Macrocyclization-based DNA-encoded Glycan Library (DEGL)

Overview of DNA-encoded Glycan Library (DEGL)

The core concept behind the revolutionary DEGL technology lies in the encoding of each compound within an expansive library using a distinctive DNA-based barcode. This approach enables the facile identification of library members enriched during selection campaigns. Identification is achieved through the amplification of the DNA tag via polymerase chain reaction (PCR), followed by decoding through conventional DNA sequencing. By seamlessly integrating novel synthetic designs with fundamental molecular biology techniques, a potent tool emerges for the swift interrogation of vast compound collections. Based on this innovative strategy, CD BioGlyco helps clients Design and construct DEGLs, aiming to revolutionize the field, paving the way for discoveries and advancements in chemical research.

Macrocyclization DEGL: Pioneering New Era in Glycan Screening!

Macrocycles are notably compelling candidates for the identification of biologically active small molecules. To construct a macrocyclization-based DEGL, several advanced techniques for macrocyclization on DNA are employed.

Wittig olefination reaction: We employ the Wittig olefination reaction to directly synthesize macrocycles on DNA.
Ruthenium-promoted ring-closing metathesis: This is a contemporary approach that involves ruthenium as a catalyst for ring-closing metathesis, facilitating olefin formation. To safeguard DNA from potential ruthenium-induced damage, a substantial excess of Mg²⁺ ions is used, alongside heterogeneous reaction conditions to ensure successful macrocyclization.
Acylation reactions: Besides, our research team uses the traditional acylation methods to achieve macrocyclization on DNA.
Copper-catalyzed azide-alkyne cycloaddition: This reaction employs copper as a catalyst to facilitate the formation of macrocycles through the azide-alkyne cycloaddition process.
Disulfide and thioether bond formation: Furthermore, our researchers achieve the macrocyclization using cysteine residues through the formation of disulfide or thioether bonds.
Palladium-catalyzed S-arylation: Additionally, S-arylation techniques are incorporated to further enhance macrocycle formation. This method utilizes palladium to catalyze intramolecular S-arylation with thiols and aryl iodides.

These varied methodologies collectively contribute to the development of a comprehensive DEGL, supporting the efficient synthesis and analysis of extensive glycan libraries.

Workflow

Workflow of DEGL construction. (CD BioGlyco)

The macrocyclization-based DEGL construction involves a systematic process to create diverse libraries of macrocyclic glycans, encoded by DNA sequences.

Starting Materials and Template Design

Begin with selected materials, including DNA templates with specific sequences and DNA-linked building blocks. The templates are designed to ensure proper alignment of these blocks and to avoid any structures that could obstruct the reactions.

DNA Template-directed Reactions

Attach building blocks to DNA templates using a series of chemical reactions. The process is monitored to ensure the formation of the desired products.

Capping Step

To avoid incomplete reactions, unreacted templates are capped, making them inactive for further reactions. This step is checked to confirm that unreacted templates are properly capped without affecting the products.

Addition of Specialized Building Block

Introduce a special building block for the macrocyclization process. The resulting products are captured and prepared for the next stage.

Macrocyclization Reaction

Expose the products to a specific treatment that reveals aldehyde groups and triggers the macrocyclization process. This step also removes the linkers used in previous steps, allowing the macrocyclic products to be released.

Purification and Verification

Purify the macrocyclic products and verify their purity and structure to ensure they are correct.

Publication Data

DOI: org/10.1002/mog2.50

Journal: MedComm-Oncology

Published: 2023

IF: 5.9

Result: In this paper, the authors explored the potential of macrocyclic molecules in cancer drug development and their critical role in cancer therapy. They highlighted cancer as a leading cause of cancer-related mortality worldwide and noted the limited efficacy of current therapies, underscoring the urgent need for novel, effective cancer treatments. Macrocyclic molecules, characterized by their cyclic backbone, have distinctive pharmacological properties, including enhanced bioavailability, improved metabolic stability, elevated binding affinity, and favorable pharmacokinetic profiles. The authors meticulously studied how these molecules target pivotal proteins involved in various cancer progression processes. The latest findings identified 14 hallmarks of cancer, with macrocyclic drug targets implicated in approximately 80% of these hallmarks, such as sustaining proliferative signaling, dysregulating cellular energetics, evading growth suppressors, and resisting cell death. Additionally, recent data revealed that macrocyclic molecules can target bone morphogenetic protein receptor type-II (BMPR2) and death-associated protein kinase 1 (DRAK1) for therapeutic purposes. Thus, macrocyclic compounds have the capacity to address nearly 80% of cancer hallmarks, potentially leading to tumor regression. Furthermore, these molecules exhibit potent inhibition of on-target drug-resistant mutants. In conclusion, macrocyclic molecules present promising therapeutic avenues for cancer patients.

Applications

DEL technology can be used for the rapid identification of macrocyclic glycosylated drug molecules with specific biological activities.
Macrocyclization-based DEGL can be utilized to identify novel glycan biomarkers associated with diseases.
Macrocyclization-based DEGL offers innovative perspectives and methodologies for the validation and optimization of drug targets.

Advantages

We use an array of cutting-edge macrocyclization methodologies, including Wittig olefination reactions, ruthenium-catalyzed ring-closing metathesis reactions, and acylation reactions to ensure the comprehensive and efficient development of macrocyclic glycan libraries.
Our technology employs DNA barcoding to uniquely encode each compound within the library, facilitating the easy identification and tracking of active molecules during screening processes.
Our research team achieves high efficiency in synthesizing and purifying extensive amounts of macrocyclic glycan compounds through systematic workflows and optimized reaction conditions.

Frequently Asked Questions

Why do we construct DEGLs with macrocyclic structures?
- Macrocycles present an exceptional opportunity in the pursuit of biologically active small molecules due to their inherently rigid frameworks, which significantly diminish the entropic penalties associated with target binding and restrict access to non-binding conformations. This results in a higher affinity and increased specificity compared to their linear counterparts. Moreover, macrocyclic peptide-mimetic structures hold distinct advantages for cell culture and in vivo applications when contrasted with their linear analogs, as they often exhibit enhanced bioavailability, improved membrane permeability, and superior resistance to degradation within biological systems.
What types of DEGLs can we construct?

CD BioGlyco provides the DEGL construction service which is an advanced method for creating large libraries of macrocyclic glycans with high purity and accuracy. Our advantages in the construction and application of macrocyclization-based DEGL are evident in its technological innovation, bespoke services, efficiency, and stringent quality control. If you are interested in our high-quality and efficient DEGL construction services, contact us!

Reference

Song, X.; et al. Applications of macrocyclic molecules in cancer therapy: target cancer development or overcome drug resistance. MedComm-Oncology. 2023, 2(3): e50.

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