Click Chemistry-based DNA-encoded Glycan Library (DEGL)
Overview of Click Chemistry
The copper(I)-catalyzed alkyne−azide cycloaddition (CuAAC) "click" reaction stands as a highly potent methodology for synthesizing 1,2,3-triazoles, which serve as critical frameworks in natural products and medicinal chemistry. Owing to their pronounced rigidity, stability, chemical inertness, and significant dipole moment, 1,2,3-triazoles emerge as compelling bioisosteres for amides, aromatic rings, and double bonds in drug discovery. Numerous triazole-bearing compounds, including tazobactam, cefatrizine, and carboxyamidotriazole, exhibit potent protein inhibition, demonstrating considerable biochemical activity. The discovery of novel small molecules capable of modulating pharmaceutical targets relied predominantly on High-throughput Screening (HTS). However, the advent of DNA-encoded Glycan Libraries (DECLs) offers a formidable alternative, enabling the relatively low-cost synthesis of extensive small-molecule libraries coupled with rapid target screening capabilities.
DEGL: Precision Glycan Diversity Engineered Through Click Chemistry!
Given the significance of 1,2,3-triazoles in medicinal chemistry, we provide comprehensive service for constructing DEGLs featuring 1,2,3-triazole scaffolds. Our click chemistry-based DEGL construction service is a highly specialized and customizable process that leverages the power of click chemistry to efficiently assemble vast arrays of glycan-DNA conjugates. Our research team provides comprehensive customization options, facilitating the creation of libraries of varying magnitudes according to client specifications. Whether the requirement is for thousands or millions of distinct glycan-DNA conjugates, we offer adaptable solutions to meet diverse research demands.
Workflow
The DEGL construction process allows for the precise assembly of complex glycan structures attached to unique DNA tags, typically involving the following key steps.
Synthesis of DNA Headpiece
Firstly, we synthesize a short DNA headpiece that incorporates a hexynyl moiety that facilitates. Besides, a restructured headpiece will be designed to adopt a looped DNA structure, featuring three alkyne modifications (Octadiynyl dU) to facilitate the attachment of three glycans.
Glycan Conjugation to DNA Headpiece
A glycan with a propyl azido linker is conjugated to the hexynyl moiety of the DNA headpiece using CuAAC click chemistry. The HPLC-purified DNA headpiece is mixed with varying glycan concentrations and click reagents, allowing the reaction to proceed for two hours. Post-reaction, the mixture is desalted, with the reaction's success monitored via MALDI-TOF to ensure complete alkyne-to-glycan conversion.
Quantification and Storage
The glycan-DNA headpiece conjugates are subsequently quantified using a nanodrop spectrophotometer and stored in preparation for subsequent encoding steps.
DNA Encoding of Glycan Conjugates
Distinct DNA sequences corresponding to each glycan are ligated to the sticky ends of the DNA headpiece using T4 DNA ligase, thereby generating DNA-encoded glycan conjugates. For monovalent conjugates, a complementary code strand is hybridized to the headpiece, followed by the ligation of the encoding DNA sequence. For multivalent conjugates, a tail DNA with the appropriate sequence is incorporated alongside ligation buffer and T4 ligase to complete the encoding.
Verification of DNA-encoded Glycans
We perform PCR to confirm the successful amplification of the full-length DNA code and to optimize melting temperature (Tm) conditions for further experiments.
Assembly of DEGL
Diverse glycans undergo synthesis followed by Hybridization-capture-chemical ligation (HCCL) to generate the corresponding DNA-encoded glycans. The assembled glycans are then organized into a first-generation DEGL, ready for validation through selection and sequencing methods.
Publication Data
Technology: HTS, Click chemistry
DOI: org/10.1002/cjoc.202000596
Journal: Communications chemistry
Published: 2020
IF: 5.9
Result: This paper provides a comprehensive overview of recent advancements in click chemistry within the realm of natural product modification, and it summarizes the pharmacological activities and mechanisms of action of active derivatives. Click chemistry, a robust synthetic technique, facilitates the acquisition of molecular diversity and unique functionalities of complex natural products. This enables the synthesis of various natural product derivatives, aimed at rectifying their shortcomings or constructing drug-screening libraries akin to natural products. The authors also highlighted other powerful screening technologies, particularly natural product DNA-encoded libraries (nDELs), which have demonstrated substantial capabilities in targeting challenging protein entities. By combining natural products with DELs and utilizing click chemistry for diversification, a vast library of natural product derivatives with unprecedented scaffold diversity can be rapidly generated. Additionally, since DEL screening is affinity-based, molecular targets of hits can be precisely identified post-screening. Besides, the authors researched the extensive achievements of click chemistry in natural product medicinal chemistry and offered perspectives, trends, and directions for future research.
Applications
- DEGL can be used in the realm of glycan-based drug development by identifying specific glycan molecules that exhibit a high affinity for disease-associated glycosylation sites.
- DEGL is useful for the screening of glycans that interact with glycosylation-related enzymes or receptors, identifying molecules that may have inhibitory effects on the glycosylation process.
- DEGL can be applied for a detailed examination of the interactions between glycans and antibodies, which is essential for the development of new antibody therapies and for understanding the role of glycans in immune responses.
Advantages
- Our offering encompasses a range of customizable library sizes, spanning from compact collections tailored for preliminary assessments to extensive libraries designed to probe an expansive chemical landscape.
- Furthermore, our systems are adeptly designed to scale, ensuring that the construction of even the most extensive libraries is efficient.
- In addition to constructing DEGLs, CD BioGlyco also offers screening and validation services, utilizing HTS technology to rapidly identify compounds with potential biological activity.
Frequently Asked Questions
- What are the advantages of DEGL?
- The core strength of DEGL technology lies in its ability to couple compound identity with specific DNA-encoding tags, enabling the affinity-based selection of highly complex mixtures against immobilized protein targets of interest. The bound fraction is then subject to amplification and deep sequencing, revealing expansive collections of hit structures in a single experiment. The statistical prowess of DEGL far surpasses that of traditional combinatorial chemistry by several orders of magnitude, providing both a high degree of confidence in the authenticity of hits and rich insights into structure-activity relationship (SAR) patterns.
- What are the advantages of Click Chemistry?
- Broad scope
- Quantitative yield
- Abundant starting material
- Mild reaction conditions
- High chemoselectivity
CD BioGlyco effectively harnesses click chemistry for the synthesis of glycan conjugates and DNA encoding, culminating in a library of glycans poised for downstream applications such as multiplexed detection through next-generation sequencing (NGS). If you are interested in screening and identification of glycans with specific functions and advancing the fields of glycan chemistry and glycobiology, contact us.
Reference
- Zhang, J.; Dong, J. Modular click chemistry library: searching for better functions. Chinese Journal of Chemistry. 2021, 39(4): 1025-1027.
For research use only. Not intended for any clinical use.
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