340
Z. Fu and J. Chen
17.1.2 Molecular Simulation of Typical Xenobiotics
Metabolism Catalyzed by P450 Enzymes
17.1.2.1 Introduction of P450 Enzymes and Related Metabolic
Reactions
P450 enzymes are commonly found in tissues of humans, wildlife, and microorganisms. In mammals, these enzymes reside mainly in the endoplasmic reticulum and
mitochondrial inner membranes of liver cells. P450 enzymes represent an enzyme
superfamily characterized by a heme-containing active center, which consists of a
protoporphyrin substituted with four methyl, two ethenyl, two ionizable propionate
groups as well as certain axial/vertical ligands (Fig. 17.2). The catalytic cycle of P450
enzymes starts from a resting (reduction) state, wherein the porphyrin iron binds with
H 2 O to give a metastable state. When H 2 O is replaced by CO, the complex displays
maximum absorbance at a wavelength of 450 nm; thus, the enzymes are termed
“P450”. P450 enzymes are known as the nature’s most versatile biological catalyst
[3]. The catalytic capability of P450 s covers a broad range of chemicals, involving
the functional groups –OH, –CHO, –COOH, –NH 2 , –CN, phenyl, and halogens.
The reactions mediated by P450 enzymes are mostly oxidations (Fig. 17.2), including alkane C–H hydroxylation, alkene C=C epoxidation, and heteroatom (N, P, S)
oxidation. In these oxidations, P450 enzymes function as “monooxygenases” that
insert an oxygen atom into substrates. Other reactions may also display the exceptional functionality of P450 enzymes, e.g., reductive dehalogenation of halogenated
alkanes and C–C bond coupling [4].
With the completion of the human genome project, it is known that human beings
have 57 P450 enzyme genes. Animals generally have more P450 genes than humans;
for instance, the number of P450 genes for a mouse is 101 and even up to 120 for
a sea urchin. The P450 superfamily is named with a nomenclature that comprises
family, subfamily, and isoforms. Enzymes in the same family require an amino acid
homology >40%, which is marked with Arabic numerals, e.g., the CYP 1 family;
enzymes in the subfamily have >55% gene sequences in common and are labeled
with capital letters, e.g., the “CYP1A subfamily”; the enzyme subfamily constitutes
various isoforms, labeled with Arabic numerals, e.g., “CYP1A2”. Different P450 isoforms accommodate their specific substrates; e.g., P4501A2 binds primarily with the
aromatic compounds [5]. Exposure to environmental contaminants can also induce
special P450 isoforms; e.g., the flame retardant PBDEs are metabolized mainly by
CYP2B6 in organisms [6]. Of all the catalytic reactions by P450 enzymes, about
90% is accomplished by isoforms of CYP1A2, CYP2C9, CYP2C19, CYP2D6, and
CYP3A4, with CYP3A4 being dominant [7].
Early studies on P450 enzymes were mainly focused on the metabolism and disposition of carcinogens, pharmaceuticals, and steroids. Two schemes are adopted in
these studies, namely (a) in vivo and (b) in vitro experiments. In the in vivo scheme,
enzyme inducers (e.g., phenobarbital) are fed to animals and possible metabolites in
the tissues, urine, and feces from these animals are then studied; the in vitro scheme
Z. Fu and J. Chen
17.1.2 Molecular Simulation of Typical Xenobiotics
Metabolism Catalyzed by P450 Enzymes
17.1.2.1 Introduction of P450 Enzymes and Related Metabolic
Reactions
P450 enzymes are commonly found in tissues of humans, wildlife, and microorganisms. In mammals, these enzymes reside mainly in the endoplasmic reticulum and
mitochondrial inner membranes of liver cells. P450 enzymes represent an enzyme
superfamily characterized by a heme-containing active center, which consists of a
protoporphyrin substituted with four methyl, two ethenyl, two ionizable propionate
groups as well as certain axial/vertical ligands (Fig. 17.2). The catalytic cycle of P450
enzymes starts from a resting (reduction) state, wherein the porphyrin iron binds with
H 2 O to give a metastable state. When H 2 O is replaced by CO, the complex displays
maximum absorbance at a wavelength of 450 nm; thus, the enzymes are termed
“P450”. P450 enzymes are known as the nature’s most versatile biological catalyst
[3]. The catalytic capability of P450 s covers a broad range of chemicals, involving
the functional groups –OH, –CHO, –COOH, –NH 2 , –CN, phenyl, and halogens.
The reactions mediated by P450 enzymes are mostly oxidations (Fig. 17.2), including alkane C–H hydroxylation, alkene C=C epoxidation, and heteroatom (N, P, S)
oxidation. In these oxidations, P450 enzymes function as “monooxygenases” that
insert an oxygen atom into substrates. Other reactions may also display the exceptional functionality of P450 enzymes, e.g., reductive dehalogenation of halogenated
alkanes and C–C bond coupling [4].
With the completion of the human genome project, it is known that human beings
have 57 P450 enzyme genes. Animals generally have more P450 genes than humans;
for instance, the number of P450 genes for a mouse is 101 and even up to 120 for
a sea urchin. The P450 superfamily is named with a nomenclature that comprises
family, subfamily, and isoforms. Enzymes in the same family require an amino acid
homology >40%, which is marked with Arabic numerals, e.g., the CYP 1 family;
enzymes in the subfamily have >55% gene sequences in common and are labeled
with capital letters, e.g., the “CYP1A subfamily”; the enzyme subfamily constitutes
various isoforms, labeled with Arabic numerals, e.g., “CYP1A2”. Different P450 isoforms accommodate their specific substrates; e.g., P4501A2 binds primarily with the
aromatic compounds [5]. Exposure to environmental contaminants can also induce
special P450 isoforms; e.g., the flame retardant PBDEs are metabolized mainly by
CYP2B6 in organisms [6]. Of all the catalytic reactions by P450 enzymes, about
90% is accomplished by isoforms of CYP1A2, CYP2C9, CYP2C19, CYP2D6, and
CYP3A4, with CYP3A4 being dominant [7].
Early studies on P450 enzymes were mainly focused on the metabolism and disposition of carcinogens, pharmaceuticals, and steroids. Two schemes are adopted in
these studies, namely (a) in vivo and (b) in vitro experiments. In the in vivo scheme,
enzyme inducers (e.g., phenobarbital) are fed to animals and possible metabolites in
the tissues, urine, and feces from these animals are then studied; the in vitro scheme