Étude de l'oligomérisation et de la fonction de canaux ioniques par spectroscopie de fluorescence et fluorométrie en voltage imposé

La fonction des canaux ioniques est finement régulée par des changements structuraux de sites clés contrôlant l’ouverture du pore. Ces modulations structurales découlent de l’interaction du canal avec l’environnement local, puisque certains domaines peuvent être suffisamment sensibles à des propriétés physico-chimiques spécifiques. Les mouvements engendrés dans la structure sont notamment perceptibles fonctionnellement lorsque le canal ouvre un passage à certains ions, générant ainsi un courant ionique mesurable selon le potentiel électrochimique. Une description détaillée de ces relations structure-fonction est cependant difficile à obtenir à partir de mesures sur des ensembles de canaux identiques, puisque les fluctuations et les distributions de différentes propriétés individuelles demeurent cachées dans une moyenne. Pour distinguer ces propriétés, des mesures à l’échelle de la molécule unique sont nécessaires. Le but principal de la présente thèse est d’étudier la structure et les mécanismes moléculaires de canaux ioniques par mesures de spectroscopie de fluorescence à l’échelle de la molécule unique. Les études sont particulièrement dirigées vers le développement de nouvelles méthodes ou leur amélioration. Une classe de toxine formeuse de pores a servi de premier modèle d’étude. La fluorescence à l’échelle de la molécule unique a aussi été utilisée pour l’étude d’un récepteur glutamate, d’un récepteur à la glycine et d’un canal potassique procaryote. Le premier volet porte sur l’étude de la stœchiométrie par mesures de photoblanchiment en temps résolu. Cette méthode permet de déterminer directement le nombre de monomères fluorescents dans un complexe isolé par le décompte des sauts discrets de fluorescence suivant les événements de photoblanchiment. Nous présentons ici la première description, à notre connaissance, de l’assemblage dynamique d’une protéine membranaire dans un environnement lipidique. La toxine monomérique purifiée Cry1Aa s’assemble à d’autres monomères selon la concentration et sature en conformation tétramérique. Un programme automatique est ensuite développé pour déterminer la stœchiométrie de protéines membranaires fusionnées à GFP et exprimées à la surface de cellules mammifères. Bien que ce système d’expression soit approprié pour l’étude de protéines d’origine mammifère, le bruit de fluorescence y est particulièrement important et augmente significativement le risque d’erreur dans le décompte manuel des monomères fluorescents. La méthode présentée permet une analyse rapide et automatique basée sur des critères fixes. L’algorithme chargé d’effectuer le décompte des monomères fluorescents a été optimisé à partir de simulations et ajuste ses paramètres de détection automatiquement selon la trace de fluorescence. La composition de deux canaux ioniques a été vérifiée avec succès par ce programme. Finalement, la fluorescence à l’échelle de la molécule unique est mesurée conjointement au courant ionique de canaux potassiques KcsA avec un système de fluorométrie en voltage imposé. Ces enregistrements combinés permettent de décrire la fonction de canaux ioniques simultanément à leur position et densité alors qu’ils diffusent dans une membrane lipidique dont la composition est choisie. Nous avons observé le regroupement de canaux KcsA pour différentes compositions lipidiques. Ce regroupement ne paraît pas être causé par des interactions protéine-protéine, mais plutôt par des microdomaines induits par la forme des canaux reconstitués dans la membrane. Il semble que des canaux regroupés puissent ensuite devenir couplés, se traduisant en ouvertures et fermetures simultanées où les niveaux de conductance sont un multiple de la conductance « normale » d’un canal isolé. De plus, contrairement à ce qui est actuellement suggéré, KcsA ne requiert pas de phospholipide chargé négativement pour sa fonction. Plusieurs mesures indiquent plutôt que des lipides de forme conique dans la phase cristalline liquide sont suffisants pour permettre l’ouverture de canaux KcsA isolés. Des canaux regroupés peuvent quant à eux surmonter la barrière d’énergie pour s’ouvrir de manière coopérative dans des lipides non chargés de forme cylindrique.

