Binding conformation of 2-oxoamide inhibitors to group IVA cytosolic phospholipase A2 determined by molecular docking combined with molecular dynamics

The group IVA cytosolic phospholipase A(2) (GIVA cPLA(2)) plays a central role in inflammation. Long chain 2-oxoamides constitute a class of potent GIVA cPLA(2) inhibitors that exhibit potent in vivo anti-inflammatory and analgesic activity. We have now gained insight into the binding of 2-oxoamide inhibitors in the GIVA cPLA(2) active site through a combination of molecular docking calculations and molecular dynamics simulations. Recently, the location of the 2-oxoamide inhibitor AX007 within the active site of the GIVA cPLA(2) was determined using a combination of deuterium exchange mass spectrometry followed by molecular dynamics simulations. After the optimization of the AX007-GIVA cPLA(2) complex using the docking algorithm Surflex-Dock, a series of additional 2-oxoamide inhibitors have been docked in the enzyme active site. The calculated binding affinity presents a good statistical correlation with the experimental inhibitory activity (r(2) = 0.76, N = 11). A molecular dynamics simulation of the docking complex of the most active compound has revealed persistent interactions of the inhibitor with the enzyme active site and proves the stability of the docking complex and the validity of the binding suggested by the docking calculations. The combination of molecular docking calculations and molecular dynamics simulations is useful in defining the binding of small-molecule inhibitors and provides a valuable tool for the design of new compounds with improved inhibitory activity against GIVA cPLA(2).     

Unusual nitrogenous derivatives from Alstonia

Five new nitrogenous compounds were isolated from the Malayan Alstonia angustifolia and their structures determined based on interpretation of spectroscopic data.     

Petasis three-component coupling reactions of hydrazides for the synthesis of oxadiazolones and oxazolidinones

An application of readily available hydrazides in the Petasis 3-component coupling reaction is presented. An investigation of the substrate scope was performed to establish a general, synthetically useful protocol for the formation of hydrazido alcohols, which were selectively converted to oxazolidinone and oxadiazolone ring systems through triphosgene-mediated cyclization reactions.     

Elucidation of matrix effects and performance of solid-phase extraction for LC-MS/MS analysis of β-N-methylamino-L-alanine (BMAA) and 2,4-diaminobutyric acid (DAB) neurotoxins in cyanobacteria

A liquid chromatography-mass spectrometry (LC-MS/MS) method using hydrophilic interaction liquid chromatography (HILIC) was developed for the analysis of neurotoxins β-N-methylamino-L-alanine (BMAA) and 2,4-diaminobutyric acid (DAB), using multiple reaction monitoring (MRM) scan mode. Oasis-MCX and Strata-X-C polymeric cation-exchange cartridges were used to clean extracts of cyanobacterial cultures, including two strains of Microcystis aeruginosa and one strain of Nostoc sp. The performance of the solid-phase extraction (SPE) cartridges for BMAA and DAB were evaluated using mixed standards and spiked cyanobacterial extracts, which demonstrated recoveries of BMAA and DAB ranging from 66% to 91%. Matrix effects in LC-MS/MS were evaluated, and while there was no effect on BMAA quantitation, suppression of DAB was found. Full scan (Q1) and enhanced product ion (EPI) monitoring showed that the DAB suppression may be due to closely eluting compounds, including lysine, histidine, arginine and three other compounds with [M + H](+) m/z of 88, 164 and 191. The procedures developed allow the sensitive and effective analysis of trace BMAA and DAB levels in cyanobacteria. While DAB was confirmed to be present, no BMAA was found in the cyanobacterial samples tested in the present study.     

Mirror symmetry breaking and chiral amplification in foldamer-based supramolecular helical aggregates

Spontaneous asymmetric generation of supramolecular chiral fibers was observed in the folding induced self-assembly of a lock-washer shaped foldamer. A secondary nucleation growth mechanism is proposed to explain the observed chiral amplification or deracemization of these supramolecular fibers.     

