The classification adopted by the Nomenclature Committee (NC) of the International Union of Biochemistry and Molecular Biology (IUBMB) classifies all hydrolases as 'EC 3.' and divides them into classes and subclasses according to the group they hydrolyze and the nature of their substrates. A further criterion in the classification of peptidases is based on the nature of their catalytic site. A constantly updated version with supplements is available online,6 as are all available PDB (Protein Data Bank) entries classified as recommended by the NC-IUBMB.7
A small and somewhat subjective selection of hydrolases of known or potential activity toward drugs and other xenobiotics is presented in Table 2. The objective of this table is first and foremost to testify to the impressive variety of functional groups that hydrolases can cleave. Also, the table illustrates the huge variety of enzymes that have evolved to cleave chemical bonds by comparatively simple nucleophilic mechanisms necessitating no high-energy electron transfer. But only a limited number of entries are of foremost significance in drug metabolism, namely:
• carboxylesterases (EC 188.8.131.52), whose sequence is encoded by a superfamily of genes (e.g., CES1A1, CES1A2, CES1A3, CES1B, CES1C, CES2, CES3, CES4)5'8'9;
• cholinesterases (EC 184.108.40.206, also known as butyrylcholinesterase);
• paraoxonases (EC 220.127.116.11, also known as aryldialkylphosphatase), whose sequence is encoded by the PON1, PON2, and PON3 genes10'11;
• epoxide hydrolases (EC 18.104.22.168), to be discussed separately in Section 5.06.2.3; and
• amidases and peptidases in general, although their individual roles in xenobiotic metabolism remain very poorly understood.
The enzymatic hydrolysis of carboxylic derivatives is far more effective than chemical hydrolysis. For example, subtilisin (EU 22.214.171.124) accelerates the hydrolysis of amide bonds at least 109- to 1010-fold. All hydrolases include the following three catalytic features in their active site, which enormously accelerate rates of hydrolysis (Figure 1). First, they contain an electrophilic component, which increases the polarization of the carbonyl group in the substrate (Z + in Figure 1). Second, they use a nucleophile (Y: in Figure 1) to attack the carbonyl carbon, leading to the formation of a tetrahedral intermediate. And finally, they use a proton donor (H-B in Figure 1) to transform the -OR' or -NR'R' moiety into a better leaving group.5,12
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