Structural, Spectral, Biological and Electrochemical Studies Of Some 3d Transition Metal Complexes of O-N-S and N-N-S Donor Ligands

The primary aim of these investigations was to probe the spectroscopic, electrochemical, biological and single crystal X-ray diffraction studies of some selected transition metal complexes of 4N-monosubstituted thiosemicarbazones. Transition metal complexes with thiosemicarbazones exhibit a wide range of stereochemistries and possess potential biological activity. Metal complexes of thiosemicarbazones are proved to have improved pharmacological and therapeutic effects. The studies are conducted to bring about a fair understanding of the structure activity relationship and to develop certain effective and economical metal-based antimicrobial agents. Study showed that the thiosemicarbazones have antibacterial, antiviral and antiproliferative properties and hence used against tuberculosis, leprosy, psoriasis, rheumatism, trypanosomiasis and coccidiosis. Certain thiosemicarbazones showed a selective inhibition of HSV and HIV infections. The insolubility of most thiosemicarbazones in water causes difficulty in the oral administration in clinical practice. Transition metal complexes are found to have more activity than uncombined thiosemicarbazones. They exhibit a variety of denticity and can be varied by proper substitution. The stereochemistry assumed by the thiosemicarbazones during the coordination with transition metal ions depends on the factors such as preparative conditions and availability of additional bonding site in the ligand moiety and charge of the ligand. The resulting complexes exhibited a wide range of stereochemistries and have biomimic activity and potential application as sensors.

Structural, Spectral, Biological and Electrochemical Studies Of Some 3d Transition Metal Complexes of O-N-S and N-N-S Donor Ligands

The primary aim of these investigations was to probe the spectroscopic, electrochemical, biological and single crystal X-ray diffraction studies of some selected transition metal complexes of 4N-monosubstituted thiosemicarbazones. Transition metal complexes with thiosemicarbazones exhibit a wide range of stereochemistries and possess potential biological activity. Metal complexes of thiosemicarbazones are proved to have improved pharmacological and therapeutic effects. The studies are conducted to bring about a fair understanding of the structure activity relationship and to develop certain effective and economical metal-based antimicrobial agents. Study showed that the thiosemicarbazones have antibacterial, antiviral and antiproliferative properties and hence used against tuberculosis, leprosy, psoriasis, rheumatism, trypanosomiasis and coccidiosis. Certain thiosemicarbazones showed a selective inhibition of HSV and HIV infections. The insolubility of most thiosemicarbazones in water causes difficulty in the oral administration in clinical practice. Transition metal complexes are found to have more activity than uncombined thiosemicarbazones. They exhibit a variety of denticity and can be varied by proper substitution. The stereochemistry assumed by the thiosemicarbazones during the coordination with transition metal ions depends on the factors such as preparative conditions and availability of additional bonding site in the ligand moiety and charge of the ligand. The resulting complexes exhibited a wide range of stereochemistries and have biomimic activity and potential application as sensors

Relacions estructura-propietat per un conjunt d'hidrocarburs a partir de nous descriptors tridimensionals derivats de la semblança molecular quàntica

En aquest article es defineixen uns nous índexs tridimensionals per a la descripció de les molècules a partir de paràmetres derivats de la Teoria de la Semblança Molecular i de les distàncies euclidianes entre els àtoms i les càrregues atòmiques efectives. Aquests indexs, anomenats 3D, s'han aplicat a l'estudi de les relacions estructura-propietat d'una família d'hidrocarburs, i han demostrat una capacitat de descripció de tres propietats de la família (temperatura d'ebullició, temperatura de fusió i densitat) molt més acurada que quan s'utilitzen els indexs 2D clàssics

Synteza, badania strukturalne i spektroskopowe oraz aktywność przeciwnowotworowa i przeciwdrobnoustrojowa nowych pochodnych salinomycyny

Wydział Chemii: Pracownia Chemii Bioorganicznej

PDBSprotEC: A web-accessible database linking PDB chains to EC numbers via SwissProt

A mapping between chains in the Protein Databank and Enzyme Classification numbers is invaluable for research into structure-function relationships. Mapping at the chain level is a non-trivial problem and we present an automatically updated Web-server, which provides this link in a queryable form and as a downloadable XML or flat file.

