Humans have 57 genes and more than 59 pseudogenes divided among 18 families of cytochrome P genes and 6 days ago Enzymes produced from the cytochrome P genes are involved in the formation (synthesis) and breakdown (metabolism) of various. Cytochrome P Cytochromes P (CYPs) belong to the superfamily of proteins Cytochrome P family 1 (CYP1) · Cytochrome P family 2 (CYP2) .
Cytochrome P450 Family The
From these, four sites were within important regions of the enzyme: For these sites, the following changing properties were identified: S1—S11 , Supplementary Material online for more methodological details. CYP2 subfamily code abbreviations indicate each one of the data sets used: The LDA constructed a single discriminant function fig.
This was due to the large degree of similarity among the number of CYP2 genes present in the two classes migratory and non-migratory , as is apparent from the average variable scores per group fig.
The minor differences found between the two classes were due to CYP2 genes scoring in the extremes of the discriminant function, with migratory bird scores tending slightly towards negative values whereas non-migratory are closer to the positive end of the function fig.
However, a Kolmogorov—Smirnoff test applied to the frequencies of scores from the linear discriminant function fig. Results of the linear discriminant function. A Average scores per class. B Individual species scores per class. The black line represents a nonparametric fit of frequency distributions. Furthermore, differences in the number of CYP2 genes were also observed when analysing feeding habits in association with the migratory behavior of birds fig.
Non-migratory carnivores have less CYP2 genes than non-migratory omnivores and herbivores, but none of these differences resulted to be significant. Globally, omnivores have a higher number of CYP2 genes than specialist birds carnivorous and herbivorous birds , except for non-migratory herbivores, which have a number of CYP2 genes similar to non-migratory omnivores fig.
Comparison of the number of CYP2 genes in birds with different migratory behaviors and feeding habits. Asterisks indicate significant differences in pairwise comparisons performed by Mann—Whitney tests. Species trait classifications are in supplementary table S2 , Supplementary Material online. The avian CYP2 subfamilies corresponded well with previous classifications Watanabe et al.
Some of our most striking results are the presence or absence of one or many CYP families in closely related species. The Adelie penguin and the closely related emperor penguin have similar habitats both live exclusively in the Antarctic region , feeding habits carnivores , and lifestyles colonial, social, specialized for swimming Williams but the number of CYP2 subfamilies between them was striking nine and only three, respectively— fig.
This is an intriguing scenario because it was expected that these species facing similar selective pressures would present a similar number of CYP2 subfamilies.
However, according to our approach the emperor penguin appears to have lost many subfamilies that the Adelie penguin still has and shares with other more distantly related bird species. In order to exclude possible false-negatives due to the strict criteria of our identification approach, we performed exploratory tBLASTn searches against the emperor penguin genome with less stringent criteria and using the Adelie penguin CYP2 sequences as query. However, due to their short lengths as opposed to complete CYP2 genes that encompass approximately 1, bp , the accurate assignment to a CYP subfamily becomes compromised.
Thus, such short sequences were not considered for further detailed evolutionary analyses. This would be consistent with other studies.
For example, a study of humans found that a functional CYP2G allele was also uncommon in humans detected in only We cannot exclude the possibility that these genes are present in the gaps of avian genome assemblies, or even that evidence of their presence in other birds can be missed, as demonstrated above, by our threshold of requiring at least 1, bp when searching for avian CYP2 nucleotide sequences.
Our selection analyses results are consistent with some findings in avian and nonavian species. Thus, it is plausible that the positively selected sites , , , and leading to changes in amino acid properties might have provided an important adaptation by facilitating the efficient inactivation and removal of several xenobiotic compounds in birds.
CYP2D is present in several mammalian species e. Therefore, the positively selected sites 54 and 74 found in the avian CYP2D subfamily, located within the SRS1 and HEM functional regions, could be particularly advantageous for an efficient dietary detoxification Yasukochi and Satta Our lineage-specific analyses of CYP2D suggest similar impacts among birds with distinct feeding habits.
