iLOGP: A Simple, Robust, and Efficient Description of n-Octanol/Water Partition Coefficient for Drug Design Using the GB/SA Approach.

The n-octanol/water partition coefficient (log Po/w) is a key physicochemical parameter for drug discovery, design, and development. Here, we present a physics-based approach that shows a strong linear correlation between the computed solvation free energy in implicit solvents and the experimental log Po/w on a cleansed data set of more than 17,500 molecules. After internal validation by five-fold cross-validation and data randomization, the predictive power of the most interesting multiple linear model, based on two GB/SA parameters solely, was tested on two different external sets of molecules. On the Martel druglike test set, the predictive power of the best model (N = 706, r = 0.64, MAE = 1.18, and RMSE = 1.40) is similar to six well-established empirical methods. On the 17-drug test set, our model outperformed all compared empirical methodologies (N = 17, r = 0.94, MAE = 0.38, and RMSE = 0.52). The physical basis of our original GB/SA approach together with its predictive capacity, computational efficiency (1 to 2 s per molecule), and tridimensional molecular graphics capability lay the foundations for a promising predictor, the implicit log P method (iLOGP), to complement the portfolio of drug design tools developed and provided by the SIB Swiss Institute of Bioinformatics.

Octanol-water partition coefficients for predicting the effects of tannins in ruminant nutrition

Tannins can cause beneficial or harmful nutritional effects, but their great diversity has until now prevented a rational distinction between tannin structures and their nutritional responses. An attempt has been made to study this problem by examining the octanol-water solubilities of tannins. A relatively simple HPLC method has been developed for screening mixtures of plant tannins for their octanol-water partition coefficients (K-ow coefficients). Tannins were isolated from the fruits and leaves of different Acacia, Calliandra, Dichrostachys, and Piliostigma species, which are known to produce beneficial or harmful effects. The K-ow coefficients of these tannins ranged from 0.061 to 13.9, average coefficients of variation were 9.2% and recoveries were 107%. Acacia nilotica fruits and leaves had the highest K-ow coefficients, that is, 2.0 and 13.9, respectively. These A. nilotica products also have high concentrations of tannins. The combined effects of high octanol solubilities and high tannin concentrations may explain their negative effects on animal nutrition and health. It is known that compounds with high octanol solubilities are more easily absorbed into tissues, and it is, therefore, proposed that such compounds are more likely to cause toxicity problems especially if consumed in large quantities. According to the literature, tannins in human foods tend to have low K-ow coefficients, and this was confirmed for the tannins in Piliostigma thonningii fruits. Therefore, unconventional feeds or browse products should be screened not only for their tannin concentrations but also for low octanol-water partition coefficients in order to identify nutritionally safe feeds and to avoid potentially toxic feeds.

New magnetic nano-absorbent for the determination of n-octanol/water partition coefficients

A novel and generic miniaturization methodology for the determination of partition coefficient values of organic compounds in noctanol/water by using magnetic nanoparticles is, for the first time, described. We have successfully designed, synthesised and characterised new colloidal stable porous silica-encapsulated magnetic nanoparticles of controlled dimensions. These nanoparticles absorbing a tiny amount of n-octanol in their porous silica over-layer are homogeneously dispersed into a bulk aqueous phase (pH 7.40) containing an organic compound prior to magnetic separation. The small size of the particles and the efficient mixing allow a rapid establishment of the partition equilibrium of the organic compound between the solid supported n-octanol nano-droplets and the bulk aqueous phase. UV-vis spectrophotometry is then applied as a quantitative method to determine the concentration of the organic compound in the aqueous phase both before and after partitioning (after magnetic separation). log D values of organic compounds of pharmaceutical interest (0.65-3.50), determined by this novel methodology, were found to be in excellent agreement with the values measured by the shake-flask method in two independent laboratories, which are also consistent with the literature data. It was also found that this new technique gives a number of advantages such as providing an accurate measurement of log D value, a much shorter experimental time and a smaller sample size required. With this approach, the formation of a problematic emulsion, commonly encountered in shake-flask experiments, is eliminated. It is envisaged that this method could be applicable to the high throughput log D screening of drug candidates. (c) 2005 Elsevier B.V. All rights reserved.

