Protease

A protease (also called a peptidase or proteolytic enzyme) catalyzes the hydrolysis of peptide bonds. Endopeptidases cleave bonds within a chain, while exopeptidases remove amino acids from the N-terminus (aminopeptidases) or C-terminus (carboxypeptidases); dipeptidyl peptidases remove two residues at a time. Proteases are classified by catalytic mechanism into serine, cysteine, aspartic, threonine and metalloproteases, and many are selective for particular amino acid sequences. They are essential for digestion, blood clotting, hormone processing and protein turnover, and they are a main reason natural peptides have short half-lives and poor oral bioavailability.

Native GLP-1 is cut within minutes by dipeptidyl peptidase-4 (DPP-4), which removes two amino acids from its N-terminus and inactivates it. Drug developers have exploited proteases in two ways: by designing peptides that resist cleavage, such as DPP-4-resistant GLP-1 receptor agonists, and by blocking the protease itself, as with DPP-4 inhibitors and the neprilysin inhibitor sacubitril, which slows the breakdown of natriuretic peptides in heart failure.

Proteases are the main obstacle to taking peptide medicines by mouth. The stomach and small intestine contain enzymes such as pepsin, trypsin and chymotrypsin whose job is to digest dietary protein, and they treat a peptide drug the same way. Together with poor absorption across the gut wall, this is why most peptide medicines are injected. Oral semaglutide reached approval only by pairing the peptide with an absorption enhancer, and even then only a small fraction is absorbed.

Proteases in blood and tissues also shorten how long a peptide lasts after it enters the body. Native GLP-1 survives only minutes before DPP-4 inactivates it, and many other hormones are cleared by enzymes such as neprilysin. Peptide chemists protect vulnerable bonds with substitutions such as D-amino acids or non-natural residues, cyclization and attached fatty acid chains. These changes explain much of the difference between a natural peptide and its approved drug version.

Blocking a protease can itself be a treatment. DPP-4 inhibitors keep the body’s own incretins active for longer and are used in type 2 diabetes. In the PARADIGM-HF trial of more than 8,000 people with heart failure, a combination of the neprilysin inhibitor sacubitril and valsartan reduced cardiovascular death and heart failure hospitalization compared with enalapril. Because proteases have several substrates, blocking one can affect many peptides, so these drugs need broad safety testing.

“Proteases only matter in the stomach”

Proteases are present throughout the body, including in blood, on the surface of blood vessels and in the kidney, liver and other tissues. A peptide that avoids the gut by injection still meets enzymes such as DPP-4 and neprilysin, which is why many natural peptides have half-lives of minutes even when injected directly into the bloodstream.

“Any peptide can be made oral with the right capsule”

Oral peptide delivery has been pursued for decades, with only a few successes. Formulations that inhibit gut enzymes or enhance absorption help, but oral bioavailability remains low and variable. Approved oral peptides rely on specialized formulations tested in clinical trials. Claims that unapproved peptides work equally well as capsules or drops are generally not backed by human pharmacokinetic data.

“A protease cuts any peptide bond at random”

Most proteases are selective. Trypsin cuts after lysine or arginine, and DPP-4 removes the first two amino acids when the second is alanine or proline, as in GLP-1 and GIP. This selectivity lets chemists protect the exact bond a given enzyme attacks, which is how DPP-4-resistant GLP-1 analogues were designed.

What is the difference between a protease and a peptidase?

The terms largely overlap. Both describe enzymes that hydrolyze peptide bonds. “Peptidase” is the formal umbrella term used in enzyme classification, while “protease” is often used informally, especially for enzymes that cut within longer protein chains. Exopeptidases trim the ends of a chain and endopeptidases cut within it.

Why are peptide drugs broken down so quickly?

Natural peptides are built from the same peptide bonds as dietary protein, so digestive and circulating proteases recognize and cut them. Many peptides are also small enough to be filtered by the kidneys. Together, these processes give many native peptides half-lives of minutes, which drug developers extend with chemical modifications.

What does DPP-4 do?

Dipeptidyl peptidase-4 is a serine protease found on cell surfaces and in circulation. It removes two amino acids from the N-terminus of peptides with alanine or proline in the second position, including GLP-1 and GIP. Human studies showed that administered GLP-1 is rapidly degraded this way, which led to DPP-4-resistant analogues and DPP-4 inhibitors.