The effect of changing amino acid properties for some of the positively selected sites , , located outside of the active site areas of the avian CYP2D subfamily could possibly be related with global protein folding or substrate recognition da Fonseca et al. CYP2H enzymes are involved in reactions of epoxygenation Kanetoshi et al.
Agonist for the CYP2H are the drugs dexamethasone and metyrapone and also the compounds okadaic acid, pregnenolone16 alpha-carbonitrile, and squalestatin1 Ourlin et al. The substrate of these enzymes is arachidonic acid Kanetoshi et al.
Since CYP2H has evolved differently among different avian groups, it is most likely that the changes have distinct adaptive relevance possibly involving feeding habits, habitats, and migratory behaviors.
The greater number of gene duplications and large variability in the amino acid patterns among the different copies of CYP2J genes among birds could also be related to different habitats and feeding adaptations.
Similar duplications events have been detected in bactrian camels, which are hypothesized to be linked with the importance of CYP2J in the conversion of arachidonic acid into 19 S -HETE—a potential vasodilator of renal preglomerular vessels—that stimulates water reabsorption Jirimutu et al. CYP2J also has epoxygenase activity and can convert arachidonic acid into epoxyeicosatrienoic acids EETS that have antihypertensive vasodilatory properties Yu et al. Thus, it has been hypothesized that an increased number of CYP2J copies would increase water absorption and could influence survival in dry conditions Jirimutu et al.
The large number of avian CYP2J copies and the extraordinary high degree of positive selection detected in the SRS suggest that this subfamily might be important to adaptation to distinct habitats by using water more efficiently. Although we have identified sites under positive selection in the avian CYP2K and CYP2AC subfamilies, further studies are necessary to infer the impact of these substitutions, since their function remains little known.
These genes have conserved synteny between birds and humans Watanabe et al. Similarly, the remaining subfamilies without positive selection CYP2W and CYP2AF also can have essential functions in the metabolism of endogenous compounds, being strongly adapted to their substrates.
Our analysis also revealed that the variation in the number of CYP2 genes is related to different feeding habits and migratory behaviors of birds. This suggests that the higher number of CYP2 genes found in avian migratory omnivores might be related with their need to adapt to a wider variety of environments and food resources, and thus the higher exposure to several toxins, would require a more efficient detoxification capacity Rainio et al.
While our study provides significant advances to our understanding of avian CYP2 evolution, the currently available genome scaffold lengths limit the number of CYP2 sequences that can be confidently classified. Ongoing efforts to increase the scaffold lengths of bird genomes will enhance our understanding of avian CYP2 identification and adaptation. To our knowledge, this is the first study of avian CYP2 subfamilies that includes representatives of the three avian evolutionary groups: Palaeognathae, Galloanserae, and Neoaves Zhang et al.
Of the six, only the CYP2C and CYP2H subfamilies had sites under positive selection in SRS5, suggesting that these two subfamilies may be under similar evolutionary pressures in this enzyme region, that allow them to phenotypically adapt and acquire similar substrate affinities.
The positive selected sites in these avian CYP2 subfamilies likely have helped them adapt to distinct chemical compounds in new habitats with distinct food resources, and facilitate the dispersion and evolutionary success of birds. Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide.
Sign In or Create an Account. Close mobile search navigation Article navigation. Abstract The cytochrome P CYP superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. View large Download slide. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.
Accuracy and power of bayes prediction of amino acid sites under positive selection. Gathering computational genomics and proteomics to unravel adaptive evolution. Transcriptional activation of cytochrome P CYP2C45 by drugs is mediated by the chicken xenobiotic receptor CXR interacting with a phenobarbital response enhancer unit.
Modeling amino acid substitution patterns in orthologous and paralogous genes. Structural divergence and adaptive evolution in mammalian cytochromes P 2C.
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Views Read Edit View history. Recently, the CYP1A1 structure was used in studies of interactions of the enzyme with a great number of CYP1A1 substrates and inhibitors summarized in Table 1 , including phytochemicals, for example, dietary flavonoids [ 32 , 41 , 47 ]; drugs, for example, melatonin, debrisoquine, theophylline, clozapine, and carvedilol [ 57 ]; environmental pollutants, for example, aromatic hydrocarbons and their derivatives [ 22 , 28 , 35 , 37 , 45 , 55 ]; and natural and synthetic derivatives of trans -stilbene [ 25 , 46 , 63 ].