Structure–activity relations (SARs) for gas-phase reactions of NO3, OH and O3 with alkenes: an update

We present updated structure-activity relations (SARs) for the prediction of rate coefficients for gas-phase reactions with alkenes of the major atmospheric oxidants NO3, OH and O-3. Such SARs provide one way of incorporating essential information about reactivity into atmospheric models. Rate coefficients obtained from correlations relating the logarithms of the rate coefficients to the energies of the highest occupied molecular orbitals (HOMOs) of the alkenes were used to refine the SARs. SARs have an advantage for the user over the direct application of the correlations in that knowledge of the structure of the alkene of interest is sufficient to estimate rate coefficients, and no quantum-mechanical calculations need to be performed. A comparison of the values predicted by the SARs with experimental data where they exist allowed us to assess the reliability of our method.

Investigating flavonoids as molecular templates for the design of small-molecule inhibitors of cell signaling

Epidemiological and clinical trials reveal compelling evidence for the ability of dietary flavonoids to lower cardiovascular disease risk. The mechanisms of action of these polyphenolic compounds are diverse, and of particular interest is their ability to function as protein and lipid kinase inhibitors. We have previously described structure-activity studies that reinforce the possibility for using flavonoid structures as templates for drug design. In the present study, we aim to begin constructing rational screening strategies for exploiting these compounds as templates for the design of clinically relevant, antiplatelet agents. We used the platelet as a model system to dissect the structural influence of flavonoids, stilbenes, anthocyanidins, and phenolic acids on inhibition of cell signaling and function. Functional groups identified as relevant for potent inhibition of platelet function included at least 2 benzene rings, a hydroxylated B ring, a planar C ring, a C ring ketone group, and a C-2 positioned B ring. Hydroxylation of the B ring with either a catechol group or a single C-4' hydroxyl may be required for efficient inhibition of collagen-stimulated tyrosine phosphorylated proteins of 125 to 130 kDa, but may not be necessary for that of phosphotyrosine proteins at approximately 29 kDa. The removal of the C ring C-3 hydroxyl together with a hydroxylated B ring (apigenin) may confer selectivity for 37 to 38 kDa phosphotyrosine proteins. We conclude that this study may form the basis for construction of maps of flavonoid inhibitory activity on kinase targets that may allow a multitargeted therapeutic approach with analogue counterparts and parent compounds.

Crystal Engineering of an Anti-HIV Drug Based on the Recognition of Assembling Molecular Frameworks

A rational strategy was employed for design of an orthorhombic structure of lamivudine with maleic acid. On the basis of the lamivudine saccharinate structure reported in the literature, maleic acid was chosen to synthesize a salt with the anti-HIV drug because of the structural similarities between the salt formers. Maleic acid has an acid-ionization constant of the anti first proton and an arrangement of their hydrogen bonding functionalities similar to those of saccharin. Likewise, there is a saccharin-like conformational rigidity in maleic acid because of the hydrogen-bonded ring formation and the Z-configuration around the C=C double bond. As was conceivably predicted, lamivudine maleate assembles into a structure whose intermolecular architecture is related to that of saccharinate salt of the drug. Therefore, a molecular framework responsible for crystal assembly into a lamivudine saccharinate-like structure could be recognized in the salt formers. Furthermore, structural correlations and structure-solubility relationships were established for lamivudine maleate and saccharinate. Although there is a same molecular framework in maleic acid and saccharin, these salt formers are Structurally different in some aspects. When compared to saccharin, neither out-of-plane SO(2) oxygens nor a benzene group occur in maleic acid. Both features could be related to higher solubility of lamivudine maleate. Here, we also anticipate that multicomponent molecular crystals of lamivudine with other salt formers possessing the molecular framework responsible for crystal assembly can be engineered successfully.

