Predicting pKa Using a Combination of Semi-Empirical Quantum Mechanics and Radial Basis Function Methods

The acid dissociation constant (pK_a) has an important influence on molecular properties crucial to compound development in synthesis, formulation, and optimization of absorption, distribution, metabolism, and excretion properties. We will present a method that combines quantum mechanical calculations, at a semi-empirical level of theory, with machine learning to accurately predict pK_a for a diverse range of mono- and polyprotic compounds. The resulting model has been tested on two external data sets, one specifically used to test pK_a prediction methods (SAMPL6) and the second covering known drugs containing basic functionalities. Both sets were predicted with excellent accuracy (root-mean-square errors of 0.7-1.0 log units), comparable to other methodologies using a much higher level of theory and computational cost.

Orai1 Channel Inhibition Preserves Left Ventricular Systolic Function and Normal Ca2+ Handling After Pressure Overload

BACKGROUND

Orai1 is a critical ion channel subunit, best recognized as a mediator of store-operated Ca²⁺ entry (SOCE) in nonexcitable cells. SOCE has recently emerged as a key contributor of cardiac hypertrophy and heart failure but the relevance of Orai1 is still unclear.

METHODS

To test the role of these Orai1 channels in the cardiac pathophysiology, a transgenic mouse was generated with cardiomyocyte-specific expression of an ion pore-disruptive Orai1^R91W mutant (C-dnO1). Synthetic chemistry and channel screening strategies were used to develop 4-(2,5-dimethoxyphenyl)-N-[(pyridin-4-yl)methyl]aniline (hereafter referred to as JPIII), a small-molecule Orai1 channel inhibitor suitable for in vivo delivery.

RESULTS

Adult mice subjected to transverse aortic constriction (TAC) developed cardiac hypertrophy and reduced ventricular function associated with increased Orai1 expression and Orai1-dependent SOCE (assessed by Mn²⁺ influx). C-dnO1 mice displayed normal cardiac electromechanical function and cellular excitation-contraction coupling despite reduced Orai1-dependent SOCE. Five weeks after TAC, C-dnO1 mice were protected from systolic dysfunction (assessed by preserved left ventricular fractional shortening and ejection fraction) even if increased cardiac mass and prohypertrophic markers induction were observed. This is correlated with a protection from TAC-induced cellular Ca²⁺ signaling alterations (increased SOCE, decreased [Ca²⁺]_i transients amplitude and decay rate, lower SR Ca²⁺ load and depressed cellular contractility) and SERCA2a downregulation in ventricular cardiomyocytes from C-dnO1 mice, associated with blunted Pyk2 signaling. There was also less fibrosis in heart sections from C-dnO1 mice after TAC. Moreover, 3 weeks treatment with JPIII following 5 weeks of TAC confirmed the translational relevance of an Orai1 inhibition strategy during hypertrophic insult.

CONCLUSIONS

The findings suggest a key role of cardiac Orai1 channels and the potential for Orai1 channel inhibitors as inotropic therapies for maintaining contractility reserve after hypertrophic stress.

Avoiding hERG-liability in drug design via synergetic combinations of different (Q)SAR methodologies and data sources: a case study in an industrial setting

In this paper, we explore the impact of combining different in silico prediction approaches and data sources on the predictive performance of the resulting system. We use inhibition of the hERG ion channel target as the endpoint for this study as it constitutes a key safety concern in drug development and a potential cause of attrition. We will show that combining data sources can improve the relevance of the training set in regard of the target chemical space, leading to improved performance. Similarly we will demonstrate that combining multiple statistical models together, and with expert systems, can lead to positive synergistic effects when taking into account the confidence in the predictions of the merged systems. The best combinations analyzed display a good hERG predictivity. Finally, this work demonstrates the suitability of the SOHN methodology for building models in the context of receptor based endpoints like hERG inhibition when using the appropriate pharmacophoric descriptors.

JPlogP: an improved logP predictor trained using predicted data

The partition coefficient between octanol and water (logP) has been an important descriptor in QSAR predictions for many years and therefore the prediction of logP has been examined countless times. One of the best performing models is to predict the logP using multiple methods and average the result. We have used those averaged predictions to develop a training-set which was able to distil the information present across the disparate logP methods into one single model. Our model was built using extendable atom-types, where each atom is distilled down into a 6 digit number, and each individual atom is assumed to have a small additive effect on the overall logP of the molecule. Beyond the simple coefficient model a consensus model is evaluated, which uses known compounds as a starting point in the calculation and modifies the experimental logP using the same coefficients as in the first model. We then test the performance of our models against two different datasets, one where many different models routinely perform well against, and another designed to more represent pharmaceutical space. The true strength of the model is represented in the pharmaceutical benchmark set, where both models perform better than any previously developed models.

New structural alerts for Ames mutagenicity discovered using emerging pattern mining techniques

The discovered patterns are used to develop new structural alerts for mutagenicity in the Derek Nexus expert system.