The authors generated and validated a ligand-based pharmacophore model using a series of known anticancer compounds acting via CYP1A1. Selected compounds were subsequently subjected to pharmacokinetic screening, MetaSite screening, a molecular docking study, and a PAINS pan-assay interference compounds filter to refine the retrieved hits. Nine compounds capable of generating reactive metabolites and good interactions with CYP1A1 were selected for further studies in vitro.
These compounds were metabolized by CYP1A1 to the N -hydroxylated products that are potential genotoxic agents and may be responsible for a toxic effect of parent compounds.
A molecular dynamics simulation analysis was used to visualize the orientation of hit molecules in a CYP1A1 binding site cavity, which promotes bioactive metabolite formation by N-hydroxylation [ 62 ].
The narrow and flat binding pocket of CYP1A2 determines the substrate specificity of the enzyme. Drug metabolism prediction with the use of docking, molecular dynamics, and quantum chemical methods was a good option to screen a library for potential inhibitors and drug-drug interactions [ 69 , 86 ].
An efficient model for in silico screening was developed to identify CYP1A2 inhibitors in databases of herbal ingredients [ 73 ].
A rationale for these studies was herb-drug interactions. First, a pharmacophore model was constructed and validated. Then, the best pharmacophore model was chosen for a virtual screening of herbal compounds. The hits herbal compounds were investigated through molecular docking and tested in vitro.
Finally, 5 inhibitors of 18 candidate compounds were found to inhibit CYP1A2 activity. Molecular dynamics simulations provided an insight into the role of molecules of water in the enzyme active site. ANF forms the hydrogen bond with a water molecule, but during the simulations, different water molecules interact with ANF at different points of time [ 70 ].
Docking studies followed by MD simulations revealed that water molecules have an effect on hydrogen bond networks formed in the enzyme active site influencing the interactions of the substrate with amino acids in the enzyme active site. It appeared that water molecules were necessary for 7-ethoxyresorufin recognition, while for ligand recognition ANF , water molecules were not required.
The amino acid residues Val and Ala determine the cavity shape in the vicinity of the heme. A comparison of CYP1 family enzyme structures points to similarities and differences among the three active sites that determine their varied substrate specificities.
ANF bound in the CYP1 cavities occupies the same plane adjacent to the heme and opposite to the I helix in each enzyme. The most meaningful differences in the structure were listed and analyzed by Walsh et al. The residue at position is known to be important in determining the functional differences between CYP1A1 and CYP1A2; mutations at this position have a significant impact on the catalytic efficiency of enzymes; the smaller residue facilitates ligand placement in the enzyme cavity.
A five-residue break in the CYP1A1 F helix has an effect on ligand binding, increasing the flexibility of the active site. A triangle with the side length of 9. To investigate the active sites of CYP1s, a series of potential inhibitors were synthesized and tested for their inhibitory activity.
Synthesizing two series of chemical probes: The authors concluded that CYP1A1 has a narrow and long cavity, The CYP1A2 cavity can accommodate a triangular molecule, showing a planar heart-like structure with a 9. According to that suggestion, a series of 14 flavone and coumarin derivatives exhibiting a triangular planar shape were designed with the use of the computer-assisted alignment assay. Most of the tested compounds 13 out of 14 appeared to be selective CYP1A2 inhibitors. The molecular modeling of enzymes differing in a selected amino acid sequence provides a rationale for substrate specificity.
Studies of the relationship between an amino acid sequence and the functionality of CYP1s were possible, thanks to mutagenesis methods. To reduce the number of mutants to be constructed, the residues for replacement should be located in the active site of the enzyme and must be different from the corresponding residues in the enzyme which is being compared.