Role of Halogen Bonds in Thyroid Hormone Receptor Selectivity: Pharmacophore-Based 3D-QSSR Studies

Most physiological effects of thyroid hormones are mediated by the two thyroid hormone receptor subtypes, TR alpha and TR beta. Several pharmacological effects mediated by TR beta might be beneficial in important medical conditions such as obesity, hypercholesterolemia and diabetes, and selective TR beta activation may elicit these effects while maintaining an acceptable safety profile, To understand the molecular determinants of affinity and subtype selectivity of TR ligands, we have successfully employed a ligand- and structure-guided pharmacophore-based approach to obtain the molecular alignment of a large series of thyromimetics. Statistically reliable three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models were obtained using the comparative molecular field analysis (CoMFA) method, and the visual analyses of the contour maps drew attention to a number of possible opportunities for the development of analogs with improved affinity and selectivity. Furthermore, the 3D-QSSR analysis allowed the identification of a novel and previously unmentioned halogen bond, bringing new insights to the mechanism of activity and selectivity of thyromimetics.

Fragment-Based QSAR and Molecular Modeling Studies on a Series of Discodermolide Analogs as Microtubule-Stabilizing Anticancer Agents

Inhibition of microtubule function is an attractive rational approach to anticancer therapy. Although taxanes are the most prominent among the microtubule-stabilizers, their clinical toxicity, poor pharmacokinetic properties, and resistance have stimulated the search for new antitumor agents having the same mechanism of action. Discodermolide is an example of nontaxane natural product that has the same mechanism of action, demonstrating superior antitumor efficacy and therapeutic index. The extraordinary chemical and biological properties have qualified discodermolide as a lead structure for the design of novel anticancer agents with optimized therapeutic properties. In the present work, we have employed a specialized fragment-based method to develop robust quantitative structure - activity relationship models for a series of synthetic discodermolide analogs. The generated molecular recognition patterns were combined with three-dimensional molecular modeling studies as a fundamental step on the path to understanding the molecular basis of drug-receptor interactions within this important series of potent antitumoral agents.

Two-dimensional QSAR studies on arylpiperazines as high-affinity 5-HT(1A) receptor ligands

5-HT(1A) receptor plays an important role in the delayed onset of antidepressant action of a class of selective serotonin reuptake inhibitors. Moreover, 5-HT(1A) receptor levels have been shown to be altered in patients suffering from major depression. In this work, hologram quantitative structure-activity relationship (HQSAR) studies were performed on a series of arylpiperazine compounds presenting affinity to the 5-HT(1A) receptor. The models were constructed with a training set of 70 compounds. The most significant HQSAR model (q(2) = 0.81, r(2) = 0.96) was generated using atoms, bonds, connections, chirality, and donor and acceptor as fragment distinction, with fragment size of 6-9. Predictions for an external test set containing 20 compounds are in good agreement with experimental results showing the robustness of the model. Additionally, useful information can be obtained from the 2D contribution maps.

Discovery of New Inhibitors of Schistosoma mansoni PNP by Pharmacophore-Based Virtual Screening

Schistosomiasis is considered the second most important tropical parasitic disease, with severe socioeconomic consequences for millions of people worldwide. Schistosoma monsoni, one of the causative agents of human schistosomiasis, is unable to synthesize purine nucleotides de novo, which makes the enzymes of the purine salvage pathway important targets for antischistosomal drug development. In the present work, we describe the development of a pharmacophore model for ligands of S. mansoni purine nucleoside phosphorylase (SmPNP) as well as a pharmacophore-based virtual screening approach, which resulted in the identification of three thioxothiazolidinones (1-3) with substantial in vitro inhibitory activity against SmPNP. Synthesis, biochemical evaluation, and structure activity relationship investigations led to the successful development of a small set of thioxothiazolidinone derivatives harboring a novel chemical scaffold as new competitive inhibitors of SmPNP at the low-micromolar range. Seven compounds were identified with IC(50) values below 100 mu M. The most potent inhibitors 7, 10, and 17 with 1050 of 2, 18, and 38 mu M, respectively, could represent new potential lead compounds for further development of the therapy of schistosomiasis.

