Quorum-sensing inhibitor potential of trans-anethole aganist Pseudomonas aeruginosa.

AIMS: Quorum sensing (QS) is a cell-cell communication system used by a broad spectrum of pathogenic bacteria to control the expression of their virulence genes. The interruption of QS systems of pathogenic bacteria has been considered as a novel way to fight bacterial diseases. In this study, trans-anethole, the main component of anise (Pimpinella anisum) oil was examined for its QS inhibitor (QSI) potential in an attempt to identify novel QSI compound effective against opportunistic pathogen Pseudomonas aeruginosa. METHODS AND RESULTS: The preliminary screening of QSI capacity of trans-anethole was determined using a quorum-sensing inhibitor screen (QSIS) assay. The QSIS assay indicated that trans-anethole has QSI properties. QSI capacity of trans-anethole was further confirmed by lasB-gfp fussion assay and virulence factor assays. A sub-MIC of trans-anethole reduced the expression of lasB by 57%, elastase production by 59%, protease production by 56%, pyocyanin production by 95% and swarming motility by 68% without inhibiting growth of Pseudomonas aeruginosa PA01. Molecular docking and protein-ligand interaction studies were performed to understand the molecular mechanism underlying inhibitory activity of trans-anethole. The results of these analysis suggested that trans-anethole fits within the binding site of the LasR protein of P. aeruginosa. CONCLUSION: Trans-anethole has the potential to inhibit QS-regulated virulence factors in P. aeruginosa by binding to LasR protein, similar to its natural ligand N-(3-oxododecanoyl)-l-homoserine lactone. SIGNIFICANCE AND IMPACT OF THE STUDY: In this study, for the first time, it was demonstrated that trans-anethole has the potential to disrupt bacterial communication and can be developed as a novel QSI to combat with P. aeruginosa and other clinically significant pathogens.

Coupling of structural fluctuations to deamidation reaction in triosephosphate isomerase by Gaussian network model.

We study the structural fluctuations of triosephosphate isomerase (TIM) by an elastic model, namely, the Gaussian network model (GNM), to identify a network of coupled motions in the allosteric communication between its deamidation and catalytic sites, and the promoting motions for the deamidation activity. For this, three TIM structures have been studied: one crystal structure and two model structures designed to describe different putative models for the deamidation reaction taking place at the subunit interface. The structural fluctuations have been mapped on the functional properties; then the differences in the fluctuations between the two models in relation to the deamidation reaction have been considered. The results demonstrate that the qualitative picture of the mean-square fluctuations and the correlations between the fluctuations are similar in both, but the differences may affect the observed barrier height of the deamidation reaction. The higher packing density at regions close to deamidation sites, reflected by the high-frequency fluctuating residues in the respective regions, the stronger positive correlation between the fluctuations of the deamidation sites, and enhanced positive correlation of the primary deamidation site with the extended vicinity of the catalytic region on the juxtaposed unit promote the probability of the deamidation reaction. The results in general emphasize the importance of structural fluctuations in enzyme reactions, as well as proposing the present methodology as a plausible approach for studies on the network of coupled promoting motions in protein functions.

Modeling the stereoselectivity of the Johnson-Claisen rearrangements in the Danishefsky synthesis of gelsemine.

[reaction: see text] The stereochemistries of [3,3] sigmatropic Johnson-Claisen (J-C) rearrangements of six intermediates studied in the synthesis of gelsemine were modeled using DFT methodology. The possible origins of the rearrangement stereoselectivity are explored and compared with the experimentally suggested rationalizations by Danishefsky et al. (J. Am. Chem. Soc. 2002, 124, 9812-9824). In the intermediate used for the J-C rearrangement in the Danishefsky synthesis (3), the closure is inhibited by the repulsive interactions between the enolate terminus and the carbon atoms of the double bond as well as with the hydrogen on C7. The closure is favored by stabilizing interactions between the enolate terminus and the H's of the oxetane ring.

Modeling the effect of substitution on the Pb(OAc)4 mediated oxidative cleavage of steroidal 1,2-diols.

[reaction: see text] We comment on the effects of angular substitution on the outcome of a Pb(OAc)4 (LTA) mediated heterodomino reaction, with selected bicyclic unsaturated 1,2-diols, which is considered to proceed through a series of transformations in a single vessel. The first two, oxidative and pericyclic, are followed by the key step, an electrophilic addition of LTA to the olefin, responsible for the course of the domino process. In this study, the electrophilic addition of LTA to the double bond has been modeled with B3LYP, where the 6-31G* basis set is used for C, O, and H atoms and the LANL2DZ method is used for Pb. The modeling in the gaseous phase and in solution has revealed the concerted nature of the addition of LTA to the double bond of the intermediate. The fact that LTA adds from the same side as the substituent R, for R=H and from the opposite side when R=CH3 has been attributed to steric hindrance, which causes deformation of the olefinic intermediate.

