Design, preparation, and selection of DNA-encoded dynamic libraries

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• Traditional methods for selecting drug candidates face limitations in library size and target protein preparation.
• Dynamic combinatorial chemistry offers a way to explore vast chemical spaces but requires efficient selection mechanisms.

Purpose of the Study:

• To develop a novel method for preparing and selecting DNA-encoded dynamic libraries (DEDLs).
• To enable the selection of high-affinity binders against protein targets without requiring modified or immobilized proteins.

Main Methods:

• Preparation of DEDLs using two sets of DNA-linked small molecules undergoing dynamic exchange via DNA hybridization.
• Utilizing a novel locking mechanism to freeze the dynamic equilibrium after target binding.
• Hit isolation and decoding through PCR amplification and DNA sequencing.

Main Results:

• The DEDL approach successfully selected high-affinity bivalent binders by shifting equilibrium upon target addition.
• A locking mechanism was introduced to stabilize selected binders for downstream analysis.
• The method circumvents limitations in library size, enabling analysis of large dynamic libraries.
• The requirement for modified and immobilized target proteins was eliminated.

Conclusions:

• DEDLs provide a powerful platform for efficient drug discovery and lead identification.
• The developed locking mechanism enhances the reliability and applicability of DEDLs.
• This approach significantly expands the scope and feasibility of screening large chemical libraries against protein targets.