Conformational Properties of Angiotensin II and Its Active and Inactive TOAC-Labeled Analogs in the Presence of Micelles. Electron Paramagnetic Resonance, Fluorescence, and Circular Dichroism Studies

The interaction between angiotensin II (AII, DRVYIHPF) and its analogs carrying 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC) and detergents-negatively charged sodium dodecyl sulfate (SDS) and zwitterionic N-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (HPS)-was examined by means of EPR, CD, and fluorescence. EPR spectra of partially active TOAC(1)-AII and inactive TOAC(3)-AII in aqueous solution indicated fast tumbling, the freedom of motion being greater at the N-terminus. Line broadening occurred upon interaction with micelles. Below SDS critical micelle concentration, broader lines indicated complex formation with tighter molecular packing than in micelles. Small changes in hyperfine splittings evinced TOAC location at the micelle-water interface. The interaction with anionic micelles was more effective than with zwitterionic micelles. Peptide-micelle interaction caused fluorescence increase. The TOAC-promoted intramolecular fluorescence quenching was more, pronounced for TOAC(3)-AII because of the proximity between the nitroxide and Tyr(4). CD spectra showed that although both AII and TOAC(1)-AII presented flexible conformations in water, TOAC(3)-AII displayed conformational restriction because of the TOAC-imposed bend (Schreier et al., Biopolymers 2004, 74, 389). In HPS, conformational changes were observed for the labeled peptides at neutral and basic pH. In SDS, all peptides underwent pH-dependent conformational changes. Although the spectra suggested similar folds for All and TOAC(1)-AII, different conformations were acquired by TOAC(3)-AII. The membrane environment has been hypothesized to shift conformational equilibria so as to stabilize the receptor-bound conformation of ligands. The fact that TOAC(3)-AII is unable to acquire conformations similar to those of native AII and partially active TOAC(1)-AII is probably the explanation for its lack of biological activity. (C) 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 525-537, 2009.

PREDICTION OF METAL CATION TOXICITY TO THE BIOLUMINESCENT FUNGUS GERRONEMA VIRIDILUCENS

A correlation between the physicochemical properties of mono- [Li(I), K(I), Na(I)] and divalent [Cd(II), Cu(II), Mn(II), Ni(II), Co(II), Zn(II), Mg(II), Ca(II)] metal cations and their toxicity (evaluated by the free ion median effective concentration. EC50(F)) to the naturally bioluminescent fungus Gerronema viridilucens has been studied using the quantitative ion character activity relationship (QICAR) approach. Among the 11 ionic parameters used in the current study, a univariate model based on the covalent index (X(m)(2)r) proved to be the most adequate for prediction of fungal metal toxicity evaluated by the logarithm of free ion median effective concentration (log EC50(F)): log EC50(F) = 4.243 (+/-0.243) -1.268 (+/-0.125).X(m)(2)r (adj-R(2) = 0.9113, Alkaike information criterion [AIC] = 60.42). Additional two- and three-variable models were also tested and proved less suitable to fit the experimental data. These results indicate that covalent bonding is a good indicator of metal inherent toxicity to bioluminescent fungi. Furthermore, the toxicity of additional metal ions [Ag(I), Cs(I), Sr(II), Ba(II), Fe(II), Hg(II), and Pb(II)] to G. viridilucens was predicted, and Pb was found to be the most toxic metal to this bioluminescent fungus (EC50(F)): Pb(II) > Ag(I) > Hg(I) > Cd(II) > Cu(II) > Co(II) Ni(II) > Mn(II) > Fe(II) approximate to Zn(II) > Mg(II) approximate to Ba(II) approximate to Cs(I) > Li(I) > K(I) approximate to Na(I) approximate to Sr(II)> Ca(II). Environ. Toxicol. Chem. 2010;29:2177-2181. (C) 2010 SETAC