Aromatic Heterocyclization-based DNA-encoded Glycan Library (DEGL)

Overview of DNA-encoded Glycan Library (DEGL) Technology

DEGLs constitute a groundbreaking collection of glycans, each covalently attached to DNA oligonucleotides, which function as amplifiable identification markers for the corresponding organic compounds. CD BioGlyco conducts the construction of DEGLs typically by utilizing a split-and-pool strategy, wherein diverse sets of building blocks are sequentially affixed to a DNA oligonucleotide-substrate conjugate, simultaneously incorporating a distinct DNA codon for each building block. Following this, the resultant products are pooled and divided into separate wells. This procedural partitioning facilitates the introduction of additional building blocks, each uniquely encoded through the ligation of a new DNA oligonucleotide, culminating in a distinct DNA sequence attributable to each final compound. Subsequently, we subject the final products to affinity selection screening as a pooled mixture, using the DNA barcode to identify successful hits that are selected by the High-Throughput Screening.

DEGL: Unlocking Complex Carbohydrates with Precision

This advanced technology necessitates that all chemical reactions remain compatible with DNA. During the library synthesis process, we maintain the integrity of the DNA oligonucleotide through diverse strategies, including Coupling Reaction, Multi-component Reaction, Photocatalytic Cycloaddition, Non-aromatic Heterocyclization, Carbocyclization, Macrocyclization, and Click Chemistry. On this page, we utilize aromatic heterocyclization to assist our clients in constructing DEGLs with aromatic heterocyclic structures. We employ the latest strategies for forming five-membered aromatic heterocyclic rings, six-membered aromatic heterocyclic rings, and fused heterocycles, directly on DNA-linked glycans. From five-membered to six-membered rings, and extending to fused aromatic heterocyclic systems, our library is designed to cater to specific biological and pharmaceutical attributes with precision.

Method for on-DNA Five-membered Aromatic Heterocycles Synthesis

The synthesis of five-membered aromatic heterocycles involves various methods, including the following reactions.

1,2,4-Oxadiazoles are synthesized from DNA-linked aryl nitriles and various carboxylic acids.
We prepare 1,3,4-oxadiazoles via Ugi four-component reactions and aza-Wittig reactions but require specific "hexT" oligonucleotides to avoid depurination.
Our researchers use Ugi-azide four-component reactions with various amines and substituted isocyanates to synthesize substituted tetrazoles.
Isoxazoles are generated from DNA-linked α,β-unsaturated ketones.
Imidazoles are synthesized via a one-pot three-component Van Leusen reaction, using DNA-linked aromatic aldehydes and primary amines.
Produce pyrroles from DNA-linked α,β-unsaturated ketones.
Synthesize pyrazoles from DNA-linked α,β-unsaturated ketones, hydrazines, and DDQ.

Method for on-DNA Six-membered Aromatic Heterocycle Synthesis

Other methods are utilized for synthesizing six-membered aromatic heterocycles.

Using advanced synthetic strategies, we engineer pyrazines through inverse electron demand Diels-Alder (IEDDA) reactions. This process employs DNA-linked 1,2,4,5-tetrazoles in conjunction with olefins or ketones/aldes to construct these heterocyclic compounds.
Our approach to synthesizing pyridines and pyrimidines involves cyclization reactions utilizing 1,5-diketones or α,β-unsaturated ketones, thus facilitating the formation of these aromatic heterocycles.

Method for on-DNA Fused Aromatic Heterocycle Synthesis

Besides, we have the ability to obtain some fused heterocycles.

We accomplish the formation of benzimidazoles by reducing DNA-linked o-nitroanilines to aryl diamines, which are then reacted with aldehydes, yielding the desired fused heterocycles.
We synthesize 2-aminobenzimidazoles starting from aryl diamines and isothiocyanates formed in situ. These intermediates undergo cyclization and subsequent desulfurization using iodine to produce the final compounds.

Workflow

Workflow for constructing aromatic heterocyclization-based DEGL. (CD BioGlyco)

We illustrate our workflow by using the construction of DGELs with a pyrrolo[2,3-d]pyrimidine structure as an example.

