Design of Three-Dimensional Core Building Blocks adapted for DECL-Synthesis

Title: Design of Three-Dimensional Core Building Blocks Adapted for DECL-Synthesis


Designing three-dimensional core building blocks is a critical aspect of synthesizing diverse libraries using DNA-Encoded Library Chemistry (DECL). DECL is a powerful technique for high-throughput screening and discovery of small molecule ligands. In this blog post, we will focus on the key points surrounding the design of three-dimensional core building blocks specifically adapted for DECL-synthesis, and their implications in drug discovery and chemical biology.

Key Points

  1. DNA-Encoded Library Chemistry (DECL): DECL combines combinatorial chemistry, DNA encoding, and high-throughput screening to enable the synthesis and screening of vast libraries of small molecules. Each molecule within the library is tagged by a unique DNA barcode, allowing for efficient identification and tracking during the screening process.
  2. Importance of Three-Dimensional (3D) Core Building Blocks: The complexity and diversity of small molecules play a significant role in their biological activity and ability to interact with target proteins. Three-dimensional core building blocks provide the necessary structural diversity to explore a wide range of chemical space and enhance the likelihood of identifying potent and selective compounds for specific targets.
  3. Rational Design Strategies: Rational design strategies are employed in the creation of 3D core building blocks for DECL-synthesis. These strategies involve the incorporation of diverse chemical functionalities and structural features, such as chiral centers, stereochemical constraints, and sp^3-rich frameworks. These elements increase the complexity and three-dimensionality of the library, giving rise to a greater chance of finding hits with desired pharmacological properties.
  4. Synthetic Approaches: Various synthetic approaches are used to generate the 3D core building blocks for DECL-synthesis. These approaches may involve the use of multicomponent reactions, diversity-oriented synthesis, or the modification of existing scaffolds. The aim is to create structurally diverse libraries that cover a wide range of chemical space and maximize the chances of finding biologically active compounds.
  5. DNA Tagging and Encoding: Each 3D core building block is conjugated to a specific DNA barcode, allowing for its identification and sorting during the screening process. The DNA tag serves as a unique identifier, enabling the efficient tracking and deconvolution of active compounds from the library. This encoding strategy is essential for high-throughput screening and hit identification.
  6. Diversity and Drug-like Properties: The design of 3D core building blocks adapted for DECL-synthesis aims to create libraries with maximum diversity while ensuring drug-like properties. This involves considerations such as molecular weight, lipophilicity, and the presence of key functional groups. By incorporating these factors into the design, it increases the likelihood of identifying hits that can be further developed into potential drug candidates.
  7. Applications in Drug Discovery and Chemical Biology: The use of 3D core building blocks in DECL-synthesis has facilitated the discovery of small molecule ligands against various biological targets. These ligands have potential applications in drug discovery, chemical biology, and target validation. In addition, the identification of novel hits through DECL-synthesis provides valuable starting points for lead optimization and drug development.


The design of three-dimensional core building blocks adapted for DECL-synthesis has revolutionized the discovery of small molecule ligands and accelerated drug discovery efforts. By systematically designing libraries with diverse 3D structures, scientists can explore vast chemical space and identify hits with high binding affinity and selectivity. The integration of DNA tagging and encoding ensures efficient screening and tracking of active compounds. The applications of DECL-synthesized libraries in drug discovery and chemical biology promise exciting opportunities for the development of novel therapeutics and the advancement of scientific knowledge.