Biomedical subjects

David F V Lewis

Publications and source records attributed to David F V Lewis.

At least 37 records · Page 2Linked to original sources

PubMed2003

Structural models for cytochrome P450-mediated catalysis.

This review focuses on the structural models for cytochrome P450 that are improving our knowledge and understanding of the P450 catalytic cycle, and the way in which substrates bind to the enzyme leading to catalytic conversion and subsequent formation of mono-oxygenated metabolites. Various stages in the P450 reaction cycle have now been investigated using X-ray crystallography and electronic structure calculations, whereas homology modelling of mammalian P450s is currently revealing important aspects of pharmaceutical and other xenobiotic metabolism mediated by P450 involvement. These features are explored in the current review on P450-based catalysis, which emphasises the importance of structural modelling to our understanding of this enzyme's function. In addition, the results of various QSAR analyses on series of chemicals, which are metabolised via P450 enzymes, are presented such that the importance of electronic and other structural factors in explaining variations in rates of metabolism can be appreciated.

Animals↗

PubMed2003

Molecular modelling of human CYP1B1 substrate interactions and investigation of allelic variant effects on metabolism.

Molecular modelling of human CYP1B1 based on homology with the mammalian P450, CYP2C5, of known three-dimensional structure is reported. The enzyme model has been used to investigate the likely mode of binding for selected CYP1B1 substrates, particularly with regard to the possible effects of allelic variants of CYP1B1 on metabolism. In general, it appears that the CYP1B1 model is consistent with known substrate selectivity for the enzyme, and the sites of metabolism can be rationalized in terms of specific contacts with key amino acid residues within the CYP1B1 heme locus. Furthermore, a mode of binding interaction for the inhibitor, alpha-naphthoflavone, is presented which accords with currently available information. The current paper shows that a combination of molecular modelling and experimental determinations on the substrate metabolism for CYP1B1 allelic variants can aid in the understanding of structure-function relationships within P450 enzymes.

Alleles↗

PubMed2003

Essential requirements for substrate binding affinity and selectivity toward human CYP2 family enzymes.

A detailed analysis of substrate selectivity within the cytochrome P450 2 (CYP2) family is reported. From a consideration of specific interactions between drug substrates for human CYP2 family enzymes and the putative active sites of CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, and CYP2E1, it is likely that the number and disposition of hydrogen bond donor/acceptors and aromatic rings within the various P450 substrate molecules determines their enzyme selectivity and binding affinity, together with directing their preferred routes of metabolism by the CYP2 enzymes concerned. Although many aliphatic residues are present in most P450 active sites, it would appear that their main contribution centers around hydrophobic interactions and desolvation processes accompanying substrate binding. Molecular modeling studies based on the recent CYP2C5 crystal structure appear to show close agreement with site-directed mutagenesis experiments and with information on substrate metabolism and selectivity within the CYP2 family.

Alleles↗

PubMed2003

A quantitative structure-activity relationship analysis on a series of alkyl benzenes metabolized by human cytochrome p450 2E1.

The results of quantitative structure-activity relationships for eight alkyl benzenes undergoing oxidative metabolism via human CYP2E1 are reported. Molecular orbital calculations via the AM1 method were employed for the generation of electronic structural descriptors against experimentally generated kinetic data for CYP2E1-mediated metabolism. The findings point to the importance of electronic structural properties of the molecules themselves, particularly the role of frontier orbitals, in determining rates of metabolism. Other factors appear to be responsible for the affinity of these substrates for the CYP2E1 enzyme however, such as its lipophilic character. The results are consistent with the interactive molecular modeling of these compounds within the putative active site of human CYP2E1 constructed from the CYP2C5 template, where it was found that pi-pi stacking interactions between aromatic rings are important for the binding of substrates to the CYP2E1 active site, together with contributions from desolvation entropy changes accompanying substrate binding.

Aged↗

PubMed2003

A quantitative structure-activity relationship (QSAR) study of mutagenicity in several series of organic chemicals likely to be activated by cytochrome P450 enzymes.

