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Biomedical subjects

Jean-Didier Maréchal

Publications and source records attributed to Jean-Didier Maréchal.

14 recordsLinked to original sources
PubMed2006

Inhibition of cancer cell growth by cyclin dependent kinase 4 inhibitors synthesized based on the structure of fascaplysin.

Tryptamine derivatives, a new structural class of cyclin dependent kinase 4 inhibitors, have been identified during extensive biological screening of synthetic molecules. The molecules were synthesized based on the structure of fascaplysin, which is not only a specific inhibitor of the Cdk4-cyclin D1 enzyme but also a relatively toxic molecule, probably because it binds and intercalates DNA. Interestingly, the new structural analogues of fascaplysin do not interact or intercalate with double-stranded DNA, although they inhibit Cdk4-cyclin D1 specifically. We found that compound CA199 was the most potent molecule, showing at least 25-fold specificity towards Cdk4-cyclin D1 (IC50 for Cdk4-cyclin D1 = 20 microM, Cdk2 > 500 microM). CA199 inhibits the growth of different cancer cell lines at concentrations ranging from 10-40 microM. It blocks growth of asynchronous cells at G0/G1 in a retinoblastoma protein (pRb) dependent manner. Moreover, CA199 blocks growth only at early G1 in synchronised cells released from a mimosine-induced G1/S block. These observations are reminiscent of a true Cdk4 inhibitor.

Antineoplastic Agents↗
PubMed2006

CA224, a non-planar analogue of fascaplysin, inhibits Cdk4 but not Cdk2 and arrests cells at G0/G1 inhibiting pRB phosphorylation.

Tryptamine derivatives, non-planar and potentially less toxic analogues of the anti-cancer agent fascaplysin, have been synthesised. They specifically inhibit Cdk4-D1 vis a vis Cdk2-A but, unlike fascaplysin, do not bind or intercalate DNA. CA224 is the most potent compound identified (Cdk4-D1 IC(50) approximately 5.5 microM). As would be expected of a Cdk4 inhibitor that does not inhibit Cdk2, it maintains a G(0)/G(1) block in synchronised cancer cells and inhibits Cdk4-specific phosphorylation of the retinoblastoma protein.

Antineoplastic Agents↗
PubMed2006

In silico prediction of drug binding to CYP2D6: identification of a new metabolite of metoclopramide.

Patients with cancer often take many different classes of drugs to treat the effects of their malignancy and the side effects of treatment, as well as their comorbidities. The potential for drug-drug interactions that may affect the efficacy of anticancer treatment is high, and a major source of such interactions is competition for the drug-metabolizing enzymes, cytochromes P450 (P450s). We have examined a series of 20 drugs commonly prescribed to cancer patients to look for potential interactions via CYP2D6. We used a homology model of CYP2D6, together with molecular docking techniques, to perform an in silico screen for binding to CYP2D6. Experimental IC50 values were determined for these compounds and compared with the model predictions to reveal a correlation with a regression coefficient of r2= 0.61. Importantly, the docked conformation of the commonly prescribed antiemetic metoclopramide predicted a new site of metabolism that was further investigated through in vitro analysis with recombinant CYP2D6. An aromatic N-hydroxy metabolite of metoclopramide, consistent with predictions from our modeling studies, was identified by high-performance liquid chromatography/mass spectrometry. This metabolite was found to represent a major product of metabolism in human liver microsomes, and CYP2D6 was identified as the main P450 isoform responsible for catalyzing its formation. In view of the prevalence of interindividual variation in the CYP2D6 genotype and phenotype, we suggest that those experiencing adverse reactions with metoclopramide, e.g., extrapyramidal syndrome, are likely to have a particular CYP2D6 genotype/phenotype. This warrants further investigation.

Antiemetics↗
PubMed2006

Mono- vs. bi-metallic assembly on a bulky bis(imino)terpyridine framework: a combined experimental and theoretical study.