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.

Determination of octanol/water distribution coefficients, water solubilities, and sediment/water partition coefficients for hydrophobic organic pollutants /

Mode of access: Internet.

A New Approach to the Prediction of Partition Coefficients in Water/Organic Interfaces

In the present work, a new approach for the determination of the partition coefficient in different interfaces based on the density function theory is proposed. Our results for log P(ow) considering a n-octanol/water interface for a large super cell for acetone -0.30 (-0.24) and methane 0.95 (0.78) are comparable with the experimental data given in parenthesis. We believe that these differences are mainly related to the absence of van der Walls interactions and the limited number of molecules considered in the super cell. The numerical deviations are smaller than that observed for interpolation based tools. As the proposed model is parameter free, it is not limited to the n-octanol/water interface.

Estudo do coeficiente de partição octanol-água de bifenilas policloradas (PCBs) utilizando parâmetros topológicos

A model based on chemical structure was developed for the accurate prediction of octanol/water partition coefficient (K OW) of polychlorinated biphenyls (PCBs), which are molecules of environmental interest. Partial least squares (PLS) was used to build the regression model. Topological indices were used as molecular descriptors. Variable selection was performed by Hierarchical Cluster Analysis (HCA). In the modeling process, the experimental K OW measured for 30 PCBs by thin-layer chromatography - retention time (TLC-RT) has been used. The developed model (Q² = 0,990 and r² = 0,994) was used to estimate the log K OW values for the 179 PCB congeners whose K OW data have not yet been measured by TLC-RT method. The results showed that topological indices can be very useful to predict the K OW.

QSAR Modeling of a Set of Pyrazinoate Esters as Antituberculosis Prodrugs

Tuberculosis is an infection caused mainly by Mycobacterium tuberculosis. A first-line antimycobacterial drug is pyrazinamide (PZA), which acts partially as a prodrug activated by a pyrazinamidase releasing the active agent, pyrazinoic acid (POA). As pyrazinoic acid presents some difficulty to cross the mycobacterial cell wall, and also the pyrazinamide-resistant strains do not express the pyrazinamidase, a set of pyrazinoic acid esters have been evaluated as antimycobacterial agents. In this work, a QSAR approach was applied to a set of forty-three pyrazinoates against M. tuberculosis ATCC 27294, using genetic algorithm function and partial least squares regression (WOLF 5.5 program). The independent variables selected were the Balaban index (I), calculated n-octanol/water partition coefficient (ClogP), van-der-Waals surface area, dipole moment, and stretching-energy contribution. The final QSAR model (N = 32, r(2) = 0.68, q(2) = 0.59, LOF = 0.25, and LSE = 0.19) was fully validated employing leave-N-out cross-validation and y-scrambling techniques. The test set (N = 11) presented an external prediction power of 73%. In conclusion, the QSAR model generated can be used as a valuable tool to optimize the activity of future pyrazinoic acid esters in the designing of new antituberculosis agents.

Cationic drug pharmacokinetics in diseased livers determined by fibrosis index, hepatic protein content, microsomal activity, and nature of drug