The results of quantitative structure-activity relationship (QSAR) studies on six series of compounds exhibiting indirect mutagenic activity are reported. These findings demonstrate the importance of frontier orbital energies and, in some cases, frontier orbital electronic populations to overall mutagenicity in diverse polyaromatic hydrocarbons, benzidines and aminobiphenyls, benzonitrofurans, nitrogenous cooked-food mutagens, benzanthracenes, and chrysenes. The correlations between structural parameters and mutagenic potency vary from R=0.81 to R=0.97, and these findings are discussed in the context of possible molecular mechanisms of mutagenicity. In particular, it is generally regarded that cytochrome P450-mediated activation of polyaromatic hydrocarbons and their amino derivatives plays an important role in mutagenic activity. In this respect, it is apparent that enzymes of the cytochrome P4501 (CYP1) family are closely associated with the metabolic activation of polyaromatic mutagens and carcinogens via the generation of reactive intermediates (usually electrophilic in nature) that attack DNA. The findings presented in this study indicate that QSAR analyses on several series of compounds are consistent with the known evidence of procarcinogen activation mechanisms, particularly for polyaromatic hydrocarbons and their heterocyclic/amino derivatives, pointing to the importance of frontier orbital energy values in particular.

Aminobiphenyl Compounds↗

PubMed2003

Baseline lipophilicity relationships in human cytochromes P450 associated with drug metabolism.

From analyses of human P450 substrates and their physicochemical properties, it is apparent that baseline lipophilicity relationships exist for over 70 substrates of eight drug-metabolizing P450 enzymes from families CYP1, CYP2, and CYP3. Equations of the general form shown below result in all cases investigated thus far: deltaG(bind) = adeltaG(part) + b where a is the slope of the line which can be termed the hydrophobicity factor of the enzyme active site, possibly being related to the extent of hydrophobic amino acid residues lining the heme pocket; b is the intercept on the y axis and can be regarded as the sum of nonhydrophobic interactions between enzyme and substrate; deltaG(bind) is the free energy change for substrate binding to P450, based on the relationship deltaG(bind) = RTlnKm where Km is the Michaelis constant, and deltaG(part) is the free energy change for partitioning between n-octanol and water based on the relationship deltaG(part) = -RTlnP where P is the n-octanol/water partition coefficient. These findings facilitate the analysis of P450 enzyme-substrate binding interactions and provide information about the likely hydrophobic character of human P450 active site regions. This shows that there are common interactions for certain numbers of substrates in each case composed of hydrogen bonding and pi-pi stacking, the extent of which varies from one P450 enzyme to another.

Cytochrome P-450 Enzyme System↗

PubMed2003

Comparative studies on the cytochrome p450-associated metabolism and interaction potential of selegiline between human liver-derived in vitro systems.

Selegiline was used as a model compound in a project aimed at comparing, evaluating, and integrating different in vitro approaches for the prediction of cytochrome p450 (p450)-catalyzed hepatic drug metabolism in humans (EUROCYP). Metabolic predictions were generated using homology modeling, cDNA-expressed p450 enzymes, human liver microsomes, primary cultured human hepatocytes, and precision-cut human liver slices. All of the in vitro systems correctly indicated the formation of two dealkylated metabolites, desmethylselegiline and methamphetamine. The metabolic instability of selegiline was demonstrated by all of the in vitro systems studied. Estimates of clearance varied from 16 l/h to 223 l/h. With the exception of one approach, all systems underpredicted the in vivo clearance in humans (236 l/h). Despite this, all approaches successfully classified selegiline as a high clearance compound. Homology modeling suggested the participation of CYP2B6 in the demethylation of selegiline and of CYP2D6 in the depropargylation of the drug. Studies with recombinant expressed enzymes and with human hepatic microsomal fraction supported the involvement of CYP2B6 but not of CYP2D6. These techniques also suggested the involvement of CYP1A2, CYP2C8, and CYP2C19 in the biotransformation of selegiline. In vitro, CYP2B6 was the most active form of p450 involved in selegiline metabolism. Metabolism by several enzymes operating in parallel implies a low interaction potential for the drug. None of the techniques alone was able to predict all aspects of the metabolic and kinetic behavior of selegiline in vivo. However, when used as an integrated package, all significant characteristics were predictable.

