DNA Encoded Compound Library - BiopharmaDirect

About DEL

In recent years, the biopharmaceutical industry has been undergoing some fundamental changes and transformation. These changes are underlined by the unwavering demands for great medicines to treat serious illness in both developed and developing countries, which highlight the urgent need for the biopharmaceutical industry to foster greater innovation, and to focus on developing various drug candidates.

Figure 1 The evolution of DELs in three stages

DNA encoded compound library (DEL) technology is an efficient small molecule discovery technology for the pharmaceutical industry. The original concept of encoding chemical library with DNA tags was proposed by Brenner and Lerner in 1992. Early works by Brenner, Janda and Gallop, have laid out the important technological foundations for the future development of DELs. DEL eventually becomes a powerful screening platform due to the availability of low-cost, genomic-scale NGS technology. This technology combines the power of molecular biology, combinatorial chemistry, high throughput sequencing and advanced informatics to create vast number of novel molecules for hit identification and lead generation. DELs are capable of interrogating drug targets with an extremely large number of compounds highly efficiently, including against targets categorized as difficult or intractable, such as protein:protein interaction (PPI), ubiquitin ligase, epigenetic and antibacterial targets. DEL selections in cell lysates have been reported. DEL may also be used as a tool to provide SAR (structure–activity relationship) information and assist medicinal chemistry optimization.

DEL Patents by Published Year

Figure 2 DEL Patents by Published Year

In a DEL, each small molecule is covalently conjugated with a unique DNA tag, serving as the identifier or barcode for the chemical structure of the compound. Therefore, the entire library can be prepared and selected simultaneously. The selection is usually performed based on the binding affinity with an immobilized protein target. After non-binders are washed away, the binders are eluted from the target under denaturing conditions. Next, the chemical structure of the selected compounds can be decoded after PCR amplification and Next Generation Sequencing (NGS) to read the corresponding DNA sequences.

Workflow of Early Discovery

• DEL Design
• On-DNA Chemistry Development
• Realize in DEL Production
• Building Blocks installation and Codes ligation
• DEL Synthesis enabled by the practice of “Split & Pool” strategy
• Screening against drug target by affinity selection
• High throughput DNA sequencing and SAR data analysis
• Resynthesize off-DNA Compounds for confirmation of activity
• Hit Validation and Optimization
• Lead Compounds Generation

Workflow for DEL Design and Synthesis

• Library Design
  • To propose the generic structures
  • Physicochemical property profiling
  • Novelty check (in publications and in in-house collection)
• Chemistry Development & Scope Study
  • To develop DNA-compatible conditions
  • To do scope study and optimization on a small set of building blocks
• Synthesis Scheme Validation Rehearse all the reactions and protocols by applying to the whole DEL synthesis step.
• Reagent Validation To get the yields and byproduct analysis of all reagents under certain conditions in model systems
• Library Production and QC To go through the “Split & Pool” procedure and collect QC data
• Library Delivery and QC To close the DELs and review the data before archive

Chemistry Development and Validation

• Key Chemistry Development To find optimal reaction conditions with model system
• Substrate Scope Study To evaluate chemistry across various substrates
• Chemistry Study on Given DNA Length To evaluate chemistry on DNA systems as DEL synthesis
• Mini Library Evaluation To test synthetic sequence
• Building Block Full Validation To select building blocks for DELs with defined validation strategy

General guidelines for developing DNA compatible reactions:

• Tolerate water and O2, modest stability of reagents in aqueous solution.
• Efficient at low concentration (~1 mM).
• No strong acidic conditions, tolerable at ph 4~14.
• No radicals or strong oxidants.

Chemical Toolbox for DNA-encoded Libraries

The in-solution DEL chemistry also started from peptide synthesis but has been expanded to become a diverse reaction toolbox. Recently, many new reactions have been added to the toolbox.

DEL Restrictions

• In the past few years, there has a significant increase in research activities to develop DEL-compatible chemistry; and in a sense, DEL chemistry is not that limited anymore. The actual limiting factor is the availability of building blocks (BBs) suitable for these reactions. The assembly geometry of BBs has a significant impact on the chemical diversity of the library.
• Besides, most of the DEL syntheses do not have a purification step and the truncated products are almost always in presence, which complicate the SAR data from DEL selection and may result in artifacts. Further development of more sophisticated data analysis methods to take into consideration the truncated products might be a potential way to address this limitation.
• It would be a major leap forward if DEL selections could be realized with endogenous proteins without overexpression or any other modification and/or manipulation, and ideally, selections should be able to target both cell surface membrane proteins and intracellular proteins. The membrane impermeability of DNA-tagged small molecules presents a formidable challenge for intracellular DEL selection. DNA molecules are vulnerable to nuclease digestion and therefore DNA tags may have stability issues in cells.
• Discerning the compounds that have induced the phenotype change from the library would be the major challenge that has yet to be addressed.

DEL Players

References:

• Guixian Zhao, et al. Future challenges with DNA-encoded chemical libraries in the drug discovery domain. Expert Opinion on Drug Discovery. 14:8, 735-753.
• Kunig V, et al. DNA-encoded libraries - an efficient small molecule discovery technology for the biomedical sciences. Biol Chem. 2018; 399(7):691-710.
• Brenner S, Lerner RA. Encoded combinatorial chemistry. Proc Natl Acad Sci USA. 1992; 89(12): 5381–5383.