Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge

In the context of the SAMPL5 blinded challenge standard free energies of binding were predicted for a dataset of 22 small guest molecules and three different host molecules octa-acids (OAH and OAMe) and a cucurbituril (CBC). Three sets of predictions were submitted, each based on different variations of classical molecular dynamics alchemical free energy calculation protocols based on the double annihilation method. The first model (model A) yields a free energy of binding based on computed free energy changes in solvated and host-guest complex phases; the second (model B) adds long range dispersion corrections to the previous result; the third (model C) uses an additional standard state correction term to account for the use of distance restraints during the molecular dynamics simulations. Model C performs the best in terms of mean unsigned error for all guests (MUE \(3.2\,<\,3.4\,<\,3.6\,\text{kcal}\,\text{mol}^{-1}\)—95 % confidence interval) for the whole data set and in particular for the octa-acid systems (MUE \(1.7\,<\,1.9\,<\,2.1\,\text{kcal}\,\text{mol}^{-1}\)). The overall correlation with experimental data for all models is encouraging (\(R^2\, 0.65\,<\,0.70<0.75\)). The correlation between experimental and computational free energy of binding ranks as one of the highest with respect to other entries in the challenge. Nonetheless the large MUE for the best performing model highlights systematic errors, and submissions from other groups fared better with respect to this metric.     

Lévy-driven GPS queues with heavy-tailed input

In this paper, we derive exact large buffer asymptotics for a two-class generalized processor sharing (GPS) model, under the assumption that the input traffic streams generated by both classes correspond to heavy-tailed Lévy processes. Four scenarios need to be distinguished, which differ in terms of (i) the level of heavy-tailedness of the driving Lévy processes as well as (ii) the values of the corresponding mean rates relative to the GPS weights. The derived results are illustrated by two important special cases, in which the queues’ inputs are modeled by heavy-tailed compound Poisson processes and by \(\alpha \)-stable Lévy motions.     

Ergodic theorems with arithmetical weights

We prove that the divisor function d(n) counting the number of divisors of the integer n is a good weighting function for the pointwise ergodic theorem. For any measurable dynamical system (X, A, ν, τ) and any f ∈ L ^p (ν), p > 1, the limit

$$\mathop {\lim }\limits_{n \to \infty } \frac{1}{{\Sigma _{k = 1}^nd\left( k \right)}}\sum\limits_{k = 1}^n {d\left( k \right)f\left( {{\tau ^k}x} \right)} $$

exists ν-almost everywhere. The proof is based on Bourgain’s method, namely the circle method based on the shift model. Using more elementary ideas we also obtain similar results for other arithmetical functions, like the θ(n) function counting the number of squarefree divisors of n and the generalized Euler totient function J _s (n) = Σ _d|n d ^s μ(n/d), s > 0.

     

Maximum likelihood estimation for stochastic volatility in mean models with heavy‐tailed distributions

In this article, we introduce a likelihood‐based estimation method for the stochastic volatility in mean (SVM) model with scale mixtures of normal (SMN) distributions. Our estimation method is based on the fact that the powerful hidden Markov model (HMM) machinery can be applied in order to evaluate an arbitrarily accurate approximation of the likelihood of an SVM model with SMN distributions. Likelihood‐based estimation of the parameters of stochastic volatility models, in general, and SVM models with SMN distributions, in particular, is usually regarded as challenging as the likelihood is a high‐dimensional multiple integral. However, the HMM approximation, which is very easy to implement, makes numerical maximum of the likelihood feasible and leads to simple formulae for forecast distributions, for computing appropriately defined residuals, and for decoding, that is, estimating the volatility of the process. Copyright © 2017 John Wiley & Sons, Ltd.     

Unexpected Radical Telomerisation of Vinylidene Fluoride with 2-Mercaptoethanol

The radical telomerisation of vinylidene fluoride (VDF) with 2-mercaptoethanol as chain transfer agent (CTA) was studied to synthesise fluorinated telomers which bear a hydroxy end-group, such as H(VDF)_nS(CH₂)₂OH, under thermal (di-tert-butyl peroxide as the initiator) or photochemical initiations. A careful structural study of a typical H-VDF-S(CH₂)₂OH telomer was performed by ¹H and ¹⁹F NMR spectroscopy. These analytical methods allowed us to explore the selective addition of the thiyl radical onto the hydrogenated side of VDF, and the telomer containing one VDF unit was obtained selectively. Surprisingly, for higher [VDF]_o initial concentrations, a monoadduct telomer was produced as well as PVDF homopolymer. This feature was related to the fast consumption of the CTA. The kinetics of radical telomerisation led to a quite high transfer constant of the CTA (40 at 140 °C) that evidences the formation of a monoadduct as the only telomer formed.     

