In a study published on December 28 in Nature Chemical Biology, scientists from EPFL (École Polytechnique Fédérale de Lausanne, Switzerland) achieved a significant milestone in drug development. Their research indicates a new class of orally available drugs, addressing a long-standing challenge in the pharmaceutical industry.
Professor Christian Heinis from EPFL explained that many diseases have identified targets, but drugs that can bind and reach these targets could not be developed. Most of these are cancer types, with many targets being protein-protein interactions, crucial for tumor growth but unable to be inhibited.
The study focused on cyclic peptides, versatile molecules known for their high affinity and specificity in binding to challenging disease targets. However, developing cyclic peptides as oral drugs has been difficult because they are quickly digested or poorly absorbed by the gastrointestinal tract.
"Cyclic peptides present a significant interest for drug development, as these molecules can bind to difficult targets for which it was hard to generate drugs using established methods," said Prof. Heinis. However, cyclic peptides usually cannot be administered orally, like a pill, which greatly limits their application.
The research team targeted the enzyme thrombin, a critical disease target due to its central role in blood coagulation; regulating thrombin is essential for preventing and treating thrombotic disorders such as strokes and heart attacks.
To generate cyclic peptides that can target thrombin and are sufficiently stable, the researchers developed a two-step combinatorial synthesis strategy to synthesize a vast archive of cyclic peptides with thioether bonds, enhancing their metabolic stability when administered orally.
"Now we have managed to generate cyclic peptides that bind to a disease target of our choice and can also be administered orally," explained Prof. Heinis. For this purpose, the team developed a new method by which thousands of small cyclic peptides with random sequences are chemically synthesized on a nanoscale and screened in a high-throughput process.
The process of the new method involves two steps and occurs in the same reaction vessel, a feature chemists call "one pot." The first step involves synthesizing linear peptides, which are then subjected to a chemical process to form a ring-like structure – technically being "cyclized."
This is done using "bis-electrophilic linkers" – chemical compounds used to connect two molecular groups – to form stable thioether bonds. In the second phase, cyclic peptides undergo acylation, a process attaching carboxylic acids, further diversifying their molecular structure.
The technique eliminates the need for intermediate purification steps, allowing high-capacity screening directly in 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.
With this method, the team managed to generate a comprehensive library of 8,448 cyclic peptides with an average molecular mass of about 650 daltons (Da), just slightly over the recommended maximum limit of 500 Da for small molecules available orally.
Cyclic peptides also showed high affinity for thrombin. When tested on rats, the peptides exhibited oral bioavailability of up to 18%, meaning that when the cyclic peptide drug is administered orally, 18% of it successfully enters the bloodstream and has a therapeutic effect.
Given that orally administered cyclic peptides generally have a bioavailability of less than 2%, increasing this figure to 18% represents a substantial advancement for biological drugs, including peptides.
By enabling the oral availability of cyclic peptides, the team has opened new possibilities for treating a range of diseases that have been difficult to address with conventional oral medications.
The versatility of the method means it can be adapted to target a wide range of proteins, potentially leading to discoveries in areas where medical needs are currently unmet.
To apply the method to more challenging disease targets, such as intracellular protein-protein interactions, it will likely be necessary to synthesize and study larger libraries, the researchers say.
In the next phase of this project, the team will target more intracellular protein-protein interaction targets for which it has been difficult to develop inhibitors based on classic small molecules.
They are confident that for at least some of these, orally applicable cyclic peptides can be developed.
