2. CYP Enzymes
CYP enzymes are a group of heme-containing enzymes that play important roles in the metabolism of many drugs and other xenobiotics. They are located in the endoplasmic reticulum of cells throughout the body, but they are most abundant in the liver
[12]. CYP enzymes can catalyze a wide variety of reactions, including oxidation
[13], reduction
[14], hydrolysis
[15], and isomerization
[16]. The most common reaction catalyzed by CYP enzymes is oxidation. This leads to the molecule being more water soluble and easier to excrete from the body, but it can also make it more reactive and potentially toxic. Moreover, CYPs are involved in more than 90% of the reported enzymatic reactions
[14].
CYP enzymes contain between 400 and 500 amino acid residues and one heme prosthetic group in the active site, iron in protoporphyrin IX
[17]. In this structure, four pyrrole rings (I–IV) are interconnected by methyl bridges α, β, γ, and δ. Iron in the trivalent (ferric, Fe
3+) form is located in the center of the protoporphyrin ring (
Figure 1) and is coordinated by pyrrolic nitrogen. In addition, a water molecule is bound to the iron in the native structure. The heme iron is bound to the apoprotein via the thiol group of the cysteine residue. These are also the places for potential CYP inactivation by a covalent heme modification, by the modification of the apoprotein or by forming a pseudo-irreversible complex with iron
[18].
Figure 1.
Hem structure formula.
CYP enzymes are part of a superfamily of enzymes that is further divided into 18 families, 43 subfamilies, and at least 57 different enzymes present in humans
[15]. The division of the nomenclature of CYP enzymes is based on the similarity of their primary structure, or protein sequence
[17], as shown in
Table 1. The enzymes are encoded by a family of genes in the CYP superfamily. The specific CYP enzymes that are expressed in a particular cell or tissue depend on the genes that are present in that cell or tissue.
Table 1.
Nomenclature of CYP enzymes based on the similarity of the protein sequence.
The role of these enzymes in the body is versatile. As mentioned earlier, these enzymes are not only present in the liver but also in the kidney, placenta, adrenal gland, gastrointestinal tract, and skin
[19]. Thanks to their distribution throughout the body and the possibility of catalyzing a large number of different chemical reactions, CYP enzymes are responsible, among other things, for drug metabolism, steroid metabolism, bile acid biosynthesis, steroid biosynthesis, vitamin D deactivation, and much more
[15]. This role of theirs extends doubly to their functions in human health and disease. CYP enzymes are responsible for numerous protective roles in the biotransformation of toxins and other harmful substances, as well as causing side effects and toxic elements through unproductive cycles of CYP enzymes
[20].
An additional aspect of the importance of CYP enzymes lies in their role in antitumor therapy. CYP enzymes have been detected in tumor cells
[21[21][22],
22], where their expression is abnormal compared to the surrounding healthy tissue
[23]. Accordingly, experts are actively working to use the CYP enzyme as a target in modeling oncology therapy, with CYP1B1
[24], CYP2J2
[25], and CYP2W1
[26] being extensively studied. The study of CYP enzymes is an important area of research in pharmacology, toxicology, and cancer biology. Understanding how CYP enzymes work can help design more effective and less toxic drugs and develop strategies for cancer prevention and treatment.
2.1. CYP3A4 Enzyme
CYP3A4 is one of the most important enzymes involved in drug metabolism. It is encoded by the
CYP3A4 gene, located on chromosome 7q at the q21–22 locus, but variations in the coding of this gene are also responsible for variations in the presence of the CYP3A4 enzyme in humans
[27]. It is not present in the fetus, but in most people, it is formed within a year of birth
[28]. CYP3A4 is distributed in different tissues, but the highest presence of this enzyme, as well as the highest significance, was observed in the liver and intestine
[29] and is responsible for more than 70% of gastrointestinal CYP activity
[30]. CYP enzymes in the body catalyze more than 95% of oxidation and reduction reactions, while the CYP3A4 enzyme is responsible for catalyzing approximately 33% of such reactions
[14]. It is believed that the large active site of this enzyme is responsible for participating in a large number of chemical reactions and, consequently, also in a large number of drug bio-transformations. The CYP3A4 enzyme is mentioned as the most important enzyme in drug metabolism, where it is considered to be involved in the metabolism of more than 50% of drugs
[31]. Therefore, it is extremely important to know all the possible characteristics of this enzyme, especially the significantly present polymorphism of this enzyme. The rate of CYP3A4 metabolism can vary between individuals. This is a consequence of genetic polymorphisms, which can cause the enzyme to be more or less active. People with certain CYP3A4 polymorphisms may have a different rate of drug metabolism than people without these polymorphisms. For example, people with the CYP3A4*2C9 polymorphism have a higher risk of side effects from statins, which are metabolized by CYP3A4
[32]. In addition to drug dose adjustments, knowledge of CYP3A4 polymorphisms can help physicians identify people who are at higher risk of side effects. Some drugs can cause side effects if they are metabolized too quickly or too slowly. It is believed that there is 1- to 20-fold interindividual ‘variability’ of enzyme activity
[30]. The levels of CYP3A4 in humans remain the same with increasing age; it is not influenced by external factors such as smoking or alcohol and is 25% more present in females
[33].
