Empirical prediction of peptide octanol-water partition coefficients

Peptides are of great therapeutic potential as vaccines and drugs. Knowledge of physicochemical descriptors, including the partition coefficient P (commonly expressed in logarithm form: logP), is useful for screening out unsuitable molecules and also for the development of predictive Quantitative Structure-Activity Relationships (QSARs). In this paper we develop a new approach to the prediction of LogP values for peptides based on an empirical relationship between global molecular properties and measured physical properties. Our method was successful in terms of peptide prediction (total r2 = 0.641). The final model consisted of 5 physicochemical descriptors (molecular weight, number of single bonds, 2D-VDW volume, 2D-VSA hydrophobic and 2D-VSA polar). The approach is peptide specific and its predictive accuracy was high. Overall, 67% of the peptides were able to be predicted within +/-0.5 log units from the experimental values. Our method thus represents a novel prediction method with proven predictive ability.

Affinity partitioning of plasmid DNA with a zinc finger protein

The affinity isolation of pre-purified plasmid DNA (pDNA) from model buffer solutions using native and poly(ethylene glycol) (PEG) derivatized zinc finger–GST (Glutathione-S-Transferase) fusion protein was examined in PEG–dextran (DEX) aqueous two-phase systems (ATPSs). In the absence of pDNA, partitioning of unbound PEGylated fusion protein into the PEG-rich phase was confirmed with 97.5% of the PEGylated fusion protein being detected in the PEG phase of a PEG 600–DEX 40 ATPS. This represents a 1322-fold increase in the protein partition coefficient in comparison to the non-PEGylated protein (Kc = 0.013). In the presence of pDNA containing a specific oligonucleotide recognition sequence, the zinc finger moiety of the PEGylated fusion protein bound to the plasmid and steered the complex to the PEG-rich phase. An increase in the proportion of pDNA that partitioned to the PEG-rich phase was observed as the concentration of PEGylated fusion protein was increased. Partitioning of the bound complex occurred to such an extent that no DNA was detected by the picogreen assay in the dextran phase. It was also possible to partition pDNA using a non-PEGylated (native) zinc finger–GST fusion protein in a PEG 1000–DEX 500 ATPS. In this case the native ligand accumulated mainly in the PEG phase. These results indicate good prospects for the design of new plasmid DNA purification methods using fusion proteins as affinity ligands.

On the hydrophobicity of peptides:comparing empirical predictions of peptide log P values

Peptides are of great therapeutic potential as vaccines and drugs. Knowledge of physicochemical descriptors, including the partition coefficient logP, is useful for the development of predictive Quantitative Structure-Activity Relationships (QSARs). We have investigated the accuracy of available programs for the prediction of logP values for peptides with known experimental values obtained from the literature. Eight prediction programs were tested, of which seven programs were fragment-based methods: XLogP, LogKow, PLogP, ACDLogP, AlogP, Interactive Analysis's LogP and MlogP; and one program used a whole molecule approach: QikProp. The predictive accuracy of the programs was assessed using r(2) values, with ALogP being the most effective (r( 2) = 0.822) and MLogP the least (r(2) = 0.090). We also examined three distinct types of peptide structure: blocked, unblocked, and cyclic. For each study (all peptides, blocked, unblocked and cyclic peptides) the performance of programs rated from best to worse is as follows: all peptides - ALogP, QikProp, PLogP, XLogP, IALogP, LogKow, ACDLogP, and MlogP; blocked peptides - PLogP, XLogP, ACDLogP, IALogP, LogKow, QikProp, ALogP, and MLogP; unblocked peptides - QikProp, IALogP, ALogP, ACDLogP, MLogP, XLogP, LogKow and PLogP; cyclic peptides - LogKow, ALogP, XLogP, MLogP, QikProp, ACDLogP, IALogP. In summary, all programs gave better predictions for blocked peptides, while, in general, logP values for cyclic peptides were under-predicted and those of unblocked peptides were over-predicted.

