For decades, a considerable number of proteins critical for treating various diseases have remained out of reach for oral drug therapy. Traditional small molecules often struggle to bind to proteins with flat surfaces or require specificity for certain protein homologs. Typically, larger biologics targeting these proteins require injection, limiting patient convenience and accessibility.
In a new study published in Nature Chemical Biology, scientists at EPFL’s lab Professor Christian Heinis have achieved a significant milestone in drug development, opening the door to a new class of orally available drugs and solving a long-standing challenge in the pharmaceutical industry.
Many diseases have identified targets, but drugs that bind and reach these targets have not been developed. Most of these are cancers, and many targets in these cancers are protein-protein interactions crucial for tumor growth, but cannot be inhibited.“
Professor Christian Heinis at EPFL
The study focused on cyclic peptides, versatile molecules known for their high affinity and specificity in binding challenging disease targets. However, the development of cyclic peptides as oral drugs has proven to be difficult as they are rapidly digested or poorly absorbed by the gastrointestinal tract.
„Cyclic peptides are of great interest in drug development, as they can bind to challenging targets for which it has been difficult to develop drugs using established methods,“ says Heinis. „However, cyclic peptides typically cannot be administered orally, limiting their application.“
Breakthrough in Drug Development
The research team focused on the enzyme thrombin, a critical target for diseases due to its central role in blood coagulation. Regulating thrombin is key to preventing and treating thrombotic diseases such as strokes and heart attacks.
To create cyclic peptides that can target thrombin and are sufficiently stable, the scientists developed a two-stage combinatorial synthesis strategy to synthesize an extensive library of cyclic peptides with thioether bonds, increasing their metabolic stability for oral administration.
„We have succeeded in generating cyclic peptides that can bind to a disease target of our choice and can also be administered orally,“ says Heinis. „We have developed a new method in which thousands of small cyclic peptides with random sequences are chemically synthesized in nanoscale and screened in high-throughput.“
Streamlining the Process
The process of the new method involves two steps occurring in the same reaction vessel, a feature chemists call a „one-pot.“
The first step involves synthesizing linear peptides, which are then cyclized in a chemical process to form a ring-like structure – termed as „cyclized.“ This is done using „bis-electrophilic linkers“ – chemical compounds that connect two molecule groups – to form stable thioether bonds.
In the second phase, the cyclized peptides undergo acylation, a process in which carboxylic acids are bound to them, further diversifying their molecular structure.
The technique eliminates intermediate purification steps and allows for high-throughput screening directly in the synthesis plates, combining the synthesis and screening of thousands of peptides to identify candidates with high affinity for specific disease targets – in this case, thrombin.
Using this method, the doctoral student leading the project, Manuel Merz, was able to create a comprehensive library of 8,448 cyclic peptides with an average molecular mass of about 650 Daltons (Da), which is only slightly above the recommended upper limit of 500 Da for available small molecules for oral administration. Furthermore, the cyclic peptides showed high affinity for thrombin.
In tests on rats, the peptides showed an oral bioavailability of up to 18%, meaning that when a cyclic peptide drug is orally administered, 18% of it successfully enters the bloodstream and exerts a therapeutic effect. Considering that orally administered cyclic peptides generally have a bioavailability of less than 2%, this increase to 18% represents a significant advancement for drugs in the biologics category, including peptides.
By enabling the oral availability of cyclic peptides, the team has opened up opportunities to treat a range of diseases that have been difficult to combat with traditional oral drugs. The versatility of the method means it can be adapted to a wide range of proteins, potentially leading to breakthroughs in areas where medical needs are currently unmet.
„To apply the method to more challenging disease targets such as protein-protein interactions, larger libraries are likely to be synthesized and screened,“ says Manuel Merz. „Further automation of method steps seems to bring libraries with more than a million molecules within reach.“
„In the next step of this project, the researchers will target several intracellular protein-protein interaction targets for which it has been difficult to develop inhibitors based on classic small molecules. They are confident that orally applicable cyclic peptides can be developed for at least some of them.“
Ecole Polytechnique Federale de Lausanne (EPFL)
Merz, ML, et al. (2023). De-novo-Entwicklung kleiner zyklischer Peptide, die oral bioverfügbar sind. Naturchemische Biologie. doi.org/10.1038/s41589-023-01496-y.