When the CYP3A4 enzyme is mentioned, the CYP3A5 enzyme is often mentioned in the same context since it is an enzyme that is highly homologous and has overlapping substrates. Therefore, the term CYP3A4/5 enzyme is often used in the literature. However, it is important to emphasize that these two enzymes have different functions in some cases. For example, in the process of
O6-demethylation of thebaine, the CYP3A5 isoform participates almost 10 times more than CYP3A4
[34]. The reaction marker for measuring CYP3A4 enzyme activity is the 6
β-hydroxylation of testosterone. Nifedipine oxidation is used as well in order to further confirm the activity of the enzyme
[17]. It has already been said that the CYP3A4 enzyme is involved in numerous chemical reactions (hydroxylation, aromatic oxidation,
N- and
O-dealkylation, etc.). Due to its large active site, it is able to both bind several substrates at once and create more complex metabolites through hydroxylation of the sp
3 bond between carbon and hydrogen
[35].
Many xenobiotics and endobiotics can act as CYP3A4 inducers, substrates, or inhibitors. The induction of CYP3A4 is less clinically significant than CYP3A4 inhibition, but it is necessary to understand because it can lead to decreased systematic exposure to co-administered drugs and result in inadequate therapeutic values of certain medications
[36]. CYP3A4 induction occurs primarily at the transcriptional level, which involves the activation of the
CYP3A4 gene promoter, the region of DNA that regulates gene expression. Two major nuclear receptors, pregnane X receptor (PXR) and constitutive androstane receptor (CAR), are primarily responsible for CYP3A4 induction
[37]. These receptors act as transcription factors, which means they bind to specific DNA sequences and recruit RNA polymerase, the enzyme responsible for DNA transcription. PXR is activated by a variety of compounds, including endogenous ligands such as bile acids and xenobiotics such as certain drugs, environmental pollutants, and pesticides. Upon binding to PXR, these ligands induce its translocation from the cytoplasm to the nucleus, where it binds to its heterodimeric partner, retinoid X receptor (RXRα), and interacts with specific DNA sequences in the
CYP3A4 gene promoter
[38]. This interaction enhances the binding of RNA polymerase, leading to increased transcription of the
CYP3A4 gene and increased CYP3A4 protein expression. While previous models have assumed that enzyme induction is a rapid process driven by immediate changes in enzyme synthesis, more recent studies suggest that the induction response may be more complex and involve a lag phase before full induction is achieved. This delayed response could be attributed to the slower kinetics of mRNA synthesis, which may take several days to reach peak levels
[39,40][39][40]. Some of the inducers of CYP3A4 include but are not limited to
[41,42,43,44,45,46,47][41][42][43][44][45][46][47] apalutamide, capsaicin, carbamazepine, efavirenz, enzalutamide, modafinil, nevirapine, phenobarbital, phenytoin, rifampicin, St. John’s wort, and topiramate. Some of the substrates, on the other hand, include
[48,49,50,51,52,53,54,55][48][49][50][51][52][53][54][55] aripiprazole, clarithromycin, cyclophosphamide, cyclosporin, doxorubicin, erythromycin, haloperidol, ifosfamide, ketoconazole, losartan, paclitaxel, sunitinib, tacrolimus, tamoxifen, verapamil, vincristine, and many others.
