General-base catalysed hydrolysis and nucleophilic substitution of activated amides in aqueous solutions

The reactivity of 1-benzoyl-3-phenyl-1,2,4-triazole (1a) was studied in the presence of a range of weak bases in aqueous solution. A change in mechanism is observed from general-base catalysed hydrolysis to nucleophilic substitution and general-base catalysed nucleophilic substitution. A slight tendency is also observed for the more hydrophobic general bases to show higher reactivity towards 1a. Aspartame is an effective nucleophile, possibly because nucleophilic substitution is subject to intramolecular general-base catalysis. A general conclusion derived from the present results is that unexpected rate effects can only be rationalised provided that the detailed reaction mechanisms are well understood. Copyright (C) 2003 John Wiley Sons, Ltd.</p

The antimicrobial effects of the alginate oligomer OligoG CF-5/20 are independent of direct bacterial cell membrane disruption

Concerns about acquisition of antibiotic resistance have led to increasing demand for new antimicrobial therapies. OligoG CF-5/20 is an alginate oligosaccharide previously shown to have antimicrobial and antibiotic potentiating activity. We investigated the structural modification of the bacterial cell wall by OligoG CF-5/20 and its effect on membrane permeability. Binding of OligoG CF-5/20 to the bacterial cell surface was demonstrated in Gram-negative bacteria. Permeability assays revealed that OligoG CF-5/20 had virtually no membrane-perturbing effects. Lipopolysaccharide (LPS) surface charge and aggregation were unaltered in the presence of OligoG CF-5/20. Small angle neutron scattering and circular dichroism spectroscopy showed no substantial change to the structure of LPS in the presence of OligoG CF-5/20, however, isothermal titration calorimetry demonstrated a weak calcium-mediated interaction. Metabolomic analysis confirmed no change in cellular metabolic response to a range of osmolytes when treated with OligoG CF-5/20. This data shows that, although weak interactions occur between LPS and OligoG CF-5/20 in the presence of calcium, the antimicrobial effects of OligoG CF-5/20 are not related to the induction of structural alterations in the LPS or cell permeability. These results suggest a novel mechanism of action that may avoid the common route in acquisition of resistance via LPS structural modification

Kinetics of hydrolysis of 1-benzoyl-1,2,4-triazole in aqueous solution as a function of temperature near the temperature of maximum density, and the isochoric controversy

At temperatures above and below the temperature of maximum density, TMD, for water at ambient pressure, pairs of temperatures exist at which the molar volumes of water are equal. First-order rate constants for the pH-independent hydrolysis of 1-benzoyl-1,2,4-triazole in aqueous solution at pairs of such isochoric temperatures show no unique features. Taken together with previously published kinetic data for the hydrolysis of a range of simple organic solutes in both water and D2O near their respective TMDs, we conclude that special significance in the context of rates of chemical reactions in aqueous solutions should not be attached to the isochoric condition

Analysis of isothermal titration calorimetry data for complex interactions using I2CITC

I2CITC allows the analysis of isothermal titration calorimetry (ITC) data for complex coupled equilibria. Here we describe how, using I2CITC, ITC data for systems involving a self-aggregating ligand and a host offering one or two binding sites can be analyzed, how interaction models can be tested, and how confidence intervals for the optimized parameters can be determined

Uncertainty of protein-ligand binding constants: asymmetric confidence intervals versus standard errors

Equilibrium binding constants (Kb) between chemical compounds and target proteins or between interacting proteins provide a quantitative understanding of biological interaction mechanisms. Reporting uncertainties of measured experimental parameters are critical for decision making in many scientific areas, e.g., in lead compound discovery processes and in comparing computational predictions with experimental results. Uncertainties in measured Kb values are commonly represented by a symmetric normal distribution, often quoted in terms of the experimental value plus-minus the standard deviation. However, in general the distributions of measured Kb (and equivalent Kd) values and the corresponding free energy change DeltaGb are all asymmetric to varying degree. Here, using a simulation approach, we illustrate the effect of asymmetric Kb distributions within the realm of isothermal titration calorimetry (ITC) experiments. Further we illustrate the known, but perhaps not widely appreciated, fact that when distributions of any of Kb, Kd and DeltaGb are transformed into each other their degree of asymmetry is changed. Consequently, we recommend that a more accurate way of expressing the uncertainties of Kb, Kd, and DeltaGb values is to consistently report 95% confidence intervals, in line with other author’s suggestions. The ways to obtain such error ranges are discussed in detail and exemplified for a binding reaction obtained by ITC