Enzyme-Powered DNA-Encoded Libraries: A Gentler Path to Small-Molecule Drug Discovery
核心洞察
Researchers at the University of Bern, ETH Zurich (搜索), and ZHAW developed an enzyme-based method to build DNA-encoded libraries under mild, water-based conditions without damaging DNA barcodes.
The team used engineered CoA ligases (搜索) and N-acyltransferases (搜索) to synthesize over 120 diverse DNA-barcoded molecules, expanding the chemical space accessible in early-stage drug discovery.
The approach combines enzymatic and classical chemical methods, enabling reactions previously too harsh for sensitive DNA tags and increasing library diversity.
A research team led by Prof. Dr. Rebecca Buller at the University of Bern has demonstrated a fundamentally gentler approach to building DNA-encoded libraries (DELs), one of the most important tools in early-stage drug discovery. In collaboration with Prof. Dr. Jörg Scheuermann's group at ETH Zurich (搜索) and the Zurich University of Applied Sciences (搜索) (ZHAW), the team engineered enzymes to synthesize more than 120 diverse DNA-barcoded molecules under mild, water-based conditions—preserving the integrity of the sensitive DNA barcodes that are essential for reliable screening. The study, supported by the Swiss National Science Foundation (SNSF) as part of a Sinergia project, was published in Nature Catalysis.
The DEL Bottleneck: Harsh Chemistry Meets Fragile Barcodes
DNA-encoded libraries allow researchers to synthesize enormous numbers of small molecules, each tagged with a unique DNA "barcode" that identifies the compound—much like scanning a product at store checkout. These libraries can then be screened in parallel against disease-relevant proteins to identify promising drug candidates. The approach is particularly valuable for traditional small-molecule drugs, which constitute the majority of medications taken in tablet form.
Yet a persistent limitation has constrained the technology: many of the chemical reactions used to construct DELs are too harsh for the DNA labels. "Once the barcodes are damaged, they no longer function properly and the results become unreliable," the researchers note. In practice, this means only molecules that can be synthesized without harming the DNA are typically included, leaving many potentially valuable molecular structures out of reach.
Nature's Catalysts as a Solution
To circumvent this problem, the team turned to two types of enzymes: CoA ligases (搜索) and specially developed N-acyltransferases (搜索). "Enzymes are Nature's catalysts: they accelerate reactions, work very precisely, and function in water under very mild conditions," explains Buller, professor at the Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP) at the University of Bern and lead author of the study.
Using protein engineering, the researchers tailored these enzymes to make them particularly well-suited for producing DNA-encoded libraries. They then combined the two enzyme classes so that they carried out several reaction steps in sequence, functioning like a small production line. In a subsequent step, the team linked the enzymatic reactions with classical chemical methods to assemble the DNA-encoded library directly on the DNA.
Protein Engineering Unlocks New Diversity
The study demonstrates that, with the help of protein engineering, enzymes can be adapted to process molecules that already carry large, bulky DNA barcodes—something that was previously very difficult. "We achieved this under mild, water-based conditions and without damaging the sensitive barcodes," says Buller.
Daniela Schaub, one of the two lead authors of the study and a researcher at the DCBP, adds: "Enzymes have long been known as versatile tools for making small molecules and are widely used in industry. Yet until now they have hardly been used to build DNA-encoded libraries."
With the new sequence of reaction steps and the combination of enzymatic and chemical methods, the researchers assembled over 120 diverse molecular structures directly on the DNA. This makes engineered enzymes well-suited as gentle tools for producing DNA-encoded libraries and for further expanding their structural diversity.
Toward More Sustainable and Efficient Drug Discovery
The implications extend beyond scientific novelty. "Our basic research and the newly developed method help increase the chemical diversity of these libraries while making the underlying chemistry more efficient and potentially more resource-efficient," says Schaub.
Buller emphasizes the broader significance: "Developing new drugs is a lengthy and costly process. If we can use methods in the early stages of drug discovery that allow for greater chemical diversity and function under mild, water-based conditions, that is a win—scientifically, economically, and in terms of sustainability."
The team plans to extend the method to additional enzyme classes and further optimize the enzymes, broadening the range of molecules accessible in DNA-encoded libraries and supporting the discovery of future therapeutics.