On July 29, 2025, a transformative study by Tse et al. in RSC Med. Chem. demonstrated how accessible DNA-encoded library (DEL) technology expands research possibilities by overcoming historical barriers. Using simple amide coupling chemistry and commercially available building blocks like Fmoc-amino acids, the team constructed a diverse 3-million-compound DEL with minimal resources, achieving 89% DNA recovery through optimized purification. Biological validation against carbonic anhydrase IX confirmed effective enrichment of known inhibitors.

Background

The landscape of early drug discovery is being transformed by DEL technology, which enables researchers to screen billions of compounds simultaneously with minimal resource requirements. A groundbreaking study demonstrates how strategic innovations are making this powerful technology accessible to broader research communities while maintaining high-quality output.

Breaking Through Traditional Barriers

DEL technology has historically faced adoption challenges due to several constraints:

• Specialized equipment requirements beyond standard laboratory capabilities
• Extensive chemical resources and expensive building blocks
• Demanding expertise in both combinatorial chemistry and molecular biology
• Significant upfront investment in DNA-conjugated starting materials

This research directly addresses these limitations through practical solutions that maintain scientific rigor while reducing complexity and cost. The approach proves that sophisticated screening libraries can be created without exotic chemistry or prohibitive resource investments.

Practical Innovations in Library Construction

The research team developed a medium-sized DEL (3 million compounds) using accessible synthetic methodology:

• Streamlined Chemical Approach
  • Utilized simple amide coupling chemistry rather than complex transformations
  • Selected commercially available Fmoc-amino acids and carboxylic acids as building blocks
  • Implemented robust reaction conditions with DMTMM-mediated couplings
  • Established validation protocols for 171 N-Fmoc amino acids and 227 carboxylic acids
• Optimized Technical Handling
  • Developed a combined centrifugal evaporation and buffer exchange purification
  • Increased DNA recovery rates from 20% to 89% after synthetic steps
  • Designed encoding strategies with a Hamming distance of 3 to minimize cross-hybridization
  • Implemented control systems to identify truncated side-products
• Quality Validation Framework
  • Conducted rigorous LC-MS analysis of all building block couplings
  • Established acceptance criteria based on conversion rates and purity
  • Created reference standards for ongoing quality assessment
  • Developed analytical methods for DNA integrity monitoring

Fig.1 Enrichment of the CAIX inhibitor 4-sulfamoylbenzoic acid from the 3 million-member DEL. (Tse, et al., 2025)

Real-World Validation and Performance

The library's effectiveness was demonstrated through biological screening against carbonic anhydrase IX, an important cancer target. The results confirmed excellent performance with clear enrichment of known sulfonamide binders and minimal background noise. The team optimized selection conditions to reduce false positives, particularly addressing challenges with histidine-rich proteins and bead-based selection artifacts.

Computational analysis revealed that the library occupies valuable chemical space with ideal drug-like properties:

• Average molecular weight: 438 Da
• Optimal lipophilicity: logP 1.7
• Appropriate polar surface area: 106 Ų
• Balanced hydrogen bond donors: 2.6
• Excellent shape diversity comparable to high-quality HTS collections

Democratizing Access to Advanced Screening

This research represents a significant step toward making DEL technology accessible to academic laboratories and smaller companies. The practical innovations and detailed protocols provide a blueprint that organizations can follow without requiring extensive previous experience with DNA-encoded chemistry. The library's design specifically addresses common pain points in DEL implementation, offering solutions that reduce both cost and technical barriers.

The implications for the research community are substantial. Previously resource-limited research groups can now leverage DEL technology to pursue novel drug targets, investigate rare diseases, or explore innovative therapeutic approaches. The dramatically reduced material requirements—micrograms rather than milligrams of target protein—make target exploration feasible even for modestly funded research programs.

Future Directions and Applications

This work establishes a foundation for continued innovation in accessible DEL technology. The validated building blocks and optimized protocols provide a starting point for further library development and specialization. Researchers can build upon this foundation to create targeted libraries for specific protein families or therapeutic areas.

The approach also enables new applications in drug discovery, particularly for challenging targets that require specialized chemical matter. The technology's accessibility means that more researchers can contribute to solving difficult problems in drug discovery, potentially accelerating progress against underserved disease areas and difficult biological targets.

CD BioGlyco provides DEL Screening Services and consultation based on these accessible approaches. Contact us to discuss how to implement these methods in your drug discovery programs.