Photocatalytic Cycloaddition-based DNA-encoded Glycan Library (DEGL)

Overview of Photocatalysis for DNA-encoded Glycan Library (DEGL)

DNA-encoded libraries (DELs) represent an exceptionally compelling method for discovering small molecule ligands. These libraries are comprised of glycans that are covalently linked to distinct DNA sequences, each carrying specific, readable information about the structure of the associated compound. Various chemical reactions are employed in the construction of DELs. These reactions include a range of strategies such as Aromatic Heterocyclization, Non-aromatic Heterocyclization, Carbocyclization, Macrocyclization, and Click Chemistry, all of which contribute to the creation of diverse and functionalized glycan libraries. The significant potential of visible-light photocatalysis for the synthesis of DEGLs. In the presence of an appropriate photocatalyst and blue light, a variety of carbon-centered radicals can be rapidly generated from numerous precursors. These radicals can subsequently be utilized to form new C(sp²)-C(sp³) or C(sp³)-C(sp³) bonds with DNA-tagged substrates.

Empowering Glycan Discovery with Photocatalytic Precision: The Future of DEGL

Therefore, CD BioGlyco employs photocatalysts in combination with blue light to directly assemble complex chemical architectures onto DNA strands. Specifically, our research team uses a wide range of knowledge for photocatalytic transformations to enable the on-DNA construction of densely functionalized cyclobutane scaffolds through photosensitized intermolecular [2 + 2] cycloaddition reactions. In the construction of DEGLs, the utilization of photocatalytic [2 + 2] cycloaddition reactions for synthesizing structurally unique cyclobutane scaffolds unfolds.

Workflow

The steps of DEGL construction. (CD BioGlyco)

Substrate Design and Synthesis

Initially, a range of α,β-unsaturated carbonyl compounds, including α,β-unsaturated ketones, and esters, are selected. These substrates commonly employ alkyl esters such as methyl, ethyl, and tert-butyl esters, more intricate ester moieties featuring heteroaryl groups, cinnamic acid derivatives, cinnamaldehydes, and cinnamitrile. We select these commercial compounds as substrates. If the substrates are not commercially available, they will be synthesized using organic chemistry techniques.

Optimize Reaction Conditions

The reactivity of various DNA-tagged styrene reagents will be explored. Besides, we utilize a transparent 96-well plate with a blue LED array (λ ≈ 450 nm) as the light source to optimize reaction conditions, including reaction time, solvent, photocatalyst, and additives. Through this step, we investigate and optimize the synthesis of highly substituted cyclobutanes by accommodating additional substituents and improving yield, thereby expanding the scope and practicality of the cyclobutane synthesis process.

DEGL Construction

Under optimized conditions, mix the DNA-tagged substrate with another glycan reactant and carry out the [2 + 2] cycloaddition reaction under blue light irradiation. Then purify and identify the products using techniques such as liquid chromatography-mass spectrometry (LC-MS) to confirm the correctness and purity of the products. Subsequently, we validate the encoding efficiency and detectability of DNA tags through biological analysis workflows to ensure accurate identification and tracking of each product. Last, we mix various encoded products to construct a DEGL.

After the construction of DEGL, we apply High-throughput Screening technologies to the DEGL to identify glycans with specific biological activities.

Publication Data

Technology: Fluorescence quenching study, Density functional theory (DFT)

DOI: org/10.1038/s42004-020-00378-x

Journal: Communications chemistry

Published: 2020

IF: 5.9

Result: In this study, the authors were inspired by the style of renowned chemist Jean-Pierre Sauvage and they unveiled an innovative [2 + 2] cycloaddition reaction coupled with ring-opening rearomatization. This approach harnessed the reactivity of electron-deficient methylene azaarenes and double bonds, resulting in the efficient synthesis of cyclobutanes. Demonstrating remarkable tolerance for a variety of functional groups, this method was adaptable to a wide array of azaarenes and different substituents on styrenes and other alkenes. Notably, the employment of visible light photocatalysis, as opposed to traditional UV methods, mitigated selectivity challenges and broadens the spectrum of feasible substrates. Complementary fluorescence quenching experiments and theoretical calculations provide robust support for a reaction mechanism where photosensitization primarily involves the pseudo-enamine form of the azaarene, rather than its alkene counterpart. This innovative technique holds considerable promise for advancing drug discovery, offering a novel pathway for the functionalization of natural products and the development of new bioactive compounds.

Applications

Photocatalytic cycloaddition-based DEGL can be applied for the identification of allosteric binding sites on target proteins that were previously unknown. Such discoveries offer profound insights into the regulatory mechanisms of proteins and open avenues for targeting these newly recognized sites in drug development.
Photocatalytic cycloaddition-based DEGL is useful for its potential to move glycans from the initial discovery phases through to clinical development.
Photocatalytic cycloaddition-based DEGL can be used for the research and discovery of numerous bioactive compounds.

Advantages

We utilize the DEGL technology to facilitate the efficient synthesis, manipulation, and examination of vast arrays of chemically synthesized, drug-like molecules.
Our researchers use a highly effective, broadly applicable assay grounded in Darwinian selection principles to evaluate these compounds.
Our research team improves the design of compound libraries to enhance their effectiveness and coverage in drug discovery efforts.

Frequently Asked Questions

What is the mechanism of photocatalytic [2 + 2] cycloaddition reaction?
- The mechanism proposed for this reaction involves the photoexcitation of a suitable photocatalyst, which then undergoes intersystem crossing (ISC) to access a triplet excited state. The photocatalyst subsequently transfers its energy from the lowest triplet state (ET(Ir(ppy)₂(dtbbpy)PF₆) = 49.2 kcal/mol) to the substrate. This process of light-induced substrate activation is commonly referred to as triplet energy transfer or sensitization.
What are the methods for high throughput screening of DEGLs?

CD BioGlyco constructs photocatalytic cycloaddition-based DEGL, involving the careful selection of substrates, optimization of reaction conditions, and the employment of photocatalytic [2 + 2] cycloaddition reactions to synthesize glycans featuring cyclobutane scaffolds, which may have promising pharmaceutical applications. Contact us if you would like the efficient creation of structurally diverse DEGLs, enriching the chemical space available for drug discovery.

Reference

Salaverri, N., et al. Visible light mediated photocatalytic [2 + 2] cycloaddition/ring-opening rearomatization cascade of electron-deficient azaarenes and vinylarenes. Communications Chemistry. 2020, 3(1): 132.

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