Based on the knowledge of which active site residues are different between CYP1A1 and CYP1A2, the effect of reciprocal mutations on substrate specificity was examined [ 31 ]. The results confirmed the importance of SRSs for enzyme-substrate interaction, proposed earlier by Gotoh [ 89 ]. Functional alterations as a result of genetic polymorphism may influence the therapeutic response of many drugs changing their efficacy and toxicity.
A functional characterization of 20 allelic variants of CYP1A2 was performed with two substrates: Four of the studied alleles, which exhibited the substitutions critical to the enzymatic function located in: SRS, the heme-binding region, the aromatic region, and the proline-rich region , showed reduced activity toward both substrates. However, the substitution ArgGln might cause a change in hydrogen bonds to alternative ones with other amino acids, which resulted in the loss of enzyme activity or decreased holoprotein level.
Two variants with the substitutions ThrIle and AspAsn showed a significantly higher activity toward phenacetin than the wild-type enzyme. Interestingly, the amino acid residues Thr and Asp are not located in the substrate binding site.
They are situated on the surface of CYP1A2 and may influence the interaction of the enzyme with cytochrome b5 [ 90 ]. For these mutations, they found a change in protein flexibility and a collective protein motion that caused the main substrate access channel to be mostly closed. Dynamics simulations were used to explain the mechanism of a changed binding of 7-ethoxyresorufin in the catalytic pocket of the FL mutant enzyme.
Despite the fact that the mutation PheLeu is located on the surface, a series of changes in the catalytic pocket were observed. PheLeu mutation enhanced the binding affinity but lowered the O-deethylation velocity of 7-ethoxyresorufin.
Homology-modeled structures of wild-type and disease-associated mutant forms were constructed on the basis of human CYP2C9.
In the mutant form of CYP1B1, changes in the geometry of the substrate binding region and the position of the heme were observed. Using molecular dynamics simulations, altered interactions of estradiol with the disease mutant of CYP1B1 in comparison with the wild type of enzyme were demonstrated [ 83 ]. More recently, the structures of eight mutants differing only in one residue were generated from the crystal structure of CYP1A2.
Mutation of only one amino acid changed the enzyme static structure even in distant regions of the protein and influenced the flexibility of the whole protein and influenced the catalytic activity of the enzyme by changing the conformation of a ligand-enzyme complex [ 81 ]. Molecular docking is a computational approach which predicts the orientation of a ligand pose in complex with a protein target and assesses its binding affinity using scoring functions.
Structure-based drug design is performed in order to identify bioactive compounds in the compound pool found in high-throughput virtual screening HTVS based on the information from the protein structure. A computational approach predicts the orientation of ligands in complex with a protein target using scoring functions specific algorithms.
Structure-based virtual screening is a quick and more economical method of lead identification than experimental screening. In research, popular open-source docking software and more advanced commercial packages are used. Nonetheless, in the opinion of many authors, they still need to be improved to obtain a better pose prediction capability.
The main factors limiting the accuracy of docking results are protein flexibility and solvation. The affinity of a ligand to a protein target is characterized by scoring functions which represent a relative binding free energy based on protein-ligand interactions. Scoring functions do not consider the contribution of thermodynamic effects on binding free energy like solvation, long-range interactions, and conformational changes.
Protein-ligand docking methods are widely used at different stages of the drug design process. They are employed at the beginning for the virtual screening VS of large ligands' databases and at the lead optimization stage. The scoring function is used by the searching algorithm to identify the best pose of a particular ligand, the most energetically favoured orientation inside the active site.
It also estimates the binding affinity of a ligand. This allows us to rank ligands in virtual screening, where large and chemically diverse databases should be docked very effectively; so here, the speed of docking is more important than its accuracy [ 5 ].
However, in lead optimization, researchers are interested in obtaining docking results that are as accurate as possible for a small set of ligands, which are often structurally related. Besides assessing binding affinities to the macromolecular target for close analogues in lead optimization, docking can also be used for predicting off-target binding to related proteins and to cytochromes as drug-metabolizing enzymes [ 5 ].
