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Molecular Modelling Studies (molecular + modelling_studies)

Distribution by Scientific Domains

Chemistry	83%

Selected Abstracts

Pyrazolo[3,4- d]pyrimidine Derivatives as COX-2 Selective Inhibitors: Synthesis and Molecular Modelling Studies

ARCHIV DER PHARMAZIE, Issue 6 2009
Demetrio Raffa
Abstract The pyrazolo[3,4- d]pyrimidine system shows a multitude of interesting pharmacological properties. Owing to the potential anti-inflammatory activity of 5-benzamido-pyrazolo[3,4- d]pyrimidin-4-one derivatives and considering the easy synthesis of this class of compounds, a set of new 5-benzamido-1H -pyrazolo[3,4- d]pyrimidin-4-ones has been prepared in 42-80% yields by reacting 5-aminopyrazole-4(N -benzoyl)carbohydrazide derivatives and the opportune triethylorthoesters. Compounds 8a, b, 10a,d, and 11a, b revealed a superior inhibitory profile against COX-2, when compared to that of reference standards NS398 and indomethacin. Molecular modelling studies confirmed the obtained biological results. [source]

Characterization of the NAD+ binding site of Candida boidinii formate dehydrogenase by affinity labelling and site-directed mutagenesis

FEBS JOURNAL, Issue 22 2000
Nikolas E. Labrou
The 2,,3,-dialdehyde derivative of ADP (oADP) has been shown to be an affinity label for the NAD+ binding site of recombinant Candida boidinii formate dehydrogenase (FDH). Inactivation of FDH by oADP at pH 7.6 followed biphasic pseudo first-order saturation kinetics. The rate of inactivation exhibited a nonlinear dependence on the concentration of oADP, which can be described by reversible binding of reagent to the enzyme (Kd = 0.46 mm for the fast phase, 0.45 mm for the slow phase) prior to the irreversible reaction, with maximum rate constants of 0.012 and 0.007 min,1 for the fast and slow phases, respectively. Inactivation of formate dehydrogenase by oADP resulted in the formation of an enzyme,oADP product, a process that was reversed after dialysis or after treatment with 2-mercaptoethanol (> 90% reactivation). The reactivation of the enzyme by 2-mercaptoethanol was prevented if the enzyme,oADP complex was previously reduced by NaBH4, suggesting that the reaction product was a stable Schiff's base. Protection from inactivation was afforded by nucleotides (NAD+, NADH and ADP) demonstrating the specificity of the reaction. When the enzyme was completely inactivated, approximately 1 mol of [14C]oADP per mol of subunit was incorporated. Cleavage of [14C]oADP-modified enzyme with trypsin and subsequent separation of peptides by RP-HPLC gave only one radioactive peak. Amino-acid sequencing of the radioactive tryptic peptide revealed the target site of oADP reaction to be Lys360. These results indicate that oADP inactivates FDH by specific reaction at the nucleotide binding site, with negative cooperativity between subunits accounting for the appearance of two phases of inactivation. Molecular modelling studies were used to create a model of C. boidinii FDH, based on the known structure of the Pseudomonas enzyme, using the modeller 4 program. The model confirmed that Lys360 is positioned at the NAD+ -binding site. Site-directed mutagenesis was used in dissecting the structure and functional role of Lys360. The mutant Lys360,Ala enzyme exhibited unchanged kcat and Km values for formate but showed reduced affinity for NAD+. The molecular model was used to help interpret these biochemical data concerning the Lys360,Ala enzyme. The data are discussed in terms of engineering coenzyme specificity. [source]

Pyrazolo[3,4- d]pyrimidine Derivatives as COX-2 Selective Inhibitors: Synthesis and Molecular Modelling Studies

Beta-helix model for the filamentous haemagglutinin adhesin of Bordetella pertussis and related bacterial secretory proteins