Delivery and stability of antisense oligonucleotide conjugates in vitro

The efficacy of antisense oligonucleotide (ODN) therapy is dependent on four major parameters: delivery to cells, intracellular stability and localisation and efficient action at the target site.The aim of this project was to study the delivery of ODNs to macrophages and to assess the stability of two ODN conjugates, in vitro. The first conjugate aimed to improve uptake of ODNs via mannose receptor mediated delivery, the second investigated the improved delivery of ODN conjugates via non-specific lipophilic interaction with the cell membrane. A mono-mannose phosphoramidite derivative was designed and synthesised and a mono-mannose ODN conjugate synthesised by standard phosphoramidite chemistry. Delivery of this conjugate was enhanced to RAW264.7 and J774 macrophage cell lines via a mechanism of receptor mediated endocytosis. The delivery of three lipophilic ODN conjugates, cholesterol (cholhex), 16-carbon alkyl chain (C16) and hexa-ethylene glycol (HEG) moieties and an unconjugated ODN were assessed in RAW264.7 macrophages. All three conjugates increased the lipophilicity of the ODN as assessed from partition coefficient data. Both the cholhex and unconjugated ODNs were found to have higher degrees of cellular association than the C16 and HEG conjugates. Cellular uptake studies implicated internalisation of these ODNs by an adsorptive endocytosis mechanism. Following endocytosis, ODNs must remain stable during their residence in endosomal/lysosomal compartments prior to exiting and exerting their biological action in either the cytosol or nucleus. Assessment of in vitro stability in a lysosomal extract revealed the cholhex conjugate and unconjugated ODNs to have a longer half-life than the C16 and HEG conjugated ODNs, highlighting the influence of conjugate moieties on lysosomal stability. The effects of base composition and length on stability in a lysosomal extract revealed the longest half-life for homo-cytidine ODNs and ODNs over 20 nucleotides in length. These studies suggest that the above conjugates can enhance cellular association and delivery of antisense ODNs to cultured macrophages. This may lead to their use in treating disorders such as HIV infection, which affects this cell type.

Formulation of topical non-steroidal anti-inflammatory agents

Reversed-pahse high-performance liquid chromatographic (HPLC) methods were developed for the assay of indomethacin, its decomposition products, ibuprofen and its (tetrahydro-2-furanyl)methyl-, (tetrahydro-2-(2H)pyranyl)methyl- and cyclohexylmethyl esters. The development and application of these HPLC systems were studied. A number of physico-chemical parameters that affect percutaneous absorption were investigated. The pKa values of indomethacin and ibuprofen were determined using the solubility method. Potentiometric titration and the Taft equation were also used for ibuprofen. The incorporation of ethanol or propylene glycol in the solvent resulted in an improvement in the aqueous solubility of these compounds. The partition coefficients were evaluated in order to establish the affinity of these drugs towards the stratum corneum. The stability of indomethacin and of ibuprofen esters were investigated and the effect of temperature and pH on the decomposition rates were studied. The effect of cetyltrimethylammonium bromide on the alkaline degradation of indomethacin was also followed. In the presence of alcohol, indomethacin alcoholysis was observed and the kinetics of decomposition were subjected to non-linear regression analysis and the rate constants for the various pathways were quantified. The non-isothermal, sufactant non-isoconcentration and non-isopH degradation of indomethacin were investigated. The analysis of the data was undertaken using NONISO, a BASIC computer program. The degradation profiles obtained from both non-iso and iso-kinetic studies show that there is close concordance in the results. The metabolic biotransformation of ibuprofen esters was followed using esterases from hog liver and rat skin homogenates. The results showed that the esters were very labile under these conditions. The presence of propylene glycol affected the rates of enzymic hydrolysis of the ester. The hydrolysis is modelled using an equation involving the dielectric constant of the medium. The percutaneous absorption of indomethacin and of ibuprofen and its esters was followed from solutions using an in vitro excised human skin model. The absorption profiles followed first order kinetics. The diffusion process was related to their solubility and to the human skin/solvent partition coefficient. The percutaneous absorption of two ibuprofen esters from suspensions in 20% propylene glycol-water were also followed through rat skin with only ibuprofen being detected in the receiver phase. The sensitivity of ibuprofen esters to enzymic hydrolysis compared to the chemical hydrolysis may prove valuable in the formulation of topical delivery systems.