Repurposing of Omarigliptin as a Neuroprotective Agent Based on Docking with A2A Adenosine and AChE Receptors,Brain GLP-1 Response and Its Brain/Plasma Concentration Ratio after 28 Days Multiple Doses in Rats Using LC-MS/MS

The authors in the current work suggested the potential repurposing of omarigliptin (OMR) for neurodegenerative diseases based on three new findings that support the preliminary finding of crossing BBB after a single dose study in the literature. The first finding is the positive results of the docking study with the crystal structures of A_2A adenosine (A2AAR) and acetylcholine esterase (AChE) receptors. A2AAR is a member of non-dopaminergic GPCR superfamily receptor proteins and has essential role in regulation of glutamate and dopamine release in Parkinson’s disease while AChE plays a major role in Alzheimer’s disease as the primary enzyme responsible for the hydrolytic metabolism of the neurotransmitter acetylcholine into choline and acetate. Docking showed that OMR perfectly fits into A2AAR binding pocket forming a distinctive hydrogen bond with Threonine 256. Besides other non-polar interactions inside the pocket suggesting the future of the marketed anti-diabetic drug (that cross BBB) as a potential antiparkinsonian agent while OMR showed perfect fit inside AChE receptor binding site smoothly because of its optimum length and the two fluorine atoms that enables quite lean fitting. Moreover, a computational comparative study of OMR docking, other 12 DPP-4 inhibitors and 11 SGLT-2 inhibitors was carried out. Secondly, glucagon-like peptide-1 (GLP-1) concentration in rats’ brain tissue was determined by the authors using sandwich GLP-1 ELISA kit bio-analysis to ensure the effect of OMR after the multiple doses’ study. Brain GLP-1 concentration was elevated by 1.9-fold following oral multiple doses of OMR (5 mg/kg/day, p.o. for 28 days) as compared to the control group. The third finding is the enhanced BBB crossing of OMR after 28 days of multiple doses that had been studied using LC-MS/MS method with enhanced liquid–liquid extraction. A modified LC-MS/MS method was established for bioassay of OMR in rats’ plasma (10–3100 ng/mL) and rats’ brain tissue (15–2900 ng/mL) using liquid–liquid extraction. Alogliptin (ALP) was chosen as an internal standard (IS) due to its LogP value of 1.1, which is very close to the LogP of OMR. Extraction of OMR from samples of both rats’ plasma and rats’ brain tissue was effectively achieved with ethyl acetate as the extracting solvent after adding 1N sodium carbonate to enhance the drug migration, while choosing acetonitrile to be the diluent solvent for the IS to effectively decrease any emulsion between the layers in the stated method of extraction. Validation results were all pleasing including good stability studies with bias of value below 20%. Concentration of OMR in rats’ plasma were determined after 2 h of the latest dose from 28 days multiple doses, p.o, 5 mg/kg/day. It was found to be 1295.66 ± 684.63 ng/mL estimated from the bio-analysis regression equation. OMR passed through the BBB following oral administration and exhibited concentration of 543.56 ± 344.15 ng/g in brain tissue, taking in consideration the dilution factor of 10. The brain/plasma concentration ratio of 0.42 (543.56/1295.66) was used to illustrate the penetration power through the BBB after the multiple doses for 28 days. Results showed that OMR passed through the BBB more effectively in the multiple dose study as compared to the previously published single dose study by the authors. Thus, the present study suggests potential repositioning of OMR as antiparkinsonian agent that will be of interest for researchers interested in neurodegenerative diseases.     

