On January 19, 2020, a seminal review by Shi et al. in RSC Advances (2021) titled "DNA-encoded libraries (DELs): a review of on-DNA chemistries and their output" unveiled the transformative role of on-DNA chemistry in revolutionizing drug discovery. This comprehensive analysis demonstrates that DELs leverage DNA barcoding to enable ultra-high-throughput screening of trillion-scale compound collections against biological targets, using minimal protein samples and resources. The study elucidates that key innovations in DNA-compatible reactions—such as cross-coupling transformations, multicomponent assemblies, and bioorthogonal strategies—have overcome historical constraints by preserving nucleic acid integrity while enabling diverse bond formations. Mechanistically, these advances facilitate precise control over chemical fidelity under mild conditions, allowing for the generation of complex scaffolds targeting previously intractable pathways. Importantly, this paradigm shift has accelerated hit identification for kinase inhibitors, protein-protein interaction disruptors, and allosteric modulators, reducing early-stage discovery timelines and costs. The work not only maps current applications but also charts future directions, including machine learning integration and cellular screening, underscoring DELs' potential to unlock novel therapeutic avenues.

Introduction

In the relentless pursuit of novel therapeutics, DELs have emerged as a transformative technology, enabling the rapid screening of billions to trillions of small molecules against biological targets. This paradigm shift is accelerating hit identification while drastically reducing the time, cost, and resources required in early drug discovery.

Fig.1 C-C sp²-sp² coupling DNA-compatible reactions. (Shi, et al., 2020)

Overview: The DEL Advantage

DELs represent a convergence of combinatorial chemistry and molecular biology, where each compound is tagged with a unique DNA barcode. This elegant encoding system allows for:

• Ultra-high-throughput screening: Simultaneously evaluate billions of compounds
• Minimal resource consumption: Requires micrograms of target protein
• Unprecedented diversity: Access to chemical spaces beyond traditional HTS

The critical breakthrough lies in developing DNA-compatible reactions that preserve both DNA integrity and chemical fidelity.

Key Innovations in On-DNA Chemistry

• Advanced Reaction Development

The review highlights sophisticated on-DNA transformations that have overcome previous limitations:

• Cross-coupling reactions: Pd-catalyzed C-C/C-N bond formations under mild conditions
• Multicomponent reactions: Groebke-Blackburn-Bienaymé and Ugi reactions for scaffold diversity
• Photoredox catalysis: Enabling radical-based transformations with DNA compatibility
• Bioorthogonal chemistry: Strain-promoted azide-alkyne cycloadditions for late-stage diversification

• Strategic Bond Formation/Cleavage

Innovative approaches to chemical bond manipulation on DNA include:

• Reversible covalent chemistry: Dynamic library generation for target-guided synthesis
• DNA-templated synthesis: Leveraging hybridization for proximity-driven reactions
• Enzyme-mediated transformations: Biocatalytic steps integrated with synthetic chemistry

DEL Output: From Screening to Clinical Candidates

The past five years have witnessed remarkable success stories where DEL screening yielded compounds with proven druggability:

• Kinase inhibitors: Achieving picomolar potency with excellent selectivity profiles
• Protein-protein interaction disruptors: Targeting previously "undruggable" interfaces
• Allosteric modulators: Discovering novel regulatory sites on GPCRs and enzymes

Case studies demonstrate hit-to-lead optimization journeys with improved pharmacokinetic properties and in vivo efficacy.

Technical Challenges and Solutions

• Encoding Fidelity
  • Next-generation sequencing error correction algorithms
  • Dual-encoding strategies for redundancy and validation
• Chemical Compatibility
  • pH- and temperature-controlled reaction conditions
  • Novel protecting groups stable to DNA manipulation

Future Directions

The field is evolving toward:

• Machine learning integration: Predictive models for reaction success and compound properties
• Spatially encoded libraries: Multiplexed screening against multiple targets
• Cellular DEL applications: Direct screening in physiological environments

Related Services

CD BioGlyco provides end-to-end DNA-Compatible Reaction Development for DEL-based drug discovery.

Conclusion

The strategic advancement of on-DNA chemistries is fundamentally reshaping the drug discovery landscape. As DEL technology continues to mature, it promises to unlock new therapeutic opportunities against challenging targets. The comprehensive review by Shi et al. provides both a roadmap for current applications and a vision for future innovations in this dynamic field.