Electrografting of poly (carbazole-co-acrylamide) onto highly oriented pyroltic graphite. A cyclovoltammetric, atomic force microscopic and ellipsometric study

The electrocopolymerization of carbazole and acrylamide on highly oriented pyrolytic graphite (HOPG) from ACN solutions via cyclovoltammetry (CV) was studied in order to evaluate the possibility to deposit uniform and thin but pinhole-free and still reactive coatings onto graphite-like substrates. The morphology of the coatings was investigated using atomic force microscopy and the coating thicknesses and optical parameters were measured using ellipsometry. It was found that under the chosen conditions thin (coating thickness hf>180 nm) and relatively smooth (root mean square surface roughness RMS<150 nm) P(Cz-co-AAm)-coatings exhibiting a uniform globuoidal morphology can be deposited onto graphite. From a certain coating thickness (hf>50 nm) no pinholes could be detected. It was found that the thickness of the deposited coatings increases almost linearly with increasing number of CV-cycles while keeping all other experimental parameters (scan rate and comonomer concentration ratio) constant. No influence of the comonomer concentration ratio on the film thickness and coating appearance could be observed, however, at quite low initial concentrations. However, the CV-scanning rate has quite a significant influence on the thickness of the deposited coatings. Higher scan rates (100 mV/s) result in thin (hf≈22 nm) coatings whereas at lower scan rates (<50 mV/s) coatings with thicknesses of approximately 50 nm were obtained. The optical coating parameters (the refractive index n and extinction coefficient k) seem to be independent of the deposition parameters and therefore averaged values of n̄=1.54±0.03 and k̄=0.08±0.03 were obtained.

A study in the application of domestic solar assisted heat pumps for heating and cooling

In the present work, the more important parameters of the heat pump system and of solar assisted heat pump systems were analysed in a quantitative way. Ideal and real Rankine cycles applied to the heat pump, with and without subcooling and superheating were studied using practical recommended values for their thermodynamics parameters. Comparative characteristics of refrigerants here analysed looking for their applicability in heat pumps for domestic heating and their effect in the performance of the system. Curves for the variation of the coefficient of performance as a function of condensing and evaporating temperatures were prepared for R12. Air, water and earth as low-grade heat sources and basic heat pump design factors for integrated heat pumps and thermal stores and for solar assisted heat pump-series, parallel and dual-systems were studied. The analysis of the relative performance of these systems demonstrated that the dual system presents advantages in domestic applications. An account of energy requirements for space and hater heating in the domestic sector in the O.K. is presented. The expected primary energy savings by using heat pumps to provide for the heating demand of the domestic sector was found to be of the order of 7%. The availability of solar energy in the U.K. climatic conditions and the characteristics of the solar radiation here studied. Tables and graphical representations in order to calculate the incident solar radiation over a tilted roof were prepared and are given in this study in section IV. In order to analyse and calculate the heating load for the system, new mathematical and graphical relations were developed in section V. A domestic space and water heating system is described and studied. It comprises three main components: a solar radiation absorber, the normal roof of a house, a split heat pump and a thermal store. A mathematical study of the heat exchange characteristics in the roof structure was done. This permits to evaluate the energy collected by the roof acting as a radiation absorber and its efficiency. An indication of the relative contributions from the three low-grade sources: ambient air, solar boost and heat loss from the house to the roof space during operation is given in section VI, together with the average seasonal performance and the energy saving for a prototype system tested at the University of Aston. The seasonal performance as found to be 2.6 and the energy savings by using the system studied 61%. A new store configuration to reduce wasted heat losses is also discussed in section VI.

