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A new class of drugs have been synthesized, which could address a long-standing pharma challenge—cyclic peptides that can be given orally. A team from École Polytechnique Fédérale de Lausanne (EPFL) has generated such cyclic peptides that can target thrombin. The study was published in Nature Chemical Biology, by scientists from the laboratory of Christian Heinis at EPFL. 

Cyclic peptides are versatile molecules known for their high affinity and specificity in binding, but they are also usually rapidly digested or poorly absorbed by the gastrointestinal tract.

“We have now succeeded in generating cyclic peptides that bind to a disease target of our choice and can also be administered orally,” says Heinis. “To this end, we have developed a new method in which thousands of small cyclic peptides with random sequences are chemically synthesized on a nanoscale and examined in a high-throughput process.”

Targeting proteins for oral drug therapy is often challenging. Traditional small molecules don’t bind well to proteins with flat surfaces or require specificity for particular protein homologs. Typically, larger biologics that can target these proteins require injection, limiting patient convenience and accessibility.

“There are many diseases for which the targets were identified but drugs binding and reaching them could not be developed,” says Heinis. “Most of them are types of cancer, and many targets in these cancers are protein-protein interactions that are important for the tumor growth but cannot be inhibited.”

This research team targeted the enzyme thrombin, which has a central role in blood coagulation. Regulating thrombin is key to preventing and treating thrombotic disorders like strokes and heart attacks.

To generate cyclic peptides that can target thrombin and are sufficiently stable to be given orally, the scientists developed a two-step combinatorial synthesis strategy to synthesize a vast library of cyclical peptides with thioether bonds, which enhance their metabolic stability when taken orally.

The new method process involves two steps, and takes place in the same reactive container, a feature that chemists refer to as “one pot.”

The first step is to synthesize linear peptides, which then undergo a chemical process of forming a ring-like structure—in technical terms, being “cyclized.” This is done with using “bis-electrophilic linkers”—chemical compounds used to connect two molecular groups together—to form stable thioether bonds.

In the second phase, the cyclized peptides undergo acylation, a process that attaches carboxylic acids to them, further diversifying their molecular structure.

The team was able to generate a comprehensive library of 8,448 cyclic peptides with an average molecular mass of about 650 Daltons (Da), only slightly above the maximum limit of 500 Da recommended for orally available small molecules. 

When tested on rats, the peptides showed oral bioavailability up to 18%. Given that orally administered cyclic peptides generally show a bioavailability below 2%, increasing that number to 18% is a substantial advance.

“To apply the method to more challenging disease targets, such as protein-protein interactions, larger libraries will likely need to be synthesized and studied,” says lead author Manuel Merz. “By automating further steps of the methods, libraries with more than one million molecules seem to be 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 classical small molecules. 

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