New Advances in DEL Technology Facilitate Synthesis of Large, Complex Molecules

Personalized cancer therapy uses modified antibodies or immune cells to target cancer. Due to their high cost and complexity, these treatments are not always widely used. As a result, most medical treatments still rely on the more affordable, large-scale production of small chemical molecules.

Billions of New Molecules in Just a Few Weeks

The small number of novel active compounds that can be discovered using current methods represents a bottleneck in the development of new molecular treatments. DNA-encoded chemical libraries (DEL), a technique created in the 2000s at ETH Zurich and Harvard, may offer a cure.

As of right now, millions of chemical compounds may be produced, and their efficacy tested all at once using DEL technology. The disadvantage of this was that scientists could only assemble tiny molecules from a limited number of chemical building components. Chemists at ETH Zurich have greatly enhanced this procedure.

Researchers can now autonomously manufacture and test billions of distinct chemicals in a matter of weeks according to a new technique that was published in the esteemed journal Science. Larger therapeutic molecules, such ring-shaped peptides, can be created using this technique and used to target different pharmacological targets.

Creating and Testing All Combinations

The first active substances developed with the help of early DEL technology are currently in advanced clinical trials. This new DEL method once again massively expands the possibilities.”

Jörg Scheuermann, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich

Jorg is credited with helping to develop DEL technology, which is seen as essential to fully utilizing combinatorial possibilities in the practical chemical manufacturing of molecules, along with his research group at the Institute of Pharmaceutical Sciences.

The goal of combinatorial chemistry is to create a wide variety of molecular variations by combining different building ingredients. The researchers select the combinations that show the desired activity from all of these combinations. The number of synthesis cycles and the variety of building blocks combined in each synthesis cycle cause the number of distinct molecules to increase exponentially.

Using DNA Code to Identify the Active Molecules

To facilitate the identification of individual active compounds within the rapidly expanding “molecular soup” during efficacy tests, the DEL approach involves attaching a specific short DNA fragment to the molecule in tandem with each building block of an active substance. This generates a distinct DNA sequence for every set of building blocks, akin to a readable barcode.

For instance, the entire soup of molecules can be examined to see if it binds to a particular protein, and using the PCR (polymerase chain reaction) method that is well-known from COVID testing, individual DNA segments can be amplified and positively identified.

Preventing Exponential Growth of Contamination

However, the potential of DEL technology has been severely constrained thus far by the realities of chemistry. Although the method of joining the DNA fragments with the chemical building blocks is always consistent, the degree to which those building blocks chemically bind together varies based on the combination. Consequently, the uniqueness of the DNA code is lost.

The same code can apply to shortened versions that just have a portion of the building blocks as well as the entire molecule with all of its building pieces. With every synthesis cycle, these contaminants likewise get exponentially more numerous. In actuality, this has restricted the number of distinct compounds that can be included in a tolerable size of DEL libraries to combinations of three to four connected blocks.

Self-Purification Built In

Now, Scheuermann's group has discovered a means to stop the molecular library from becoming more and more contaminated: they can purify the DEL that has been synthesized all the way down to the last building block. The methodology of the ETH researchers is built around two key components.

Initially, the molecules are synthesized in conjunction with easily managed magnetic particles. Among other things, this makes washing cycles possible. Secondly, the group added to the particles a second chemical coupling element that can only bind to the final designed building block.

In one washing step, all truncated molecules that lack, say, the final building block, can be eliminated. Ultimately, the molecules in the library are limited to those that comprise all of the designated building blocks.

Conflict with the Combinatorial Chemistry

Despite its elegance on paper, implementing the method proved to be challenging, as Scheuermann said, “It was particularly challenging to find magnetic particles that do not interfere with the enzymatic coupling of DNA fragments. In the course of their doctoral projects, Michelle Keller and Dimitar Petrov from my group invested a lot of time and energy to make sure the method works reliably.”

While the concept of combinatorial chemistry on particles dates back to the 1990s, ETH researchers were not able to implement it for library synthesis until recently.

More Diverse and Larger Molecules

Beyond handling significantly larger libraries of several billion compounds, the self-purifying DEL technology enables researchers to construct larger molecules made up of five or more building blocks.

Before, we could search for small active substances that fit like a key into the lock of the active site of therapeutically relevant proteins, but now we can search for larger ones as well. These larger active substances can dock not only in a protein’s active centers but also to other specific areas of a protein’s surface, for example, to prevent it from binding to a receptor.”

Jörg Scheuermann, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich

The discovery of compounds that bind to specific protein surfaces is particularly advantageous for fundamental biological research. It allows proteins to be labeled and studied in the context of cells.

Additionally, the ETH technique may prove beneficial for large-scale multinational research projects like Target 2035. The goal of this program is to identify, by 2035, a chemical that binds precisely to each of the approximately 20,000 human proteins, therefore influencing the protein's function.

Spin-Off Service for Industry and Science

To maximize the efficiency of the technology for basic research and the pharmaceutical business, Scheuermann and his team plan to launch a spin-off company. This business will provide the full procedure, including automated synthesis, automated efficacy testing, and DNA-based molecular identification, in addition to developing DEL collections.

We are seeing immense interest from industry and research, especially in cyclic molecules, which to date have not been accessible in large numbers.”

Jörg Scheuermann, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich