A protease is an enzyme that begins protein catabolism (proteolysis) by hydrolysis of the peptide bonds that link the amino acids together in the polypeptide chain. Cysteine proteases are one of six classes of proteases known to man.

Cysteine proteases have a common catalytic mechanism that involves a nucleophilic cysteine thiol in a catalytic triad.

Step 1: Deprotonation of a thiol in the enzyme's active site by an adjacent amino acid with a basic side chain, usually a histidine residue.

Step 2: Nucleophilic attack by the deprotonated cysteine's anionic sulfur on the substrate carbonyl carbon. In this step, a fragment of the substrate is released with an amine terminus, the histidine residue in the protease is restored to its deprotonated form.

Step 3: A thioester intermediate linking the new carboxy-terminus of the substrate to the cysteine thiol is formed.

Step 4: The thioester bond is subsequently hydrolyzed to generate a carboxylic acid moiety on the remaining substrate fragment, while regenerating the free enzyme.

The mechanism used to cleave the peptide bond involves making an amino acid residue that has the cysteine and threonine (peptidases) or a water molecule (aspartic acid, mello and glutamic acid peptidases) nucleophillic so that it can attack the peptide carbonyl  group. One way to make a nucleophile is by a catalytic triad, where a histadine residue is used to activate serine, cisteine or threonine as a nucleophile.

Research has shown that once DERp1 has entered the body (usually by inhalation) that it cleaves the low affinity IgE Fc receptor (CD23) from B lymphocytes. This deprives the B cell of an important mechanism to limit IgE synthesis and it generates CD23 fragments that directly inhance IgE synthesis. This leads to a presentation of the symptoms previously discussed.