Trifluoromethyldiazirine: an effective photo-induced cross-linking probe for exploring amyloid formation

The separative and analytical power of ion mobility spectrometry-mass spectrometry combined with photo-induced cross-linking of site-specifically incorporated trifluoromethyldiazirine provides a powerful approach towards structural characterisation of amyloid fibrils.

Synthesis of functionalised aromatic oligamide rods

A current goal in synthetic chemistry is the design and synthesis of molecules that adopt well defined conformations-so called foldamers. In this manuscript we describe a modular approach for construction of rod shaped para-oligobenzamide molecules. Our approach permits regiospecific incorporation of side chains through a phenolic ether linkage on the scaffold; a feature that partly restricts the conformation of the rod through intramolecular hydrogen-bonding.

Macrocyclic scaffolds derived from p-aminobenzoic acid

The regiospecific synthesis of C3 macrocyclic scaffolds possessing multiple different functional groups is described.

Most obstructive sleep apnoea patients exhibit vigilance and attention deficits on an extended battery of tests

Excessive daytime sleepiness, fatigue and altered attention are often experienced by obstructive sleep apnoea (OSA) patients. Although attentional problems are presumably responsible for part of the daytime functioning impairment in OSA, thorough investigation is unusual. Clinicians usually attribute these symptoms to somnolence. In clinical practice, only one isolated test is generally used to assess vigilance and attentional defects. It was hypothesised that most OSA patients exhibit a broad range of attentional deficits, beyond impaired maintenance of wakefulness, and a specific battery of tests is needed to correctly assess them. Three attentional tests were performed at 9:00, 11:00 and 13:30 h, measuring maintenance of wakefulness, sustained attention and divided attention. Twenty OSA patients (aged 51+/-12 yrs, apnoea/hypopnoea index 45+/-22 h) and 40 control subjects (aged 48.4+/-9.9 yrs) were tested. OSA patients performed significantly less well on the three tests than the controls at the three sessions. This battery of tests demonstrated that 95% of patients had vigilance and/or attentional impairment. Impairment patterns varied between patients. Vigilance is impaired in obstructive sleep apnoea patients over a wide range of attentional processes. Not only is their ability to remain awake in monotonous situations impaired but their ability to maintain attention in more stimulating conditions is also affected. A single test of vigilance is not sufficient and could underestimate impaired vigilance and attention in some patients.

Quality assessment of seven types of fresh-frozen plasma leucoreduced by specific plasma filtration

BACKGROUND AND OBJECTIVES

A study was undertaken to determine plasma quality after specific filtration.

MATERIALS AND METHODS

Seven types of plasma were tested, after filtration of plasma from filtered or non-filtered whole blood. Leucocyte counting was carried out after a 30-fold concentration of the sample. Twenty-nine parameters (including coagulation testing, proteins, coagulation factors and activation markers) were measured before and after filtration, and after 6 months of storage.

RESULTS

After specific plasma filtration, the average residual leucocyte counts were less than 2250/l. In spite of small statistically significant changes in proteins, coagulation factors and complement activation, this study showed that plasma filtration did not alter plasma quality. After 6 months of storage at -30 degrees C, factor VIII recovery varied between 91 and 109%. Haemostasis parameters and activation markers remained within the normal range.

CONCLUSIONS

Specific plasma filtration reduced the leucocyte number to < 104 leucocytes/l. The quality of plasma was not altered by the additional step of specific plasma filtration.

[Evaluation of nutrition instruction in a group of Senegalese students at the secondary level]

BACKGROUND

In Senegal, nutrition instruction was implanted in 1981 in the national curriculum of biology and has never been evaluated since.

METHODS

The purpose of this study, was to evaluate the effect of a six weeks nutrition instruction program on improving nutrition knowledge and nutrition attitudes in an experimental group including 81 subjects aged 16.7+/-1.2 years and a control group including 80 subjects aged 15.7+/-1.3 years. These subjects came respectively from third and fourth grade. A questionnaire on knowledge and one on attitudes were administered to the experimental group, before and after the nutrition instruction, while the control group, who did not received any nutrition instruction, also answered the questionnaires.

RESULTS

Results indicate that the adjusted mean knowledge posttest scores did not significantly increase in the experimental group compared to the control group. In addition, the adjusted mean attitude postscores of the boys and girls of the experimental group on the attitude scale "Nutrition affects health" were significantly higher from that of the control group.

CONCLUSION

An evaluation of the nutrition curriculum and the teaching methods is suggested in order to improve the effectiveness of this nutrition program.

ADP-ribosylation of rye histones

Chromatin from etiolated rye seedlings synthesized protein-bound, acid-insoluble material from [3H]NAD, presumably poly(ADP-ribose). [3H]ADP-ribosylated histone fractions were isolated from crude chromatin and characterized by gel electrophoresis and exclusion chromatography. It was found that histone H2B was the main acceptor, that H2A and H1 were modified to a lesser extent, and that H3 and H4 were only slightly modified. The average chain length on purified histones was 2.5 units of polymer.