The role of a docking algorithm is to generate ligand poses inside the binding site. The scoring function should correctly recognize the bioactive orientation and assign a sufficiently high score to it, allowing us to discriminate binders from nonbinders in terms of calculated binding affinity [ 5 ]. Scoring functions are classified as force field-based, empirical, and knowledge-based [ 95 ].
Force field-based functions account for electrostatic and van der Waals interactions in protein-ligand complexes using force field parameters. In empirical scoring, functions are terms describing specific ligand-protein interactions, for example, hydrogen bonds, ionic interactions, or hydrophobic effects.
Another class of scoring functions, knowledge-based, was derived from a statistical analysis of the crystal structures of ligand-protein complexes. It does not use information about experimental activity but analyzes the distribution of ligand-protein atom pairs giving pairwise potentials [ 95 ]. All scoring functions have some limitations. They perform much better in identifying correct poses of individual ligands than in ranking ligands according to their activity for respective targets.
Difficulty in differentiating between nano- and micromolar compounds limits the reliability of docking [ 5 ]. To overcome this issue, more than one scoring function can be employed in assessing binding affinity.
Consensus scoring combines the results of several scoring functions; this approach is in some cases more successful in predicting activity than a single function [ 95 ]. Some specific interactions, for example, cation-pi, CH-pi, or weak hydrogen bonds, are not captured by commonly used scoring functions. Also, many simplifications, such as treating solvation effects and contributions of entropy to the binding energy, result in a poor ranking of compounds in VS [ 95 ].
Therefore, more advanced and computationally demanding methods for rescoring docked poses are applied. For this purpose, physics-based methods and simulations based on force fields and implicit solvent models are employed. Many docking algorithms treat the receptor as conformationally rigid, which is a severe approximation influencing the final results.
In fact, upon binding to a protein, ligands often induce changes in its conformation [ 5 , 96 ]. The flexibility of a protein can be included in the macromolecular model in several ways. There are many examples of ligand-target interactions via water molecules e.
Usually, before docking, water molecules are removed from the binding site, but there are also other options, such as keeping or displacing water molecules which are placed in the binding site or are important for the binding of ligands [ 5 , 95 ]. Existing scoring functions are not perfect in ranking compounds in virtual screening and estimating absolute binding affinities in lead optimization.
Also, receptor flexibility needs to be taken into account during docking experiments. Therefore, docking methods are still under development regarding aspects such as receptor flexibility, structural water or the solvation, and entropic effect [ 98 ].
Docking can predict a plausible orientation and conformation of ligands inside the binding site of the receptor, although this method gives only a static picture of ligand-receptor interactions.
A deeper insight into the time-dependent properties of ligand-protein complexes could be obtained with the use of molecular dynamics MD simulations.
In molecular dynamics simulations, solvent molecules are included explicitly or with the use of implicit solvent models. Before docking, MD simulations could be used to give an ensemble of protein structures, but for postdocking complexes, this method allows for a computational testing of its stability and is often used to rescore docked ligands because of the improvement in the mutual fit and optimization of interactions that occur during the simulation.
There are many examples of successful applications of MD in the characterization of ligand-macromolecular target complexes [ 4 , 99 ]. Protein-ligand binding energy should be determined as a nonadditive effect, which depends on the chemical environment and protein-ligand cooperative dynamic processes. Molecular dynamics simulation improves predictions of binding free energy by considering the time-dependent behaviour of the macromolecular system in response to changes in its molecular environment.
However, docking results are not always consistent with MD simulation different poses observed by docking and MD; a ligand does not form a long-lasting complex. It also happens that docking results are not proved by the biochemical assay in vitro , and vice versa; compounds with high bioactivities are shown to have a poor docking score.
Cytochrome P, named in the s as a 'chromatic (coloured) pigment in the most vertebrates) are divided into 18 CYP gene families – based on amino. Cytochrome P (CYP) is a large family consisting of multiple sub-families and many were found to be related to CRC susceptibility, especially CYP1A and . Cytochromes P (CYPs) are the principal enzymes responsible for the oxidation . drug metabolism are found in the CYP1, CYP2, and CYP3 gene families.