The bis(imino)terpyridine ligands, 6,6''-{(2,6-i-Pr2C6H3)N=CR}2-2,2':6',2''-C15H9N3 (R = H L1, Me L2), have been prepared in high yield from the condensation reaction of the corresponding carbonyl compound with two equivalents of 2,6-diisopropylaniline. The molecular structure of L2 reveals a transoid relationship between the imino and pyridyl nitrogen groups throughout the ligand framework. Treatment of aldimine-containing L1 with one equivalent or an excess of MX2 in n-BuOH at 110 degrees C gives the mononuclear five-coordinate complexes, [(L1)MX2] (M = Fe, X = Cl 1a; M = Ni, X = Br 1b; M = Zn, X = Cl 1c), in which the metal centre occupies the terpyridine cavity and the imino groups pendant. Conversely, reaction of ketimine-containing L2 with excess MX2 in n-BuOH at 110 degrees C affords the binuclear complexes, [(L2)M2X4] (M = Fe, X = Cl 3a; M = Ni, X = Br 3b; M = Zn, X = Cl 3c), in which one metal centre occupies a bidentate pyridylimine cavity while the other a tridentate bipyridylimine cavity. 1H NMR studies on diamagnetic 3c suggests a fluxional process is operational at ambient temperature in which the central pyridine ring undergoes an exchange between metal coordination. Under less forcing conditions (room temperature in dichloromethane), the monometallic counterpart of 1b [(L2)NiBr2] (2b) has been isolated which can be converted to 3b by addition of one equivalent of (DME)NiBr2 (DME = 1,2-dimethoxyethane) in n-BuOH at 110 degrees C. Quantum mechanical calculations (DFT) have been performed on [(L1)ZnCl2] and [(L2)ZnCl2] for different monometallic conformations and show that 1a is the energetically preferred structure for L1 while there is evidence for dynamic behaviour in L2-containing species leading to bimetallic formation. Single-crystal X-ray diffraction studies have been performed on 1a, 1b, 1c, 2b, 3a, 3b(H2O) and 3c.

Aniline Compounds↗
PubMed2006

A DFT study on the relative affinity for oxygen of the alpha and beta subunits of hemoglobin.

DFT calculations are carried out on computational models of the active center of the alpha and beta subunits of hemoglobin in both its oxygenated (R) and deoxygenated (T) states. The computational models are defined by the full heme group, including all porphyrin substituents, and the four amino acids closer to it. The role of the protein environment is introduced by freezing the position of the alpha carbon atom of each of the four amino acids to the positions they have in the available PDB structures. Oxygen affinity is then evaluated by computing the energy difference between the optimized structures of the oxygenated and deoxygenated forms of each model. The results indicate a higher affinity of the alpha subunits over the beta ones. Analysis of the computed structures points out to the strength of the hydrogen bond between the distal histidine and the oxygen molecule as a key factor in discriminating the different systems.

Computer Simulation↗
PubMed2006

Insights into drug metabolism from modelling studies of cytochrome P450-drug interactions.

The cytochromes P450 (CYPs) comprise a vast superfamily of enzymes found in virtually all life forms. In mammals, xenobiotic metabolising CYPs provide crucial protection from the harmful effects of exposure to a wide variety of chemicals, including environmental toxins and therapeutic drugs. Elucidating the structural features of CYPs that contribute to their metabolism of structurally diverse substrates impacts on the rational design of improved therapeutic drugs and specific inhibitors. Models capable of predicting the possible involvement of CYPs in the metabolism of drugs or drug candidates are thus important tools in drug discovery and development. Ideally, functional information would be obtained from crystal structures of all the CYPs of interest. Initially only crystal structures of distantly related bacterial CYPs were available - comparative modelling techniques were used to bridge the gap and produce structural models of human CYPs, and thereby obtain some useful functional information. A significant step forward in the reliability of these models came six years ago with the first crystal structure of a mammalian CYP, rabbit CYP2C5, followed by the structures of five human enzymes, CYP2A6, CYP2C8, CYP2C9, CYP2D6 and CYP3A4, and a second rabbit enzyme, CYP2B4. The evolution of a CYP2D6 model, leading to the validation of the model as an in silico tool for predicting binding and metabolism, is presented as a case study.

Animals↗
PubMed2005

Why is quinidine an inhibitor of cytochrome P450 2D6? The role of key active-site residues in quinidine binding.

