In silico study of VP35 inhibitors: from computational alanine scanning to essential dynamics.

In recent years the Ebola virus has spread through several countries in Africa, highlighting the need to develop new treatments for this disease and boosting a new research effort on this subject. The Ebola virus Viral Protein 35 (VP35) carries out multiple functions necessary for virus replication and infection, in particular interfering with (IFN)-α/ß signaling. Recently, VP35 has been crystallized in complex with small organic molecules able to inhibit its interaction with viral nucleoproteins, thus reducing Ebola infections of cultured cells. In this work, starting from these structures, we carry out a computational study aimed at investigating the energetic and dynamical aspects of the interaction between VP35 and its ligands at the atomic level. Molecular dynamics simulations, computational alanine scanning, root mean square fluctuations bootstrap analysis and essential dynamics analysis were performed. Our results expand the experimental ones obtained in previous works, adding information about the interactions landscape with the identification of a set of new hot-spots residues exerting a critical function in the protein-ligand interaction. Moreover we characterized the dynamics of the complexes, showing that the presence of ligands modifies the overall protein dynamics as well as the behavior of particular protein segments.

Electrophysiological and metabolic effects of CHF5074 in the hippocampus: protection against in vitro ischemia.

CHF5074 is a non-steroidal anti-inflammatory derivative holding disease-modifying potential for the treatment of Alzheimer's disease. The aim of the present study was to characterize the electrophysiological and metabolic profile of CHF5074 in the hippocampus. Electrophysiological recordings show that CHF5074 inhibits in a dose-dependent manner the current-evoked repetitive firing discharge in CA1 pyramidal neurons. This result is paralleled by a dose-dependent reduction of field excitatory post-synaptic potentials with no effect on the paired-pulse ratio. The effects of CHF5074 were not mediated by AMPA or NMDA receptors, since the inward currents induced by local applications of AMPA and NMDA remained constant in the presence of this compound. We also suggest a possible activity of CHF5074 on ASIC1a receptor since ASIC1a-mediated current, evoked by application of a pH 5.5 solution, is reduced by pretreatment with this compound. Moreover, we demonstrate that CHF5074 treatment is able to counteract in hippocampal slices the OGD-induced increase in alanine, lactate and acetate levels. Finally, CHF5074 significantly reduced the apoptosis in hippocampal neurons exposed to OGD, as revealed by cleaved-caspase-3 immunoreactivity and TUNEL staining. Overall, the present work identifies novel mechanisms for CHF5074 in reducing metabolic acidosis, rendering this compound potentially useful also in conditions of brain ischemia.

Small-angle X-ray scattering study of self-assembling lipophilic guanines in organic solvents: G-quadruplex formation and cation effects in cyclohexane.

Lipophilic guanilic derivatives (lipoGs) dissolved in organic solvents can undergo different self-assembly pathways based on different H-bonded motifs, e.g., the cyclic discrete G-quartet, which forms in the presence of alkali-metal ions, and the "infinite" tape-like G-ribbon observed in the absence of ions. Using in-solution small-angle X-ray scattering, we analyzed a series of lipoGs dissolved in cyclohexane in the presence of different salts. The formation of G-quartet based supramolecular aggregates has been confirmed, evidencing the coexistence equilibrium of octamers and noncovalent molecular nanowires (the so-called G-quadruplexes). By global fitting the scattering data, the concentration of the two kinds of particles as well as the nanowire length have been derived as a function of temperature for the different compounds and salts. The thermodynamic parameters show that the self-assembly aggregation process is enthalpy driven, while the observed enthalpy-entropy compensation suggests that similar stacking interactions control the self-assembly of the different compounds. However, the strength of the stacking interactions, and then the nanowire stability, depends on the nature of templating cations and on their capacity to fill the central cavity of quadruplexes, with the order Sr(+) < Na(+) ≲ K(+).

A Simple Mechanism Underlying the Effect of Protecting Osmolytes on Protein Folding.

Osmolytes are small organic compounds that confer to the cell an enhanced adaptability to external conditions. Many osmolytes not only protect the cell from osmotic stress but also stabilize the native structure of proteins. While simplified models able to predict changes to protein stability are available, a general physicochemical explanation of the underlying microscopic mechanism is still missing. Here, we address this issue by performing very long all-atom MD simulations, free energy calculations, and experiments on a well-characterized mini-protein, the villin headpiece. Comparisons between the folding free energy landscapes in pure water and osmolyte solutions, together with experimental validation by means of circular dichroism, unfolding experiments, and NMR, led us to formulate a simple hypothesis for the protecting mechanism. Taken together, our results support a novel mechanistic explanation according to which the main driving force behind native state protection is a change in the solvent rotational diffusion.