Cells, Cultured↗

PubMed2003

Quantitative structure-activity relationships (QSARs) within the cytochrome P450 system: QSARs describing substrate binding, inhibition and induction of P450s.

Quantitative structure-activity relationships (QSARs) within substrates, inducers and inhibitors of cytochromes P450 involved in xenobiotic metabolism are reported, together with QSARs associated with induction, inhibition and metabolic rate. The importance of frontier orbitals and shape descriptors, such as planarity (estimated by the area/depth(2) parameter) and rectangularity (estimated by the length/width parameter) is discussed, particularly in the context of the COMPACT system which discriminates between several P450 families associated with the activation and detoxication of xenobiotics. The use of parameters, particularly those derived from homology modelling of mammalian (especially human) P450s that are involved in exogenous metabolism, in generating QSARs for P450 substrates is discussed in the context of explaining differences in the binding affinities of human P450 substrates which are pharmacologically active.

Journal Article↗

PubMed2003

A molecular model of CYP2D6 constructed by homology with the CYP2C5 crystallographic template: investigation of enzyme-substrate interactions.

The results of homology modelling of CYP2D6 based on the mammalian P450 crystal structure of rabbit CYP2C5 are reported. It is found that many CYP2D6-selective substrates are able to fit closely within the putative active site of the enzyme where there are favourable contacts with complementary amino acid residues, including aspartate-301 which has been probed via site-directed mutagenesis. The homology model of CYP2D6 is consistent with available experimental evidence from selective substrate metabolism and site-specific mutation data. Quantitative structure-activity relationships (QSARs) with substrate binding affinity based on KD values and inhibition data (Ki values) demonstrate the importance of hydrogen bonding, pi-pi stacking and relative molecular mass in describing variations in avidity towards the CYP2D6 enzyme, although the compound lipophilicity (log D(7.4)) appears to be the most important single descriptor for CYP2D6 inhibition. Calculation of substrate binding affinity based on contributions from active site interactions and lipophilic character gives satisfactory agreement with experimentally determined KD values.

Chemical Phenomena↗

PubMed2003

Investigation of enzyme selectivity in the human CYP2C subfamily: homology modelling of CYP2C8, CYP2C9 and CYP2C19 from the CYP2C5 crystallographic template.

Homology modelling of human CYP2C subfamily enzymes, CYP2C8, CYP2C9 and CYP2C19, based on the rabbit CYP2C5 crystal structure template is reported. The relatively high sequence homologies (75-80%) between the rabbit CYP2C5 and human CYP2C subfamily enzymes tend to indicate that the resulting structures should prove adequate models of these major catalysts of human drug metabolism. Selective substrates of all three human CYP2C enzymes are found to fit closely within the putative active sites in a manner which is consistent with site-directed mutagenesis experiments and known positions of substrate metabolism. The specific interactions between substrates and enzymes can be used to rationalize the variation in substrate binding affinity and generate QSAR models for both inhibition and metabolism via CYP2C family enzymes, yielding a generally good agreement with experimental binding data obtained from Km values, with correlation coefficients (R values) of between 0.97 and 0.99 depending on the QSAR equation produced.

Aryl Hydrocarbon Hydroxylases↗

PubMed2003

P450 structures and oxidative metabolism of xenobiotics.

This review focuses on the structural models for cytochrome P450, which are improving our knowledge and understanding of the P450 catalytic cycle, and the way in which substrates bind to the enzyme leading to catalytic conversion and subsequent formation of mono-oxygenated metabolites. Various stages in the P450 reaction cycle have now been investigated using X-ray crystallography and electronic structure calculations, whereas homology modeling of mammalian P450s is currently revealing important aspects of pharmaceutical and other xenobiotic metabolism mediated by P450 involvement. These features are explored in the current review on P450-based catalysis, which emphasizes the importance of structural modeling to our understanding of this enzyme's function. In addition, the results of various quantitative structure-activity relationships (QSAR) analyses on series of chemicals, which are metabolized via P450 enzymes, are presented such that the importance of electronic and other structural factors in explaining variations in rates of metabolism can be appreciated. As an important example of biocatalysis, the P450 system has a major future as an enzyme for use in many biotechnological applications, including biodegradation and bioremediation.

