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Thierry Prangé

Publications and source records attributed to Thierry Prangé.

At least 19 recordsLinked to original sources
PubMed2006

Protein crystallography under xenon and nitrous oxide pressure: comparison with in vivo pharmacology studies and implications for the mechanism of inhaled anesthetic action.

In contrast with most inhalational anesthetics, the anesthetic gases xenon (Xe) and nitrous oxide (N(2)O) act by blocking the N-methyl-d-aspartate (NMDA) receptor. Using x-ray crystallography, we examined the binding characteristics of these two gases on two soluble proteins as structural models: urate oxidase, which is a prototype of a variety of intracellular globular proteins, and annexin V, which has structural and functional characteristics that allow it to be considered as a prototype for the NMDA receptor. The structure of these proteins complexed with Xe and N(2)O were determined. One N(2)O molecule or one Xe atom binds to the same main site in both proteins. A second subsite is observed for N(2)O in each case. The gas-binding sites are always hydrophobic flexible cavities buried within the monomer. Comparison of the effects of Xe and N(2)O on urate oxidase and annexin V reveals an interesting relationship with the in vivo pharmacological effects of these gases, the ratio of the gas-binding sites' volume expansion and the ratio of the narcotic potency being similar. Given these data, we propose that alterations of cytosolic globular protein functions by general anesthetics would be responsible for the early stages of anesthesia such as amnesia and hypnosis and that additional alterations of ion-channel membrane receptor functions are required for deeper effects that progress to "surgical" anesthesia.

Anesthetics↗
PubMed2006

Efficient synthesis of calix[6]tmpa: a new calix[6]azacryptand with unique conformational and host-guest properties.

A new C(3v)-symmetrical calix[6]azacryptand, that is, calix[6]tmpa (11), was synthesized by efficient [1+1] macrocyclization reactions. Remarkably, both linear and convergent synthetic strategies that were applied lead to equally good overall yields. Calix[6]tmpa behaves as a single proton sponge and appeared reluctant to undergo polyprotonation, unlike classical tris(2-pyridylmethyl)amine (tmpa) derivatives. It also acts as a good host for ammonium ions. Interestingly, it strongly binds a sodium ion and a neutral guest molecule, such as a urea, an amide, or an alcohol, in a cooperative way. A (1)H NMR study indicated that the ligand, as well as its complexes, adopt a major flattened cone conformation that is the opposite of that observed with the previously reported calix[6]cryptands. Characterization of the monoprotonated derivative 11H(+) by X-ray diffraction also revealed the presence of a 1,3-alternate conformation, which is the first example of its kind in the calix[6]arene family. This conformer is probably also present in solution as a minor species. The important covalent constraint induced by the polyaromatic tmpa cap on the calixarene skeleton, and conversely from the calix core onto the tmpa moiety, is the likely basis for the unique conformational and chemical properties of this host.

Journal Article↗
PubMed2006

On the edge of the denaturation process: application of X-ray diffraction to barnase and lysozyme cross-linked crystals with denaturants in molar concentrations.

Structural data about the early step of protein denaturation were obtained from cross-linked crystals for two small proteins: barnase and lysozyme. Several denaturant agents like urea, bromoethanol or thiourea were used at increasing concentrations up to a limit leading to crystal disruption (>or=2 to 6 M). Before the complete destruction of the crystal order started, specific binding sites were observed at the protein surfaces, an indication that the preliminary step of denaturation is the disproportion of intermolecular polar bonds to the benefit of the agent "parasiting" the surface. The analysis of the thermal factors first agree with a stabilization effect at low or moderate concentration of denaturants rapidly followed by a destabilization at specific weak points when the number of sites increase (overflooding effect).

Animals↗
PubMed2006

Recapture of [S]-allantoin, the product of the two-step degradation of uric acid, by urate oxidase.

Urate oxidase from Aspergillus flavus catalyzes the degradation of uric acid to [S]-allantoin through 5-hydroxyisourate as a metastable intermediate. The second degradation step is thought either catalyzed by another specific enzyme, or spontaneous. The structure of the enzyme was known at high resolution by X-ray diffraction of I222 crystals complexed with a purine-type inhibitor (8-azaxanthin). Analyzing the X-ray structure of urate oxidase treated with an excess of urate, the natural substrate, shows unexpectedly that the active site recaptures [S]-allantoin from the racemic end product of a second degradation step.