Novel chiral macrocycles containing two electronically interacting arylene chromophores.

Novel chiral macrocycles consisting of two rigid oligoarylene rods and two chiral spiroindane clips have been synthesized by condensation of spiroindane diols and CF3-activated alpha-omega-difluorooligoaryls. Since a broad variety of planar aromatic macrocycles is known, our non-planar, chiral rings represent a new class of macrocyclic compounds. The first two examples, which contain quaterphenylene and diphenylbithiophene rods, are presented in this communication; for one of them a crystal structure is given. The chiroptical properties of the macrocycles can be interpreted as an interplay of the "intra-rod" helicity of individual oligoarylene rods and the "inter-rod" helicity between both chromophores of the macrocycle. The macrocycles can act as chiral dopands of commercially available, and novel, polymeric nematic liquid crystals (emissive polyfluorenes). The "intra-rod" helicity of individual oligoarylene rods is the main feature in determining the resulting helical twisting power (HTP). The cholestric induction in mesogenic, emissive polyfluorenes is of special interest for a realization of electronic devices that have a circularly polarized electroluminescence. The results are also important for an understanding of larger ensembles of chiral rodlike molecules, especially their pi-pi interactions.

The self-assembly of a lipophilic guanosine nucleoside into polymeric columnar aggregates: the nucleoside strucutre contains sufficient information to drive the process towards a strikingly regular polymer.

Lipophilic guanosine derivatives act as self-assembled ionophores. In the presence of alkali metal ions in organic solvents, these G derivatives can form tubular polymeric structures. The molecular aggregates formed by 3',5'-didecanoyl-2'-deoxyguanosine (1) have been characterised by SANS and NMR spectroscopy. The polymer is structured as a pile of stacked G quartets held together by the alkali metal ions that occupy the column's central channel. The deoxyribose moieties, with their alkyl substituents, surround the stacked G quartets, and the nucleoside's long-chain alkyl tails are in intimate contact with the organic solvent. In this polymeric structure, there is an amazing regularity in the rotamers around the glycosidic bond within each G quartet and in the repeat sequence of the G quartets along the columns. In hydrocarbon solvents, these columnar aggregates form lyomesophases of the cholesteric and hexagonal types.

Columnar lyomesophases formed in hydrocarbon solvents by chiral lipophilic guanosine-alkali metal complexes.

The lipophilic guanosine derivative 1 acts as a self-assembled ionophore and, in the presence of alkali metal ions, forms chiral polymeric structures in organic solvents. These polymeric columnar aggregates are comprised of G-quartets held together by alkali metal ions which are located inside the tubular structure; the quartets are surrounded by hydrocarbon chains. In hydrocarbon solvents, these columnar aggregates form lyomesophases of the cholesteric and hexagonal type. Copyright 2000 Wiley-Liss, Inc.

The self-assembly of lipophilic guanosine derivatives in solution and on solid surfaces

The self-assembly of lipophilic deoxyguanosine derivatives 1 and 2 has been studied in solution by NMR spectroscopy and ESI-MS (electrospray ionization mass spectrometry). NMR data show the existence of two types of self-assembled, ribbonlike structures (A and B), which are connected at the guanine moieties through two different H-bonded networks. The first species (A), which is stable in the solid state and characterised by cyclic NH(2)-O(6) and NH(1)-N(7) hydrogen bonds, is detected soon after dissolving the polycrystalline powder in rigorously anhydrous CDCl3. In solution it slowly undergoes a structural transition towards a thermodynamically stable ribbon characterised by NH(1)-O(6) and NH(2)-N(3) cyclic hydrogen bonds (B). On the other hand, at surfaces, self-assembled ribbon nanostructures have been grown from solutions of derivative 1 both on mica and at the graphite-solution interface. They have been investigated by means of tapping mode scanning force microscopy (SFM) and scanning tunnelling microscopy (STM), respectively. SFM revealed dry, micrometer-long nanoribbons with a molecular cross-section. while STM imaging at submolecular resolution indicates a molecular packing of type A, like the one detected in the solid state. This indicates that, upon adsorption at the solid-liquid interface, the guanosine moieties undergo a structural rearrangement from a B-type to an A-type ribbon.

Enantioselective Extraction of Dinitrophenyl Amino Acids Mediated by Lipophilic Deoxyguanosine Derivatives: Chiral Discrimination by Self-Assembly.

The transfer of potassium salts of dinitrophenyl amino acids from water to chloroform by the lipophilic guanosine derivative 1 takes place enantioselectively. Depending on the K(+):1 ratio, G-quartets of 1 self-assemble into octamers (O) or polymers.