Oxidational wear of low alloy steel in gases other than air

A pin on disc wear machine has been used to study the oxidational wear of low alloy steel in a series of experiments which were carried out under dry wear sliding conditions at range of loads from 11.28 to 49.05 N and three sliding speeds of 2 m/s, 3.5 m/s and 5 m/s, in atmosphere of air, Ar, CO2, 100% O2, 20% O2-80% Ar and 2% O2-98% Ar. Also, the experiments were conducted to study frictional force, surface and contact temperatures and surface parameters of the wearing pins. The wear debris was examined using x-ray diffraction technique for the identification of compounds produced by the wear process. Scanning electron microscopy was employed to study the topographical features of worn pins and to measure the thickness of the oxide films. Microhardness tests were carried out to investigate the influence of the sub-surface microhardness in tribological conditions. Under all loads, speeds and atmospheres parabolic oxidation growth was observed on worn surfaces, although such growth is dependent on the concentration of oxygen in the atmospheres employed. These atmospheres are shown to influence wear rate and coefficient of friction with change in applied load. The nature of the atmosphere also has influence on surface and contact temperatures as determined from heat flow analysis. Unlubricated wear debris was found to be a mixture of αFe2O3, Fe3O4 and FeO oxide. A model has been proposed for tribo-oxide growth demonstrating the importance of diffusion rate and oxygen partial pressure, in the oxidation processes and thus in determination of wear rates.

Measurements of stress-optic coefficient in polymer optical fibers

We have systematically measured the differential stress-optic coefficient, ?C, in a number of poly(methyl methacrylate) (PMMA) fibers drawn with different stress, ranging from 2 up to 27 MPa. ?C was determined in transverse illumination by measuring the dependence of birefringence on additional axial stress applied to the fiber. Our results show that ?C in PMMA fibers has a negative sign and ranges from -4.5 to -4.5×10-12 Pa-1, depending on the drawing stress. Increase of the drawing stress results in greater initial fiber birefringence and lower ?C.

Computational modelling of the impact of particle size to the heat transfer coefficient between biomass particles and a fluidised bed

The fluid–particle interaction and the impact of different heat transfer conditions on pyrolysis of biomass inside a 150 g/h fluidised bed reactor are modelled. Two different size biomass particles (350 µm and 550 µm in diameter) are injected into the fluidised bed. The different biomass particle sizes result in different heat transfer conditions. This is due to the fact that the 350 µm diameter particle is smaller than the sand particles of the reactor (440 µm), while the 550 µm one is larger. The bed-to-particle heat transfer for both cases is calculated according to the literature. Conductive heat transfer is assumed for the larger biomass particle (550 µm) inside the bed, while biomass–sand contacts for the smaller biomass particle (350 µm) were considered unimportant. The Eulerian approach is used to model the bubbling behaviour of the sand, which is treated as a continuum. Biomass reaction kinetics is modelled according to the literature using a two-stage, semi-global model which takes into account secondary reactions. The particle motion inside the reactor is computed using drag laws, dependent on the local volume fraction of each phase. FLUENT 6.2 has been used as the modelling framework of the simulations with the whole pyrolysis model incorporated in the form of User Defined Function (UDF).

Mechanisms of heat and mass transfer to and from single drops freely-suspended in an air stream

A specially-designed vertical wind tunnel was used to freely suspend individual liquid drops of 5 mm initial diameter to investigate drop dynamics, terminal velocity and heat and mass transfer rates. Droplets of distilled, de-ionised water, n-propanol, iso-butanol, monoethanolamine and heptane were studied over a temperature range of 50oC to 82oC. The effects of substances that may provide drop surface rigidity (e.g. surface active agents, binders and polymers) on mass transfer rates were investigated by doping distilled de-ionised water drops with sodium di-octyl sulfo-succinate surfactant. Mass transfer rates decreased with reduced drop oscillation as a result of surfactant addition, confirming the importance of droplet surface instability. Rigid naphthalene spheres and drops which formed a skin were also studied; the results confirmed the reduced transfer rates in the absence of drop fluidity. Following consideration of fundamental drop dynamics in air and experimental results from this study, a novel dimensionless group, the Oteng-Attakora, (OT), number was included in the mass transfer equation to account for droplet surface behaviour and for prediction of heat and mass transfer rates from single drops which exhibit surface instability at Re>=500. The OT number and the modified mass transfer equation are respectively: OT=(ava2/d).de1.5(d/) Sh = 2 + 0.02OT0.15Re0.88Sc0.33 Under all conditions drop terminal velocity increased linearly with the square root of drop diameter and the drag coefficient was 1. The data were correlated with a modified equation by Finlay as follows: CD=0.237.((Re/P0.13)1.55(1/We.P0.13) The relevance of the new model to practical evaporative spray processes is discussed.