Preparation of Model Compounds

Initially, we utilize resin to prepare several model compounds encoded with DNA sequences, aiming to assess both the synthetic efficiency and the compatibility with DNA tags. The resin undergoes a series of chemical transformations, including Fmoc-based chemistry for attaching spacer groups (Ahx) and linker groups (for DNA tag coupling), followed by the incorporation of a photolytic linker (ANP) and the synthesis of the DNA-encoded tags.

Construction of the Glycan Library

We will construct a DEGL of pyrrolo[2,3-d]pyrimidines using various amines and aldehydes. With the split-and-pool synthesis method, we generate a library of tetra-substituted pyrrolo[2,3-d]pyrimidines on beads, achieving tens of thousands of glycan compounds. On the resin, we will synthesize target compounds through chloracetylation and amine substitution, incorporating DNA tags. We then add a third DNA sequence for the R3 group using T4 DNA ligase. Finally, we synthesize the pyrrolo[2,3-d]pyrimidine structures via intramolecular aldol condensation with DIPEA and sodium methoxide. Last, time-of-flight mass spectrometry (TOF-MS) verifies successful library generation.

Publication Data

Technology: Pharmacokinetic, Toxicological, Drug design, Drug discovery

DOI: 10.3390/pharmaceutics15112554

Journal: Pharmaceutics

Published: 2023

IF: 4.9

Results: In this study, authors described the pivotal role of five-membered aromatic heterocycles within antibacterial agents, such as isoxazoles and thiophenes. The biological activity of drugs is significantly influenced by the physicochemical characteristics of these heterocycles, impacting their spectrum of activity, efficacy, pharmacokinetics, and toxicological profiles. Utilizing scientific databases, the authors identified and analyzed antibacterial agents featuring five-membered heterocycles in their molecular structures. These heterocycles incorporate one to four heteroatoms, such as nitrogen, oxygen, or sulfur. They also discussed that how these heterocycles impart distinct biological properties to the antibacterials, often serving as crucial pharmacophores that drive specific antibacterial activities. By acting as pharmacophores, these heterocycles facilitate the design of novel therapeutic molecules, enhancing their potency and selectivity, and providing insights into the structure-activity relationships of antibiotics.

Applications

DEGLs can be used for their ability to empower the identification of unprecedented glycan-based ligands with specific receptor interactions, thus driving the development of novel therapeutic agents with potentially groundbreaking applications.
DEGLs can be researched for the design of advanced diagnostic tools, leveraging glycan interactions with enzymes and other biomolecules to enhance detection and diagnostic precision.
DEGLs provide critical insights into intricate biological pathways, thereby facilitating the creation of more targeted and effective therapeutic interventions.

Advantages of Us

Our DEGL technology embodies a formidable methodology for discovering hit compounds during drug development initiatives, standing robustly alongside more conventional techniques like high-throughput screening.
Our research team exploits the diverse capabilities of aromatic heterocyclization reactions to produce an unparalleled variety of glycan structures.
Our DEGL construction is fully customizable, enabling clients to specify the types of aromatic heterocycles, glycan structures, and screening assays they are interested in.

Frequently Asked Questions

What are the advantages of DEGL?
- By leveraging cutting-edge technologies, rapid and efficient synthesis of extensive libraries is achieved, enabling researchers to explore expansive chemical spaces with minimal effort and time.
- Each glycan in the library is distinctly labeled with a DNA barcode, facilitating high-throughput screening and precise identification of bioactive compounds. This DNA-encoded strategy revolutionizes conventional glycan synthesis and discovery methodologies.
In addition to the DEGLs mentioned above, what other structures of DEGLs can you synthesize?
- We have the ability to synthesize other heterocyclic compounds such as imidazo[1,2-a]pyridines, indole-3-carboxamides, quinolines on DNA, and so on.

Through the advanced principles of aromatic heterocyclization chemistry applied to DNA, CD BioGlyco provides clients with an exceptional and potent resource for delving into the extensive realm of glycan structures. Our platform, which is both customizable and scalable, coupled with its high-throughput capabilities, is set to transform the domain of glycan science. Contact us if you want to facilitate the rapid and efficient discovery of novel bioactive molecules.

Reference

Rusu, A.; et al. The role of five-membered heterocycles in the molecular structure of antibacterial drugs used in therapy. Pharmaceutics. 2023, 15(11): 2554.

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