Structure elucidation of a complex CO2-based organic framework material by NMR crystallography.

A three-dimensional structural model of a complex CO2-based organic framework made from high molecular weight, self-assembled, flexible and multi-functional oligomeric constituents has been determined de novo by solid-state NMR including DNP-enhanced experiments. The complete assignment of the 15N, 13C and 1H resonances was obtained from a series of two-dimensional through space and through bond correlation experiments. MM-QM calculations were used to generate different model structures for the material which were then evaluated by comparing multiple experimental and calculated NMR parameters. Both NMR and powder X-ray diffraction were evaluated as tools to determine the packing by crystal modelling, and at the level of structural modelling used here PXRD was found not to be a useful complement. The structure determined reveals a highly optimised H-bonding network that explains the unusual selectivity of the self-assembly process which generates the material. The NMR crystallography approach used here should be applicable for the structure determination of other complex solid materials.

Single molecule probing of the local segmental relaxation dynamics in polymer above the glass transition temperature.

We investigate the temporal dynamics of terrylene diimide molecule with four phenoxy rings (TDI) in a poly(styrene) (PS) matrix in the supercooled regime by use of single molecule spectroscopy. By recording both fluorescence lifetime and linear dichroism observables simultaneously, we show that the TDI dye molecule is a versatile probe of the local dynamics in the polymer. The molecule is able to undergo conformational changes, as indicated by lifetime fluctuations and/or reorientation jumps, as indicated by both observables on different time scales. Owing to molecular mechanics and quantum calculations, we could assign the conformational changes to folding/unfolding event(s) of one or more arms with respect to the conjugated core. We tentatively attribute the different spatial extents of the locally probed motions to the alpha and beta relaxation processes occurring in the PS matrix.

Resistance of hepatitis C virus to NS3-4A protease inhibitors: mechanisms of drug resistance induced by R155Q, A156T, D168A and D168V mutations.

BACKGROUND/AIMS: One of the main issues in the development of antiviral therapy is the emergence of drug-resistant viruses. In the case of hepatitis C virus (HCV), selection of drug-resistant mutants was evidenced by in vitro studies on protease inhibitors (PIs); for example, BILN-2061, VX-950 and SCH-6. Four mutations in the HCV protease (R155Q, A156T, D168A and D168V) have been identified in vitro in the HCV replicon system that confer resistance to BILN-2061 (a reference inhibitor). However, the molecular mechanism of drug resistance is still unknown. The aim of this study is to unravel, using an molecular modelling strategy, the structural basis of such molecular mechanism of HCV resistance to PIs. We focused on protease mutations conferring HCV resistance to BILN-2061 and described for the first time such mechanism at a molecular level. METHODS: The structures of drug-resistant NS3 proteases were obtained by mutation of selected residues (R155Q, A156T, D168A and D168V) and the ternary complexes formed between NS3-4A and BILN-2061 were optimized using GenMol software (www.3dgenoscience.com; Genoscience, Marseille, France). RESULTS: Two mechanisms were evidenced for viral resistance to BILN-2061. A 'direct' resistance mechanism is based on contacts between the mutated R155Q and A156T protease residues and its inhibitor. In the 'indirect' resistance mechanism, the mutated D168A/V residue is not in close contact with the drug itself but interacts with other residues connected to the drug. CONCLUSIONS: These data provide new insights in the understanding of the mechanisms of HCV drug escape, and may allow predicting potential cross-resistance phenomenon with other PIs. This approach can be used as a basis for future rational PI drug design candidates.

Synthesis and antiviral evaluation of cis-substituted cyclohexenyl and cyclohexanyl nucleosides.

Starting from commercially available (rac)-3-cyclohexene-1-carboxylic acid, a series of purine and pyrimidine cis-substituted cyclohexenyl and cyclohexanyl nucleosides were synthesized through a key Mitsunobu reaction. Antiviral evaluations were performed on HIV, coxsackie B3, and herpes viruses (HSV-1, HSV-2, VZV, HCMV). Three compounds showed moderate activity against HSV-1 and coxsackie viruses. Specific computer modeling studies were performed on HSV-1 thymidine kinase in order to understand the enzyme activation of an analogue showing moderate antiviral activity.

A novel photoreversible photochromic system involving a hydrogen transfer/cyclization sequence.

A novel photoreversible photochromic system, 3-(2-benzylbenzoyl)-1,2-R,R(1)-4(1H)-quinolinones/12-hydroxy-5-R-5a-R(1)-6-phenyl-5a,6-dihydrobenzo[b]acridin-11(5H)-ones, is described.

Hydration free energy a fragmental model and drug design.

The aim of this work was to provide a simple model to determine hydration free energies of molecular compounds at ambient temperature in order to help drug design. Since the free energy of interaction between molecules and water can be approximated by an additive function of their constituent groups, a model based on a fragmental analysis was developed with all the hydration free energies determined from experimental values. The model gives accurate hydration free energies on small molecules by simply adding the hydration energies of the fragments constituting the molecule. The correlation factor r(2) is 0.990 on the 125 molecules used to establish the model parameters. As experimental values are determined at ambient temperature (25 degrees C), the values obtained from the model will correspond to this temperature. For mean size molecules or big molecules as proteins, it was not possible to calibrate the model owing to the absence of experimental values. However, the model makes it possible to estimate the hydration free energy of such molecules. The fragmental representation of any molecule with coded colours, depending on the fragment nature (hydrophobic, hydrophilic or neutral), can be useful to understand molecule behaviour and help drug design.

A Proton-Ionizable Ester Crown of 3,5-Disubstituted 1H-Pyrazole Able To Form Stable Dinuclear Complexes with Lipophilic Phenethylamines.

A convenient synthesis of the proton-ionizable crown 3 is reported that uses dibutyltin oxide. In acetonitrile, the reaction of 3 (LH(2)) with phenethylamine and homoveratrylamine (molar ratio 1:2) affords solid dinuclear complexes [LH(2)]2RNH(2) (4a,b), which spectroscopic (FAB-MS, IR, (1)H and (13)C NMR) data point toward a strong participation of the pyrazole nitrogens in the amine complexation. In DMSO-d(6) solution, a (13)C NMR study demonstrates the formation in situ of analogous neutral 4a-d[LH(2)]2RNH(2) or charged 5a-d[L(2)(-)]2RNH(3)(+) dinuclear complexes by reaction of 3 [LH(2)] or 3'[L(2)(-)]2Na(+) with RNH(2) (phenethylamine, homoveratrylamine, dopamine, and norepinephrine) or their RNH(3)(+)Cl(-) salts, respectively. Differences between the structure of complexes 4 and 5 have been evaluated by taking the homoveratrylamine derivatives 4b and 5bas models. An (1)H and (13)C NMR study (by raising the temperature) and measurements of intermolecular NOE effects (from NOESY and ROESY spectra) demonstrate that both complexes behave as prototropic isomers showing different conformations. By increasing the ionic strength, the 4b isomer structure becomes similar to that of 5b. The molecular modeling (GenMol software) of 4a-d and 5a-d shows that the assemblage in which both amine molecules are on the same side of the crown is the more stable. Lipophilic amines afford more stable complexes than hydrophilic ones and charged species are much more stable than the neutral ones.