Multinuclear copper(I) guanidinate complexes

A series of multinuclear Copper(I) guanidinate complexes have been synthesized in a succession of reactions between CuCl and the lithium guanidinate systems Li{L} (L = Me(2)NC((i)PrN)(2) (1a), Me(2)NC(CyN)(2) (1b), Me(2)NC((t)BuN)(2)(1c), and Me(2)NC(DipN)(2) (2d) ((i)Pr = iso-propyl, Cy = cyclohexyl, (t)Bu = tert-butyl, and Dip = 2,6-disopropylphenyl) made in situ, and structurally characterized. The di-copper guanidinates systems with the general formula [Cu(2){L}(2)] (L = {Me(2)NC((i)PrN)(2)} (2a), {Me(2)NC(CyN)(2)} (2b), and {Me(2)NC(DipN)(2)} (2d) differed significantly from related amidinate complexes because of a large torsion of the dimer ring, which in turn is a result of transannular repulsion between adjacent guanidinate substituents. Attempts to synthesis the tert-butyl derivative [Cu(2){Me(2)NC((t)BuN)(2)}(2)] result in the separate formation and isolation of the tri-copper complexes [Cu(3){Me(2)NC((t)BuN)(2)}(2)(μ-NMe(2))] (3c) and [Cu(3){Me(2)NC((t)BuN)(2)}(2)(μ-Cl)] (4c), both of which have been unambiguously characterized by single crystal X-ray diffraction. Closer inspection of the solution state behavior of the lithium salt 1c reveals a previously unobserved equilibrium between 1c and its starting materials, LiNMe(2) and N,N'-di-tert-butyl-carbodiimide, for which activation enthalpy and entropy values of ΔH(?) = 48.2 ± 18 kJ mol(-1) and ΔS(?) = 70.6 ± 6 J/K mol have been calculated using 1D-EXSY NMR spectroscopy to establish temperature dependent rates of exchange between the species in solution. The molecular structures of the lithium complexes 1c and 1d have also been determined and shown to form tetrameric and dimeric complexes respectively held together by Li-N and agostic Li···H-C interactions. The thermal chemistry of the copper complexes have also been assessed by thermogravimetric analysis.     

Dielectric relaxation and ultrafast transient absorption spectroscopy of [C6mim]+[Tf2N]−/acetonitrile mixtures

Mixtures of the ionic liquid (IL) [C(6)mim](+)[Tf(2)N](-) and acetonitrile have been investigated by a combination of dielectric relaxation spectroscopy (DRS) and ultrafast transient absorption techniques using the molecular probe 12'-apo-β-carotenoic-12'-acid (12'CA). Steady-state absorption spectra of the 12'CA molecule have also been recorded. The position of the probe's S(0)→ S(2) absorption maximum correlates linearly with the polarizability of the mixture, suggesting that the bulk composition is a good approximation to the local composition. The lifetime τ(1) of the S(1)/ICT state of 12'CA varies rather smoothly with composition between the value for pure acetonitrile (42 ps) and neat [C(6)mim](+)[Tf(2)N](-) (94 ps). At low IL contents there appears to be an influence of discrete ion pairs. Employing static dielectric constants from the DRS experiments, one finds that the lifetime of the probe in the IL mixtures is shorter than that in pure organic solvents with the same polarity parameter. This suggests an increased stabilization of the S(1)/ICT state in IL-containing mixtures, most likely due to IL-specific Coulombic interactions between the cation and the negative end of the probe's dipole. An ultrafast solvation component is observed which is ca. 0.5 ps in pure acetonitrile, and approaches the value for the pure IL (2.0 ps) already around x(IL) = 0.3. This is interpreted in terms of an efficient perturbation of the cooperative solvation response of acetonitrile by the presence of small amounts of IL and possibly also the viscosity increase when adding IL. This view is also supported by the increase of the average longitudinal relaxation time of acetonitrile upon addition of small IL amounts extracted from the DRS experiments.     

On the applicability of elastic network normal modes in small-molecule docking

Incorporating backbone flexibility into protein-ligand docking is still a challenging problem. In protein-protein docking, normal mode analysis (NMA) has become increasingly popular as it can be used to describe the collective motions of a biological system, but the question of whether NMA can also be useful in predicting the conformational changes observed upon small-molecule binding has only been addressed in a few case studies. Here, we describe a large-scale study on the applicability of NMA for protein-ligand docking using 433 apo/holo pairs of the Astex data sets. On the basis of sets of the first normal modes from the apo structure, we first generated for each paired holo structure a set of conformations that optimally reproduce its C(α) trace with respect to the underlying normal mode subspace. Using AutoDock, GOLD, and FlexX we then docked the original ligands into these conformations to assess how the docking performance depends on the number of modes used to reproduce the holo structure. The results of our study indicate that, even for such a best-case scenario, the use of normal mode analysis in small-molecule docking is restricted and that a general rule on how many modes to use does not seem to exist or at least is not easy to find.     

Interfacial free energy driven nanophase separation in poly(3-hexylthiophene)/[6,6]-phenyl-C61-butyric acid methyl ester thin films

The nanostructure of thermally annealed thin films of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) blends on hydrophobic and hydrophilic substrates was studied to unravel the relationship between the substrate properties and the phase structure of polymer blends in confined geometry. Indeed, the nature of the employed substrates was found to affect the extent of phase separation, the PCBM aggregation state and the texture of the whole system. In particular, annealing below the melting temperature of the polymer yielded the formation of PCBM nanometric crystallites on the hydrophobic substrates, while mostly amorphous microscopic aggregates were formed on the hydrophilic ones. Moreover, while an enhanced in-plane orientation of P3HT lamellae was promoted on hydrophobic substrates, a markedly tilted geometry was produced on the hydrophilic ones. The observed effects were interpreted in terms of a simple model connecting the interface free energy for the blend films to the different polymer chain mobility and diffusion velocity of PCBM molecules on the different substrates.