Animals↗

PubMed2003

Human cytochromes P450 associated with the phase 1 metabolism of drugs and other xenobiotics: a compilation of substrates and inhibitors of the CYP1, CYP2 and CYP3 families.

This review represents a compilation of typical substrates and inhibitors for human cytochrome P450 (CYP) enzymes that are involved in drug metabolism, specifically those from the CYP1, CYP2 and CYP3 families. Relatively recent literature on substrates and inhibitors has been collected and the relevant K(m) and K(i) values, respectively, are tabulated. Furthermore, physicochemical properties in the form of lipophilicity (log P and log D(7.4) values) and acidity/basicity (pK(a) values) are also tabulated for a significant number of substrates, together with some information on inhibitors, although only key inhibitors have been selected as the main focus is on substrates. The collated information indicates that there are certain commonalities between substrates for the same enzyme, especially with respect to their positions of metabolism and likely interactions with the relevant enzyme active site regions. The compilation therefore assists in establishing substrate structure-activity relationships (SSARs) within human drug-metabolizing P450s.

Cytochrome P-450 Enzyme Inhibitors↗

PubMed2003

On the estimation of binding affinity (deltaGbind) for human P450 substrates (based on Km and KD values).

A straightforward methodology, based on first principles, for the estimation of human cytochrome P450-substrate binding energies is outlined, and the system has then been applied successfully to a relatively large dataset of P450 substrates totalling 90 compounds. The results of Quantitative Structure-Activity Relationship (QSAR) analysis on the same dataset of cytochrome P450 (CYP) substrates from the CYP1, CYP2, and CYP3 families, involving a total of 90 compounds, agree favourably with the original analysis based on first principles, thus confirming the use of average values for hydrogen bond and pi-pi stacking energies, together with utilizing log P values as an estimation of desolvation energies. This method is based on a linear summation of the various contributary factors to the process, including: desolvation, hydrogen bonding, pi-pi stacking, restricted bond rotation and other energies relating to loss in translational and rotational energy. It is found that, for the majority of P450 substrates investigated, the first four terms are required for a relatively good estimation (R = 0.98) of the substrate binding affinity (deltaGbind) towards CYP1 and CYP2 enzymes. Consequently, it would appear that the loss in rotational and translational energy, which is thought to occur on substrate binding, apparently has little effect in most cases, possibly due to some degree of residual motion of the enzyme-substrate complex within the endoplasmic reticulum membrane. However, the appearance of a small constant term in the QSAR equation could possibly relate to an average loss in translational and rotational energy for the 90 compounds studied in this investigation.

Amino Acid Sequence↗

PubMed2002

Modelling human cytochromes P450 involved in drug metabolism from the CYP2C5 crystallographic template.

A historical background to homology modelling of human P450s involved in drug metabolism is outlined, showing that the progress in crystallographic studies of bacterial forms of enzyme and, latterly, determination of a mammalian P450 crystal structure, has enabled the production of increasingly satisfactory models of human P450 enzymes. The methodology for the generation of P450 models by homology with crystallographic template structures is summarized, and recent results of CYP2C5-constructed models of P450s are described. These indicate that selective substrates are able to fit within the putative active sites of each enzyme, where key contacts with complementary amino acid residues are largely consistent with the results of site-directed mutagenesis experiments and metabolic studies. Consequently, the CYP2C5 crystal structure can be regarded at the current paradigm for homology modelling of the drug metabolizing P450s, especially those from the CYP2 family.

Amino Acid Sequence↗

PubMed2002

Substrate SARs in human P450s.