Allantoin↗
PubMed2006

Supramolecular assemblies with calix[6]arenes and copper ions: from dinuclear to trinuclear linear arrangements of hydroxo-Cu(II) complexes.

Complexation of copper(II) by calix[6]arene-based ligands bearing either two or three N-benzylimidazole coordinating arms under basic conditions has been studied. Whereas the tris(imidazole) derivative stabilizes dicationic 5-coordinate aqua complexes in a mononuclear state with an intracavity bound guest, in the presence of hydroxide ions, the latter undergo dimerization. An X-ray structure revealed decoordination of one imidazole arm and formation of a bis(hydroxo) bridged Cu(II) core with a square-planar geometry for both metal centers sandwiched by two empty calixarene cavities. Upon methanolysis, the dinuclear complex underwent an unexpected rearrangement leading to the clean formation of a trinuclear complex. X-ray diffraction analyses of this novel species revealed a trinuclear core constructed around a central Cu(II) ion that is doubly bridged through either methoxide or hydroxide anions to two Cu(II) ions hold by two calixarene units. The same complex could be directly synthesized by reacting the ligand with copper(II) perchlorate in a 2:3 ratio in the presence of base. In solution, the tetrahydroxo Cu(3) complex was characterized by UV-vis and (1)H NMR spectroscopies and displayed an electron paramagnetic resonance (EPR) signal only below 100 K that accounts for a S = 1/2 fundamental state. Formation of the same di- and trinuclear species was observed with a calix[6]arene-based bis(imidazole) ligand, which demonstrates the generality of the reaction schemes. All these results emphasize the versatility of the calix[6]arene scaffold for the stabilization of metal complexes with various nuclearities.

Calixarenes↗
PubMed2006

Andropanolide and isoandrographolide, minor diterpenoids from Andrographis paniculata: structure and X-ray crystallographic analysis.

Phytochemical investigation of the leaves of Andrographis paniculata has led to the isolation of a new labdane type diterpenoid, andropanolide (1), along with seven known diterpenoids including isoandrographolide (2), previously reported as a rearrangement product of andrographolide. The structures and stereochemistry of compounds 1 and 2 were established by X-ray crystallographic analysis.

Andrographis↗
PubMed2006

Saradaferin, a new sesquiterpenoid coumarin from Ferula assafoetida.

Phytochemical investigation of the gum resin of Ferula assafoetida resulted in the isolation and characterization of a new sesquiterpenoid coumarin, Saradaferin (1) named as [Decahydro-(3-alpha-hydroxy-4,4,10-trimethyl-8-methylene-9-naphthenyl)-alpha-hydroxymethyl] ether of umbelliferone.

Coumarins↗
PubMed2005

X-ray diffraction and EXAFS studies of hydroxo-Cu(II) complexes based on a calix[6]arene-N3 ligand: evidence for a mononuclear-dinuclear equilibrium controlled by supramolecular features.

The formation of hydroxo complexes based on a calix[6]trisimidazole ligand is described. Deprotonation of the mononuclear Cu(II)-aqua complex gives rise to a dinuclear bis(mu-hydroxo) complex that has been characterized by X-ray diffraction analysis. Spectroscopic studies (EPR and UV-vis), conducted in dichloromethane solutions in the presence of various coordinating cosolvents (DMF, EtOH, or RCN) or with acetamide, revealed the coexistence of a mononuclear hydroxo species. The latter could be trapped by acetic acid to provide an acetato-Cu(II) complex that presents close spectroscopic features. An EXAFS study first conducted on the hydroxo-Cu(II) complex led to an excellent fit for the dinuclear core. It then allowed for the characterization of the mononuclear acetato complex with an acetamide guest included in the calixarene cavity. Hence, this study illustrates the flexibility of calixarene-based ligands and the role of the second coordination sphere in the stabilization of acidic or basic Cu(II) complexes.