We have previously shown that Phe(120), Glu(216), and Asp(301) in the active site of cytochrome P450 2D6 (CYP2D6) play a key role in substrate recognition by this important drug-metabolizing enzyme (Paine, M. J., McLaughlin, L. A., Flanagan, J. U., Kemp, C. A., Sutcliffe, M. J., Roberts, G. C., and Wolf, C. R. (2003) J. Biol. Chem. 278, 4021-4027 and Flanagan, J. U., Maréchal, J.-D., Ward, R., Kemp, C. A., McLaughlin, L. A., Sutcliffe, M. J., Roberts, G. C., Paine, M. J., and Wolf, C. R. (2004) Biochem. J. 380, 353-360). We have now examined the effect of mutations of these residues on interactions of the enzyme with the prototypical CYP2D6 inhibitor, quinidine. Abolition of the negative charge at either or both residues 216 and 301 decreased quinidine inhibition of bufuralol 1'-hydroxylation and dextromethorphan O-demethylation by at least 100-fold. The apparent dissociation constants (K(d)) for quinidine binding to the wild-type enzyme and the E216D and D301E mutants were 0.25-0.50 microm. The amide substitution of Glu(216) or Asp(301) resulted in 30-64-fold increases in the K(d) for quinidine. The double mutant E216Q/D301Q showed the largest decrease in quinidine affinity, with a K(d) of 65 microm. Alanine substitution of Phe(120), Phe(481),or Phe(483) had only a minor effect on the inhibition of bufuralol 1'-hydroxylation and dextromethorphan O-demethylation and on binding. In contrast to the wild-type enzyme, a number of the mutants studied were found to be able to metabolize quinidine. E216F produced O-demethylated quinidine, and F120A and E216Q/D301Q produced both O-demethylated quinidine and 3-hydroxyquinidine metabolites. Homology modeling and molecular docking were used to predict the modes of quinidine binding to the wild-type and mutant enzymes; these were able to rationalize the experimental observations.

Alanine↗
PubMed2005

Internal cavities and ligand passageways in human hemoglobin characterized by molecular dynamics simulations.

Molecular dynamics simulations of the unliganded T state of human hemoglobin showed the existence of a spontaneous, very wide cavity on the distal side of the alpha subunit. This cavity consists of three tunnels spreading from the vicinity of the iron atom (the ligand binding site) to the surface of the subunit, constituting possible passageways for the entrance of the ligand. A fourth passageway was characterized due to the trajectory of water molecules entering or leaving the heme pocket. Analogous passages were observed in the beta subunits. They all appear and disappear dynamically, although some parts of them are more persistent along the trajectories. The most persistent regions within these tunnels correspond to all the xenon docking sites of human cytoglobin and to some of those of sperm whale and horse heart myoglobins and group I truncated hemoglobins.

Binding Sites↗
PubMed2005

Progress in cytochrome P450 active site modeling.

Models capable of predicting the possible involvement of cytochromes P450 in the metabolism of drugs or drug candidates are important tools in drug discovery and development. Ideally, functional information would be obtained from crystal structures of all the cytochromes P450 of interest. Initially, only crystal structures of distantly related bacterial cytochromes P450 were available-comparative modeling techniques were used to bridge the gap and produce structural models of human cytochromes P450, and thereby obtain some useful functional information. A significant step forward in the reliability of these models came four years ago with the first crystal structure of a mammalian cytochrome P450, rabbit CYP2C5, followed by the structures of two human enzymes, CYP2C8 and CYP2C9, and a second rabbit enzyme, CYP2B4. The evolution of a CYP2D6 model, leading to the validation of the model as an in silico tool for predicting binding and metabolism, is presented as a case study.

Amino Acid Sequence↗
PubMed2004

Validation of model of cytochrome P450 2D6: an in silico tool for predicting metabolism and inhibition.

There has been much interest in the development of a predictive model of cytochrome P450 2D6 particularly because this enzyme is involved in the oxidation of at least 50 drugs. Previously we have described the combined use of homology modeling and molecular docking to correctly position a range of substrates in the CYP2D6 active site with the known sites of metabolism above the heme. Here, our approach identifies correctly the site of metabolism of the atypical (no basic nitrogen) cytochrome P450 2D6 substrate, spirosulfonamide. The same method is used to screen a small compound database for cytochrome P450 2D6 inhibition. A database containing 33 compounds from the National Cancer Institute database was docked into our cytochrome P450 2D6 homology model using the program GOLDv2.0. Experimental IC50 values for the 33 compounds were determined; comparison with the corresponding docked scores revealed a correlation with a regression coefficient of r2 = 0.61 (q2 = 0.59). The method was able to discriminate between tight and weak binding compounds and correctly identified several novel inhibitors. The results therefore suggest that our approach, which combines homology modeling with molecular docking, has produced a useful predictive in silico tool for cytochrome P450 2D6 inhibition, which is best used as one filter in a multifilter database screen.

