Estimation of pKa using semiempirical molecular orbital methods. Part 2 : application to amines, anilines and various nitrogen containing heterocyclic compounds

The pKa of a compound directly influences its biopharmaceutical profile. This article describes the development of a method for estimating pKa values for a number of nitrogen containing chemical structures using semiempirical QM properties derived from frontier electron theory. Typically, the property giving the best correlation with pKa was the electrophilic superdelocalisability of the nitrogen atom resulting in regression equations with r2 values up to 0.94. The advantages of this technique are in the simplicity of the models and the speed of calculation, suggesting that this method could be widely applied to the estimation of pKa values. The success of this approach is discussed in relation to other methods

Estimation of pKa using semiempirical molecular orbital methods. Part 1: application to phenols and carboxylic acids

The electronic properties of small molecules can be calculated quickly and with a reasonable degree of accuracy using semiempirical QM methods. In this study a set of QM properties derived from frontier electron theory have been used to produce a predictive model of the dissociation constants of phenols, benzoic acids and aliphatic carboxylic acids. The pKa values and structures of nearly 500 compounds were extracted from the Physprop database for this purpose. Multiple linear regression was used to search for relationships between pKa and the calculated QM properties. In most cases only a single independent variable, electrophilic superdelocalisability, was needed to produce a good model of pKa. The advantages of our approach are in the speed of calculation and the simplicity of the resultant models. The merits of using semiempirical methods to predict pKa are discussed in relation to previous studies

A longitudinal 1H-NMR metabolomics analysis of urine from newborns with hypoxic-ischemic encephalopathy undergoing hypothermia therapy. Clinical and medical legal insights.

Perinatal asphyxia is an event affecting around four million newborns worldwide. The 0.5 to 2 per 1000 of full term asphyxiated newborns suffer from hypoxic-ischemic encephalopathy (HIE), which is a frequent cause of death or severe disability and, as consequence, the most common birth injury claim for obstetrics, gynaecologists, and paediatricians. Perinatal asphyxia results from a compromised gas exchange that leads to hypoxemia, hypercapnia, and metabolic acidosis. In this work, we applied a metabolomics approach to investigate the metabolic profiles of urine samples collected from full term asphyxiated newborns with HIE undergoing therapeutic hypothermia (TH), with the aim of identifying a pattern of metabolites associated with HIE and to follow their modifications over time. Urine samples were collected from 10 HIE newborns at birth, during hypothermia (48 hours), at the end of the therapeutic treatment (72 hours), at 1 month of life, and compared with a matched control population of 16 healthy full term newborns. The metabolic profiles were investigated by H-1 NMR spectroscopy coupled with multivariate statistical methods such as principal component analysis and orthogonal partial least square discriminant analysis. Multivariate analysis indicated significant differences between the urine samples of HIE and healthy newborns at birth. The altered metabolic patterns, mainly originated from the depletion of cellular energy and homeostasis, seem to constitute a characteristic of perinatal asphyxia. The HIE urine metabolome changes over time reflected either the effects of TH and the physiological growth of the newborns. Of interest, the urine metabolic profiles of the HIE non-surviving babies, characterized by the increased excretion of lactate, resulted significantly different from the rest of HIE population

Clinical parameters of the study population at birth.

<p>Clinical parameters of the study population at birth.</p

Comparative analysis of urine samples of HIE newborns at birth and at 30 days of life.

<p>Score scatter plots of (<b>A</b>) PCA and (<b>B</b>) OPLS-DA models of urine samples collected from HIE babies at birth (HIE day 1, empty circles) and at 30 days of life (HIE day 30, light blue diamonds). (<b>C</b>) Permutation test of the corresponding PLS-DA model (n = 400 random permutations). (<b>D</b>) OPLS-DA loading column plot of discriminant variables.</p

The effect of 72 hours of TH on the urine metabolome of HIE newborns.

<p>(<b>A</b>) Score scatter plot of the PCA model of urine samples collected from HIE newborns (HIE day 1, empty circles) and at the end of TH treatment (HIE day 3, blue triangles). The label NS indicates the non-surviving newborns. (<b>B</b>) Score scatter plot of the PCA model after removal of the samples belonging to non-surviving newborns (<b>C</b>) Score scatter plot of the OPLS-DA model of the samples belonging to surviving newborns. (<b>D</b>) Permutation test of the corresponding PLS-DA model (n = 400 random permutations). (<b>E</b>) OPLS-DA loading column plot of discriminant variables.</p

Comparative analysis of urine samples of HIE newborns and healthy controls at birth.

<p>Score scatter plots of (<b>A</b>) PCA and (<b>B</b>) OPLS-DA models of urine samples collected from HIE newborns (HIE day 1, empty circles) and from healthy newborns (Healthy day 1, green circles). The label NS indicates the non-surviving babies. (<b>C</b>) Permutation test of the corresponding PLS-DA model (n = 400 random permutations). (<b>D</b>) OPLS-DA loading column plot of discriminant variables.</p

The effect of 48 hours of TH on the urine metabolome of HIE newborns.

<p>Score scatter plots of (A) PCA model of urine samples collected from HIE babies at birth (HIE day 1, empty circles) and during the TH treatment at 48 hours (HIE day 2, red squares). The label NS indicates the non-surviving babies, and (<b>B</b>) corresponding PCA model after removal of the samples belonging to non-surviving newborns.</p

Clinical parameters of the study population in the first 30 days of life.

<p>Clinical parameters of the study population in the first 30 days of life.</p

Mycobacterium tuberculosis Chaperonin 10 Is Secreted in the Macrophage Phagosome: Is Secretion Due to Dissociation and Adoption of a Partially Helical Structure at the Membrane?

To confirm that Mycobacterium tuberculosis chaperonin 10 (Cpn10) is secreted outside the live bacillus, infected macrophages were examined by electron microscopy. This revealed that the mycobacterial protein accumulates both in the wall of the bacterium and in the matrix of the phagosomes in which ingested mycobacteria survive within infected macrophages. To understand the structural implications underlying this secretion, a structural study of M. tuberculosis Cpn10 was performed under conditions that are generally believed to mimic the membrane environment. It was found that in buffer-organic solvent mixtures, the mycobacterial protein forms two main species, namely, a partially helical monomer that prevails in dilute solutions at room temperature and a dimer that folds into a β-sheet-dominated structure and prevails in either concentrated protein solutions at room temperature or in dilute solutions at low temperature. A partially helical monomer was also found and was completely associated with negatively charged detergents in a micelle-bound state. Remarkably, zwitterionic lipids had no effect on the protein structure. By using N- and C-truncated forms of the protein, the C- and N-terminal sequences were identified as possessing an amphiphilic helical character and as selectively associating with acidic detergent micelles. When the study was extended to other chaperonins, it was found that human Cpn10 is also monomeric and partially helical in dilute organic solvent-buffer mixtures. In contrast, Escherichia coli Cpn10 is mostly dimeric and predominately β-sheet in both dilute and concentrated solutions. Interestingly, human Cpn10 also crosses biological membranes, whereas the E. coli homologue is strictly cytosolic. These results suggest that dissociation to partially helical monomers and interaction with acidic lipids may be two important steps in the mechanism of secretion of M. tuberculosis Cpn10 to the external environment