Journal Article↗
PubMed2005

Biomimetic zinc funnel complexes based on calix[6]N3ArO ligands: an acid-base switch for guest binding.

The coordination chemistry of Zn in an N(3)ArOH environment has been explored. The ligands are based on calix[6]arenes that present two imidazole arms and an amino phenol moiety at the narrow rim. Three different types of complexes have been characterized. One is dicationic with Zn(2+) coordinated to the three nitrogen atoms and to the oxygen of the phenol group of the calix[6]ligand. This complex is very sensitive to exogenous coordinating molecules and exists as a 5-coordinate species due to the endo-complexation of a guest. The second species is a monocationic complex for which the phenol group has been deprotonated. The resulting N(3)ArOZn complex can also bind a guest ligand albeit with a lower affinity than the dicationic complex. The third species is neutral. It can be obtained upon reaction with a base to yield a hydroxo complex or with an anion such as a chloride that coordinates the metal center from the outside of the calixarene cavity. The simultaneous binding of two anionic donors decreases the Zn Lewis acidity, allowing an impressive conformational reorganization of the system. One imidazole arm is released by the metal center. The other one undergoes self-inclusion into the pi-basic calixarene cavity because the low affinity of the metal center for neutral ligand does not allow the endo-coordination of an exogenous guest. Hence, the calix[6]N(3)ArOH-based Zn complexes act as an acid-base switch for guest binding. Several aspects of this system appear reminiscent of Zn-peptidases of the astacin and serralisin families.

Acid-Base Equilibrium↗
PubMed2005

Synthesis and glycosidase inhibitory activity of new hexa-substituted C8-glycomimetics.

BACKGROUND: Glycosidases are involved in several metabolic pathways and the development of inhibitors is an important challenge towards the treatment of diseases, such as diabetes, cancer and viral infections including AIDS. Thus, inhibition of intestinal alpha-glucosidases can be used to treat diabetes through the lowering of blood glucose levels, and alpha-glucosidase inhibitors are being marketed against type 2 (non-insulinodependent mellitus) diabetes (i.e.: Glyset or Diastabol, Basen and Glucor or Precose). RESULTS: In that context, new C8-carbasugars and related aminocyclitols have been targeted in order to study the effect of the enhanced flexibility and of the new spatial distribution displayed by these structures on their adaptability in the active site of the enzymes. The synthesis of these new C8-glycomimetics is described from enantiomerically pure C2-symmetrical polyhydroxylated cyclooctenes. Their obtention notably involved a syn-dihydroxylation, and more extended functionalization through formation of a cis-cyclic sulfate followed by amination and subsequent reductive amination. This strategy involving the nucleophilic opening of a cis-cyclic sulfate by sodium azide is to our knowledge the first example in C8-series. It revealead to be an efficient alternative to the nucleoplilic opening of an epoxide moiety which proved unsuccessful in this particular case, due to the hindered conformation of such epoxides as demonstrated by X-ray cristallographic analysis. CONCLUSION: The biological activity of the synthesized glycomimetics has been evaluated towards 24 commercially available glycosidases. The weak observed activities can probably be related to the spatial disposition of the hydroxy and amino groups which depart too much from that realized in glycomimetics such as valiolamine, voglibose and valienamine. Nevertheless, the synthetic strategy described here is efficient and general, and could be extended to increase the diversity of the glycosidase inhibitors obtained since this diversity is introduced in an ultimate step of the synthesis.

Journal Article↗
PubMed2005

Calix[6]tren and copper(II): a third generation of funnel complexes on the way to redox calix-zymes.

