan units with DNA tags through precisely designed chemical synthesis strategies to construct a library of glycan compounds with diverse structures and rich information. This innovative platform not only greatly expands the explorable space of glycans but also realizes high-throughput screening and rapid data analysis.

Revolutionize Your Discoveries with Scaffold-based DEGL

The scaffold-based DEGL construction is a sophisticated process that capitalizes on our extensive expertise in both synthetic chemistry and molecular biology. The DEGL synthesis workflow is characterized by multiple iterative cycles of chemical reactions, encoding, and amplification, ensuring a diverse and high-quality library for screening.

Schematic diagram of the construction process of scaffold-based DEGL. (CD BioGlyco)

Scaffold Specification and Design

The process begins with the client specifying a molecular scaffold, which can be a lead compound or a proprietary molecule. This scaffold serves as the core structure around which the glycan diversity is constructed.

Generation of Glycan Diversity

Cycle 1: Attachment of Glycan Building Blocks
- We initiate the first cycle by conjugating the scaffold to the DNA starting material, which is named headpiece, using robust chemistries such as nucleophilic substitution or condensation. Then, each building block reacts with the headpiece-scaffold conjugates after being uniquely tagged by a different sequence of DNA, facilitating subsequent identification.
- The products are purified, characterized, and quantified, ensuring sufficient material for subsequent cycles.
Cycle 2 and Beyond: Iterative Expansion
- In subsequent cycles, additional glycan building blocks are attached to the growing scaffold using orthogonal chemistries. Each addition is accompanied by a corresponding DNA code that records the synthetic history of the molecule.
- Common reactions include but are not limited to amide bond formation, thiol-ene click reactions, and glycosylation reactions, each selected based on the nature of the building blocks and the desired final library structure.
- With each cycle, the complexity and diversity of libraries increase exponentially, allowing for the construction of libraries containing millions to tens of millions of unique glycan-scaffold conjugates.

Encoding and Synthesis

The scaffold and the building blocks could be glycan compounds, we make the library design scheme according to your specific needs. And the scaffold can be the commercially available compound or the compound that you provided which is synthesized in your lab. Our synthesis is highly customizable, accommodating the construction of libraries in various scales and sizes. We offer synthesis flexibility that spans from focused libraries containing a few thousand compounds to expansive libraries with several million compounds, tailored precisely to the experimental needs and scale required by our clients.

Final Library Structure

The end products of our DEGL construction are glycan-scaffold conjugates and each is uniquely identifiable by its DNA tag. These libraries consist of a vast array of structurally diverse molecules ready for high-throughput screening against various biological targets.

Quality Control and Validation

Throughout the synthesis process, we employ rigorous quality control measures, including the confirmation of the "ligation" result of DNA tags and the verification of chemical transformations via analytical techniques such as mass spectrography.
Final libraries undergo thorough validation to ensure integrity, diversity, and readiness for downstream applications.

Workflow

Client Consultation and Scaffold Specification

Initial discussions to understand the client's requirements and specification of the scaffold molecule.

Design and Planning

Customized library design, selecting appropriate glycan building blocks and corresponding chemical reactions.
Planning of iterative cycles for scaffold diversification.

Synthesis and Encoding Cycles

First cycle: Attachment of initial glycan building blocks and DNA tagging.
Second cycle: Iterative diversifications via chemical reactions, each step followed by DNA tagging.

Library Construction and Purification

Construction completion after the desired number of cycles.
Purification of the final library to ensure high quality.

Quality Control and Delivery

Comprehensive quality control and validation.
Delivery of the final DEGL to the client, along with detailed documentation of the synthesis process and diversity analysis.

Applications of Scaffold-based DEGL

Biomarker discovery: Scaffold-based DEGLs have broad applications in the field of biomarker discovery. Researchers systematically explore changes in glycosylation patterns associated with specific biological processes or disease states by constructing scaffold-based DEGLs containing rich glycan diversity.
Drug target validation: Scaffold-based DEGLs can be used to validate potential drug targets. Researchers identify ligands with high affinity for specific targets by screening compounds in DEGLs.
Bioinformatics analysis: The large amount of data generated by the construction and screening process of scaffold-based DEGLs provides rich resources for bioinformatics analysis.

Advantages

Highly customized and flexible: The scaffold-based DEGL construction service we provide is highly customized according to the specific needs of clients, including the choice of a scaffold, the diversity of glycan units, and the size of the library.
Efficient DNA encoding technology: We use advanced DNA encoding technology to assign unique DNA tags to each glycan, enabling efficient tracking and rapid identification of compounds.
Extensive chemical synthesis capabilities: We have a strong chemical synthesis team to support a variety of glycosylation reactions from simple to complex.

Publication

Technology: Construction of a versatile and Lipinski-compliant DNA-encoded library (DEL)

Journal: Advanced Science

IF: 14.3

Published: 2020

Results: The authors designed, constructed, and characterized a versatile DEL that adhered to Lipinski's rules, consisting of 366,600 glutamic acid derivatives attached to oligonucleotides acting as amplifiable identification barcodes. This GB-DEL library, formulated in single-stranded DNA, facilitated the de novo identification of specific binders targeting various pharmaceutically significant proteins. Furthermore, by hybridizing the single-stranded DEL with a collection of known protein ligands displaying low to medium affinity, which were linked to a complementary DNA strand, self-assembled selectable chemical structures emerged, ultimately enabling the identification of affinity-matured compounds.

Fig.1 Schematic representation of the synthetical steps involved in GB-DEL formation. (Bassi, et al., 2020)

Frequently Asked Questions

How long does it take to customize scaffold-based DEGL? What factors affect the lead time?
- The lead time of customized scaffold-based DEGL usually depends on multiple factors, including the complexity, quantity, and synthesis difficulty of the required compounds, and the specific needs of the client. Generally speaking, it may take weeks to months from designing the synthesis scheme to the final delivery of DEGL. To shorten the lead time, we will communicate closely with clients to clarify their needs, and continuously optimize the scheme during the synthesis process to improve the synthesis efficiency.
What follow-up support can I get after using your DEGL?
- After clients use our DEGL, we provide a full range of follow-up support. This includes but is not limited to:
- We provide detailed experimental guidance and technical training to help clients master the use and precautions of scaffold-based DEGL.
- We provide data analysis services to help clients interpret screening results and discover potential research directions.
- We provide further customized services according to client needs, such as optimizing synthesis schemes and expanding the scale of scaffold-based DEGL.

At CD BioGlyco, our scaffold-based DEGL construction service combines advanced techniques, expert knowledge, and customization to deliver unparalleled solutions in drug discovery and glycobiology research. Please feel free to contact us for more details if you are interested in our scaffold-based DEGL construction service!

Reference

Bassi, G.; et al. A single-stranded DNA-encoded chemical library based on a stereoisomeric scaffold enables ligand discovery by modular assembly of building blocks. Advanced Science. 2020, 7(22): 2001970.

For research use only. Not intended for any clinical use.