2.2. CYP3A4 Inhibitors
Probably the most important item in the study of interactions of CYP enzymes with endobiotics and xenobiotics is the process of inhibition of CYP enzymes. Inhibitors are compounds that can bind to the active site or prevent the enzyme from catalyzing chemical reactions. In some cases, inhibitors can do both, which leads to a decrease in enzyme activity. A decrease in enzyme activity will consequently lead to a decrease in the biotransformation of substrates, in some cases of drugs, and may lead to an increased concentration of drugs in the blood system. Because of this, but also because of the influence on the development of new drugs, the processes of inhibition of various types of enzymes, including the CYP3A4 enzyme, are significantly studied. One of the most common criteria used to determine inhibitor strength is the 50% inhibitory concentration (
IC50). The
IC50 value determines half of the maximum inhibitory concentration, a measure of the strength by which a certain compound can inhibit a biological or biochemical function
[56].
IC50 values are usually calculated using kinetic methods. One of the most common methods is the inhibition quadrant method. In this method, the enzyme is incubated with different concentrations of inhibitors, and the reaction rate is measured. The
IC50 value is then determined from the graph of the reaction rate in relation to the concentration of the inhibitor. A lower
IC50 value indicates a higher potency of the inhibitor. This means that a lower inhibitor concentration is required to achieve 50% inhibitory inactivation of the enzyme. According to the current literature guidelines on this topic, inhibitors are divided into strong, medium, and weak. Strong inhibitors are those that show an
IC50 value at a concentration of less than 1 μM, medium inhibitors are those that show an
IC50 value from 1 μM to 50 μM, and weak inhibitors are those that show an
IC50 value greater than 50 μM
[57,58][57][58].
2.3. Types of CYP3A4 Inhibitions
When CYP3A4 enzyme inhibition is mentioned, it should be kept in mind that there are significantly different types of inhibition and, therefore, different clinical implications. CYP3A4 enzymes can be subject to reversible inhibition, in which the enzyme is bound by non-covalent bonds, which allows it to be easily removed from the enzyme and return to enzymatic activity. An example of a reversible inhibitor of the CYP3A4 enzyme is ketoconazole
[59], which shows different types of inhibition—competitive and non-competitive inhibition. The third subtype of reversible inhibition, uncompetitive inhibition, is not a common case for CYP3A4 enzymes and is mentioned only sporadically
[60]. A much more significant type of CYP3A4 enzyme inhibition is irreversible inhibition, in which the inhibitor is irreversibly bound to the enzyme by covalent bonds. Such a bond cannot be easily broken; therefore, the enzyme remains permanently inactive. One of the main characteristics of these inhibitions of the CYP3A4 enzyme is that it takes time; that is, it is a time-dependent inhibition
[18].
As mentioned earlier, inhibition can be caused by the drug directly (or, in this case, by the flavonoid directly), or it can be caused by the metabolite that is produced by the CYP catalytic cycle
[61]. An inhibition that is caused by the flavonoid directly can be classified as direct or time dependent. An inhibition that is caused by the metabolite can be classified as mechanism dependent (reversible or irreversible) or quasi-irreversible.
2.4. Methods for Testing out CYP3A4 Inhibitions
To test out the time-dependent type of inhibition, special experimental guidelines are implemented that suggest prior pre-incubation of the enzyme with the inhibitor to ensure sufficient time for enzyme inactivation. Only then is nicotinamide adenine dinucleotide phosphate (NADPH) added to the incubation mixture, which serves as a source of electrons in the case of testing CYP3A4 inhibition. NADPH is most often added in the form of a generating system. Another characteristic of this type of inhibition is that the
IC50 value cannot be reliably used as a basic indicator of inhibition potency, but other parameters must be considered
[62]. Such inhibitions are not characteristic of CYP3A4 enzymes
[63], but direct inhibition, as well as metabolism-dependent inhibition, are most often observed.
When testing direct inhibition, the generating system is immediately added to the incubation mixture, while for metabolism-dependent inhibition, pre-incubation with NADPH is carried out. Certain inhibitors of the CYP3A4 enzyme can also act in such a way as to show pseudo-irreversible inhibition. Pseudo-irreversible inhibition or quasi-irreversible inhibition occurs when the inhibitor binds to heme, that is, to the ferrous form of heme iron, whereby a stable complex is formed. Apparently, this type of inhibition should be considered irreversible. However, if there is a possibility for the same enzyme to return to its active form in in vitro conditions (for example, by using an oxidant along with dialysis), then one can observe this unusual phenomenon. One such example of an inhibitor is diltiazem
[64]. Some of the selected CYP3A4 inhibitors and their mechanisms of inhibition (binding of the inhibitor to the protein and/or heme) are shown in
Table 2.
Table 2.
Selected drugs as CYP3A4 inhibitors.