Mono-copper enzymes play an important role in biology and their functionality is based on Cu(II)/Cu(I) redox processes. Modeling a mono-nuclear site remains a challenge for a better understanding of its intrinsic reactivity. The first member of a third generation of calixarene-based mono-copper "funnel" complexes is described. The ligand is a calix[6]arene capped by a tren unit, hence presenting a N(4) coordination site confined in a cavity. Its Cu(II) complexes were characterized by electronic and EPR spectroscopies. The x-ray structure of one of them shows a five-coordinated metal ion in a slightly distorted trigonal bipyramidal geometry thanks to its coordination to a guest ligand L (ethanol). The latter sits in the heart of the hydrophobic calixarene cone that mimics the active site chamber and the hydrophobic access channel of enzymes. Competitive binding experiments showed a preference order dimethylformamide > ethanol > MeCN for L binding at the single exchangeable metal site. Cyclic voltammetry studies showed irreversible redox processes in CH(2)Cl(2) when L is an oxygen donor caused by the redox-driven ejection of the guest at the Cu(I) level. In the presence of MeCN, a pseudoreversible process was obtained, owing to a fast equilibrium between a four and a five-coordinate Cu(I) species. Finally, a redox-driven ligand interchange of dimethylformamide for MeCN at the Cu(I) state allowed the trapping of the thermodynamically less stable Cu(II)-MeCN adduct. Hence, this work represents an important step toward the elaboration of a functional supramolecular model for redox mono-copper enzymes, named redox calix-zymes.

Binding Sites↗
PubMed2005

Urate oxidase from Aspergillus flavus: new crystal-packing contacts in relation to the content of the active site.

Urate oxidase from Aspergillus flavus (uricase or Uox; EC 1.7.3.3) is a 135 kDa homotetramer with a subunit consisting of 301 amino acids. It catalyses the first step of the degradation of uric acid into allantoin. The structure of the extracted enzyme complexed with a purine-type inhibitor (8-azaxanthin) had been solved from high-resolution X-ray diffraction of I222 crystals. Expression of the recombinant enzyme in Saccharomyces cerevisiae followed by a new purification procedure allowed the crystallization of both unliganded and liganded enzymes utilizing the same conditions but in various crystal forms. Here, four different crystal forms of Uox are analyzed. The diversity of the Uox crystal forms appears to depend strongly on the chemicals used as inhibitors. In the presence of uracil and 5,6-diaminouracil crystals usually belong to the trigonal space group P3(1)21, the asymmetric unit (AU) of which contains one tetramer of Uox (four subunits). Chemical oxidation of 5,6-diaminouracil within the protein may occur, leading to the canonical (I222) packing with one subunit per AU. Coexistence of two crystal forms, P2(1) with two tetramers per AU and I222, was found in the same crystallization drop containing another inhibitor, guanine. Finally, a fourth form, P2(1)2(1)2 with one tetramer per AU, resulted fortuitously in the presence of cymelarsan, an additive. Of all the reported forms, the I222 crystal forms present by far the best X-ray diffraction resolution (approximately 1.6 angstroms resolution compared with 2.3-3.2 angstroms for the other forms). The various structures and contacts in all crystalline lattices are compared. The backbones are essentially conserved except for the region near the active site. Its location at the dimer interface is thus likely to be at the origin of the crystal contact changes as a response to the various bound inhibitors.

Aspergillus flavus↗
PubMed2004

Tuning organogels and mesophases with phenanthroline ligands and their copper complexes by inter- to intramolecular hydrogen bonds.

A novel family of highly functionalized molecules consisting of a central 4-methyl-3,5-diacylaminobenzene platform linked in close proximity to the methyl group by two lateral aromatic rings each equipped with two long alkoxy chains has been rationally designed. The presence of amide tethers and a chelating phenanthroline fragment connected via an ester dipole formed a new class of gelating reagents and mesomorphic materials. A few of these compounds have the tendency to form macromolecule-like aggregates through noncovalent interactions in hydrocarbon solvents and were found to exhibit thermotropic cubic mesophases. In light of the X-ray molecular structure of the methoxy ligand, an infinite network maintained by intermolecular hydrogen bonds as well as by pi-pi stacking of the phenyl subunits was evidenced. FT-IR studies confirm that the common driving force for aggregation in the organogels and microsegregation in the mesophase is the occurrence of a tight intermolecular H-bonded network that does not persist in diluted solution. This situation is switched when the ligands are interlocked by a copper(I) cation. A strong intramolecular H-bond confirmed by X-ray diffraction of a single crystal for the methoxy case provides very stable complexes but inhibits the gelation of the solvents. Heating the complexes bearing long paraffin chains (n = 12 and 16) in the dried state leads to a self-organization into a columnar liquid-crystalline phase in which the columns are arranged along a 2D oblique symmetry as deduced from powder XRD experiments. In this case, the complexes with the appended counteranions self-assemble in a specific way to form columns. A striking observation is that the intramolecular hydrogen bond persists in the mesophase as it does in solution without any evidence of an extended network. As far as we are aware, these ligands and complexes are rare examples in which organogelation and thermotropic mesomorphic behavior could be observed in parallel with molecules bearing a chelating platform. Due to the synthetic availability of the 4-methyl-3,5-diacylaminobenzene core and the simplicity by which the chelating platforms can be graphed, this methodology represents a practical alternative to the production of functionalized organogelators and mesomorphic materials.