Phytochemical Investigation and Biological Activities of Lantana rhodesiensis

Lantana rhodesiensis Moldenke is a plant widely used to treat diseases, such as rheumatism, diabetes, and malaria in traditional medicine. To better understand the traditional uses of this plant, a phytochemical study was undertaken, revealing a higher proportion of polyphenols, including flavonoids in L. rhodesiensis leaf extract and moderate proportion in stem and root extracts. The antioxidant activity of the extracts was also determined using three different assays: the radical 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity, the FRAP method (Ferric-reducing antioxidant power) and the β-carotene bleaching test. The anti-malarial activity of each extract was also evaluated using asexual erythrocyte stages of Plasmodium falciparum, chloroquine-sensitive strain 3D7. The results showed that the leaf extract exhibited higher antioxidant and anti-malarial activities in comparison with the stem and root extracts, probably due to the presence of higher quantities of polyphenols including flavonoids in the leaves. A positive linear correlation was established between the phenolic compound content (total polyphenols including flavonoids and tannins; and total flavonoids) and the antioxidant activity of all extracts. Furthermore, four flavones were isolated from leaf dichloromethane and ethyl acetate fractions: a new flavone named rhodescine (5,6,3′,5′-tetrahydroxy-7,4′-dimethoxyflavone) (1), 5-hydroxy-6,7,3′,4′,5′-pentamethoxyflavone (2), 5-hydroxy-6,7,3′,4′-tetramethoxyflavone (3), and 5,6,3′-trihydroxy-7,4′-dimethoxyflavone (4). Their structures were elucidated by ¹H, ¹³CNMR, COSY, HSQC, HMBC, and MS-EI spectral methods. Aside from compound 2, all other molecules were described for the first time in this plant species.     

Palatability Enhancement Potential of Hermetia illucens Larvae Protein Hydrolysate in Litopenaeus vannamei Diets

Marine feed ingredients derived from cephalopods (e.g., squid) and crustaceans (e.g., krill) are commercially used to improve the palatability of shrimp diets. Increase in global demand for shrimps has resulted in overfishing of these marine organisms and is a matter of concern. Insect protein hydrolysate could be a sustainable alternative for the possible replacement of these marine feed ingredients. During this study, four formulations: diet A (control: not containing any palatability enhancer), diet B (containing squid meal and krill oil), diet C (containing 1% insect protein hydrolysate), and diet D (containing 2% insect protein hydrolysate) were tested for (1) time required by first subject to begin feeding (time to strike) and (2) palatability in Litopenaeus vannamei. Additionally, the chemical composition of all four diet formulations was also analyzed. Results indicate that all diets had similar crude composition. The major essential amino acids in all diets were leucine and lysine, whereas eicosapentaenoic acid was the major omega-3 fatty acid in all diets. There were no significant differences between the mean time to strike for all the tested formulations. Palatability of tested formulations was found in the following order: diet D > diet C > diet B = diet A (p < 0.05), indicating that addition of squid meal and krill oil has no effect on palatability in comparison to control, whereas inclusion of insect protein hydrolysates significantly improves the palatability of formulations. Palatability enhancement potential of insect protein hydrolysate could be attributed to the high free amino acid content and water solubility in comparison to squid meal.     

In Vitro Antiplasmodial and Cytotoxic Activities of Compounds from the Roots of Eriosema montanum Baker f. (Fabaceae)

Malaria remains one of the leading causes of death in sub-Saharan Africa, ranked in the top three infectious diseases in the world. Plants of the Eriosema genus have been reported to be used for the treatment of this disease, but scientific evidence is still missing for some of them. In the present study, the in vitro antiplasmodial activity of the crude extract and compounds from Eriosema montanum Baker f. roots were tested against the 3D7 strain of Plasmodium falciparum and revealed using the SYBR Green, a DNA intercalating compound. The cytotoxicity effect of the compounds on a human cancer cell line (THP-1) was assessed to determine their selectivity index. It was found that the crude extract of the plant displayed a significant antiplasmodial activity with an IC₅₀ (µg/mL) = 17.68 ± 4.030 and a cytotoxic activity with a CC₅₀ (µg/mL) = 101.5 ± 12.6, corresponding to a selective antiplasmodial activity of 5.7. Bioactivity-guided isolation of the major compounds of the roots’ crude extract afforded seven compounds, including genistein, genistin and eucomic acid. Under our experimental conditions, using Artemisinin as a positive control, eucomic acid showed the best inhibitory activity against the P. falciparum 3D7, a well-known chloroquine-sensitive strain. The present results provide a referential basis to support the traditional use of Eriosema species in the treatment of malaria.