A theoretical study on the mechanism of the cyclopolymerization of diallyl monomers.

The cyclization and intermolecular propagation steps of the cyclopolymerization mechanism are studied with density functional theory. In addition to standard cyclization and intermolecular propagation reactions of cyclopolymerization, competing reactions that lead to chain transfer and termination are also discussed. The mechanistic study of the cyclopolymerization reaction of two representative monomers, N,N-diallylamine (1) and N,N-dimethyl-N,N-diallylamonium (2), was carried out with B3LYP/6-31G computations. Monomer 1 has almost the same activation barriers for homopolymerization and cyclization. In monomer 2, cyclization is much more facile than homopolymerization, leading to the higher cyclopolymerization efficiency. In the case of 2, methyl substituents on nitrogen inhibit hydrogen abstraction, whereas in 1, hydrogen abstraction reactions from the neutral monomer yield stabilized products leading to chain transfer. Calculations show that facile competing reactions of monomer 1 lower the polymerization efficiency. Monomer 2 displays a stronger preference for cyclization relative to other processes.

Theoretical study of factors controlling rates of cyclization of radical intermediates from diallylamine and diallylammonium monomers in radical polymerizations.

The radical cyclization reactions of models for the growing radical chains formed from N,N-diallylamine (1), N-methyl-N,N-diallylamine (2), N,N-diallylammonium (3), N-methyl-N,N-diallylammonium (4) and N,N-dimethyl-N,N-diallylammonium (5) have been investigated computationally by DFT theory, using the B3LYP functional. Models formed by hydrogen atom addition to dienes 1-5 undergo five-membered ring cyclization reactions with activation energies predicted to be 7.2, 5.0, 8.6, 6.4, and 6.2 kcal/mol, respectively. Methyl substitution on nitrogen decreases the barrier to cyclization. One methyl has a larger effect on the cyclization rate than the second methyl. This rate enhancement is attributed to a decrease in gauche interactions in the transition state as compared to the initial structure and to different destabilizing effects when an H is replaced by a methyl group. These predicted rate effects are in agreement with the experimental data on polymerization efficiencies.

Conformational properties of amphotericin B amide derivatives--impact on selective toxicity.

Even though it is highly toxic, Amphotericin B (AmB), an amphipathic polyene macrolide antibiotic, is used in the treatment of severe systemic fungal infections as a life-saving drug. To examine the influence of conformational factors on selective toxicity of these compounds, we have investigated the conformational properties of five AmB amide derivatives. It was found that the extended conformation with torsional angles (phi,psi)=(290 degrees,180 degrees) is a common minimum of the potential energy surfaces (PES) of unsubstituted AmB and its amide derivatives. The extended conformation of the studied compounds allows for the formation of an intermolecular hydrogen bond network between adjacent antibiotic molecules in the open channel configuration. Therefore, the extended conformation is expected to be the dominant conformer in an open AmB (or its amide derivatives) membrane channel. The derivative compounds for calculations were chosen according to their selective toxicity compared to AmB and they had a wide range of selective toxicity. Except for two AmB derivatives, the PES maps of the derivatives reveal that the molecules can coexist in more than one conformer. Taking into account the cumulative conclusions drawn from the earlier MD simulation studies of AmB membrane channel, the results of the potential energy surface maps, and the physical considerations of the molecular structures, we hypothesize a new model of structure-selective toxicity of AmB derivatives. In this proposed model the presence of the extended conformation as the only well defined global conformer for AmB derivatives is taken as the indicator of their higher selective toxicity. This model successfully explains our results. To further test our model, we also investigated an AmB derivative whose selective toxicity has not been experimentally measured before. Our prediction for the selective toxicity of this compound can be tested in experiments to validate or invalidate the proposed model.

Tandem mass spectrometry studies of acetone and acetone/water cluster ions.

Ion clusters were formed in a temperature-variable high-pressure ion source from neat acetone and acetone/water mixtures and subjected to tandem mass spectrometry studies-unimolecular and collisionally activated mass-analyzed ion kinetic energy spectroscopy. The predominance of water loss from H(+)(H20)(A) l=3, where A = acetone, suggests that the solvation sphere around H3O(+) does not close at l = 3, contrary to the case of acetonitrile or dimethyl ether. The results may be interpreted in terms of suggested ion structures which involve isomerization enroute to dissociation. The virtual absence of H/D scrambling in the collisionally activated dissociation of H3O(+)(DA)3, DA =acetone-d 6, and of D3O(+)(A)3 means that if enolization takes place, it is a rate-determining step in an irreversible isomerization. The stability of H(+)(H2O)(A)3 is a dominant factor in the observation of acetone loss from H(+)(H20)(A)4.