Journal Article↗
PubMed2004

Complexed and ligand-free high-resolution structures of urate oxidase (Uox) from Aspergillus flavus: a reassignment of the active-site binding mode.

High-resolution X-ray structures of the complexes of Aspergillus flavus urate oxidase (Uox) with three inhibitors, 8-azaxanthin (AZA), 9-methyl uric acid (MUA) and oxonic acid (OXC), were determined in an orthorhombic space group (I222). In addition, the ligand-free enzyme was also crystallized in a monoclinic form (P2(1)) and its structure determined. Higher accuracy in the three new enzyme-inhibitor complex structures (Uox-AZA, Uox-MUA and Uox-OXC) with respect to the previously determined structure of Uox-AZA (PDB code 1uox) leads to a reversed position of the inhibitor in the active site of the enzyme. The corrected anchoring of the substrate (uric acid) allows an improvement in the understanding of the enzymatic mechanism of urate oxidase.

Amino Acid Sequence↗
PubMed2004

Purification, crystallization and preliminary X-ray studies of sylvaticin, an elicitin-like protein from Pythium sylvaticum.

Sylvaticin belongs to the elicitin family. These 10 kDa oomycetous proteins induce a hypersensitive response in plants, including necrosis and cell death, but subsequently leading to a non-specific systemic acquired resistance (SAR) against other pathogens. Sylvaticin has been crystallized using PEG 2000 MME as a precipitant agent in the presence of nickel chloride. The crystals belong to space group C2, with unit-cell parameters a = 99.29, b = 25.67, c = 67.45 A, beta = 99.66 degrees. Diffraction data were recorded to 2.1 A resolution at a synchrotron-radiation source.

Algal Proteins↗
PubMed2003

Cation sensors based on terpyridine-functionalized boradiazaindacene.

A new class of highly luminescent dyes is reported. The characteristic feature of these compounds is that a terpyridine fragment is closely appended to a boradiazaindacene moiety in such a way that cation binding to the vacant terpyridine causes strong perturbations of the photophysical properties of the boradiazaindacene unit. In particular, these sensors are especially applicable to the fluorescence detection of trace quantities of zinc(II) ions in solution. The mechanism of the cation-induced quenching process has been investigated by a combination of electrochemistry, UV/Vis absorption, emission, and NMR spectroscopy. Highly luminescent arrays can be formed by doping transparent polymers with low concentrations of these new dyes. In such materials, the change in photophysical properties upon cation binding is so marked that "cation writing" becomes feasible under routine conditions.

Journal Article↗
PubMed2003

Interactions of a new alpha-aminophosphinic derivative inside the active site of TLN (thermolysin): a model for zinc-metalloendopeptidase inhibition.

A new alpha-aminophosphinic compound able to inhibit both zinc-containing exopeptidases and endopeptidases has been crystallized with TLN as a model in order to investigate the mode of zinc recognition by the phosphinic moiety and to evaluate the potential role of the free alpha-amino group in the formation of enzyme-inhibitor complexes. In addition to the main interactions between the backbone of the inhibitor and the enzyme active site, it is observed that the phosphinic group acts as a distorted bidentate ligand for the zinc ion, while the free alpha-amino function does not directly participate in interactions within the active site. Association of the present data and the K(i) values of various analogues of the inhibitor towards TLN and neprilysin suggests differences in the hydrophobicity of the S(1)-S(2) domains of the enzymes. This could be taken into account in the design of selective inhibitors.

Binding Sites↗