Protease

A protease (or peptidase) is an enzyme that catalyzes the hydrolysis of peptide bonds between two amino acids. These enzymes play a central role in digestion, signaling pathway regulation, apoptosis, tissue remodeling and bioactive peptide turnover — all critical dimensions for understanding pharmacokinetics and metabolic stability of research peptides.

The MEROPS classification distinguishes seven major classes by catalytic residue: serine proteases (trypsin, chymotrypsin, elastase, thrombin), cysteine proteases (papain, caspases, cathepsins B/L), aspartyl proteases (pepsin, renin, BACE-1), metalloproteases (MMPs, ACE, neprilysin, DPP-4 in some acceptions), threonine proteases (proteasome), glutamic and asparagine proteases.

Two functional subcategories complete the picture: endopeptidases cleave mid-chain, exopeptidases remove residues from termini (aminopeptidases at the N-terminus, carboxypeptidases at the C-terminus).

For catalog research peptides, the most feared protease is DPP-4 (dipeptidyl peptidase 4): it cleaves N-terminal dipeptides from many regulatory peptides (native GLP-1 cleaved within 2 minutes, GIP, substance P, NPY). DPP-4-resistant analogs (semaglutide, liraglutide, tirzepatide, retatrutide) were engineered via amino acid substitution or chemical modifications to block this cleavage. Neprilysin (neutral endopeptidase) also degrades natriuretic peptides, enkephalins, amylin. MMPs remodel extracellular matrices.

Understanding which protease targets which peptide allows choosing the right inhibitor, modeling in vitro half-life, interpreting serum incubation results and anticipating expected metabolic stability. It is a prerequisite for any rigorous peptide research protocol, whether native or modified analogs.

Proteases (or peptidases) are the largest catalogued enzyme family: the MEROPS database lists over 3500 entries classified into 9 catalytic types by mechanism (serine S, cysteine C, aspartyl A, glutamyl G, threonine T, metalloprotease M, asparagine N, mixed P, unknown U). Their biological roles are universal: digestion (pepsin, trypsin, chymotrypsin), coagulation (thrombin, factors Xa/IXa), hormonal activation (renin, angiotensin-converting enzyme ACE), apoptosis (caspases), cell signalling (proprotein convertase PC1/PC3), proteasomal degradation (26S complex), matrix remodelling (MMPs).

In peptide research two aspects dominate: susceptibility of the research peptide to physiological proteases (determining in vivo half-life) and stabilisation strategies (D-amino acid substitutions, Aib, α-methylation, modified amide bond, N-methylation, cyclisation, C20 acylation, albumin binding). DPP-4 (dipeptidyl peptidase 4) is the most documented serum protease in peptide pharmacology: it cleaves N-terminal Xaa-Pro and Xaa-Ala dipeptides, rapidly degrading native GLP-1, GIP, GHRH. Modern research peptides (tirzepatide, semaglutide, CJC-1295) bear Aib or D-Ala substitutions at position 2 to block this degradation.