The effects of relocation on Royal Air Force families

This doctoral research project examines the effects that geographical transience has on Royal Air Force families. The methodology employed in this exploratory and qualitative study consisted largely of open-ended interview questions but also included a series of demographic variables. In total, 29 RAF personnel without families, 33 RAF personnel with families, 33 RAF spouses, and 15 RAF children participated in this research (N = 110). All respondents volunteered to take part in the study and were based in the United Kingdom at the time of data collection. The interviews were transcribed and content coded according to six major relocation themes arising from the literature (change, tasks, support, coping, difficulty, and outcome). QSR NVIVO 2.0, a qualitative data analysis software package, was used to facilitate the process. Through the utilisations of qualitative methodology, the researcher was able to offer various novel and reoccurring variables that appear to play an important role (at least subjectively) in relocation. Additionally, frequencies associated with these factors were presented. The findings were integrated with those from the literature in order to offer an initial comparison and differentiation between civilian and military samples. The main theoretical contributions were the introduction of the concept of mobile mentality, the creation of a novel relocation model that takes familial interaction into account, and the development of a taxonomy for the classification of relocation outcomes. Finally, additional observations, recommendations for future research, and practical implications are reviewed.

Mass transfer coefficient for drying of moist particulate in a bubbling fluidized bed

Experiments on drying of moist particles by ambient air were carried out to measure the mass transfer coefficient in a bubbling fluidized bed. Fine glass beads of mean diameter 125?µm were used as the bed material. Throughout the drying process, the dynamic material distribution was recorded by electrical capacitance tomography (ECT) and the exit air condition was recorded by a temperature/humidity probe. The ECT data were used to obtain qualitative and quantitative information on the bubble characteristics. The exit air moisture content was used to determine the water content in the bed. The measured overall mass transfer coefficient was in the range of 0.0145–0.021?m/s. A simple model based on the available correlations for bubble-cloud and cloud-dense interchange (two-region model) was used to predict the overall mass transfer coefficient. Comparison between the measured and predicted mass transfer coefficient have shown reasonable agreement. The results were also used to determine the relative importance of the two transfer regions.

Elemental partitioning and microstructural development in duplex stainless steel weld metal

A thermodynamic analysis which is capable of estimating the austenite/ferrite equilibria in duplex stainless steels has been carried out using the sublattice thermodynamic model. The partitioning of alloying elements between the austenite and ferrite phases has been calculated as a function of temperature. The results showed that chromium partitioning was not influenced significantly by the temperature. The molybdenum, on the other hand, was found to partition preferentially into ferrite phase as the temperature decreases. A strong partitioning of nickel into the austenite was observed to decrease gradually with increasing temperature. Among the alloying elements, average nitrogen concentration was found to have the most profound effect on the phase balance and the partitioning of nitrogen into the austenite. The partitioning coefficient of nitrogen (the ratio of the mole fraction of nitrogen in the austenite to that in the ferrite) was found to be as high as 7.0 around 1300 K. Consequently, the volume fraction of austenite was influenced by relatively small additions of nitrogen. The results are compared with the experimentally observed data in a duplex stainless steel weld metal in conjunction with the solid state δ → δ + γ phase transformation. Particular attention was given to the morphological instability of grain boundary austenite allotriomorphs. A compariso between the experimental results and calculations indicated that the instability associated with irregular austenite perturbations results from the high degree of undercooling. The results suggest that the model can be used successfully to understand the development of the microstructure in duplex stainless steel weld metals.

The impact of general sales agents on the air cargo industry

A General Sales Agent (GSA) is an airline's outsourcing counter part that markets and manages cargo services. An empirical investigation is undertaken to ascertain whether GSAs contribute economically to the air cargo industry using three 'litmus test' indicators:1) contribution to the airline's sales and profitability by expanding o perating networks; 2) viability as a marketing option for emerging or struggling airlines to help cut operating costs to reduce prices; 3) cost-effective GSAs were found to establish an airline's market presence through wide network coverage and good local knowledge, leading to an expansion of airline's operating networks and generating greater sales revenue. Copyright © 2012 Inderscience Enterprises Ltd.