The concentration effect on the ‘hydrophobic’ and ‘hydrophilic’ behaviour around DMSO in dilute aqueous DMSO solutions. A computer simulation study

We have carried out a molecular dynamics study of dimethyl sulfoxide (DMSO) in water at 298 K at two different densities by simulating two different concentrations: 0.055 and 0.19 mole fraction. We have found an enhancement in the structure of water, an effect that becomes more pronounced as the concentration of DMSO increases. At both concentrations there is a well-defined hydration structure around the oxygen atom of DMSO, which is able to establish strong hydrogen bonds with surrounding water molecules. An increase in the concentration of DMSO depletes the solution of bulk water molecules, reducing the number of hydrogen bonds that water can have in the immediate vicinity of DMSO but increasing the strength of the hydrogen bonds made between the oxygen atom of DMSO and water. There is clear evidence of ‘hydrophobic’ hydration around the methyl groups of DMSO, which is enhanced as the concentration of DMSO increases.     

Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

Reaction of tetrahydrobenz[a]acridinones with hydroxylamine hydrochloride. VII

Oximation of ortho-substituted phenylbenz[a]acridinones using hydroxylamine hydrochloride, sodium hydroxide and ethanol as the solvent gave always the benzoquinacridine N-oxide 2 . Oximation of para-substituted phenylbenz[a]acridinones, however, gave only the corresponding oximes. The structure of all products was corroborated by ir, ¹H and ¹³C-nmr and mass spectral data. Theoretical calculations support the experimental findings.     

Diels-Alder reaction mechanisms of substituted chiral anthracene: A theoretical study based on the reaction force and reaction electronic flux

Quantum chemical calculations were used to study the mechanism of Diels-Alder reactions involving chiral anthracenes as dienes and a series of dienophiles. The reaction force analysis was employed to obtain a detailed scrutiny of the reaction mechanisms, it has been found that thermodynamics and kinetics of the reactions are quite consistent: the lower the activation energy, the lower the reaction energy, thus following the Bell-Evans-Polanyi principle. It has been found that activation energies are mostly due to structural rearrangements that in most cases represented more than 70% of the activation energy. Electronic activity mostly due to changes in σ and π bonding were revealed by the reaction electronic flux (REF), this property helps identify whether changes on σ or π bonding drive the reaction. Additionally, new global indexes describing the behavior of the electronic activity were introduced and then used to classify the reactions in terms of the spontaneity of their electronic activity. Local natural bond order electronic population analysis was used to check consistency with global REF through the characterization of specific changes in the electronic density that might be responsible for the activity already detected by the REF. Results show that reactions involving acetoxy lactones are driven by spontaneous electronic activity coming from bond forming/strengthening processes; in the case of maleic anhydrides and maleimides it appears that both spontaneous and non-spontaneous electronic activity are quite active in driving the reactions.     

Low-molecular-weight poly(alpha-methyl beta,L-malate) of microbial origin: synthesis and crystallization

Low-molecular-weight poly(alpha-methyl beta,L-malate) made of approximately 25-30 units was prepared from microbial poly(beta,L-malic acid) by treatment with diazomethane. The thermal characterization of the polymalate methyl ester was carried out and its crystalline structure was preliminary examined. Its ability to crystallize both from solution and from the melt was comparatively evaluated.     

Molecular dynamics simulations of CXCL-8 and its interactions with a receptor peptide, heparin fragments, and sulfated linked cyclitols

CXCL-8 (Interleukin 8) is a CXC chemokine with a central role in the human immune response. We have undertaken extensive in silico analyses to elucidate the interactions of CXCL-8 with its various binding partners, which are crucial for its biological function. Sequence and structure analyses showed that residues in the thirdq β-sheet and basic residues in the heparin binding site are highly variable, while residues in the second β-sheet are highly conserved. Molecular dynamics simulations in aqueous solution of dimeric CXCL-8 have been performed with starting geometries from both X-ray and NMR structures showed shearing movements between the two antiparallel C-terminal helices. Dynamic conservation analyses of these simulations agreed with experimental data indicating that structural differences between the two structures at quaternary level arise from changes in the secondary structure of the N-terminal loop, the 3(10)-helix, the 30s, 40s, and 50s loops and the third β-sheet, resulting in a different interhelical separation. Nevertheless, the observation of these different states indicates that CXCL-8 has the potential to undergo conformational changes, and it seems likely that this feature is relevant to the mode of binding of glycosaminoglycan (GAG) mimetics such as cyclitols. Simulations of the receptor peptide fragment-CXCL-8 complex identified several specific interactions of the receptor peptide with CXCL-8 that could be exploited in the structure-based design of competitive peptides and nonpeptidic molecules targeting CXCL-8 for combating inflammatory diseases. Simulations of the CXCL-8 dimer complexed with a 24-mer heparin fragment and of the CXCL-8-receptor peptide complex revealed that Arg60, Lys64, and Arg68 in the dimer bind to cyclitols in a horseshoe pattern, defining a region which is spatially distinct from the receptor binding site. There appears to be an optimum number of sulfates and an optimum length of alkyl spacers required for the interaction of cyclitol inhibitors with the dimeric form of CXCL-8. Calculation of the binding affinities of cyclitol inhibitors reflected satisfactorily the ranking of experimentally determined inhibitory potencies. The findings of these molecular modeling studies will help in the search for inhibitors which can modulate various CXCL-8 biological activities and serve as an excellent model system to study CXC-inhibitor interactions.     

Aromatic polyesters from naturally occurring monosaccharides: Poly(ethylene terephthalate) and poly(ethylene isophthalate) analogs derived from D‐mannitol and galactitol

The synthesis and characterization of a new series of aromatic polyesters based on D‐mannitol and galactitol are described. These polyesters were obtained by polycondensation reaction of the terephthaloyl chloride or isophthaloyl chloride and 2,3,4,5‐tetra‐O‐methyl‐D‐mannitol or 2,3,4,5‐tetra‐O‐methyl‐galactitol in o‐dichlorobenzene. All the new polyesters were characterized by elemental analyses, GPC, IR, and NMR. They were soluble in chloroform, but insoluble in water and other polar oxygenated solvents. They showed a notable hygroscopicity, lower for those containing isophthalic units. DSC and X‐ray diffraction studies showed that D‐mannitol‐based polyesters were stiffer and less crystalline than those derived from galactitol, which presented a noticeably lower thermal stability. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4570–4577, 2005     

Ligand-protein docking with water molecules

The presence of water molecules plays an important role in the accuracy of ligand-protein docking predictions. Comprehensive docking simulations have been performed on a large set of ligand-protein complexes whose crystal structures contain water molecules in their binding sites. Only those water molecules found in the immediate vicinity of both the ligand and the protein were considered. We have investigated whether prior optimization of the orientation of water molecules in either the presence or absence of the bound ligand has any effect on the accuracy of docking predictions. We have observed a statistically significant overall increase in accuracy when water molecules are included during docking simulations and have found this to be independent of the method of optimization of the orientation of water molecules. These results confirm the importance of including water molecules whenever possible in a ligand-protein docking simulation. Our findings also reveal that prior optimization of the orientation of water molecules, in the absence of any bound ligand, does not have a detrimental effect on the improved accuracy of ligand-protein docking. This is important, given the use of docking simulations to predict the binding modes of new ligands or drug molecules.