Binding Sites↗
PubMed2004

Flexible N,N,N-chelates as supports for iron and cobalt chloride complexes; synthesis, structures, DFT calculations and ethylene oligomerisation studies.

The aryl-substituted N-picolylethylenediamine and diethylenetriamine ligands, (ArNHCH(2)CH(2))[(2-C(5)H(4)N)CH(2)]NH and (ArNHCH(2)CH(2))(2)NH (Ar = 2,6-Me(2)C(6)H(3), 2,4,6-Me(3)C(6)H(2)), have been prepared by employing palladium-catalysed N-C(aryl) coupling reactions of the corresponding primary amines with aryl bromide. Treatment of MCl(2) with (ArNHCH(2)CH(2))[(2-C(5)H(4)N)CH(2)]NH affords [[(ArNHCH(2)CH(2))((2-C(5)H(4)N)CH(2))NH]CoCl(2)](Ar = 2,6-Me(2)C(6)H(3) 1a; 2,4,6-Me(3)C(6)H(2)) 1b and [[(ArNHCH(2)CH(2))((2-C(5)H(4)N)CH(2))NH]FeCl(2)](n)(n= 1, Ar = 2,6-Me(2)C(6)H(3) 2a; n= 2, 2,4,6-Me(3)C(6)H(2) 2b) in high yield. The X-ray structures of 1a and 1b are isostructural and reveal the metal centres to adopt distorted trigonal bipyramidal geometries with the N,N,N-chelates adopting fac-structures. A facial coordination mode of the ligand is also observed in bimetallic 2b, however, in 2a the N,N,N-chelate adopts a mer-configuration with the metal centre adopting a geometry best described as square pyramidal. Solution studies indicate that mer-fac isomerisation is a facile process for these systems at room temperature. Quantum mechanical calculations (DFT) have been performed on 1a and 2a, in which the ligands employed are identical, and show the fac- to be marginally more stable than the mer-configuration for cobalt (1a) while for iron (2a) the converse is evident. Reaction of (ArNHCH(2)CH(2))(2)NH with CoCl(2) gave the five-coordinate complexes [[(ArNHCH(2)CH(2))(2)NH]CoCl(2)](Ar = 2,6-Me(2)C(6)H(3) 3a, 2,4,6-Me(3)C(6)H(2) 3b), in which the ligand adopts a mer-configuration; no reaction occurred with FeCl(2). All complexes 1-3 act as modest ethylene oligomerisation catalysts on activation with excess methylaluminoxane (MAO); the iron systems giving linear alpha-olefins while the cobalt systems give mixtures of linear and branched products.

Journal Article↗
PubMed2004

Phe120 contributes to the regiospecificity of cytochrome P450 2D6: mutation leads to the formation of a novel dextromethorphan metabolite.

Although the residues that determine the preference of CYP2D6 (cytochrome P450 2D6) for compounds containing a basic nitrogen are well characterized, the contribution of other active site residues to substrate binding and orientation is less well understood. Our structural model of CYP2D6 identifies the aromatic residue Phe120 as a likely major feature of the active site. To examine the role of Phe120, mutants of CYP2D6 in which this residue has been substituted by alanine, leucine, tyrosine, serine, histidine, tryptophan or methionine residues have been prepared in bacterial membranes co-expressing human cytochrome NADPH cytochrome P450 oxidoreductase. The mutants have been characterized using the prototypical bufuralol 1' hydroxylase and dextromethorphan O- and N-demethylase activities of CYP2D6. Larger effects on K(m) values are observed for dextromethorphan O-demethylation than for bufuralol 1' hydroxylation, indicating that the Phe120 side chain is more important in dextromethorphan than in bufuralol binding. A role for this side chain in determining the regiospecificity of substrate oxidation was indicated by changes in the relative rates of O- and N-demethylation of dextromethorphan and, notably, by the formation of 7-hydroxy dextromethrophan, a novel dextromethorphan metabolite, in mutants in which it had been substituted. Computational studies of dextromethorphan binding to the active site of the Phe120-->Ala mutant were carried out to throw light on the way in which the removal of this side chain leads to different modes of ligand binding.

Cytochrome P-450 CYP2D6↗