MOLECULAR MICROBIOLOGY, Issue 2 2001
Andrey V. Kajava
Bordetella pertussis establishes infection by attaching to epithelial cells of the respiratory tract. One of its adhesins is filamentous haemagglutinin (FHA), a 500-Å-long secreted protein that is rich in ,-structure and contains two regions, R1 and R2, of tandem 19-residue repeats. Two models have been proposed in which the central shaft is (i) a hairpin made up of a pairing of two long antiparallel ,-sheets; or (ii) a ,-helix in which the polypeptide chain is coiled to form three long parallel ,-sheets. We have analysed a truncated variant of FHA by electron microscopy (negative staining, shadowing and scanning transmission electron microscopy of unstained specimens): these observations support the latter model. Further support comes from detailed sequence analysis and molecular modelling studies. We applied a profile search method to the sequences adjacent to and between R1 and R2 and found additional ,covert' copies of the same motifs that may be recognized in overt form in the R1 and R2 sequence repeats. Their total number is sufficient to support the tenet of the ,-helix model that the shaft domain , a 350 Å rod , should consist of a continuous run of these motifs, apart from loop inserts. The N-terminus, which does not contain such repeats, was found to be weakly homologous to cyclodextrin transferase, a protein of known immunoglobulin-like structure. Drawing on crystal structures of known ,-helical proteins, we developed structural models of the coil motifs putatively formed by the R1 and R2 repeats. Finally, we applied the same profile search method to the sequence database and found several other proteins , all large secreted proteins of bacterial provenance , that have similar repeats and probably also similar structures. [source]

Factors Mediating Activity, Selectivity, and Substrate Specificity for the Thiamin Diphosphate-Dependent Enzymes Benzaldehyde Lyase and Benzoylformate Decarboxylase

CHEMBIOCHEM, Issue 12 2006
Michael Knoll
Abstract Benzaldehyde lyase from Pseudomonas fluorescens and benzoylformate decarboxylase from Pseudomonas putida are homologous thiamin diphosphate-dependent enzymes that catalyze carboligase and carbolyase reactions. Both enzymes catalyze the formation of chiral 2-hydroxy ketones from aldehydes. However, the reverse reaction has only been observed with benzaldehyde lyase. Whereas benzaldehyde lyase is strictly R specific, the stereoselectivity of benzoylformate decarboxylase from P. putida is dependent on the structure and orientation of the substrate aldehydes. In this study, the binding sites of both enzymes were investigated by using molecular modelling studies to explain the experimentally observed differences in the activity, stereo- and enantioselectivity and substrate specificity of both enzymes. We designed a detailed illustration that describes the shape of the binding site of both enzymes and sufficiently explains the experimental effects observed with the wild-type enzymes and different variants. These findings demonstrate that steric reasons are predominantly responsible for the differences observed in the (R)-benzoin cleavage and in the formation of chiral 2-hydroxy ketones. [source]

Molecular modelling of inclusion compounds from hydrophobic dyes and ,-cyclodextrin

COLORATION TECHNOLOGY, Issue 4 2009
Ahmed El-Shafei
This paper arises from studies aimed at developing new approaches to combining the fabric formation and coloration steps of fabric processing. A key aspect of these studies involved the evaluation of cyclodextrin (CD)-based compounds as hosts for dye molecules that could be released onto a fabric surface following fabric formation. In this study, experimental data from wide-angle X-ray diffraction and differential scanning calorimetry experiments were used in tandem with molecular modelling studies to confirm the formation of ,-CD,dye complex inclusion compounds and to demonstrate the utility of parameterised model number 3 (PM3) semi-empirical molecular modelling methods for predicting the nature of the preferred ,-CD,dye inclusion compounds. Calculations revealed that the inclusion compounds containing two dye molecules was preferred over the inclusion compound containing one dye molecule. Further, molecular modelling of the inclusion compound obtained using ,-CD linked to an epichlorohydrin-based oligomer and commercial disperse dyes showed inclusion compound formation to be an energetically favourable process. [source]