Drug metabolism is now an integral part of the drug discovery process, and the cytochromes P450 (CYPs) are the most important family of enzymes involved in human drug metabolism. An increased understanding of the properties of the substrates for the major human CYPs is thus highly desirable. This article shows how key characteristics of CYP substrates, such as lipophilicity, molecular mass and hydrogen-bonding potential, govern selectivity towards individual CYPs. Importantly, the variation in binding affinities of 60 human CYP substrates can be explained by understanding the key physicochemical, structural and electronic characteristics that govern substrate binding to each isozyme.

Clinical Trials, Phase I as Topic↗

PubMed2002

Molecular binding interactions: their estimation and rationalization in QSARs in terms of theoretically derived parameters.

An extensive survey of molecular binding interactions and parameters used in QSARs is reported, which includes consideration of lipophilicity and the derivation of Linear Free Energy Relationships associated with drug-receptor binding, together with an overview of the various contributions to binding energy. The lipophilic parameter, log P, and its relevance to desolvation energy is outlined and explanation of the parameters derived from electronic structure calculation is provided, leading into a summary of molecular dynamics simulations.

Models, Theoretical↗

PubMed2002

Steroid hormone receptors and dietary ligands: a selected review.

Members of the nuclear steroid hormone superfamily mediate essential physiological functions. Steroid hormone receptors (SHR) act directly on DNA, regulate the synthesis of their target genes and are usually activated by ligand binding. Both endogenous and exogenous compounds and their metabolites may act as activators of SHR and disruptors of endocrine, cellular and lipid homeostasis. The endogenous ligands are generally steroids such as 17beta-oestradiol, androgens, progesterone and pregnenolone. The exogenous compounds are usually delivered through the diet and include non-steroidal ligands. Examples of such ligands include isoflavanoids or phytooestrogens, and food contaminants such as exogenous oestrogens from hormone-treated cattle, pesticides, polychlorinated biphenyls and plasticisers. Certain drugs are also ligands; so nuclear receptors are also important drug targets for intervention in disease processes. The present review summarises recent reports on ligand-activated SHR that describe the selective regulation of a tightly-controlled cross-talking network involving exchange of ligands, and the control of major classes of cytochrome P450 (CYP) isoforms which metabolise many bioactive exogenous compounds. Many CYP have broad substrate activity and appear to be integrated into a coordinated metabolic pathway, such that whilst some receptors are ligand specific, other sensors may have a broader specificity and low ligand affinity to monitor aggregate levels of inducers. They can then trigger production of metabolising enzymes to defend against possible toxic nutrients and xenobiotic compounds. The influence of dietary intakes of nutrients and non-nutrients on the human oestrogen receptors (alpha and beta), the aryl hydrocarbon receptor, the pregnane X receptor, the constitutive androstane receptor, and the peroxisome proliferator-activated receptors (alpha and gamma), can be examined by utilising computer-generated molecular models of the ligand-receptor interaction, based on information generated from crystallographic data and sequence homology. In relation to experimental and observed data, molecular modelling can provide a scientifically sound perspective on the potential risk and benefits to human health from dietary exposure to hormone-mimicking chemicals, providing a useful tool in drug development and in a situation of considerable public concern.

Animals↗

PubMed2002

Molecular modelling of CYP2B6 based on homology with the CYP2C5 crystal structure: analysis of enzyme-substrate interactions.

The results of homology modelling of CYP2B6 based on the CYP2C5 crystal structure is described in terms of substrates and inhibitors binding within the putative active site. In general these results are in agreement with currently available evidence from substrate metabolism, mode of inhibitor action and site-directed mutagenesis experiments within the CYP2B subfamily of enzymes. Consequently, the model based on the CYP2C5 template represents an advance on those models produced from bacterial P450s, such as CYP101 and CYP102. Quantitative Structure-Activity Relationships (QSARs) for substrates binding to CYP2B6 indicate a key role for hydrogen bonding, and lipophilic character, as determined by the log P parameter (where P is the octanol/water partition coefficient), is also of importance for explaining the variation in experimental binding affinity for CYP2B6 substrates. It is possible to estimate the binding energies for typical CYP2B6 substrates based on their properties and interactions with the enzyme, which show good concordance with experimental data in the form of apparent Km values.

Aryl Hydrocarbon Hydroxylases↗