The disposition kinetics of six cationic drugs in perfused diseased and normal rat livers were determined by multiple indicator dilution and related to the drug physicochemical properties and liver histopathology. A carbon tetrachloride (CCl4)induced acute hepatocellular injury model had a higher fibrosis index (FI), determined by computer-assisted image analysis, than did an alcohol-induced chronic hepatocellular injury model. The alcohol-treated group had the highest hepatic alpha(1)- acid glycoprotein, microsomal protein (MP), and cytochrome P450 (P450) concentrations. Various pharmacokinetic parameters could be related to the octanol-water partition coefficient (log P-app) of the drug as a surrogate for plasma membrane partition coefficient and affinity for MP or P450, the dependence being lower in the CCl4-treated group and higher in the alcohol-treated group relative to controls. Stepwise regression analysis showed that hepatic extraction ratio, permeability-surface area product, tissue-binding constant, intrinsic clearance, partition ratio of influx (k(in)) and efflux rate constant (k(out)), and k(in)/k(out) were related to physicochemical properties of drug (log P-app or pK(a)) and liver histopathology (FI, MP, or P450). In addition, hepatocyte organelle ion trapping of cationic drugs was evident in all groups. It is concluded that fibrosis-inducing hepatic disease effects on cationic drug disposition in the liver may be predicted from drug properties and liver histopathology.

Study on solubility of pharmaceutical compounds in ionic liquids

Dissertation to obtain the degree of master in Chemical and Biochemical Engineering

The value of selected in vitro and in silico methods to predict acute oral toxicity in a regulatory context: results from the European Project ACuteTox.

ACuteTox is a project within the 6th European Framework Programme which had as one of its goals to develop, optimise and prevalidate a non-animal testing strategy for predicting human acute oral toxicity. In its last 6 months, a challenging exercise was conducted to assess the predictive capacity of the developed testing strategies and final identification of the most promising ones. Thirty-two chemicals were tested blind in the battery of in vitro and in silico methods selected during the first phase of the project. This paper describes the classification approaches studied: single step procedures and two step tiered testing strategies. In summary, four in vitro testing strategies were proposed as best performing in terms of predictive capacity with respect to the European acute oral toxicity classification. In addition, a heuristic testing strategy is suggested that combines the prediction results gained from the neutral red uptake assay performed in 3T3 cells, with information on neurotoxicity alerts identified by the primary rat brain aggregates test method. Octanol-water partition coefficients and in silico prediction of intestinal absorption and blood-brain barrier passage are also considered. This approach allows to reduce the number of chemicals wrongly predicted as not classified (LD50>2000 mg/kg b.w.).

A database to aid the identification of chemicals potentially posing a health risk through percutaneous exposure

In the context of recent attempts to redefine the 'skin notation' concept, a position paper summarizing an international workshop on the topic stated that the skin notation should be a hazard indicator related to the degree of toxicity and the potential for transdermal exposure of a chemical. Within the framework of developing a web-based tool integrating this concept, we constructed a database of 7101 agents for which a percutaneous permeation constant can be estimated (using molecular weight and octanol-water partition constant), and for which at least one of the following toxicity indices could be retrieved: Inhalation occupational exposure limit (n=644), Oral lethal dose 50 (LD50, n=6708), cutaneous LD50 (n=1801), Oral no observed adverse effect level (NOAEL, n=1600), and cutaneous NOAEL (n=187). Data sources included the Registry of toxic effects of chemical substances (RTECS, MDL information systems, Inc.), PHYSPROP (Syracuse Research Corp.) and safety cards from the International Programme on Chemical Safety (IPCS). A hazard index, which corresponds to the product of exposure duration and skin surface exposed that would yield an internal dose equal to a toxic reference dose was calculated. This presentation provides a descriptive summary of the database, correlations between toxicity indices, and an example of how the web tool will help industrial hygienist decide on the possibility of a dermal risk using the hazard index.

Steroidien selektiivinen erottaminen sähköavusteisesti mikroemulsioita käyttäen

Mikroemulsiosähkökineettinen kromatografia on sähköavusteinen erotusmenetelmä. Yhdisteiden erottuminen tapahtuu mikroemulsiopisaroiden vaikutuksesta, kun nanometrien kokoiset öljypisarat ovat dispergoituneena veteen valmistettuun puskuriliuokseen. Yleensä mikroemulsiot valmistetaan raakaöljynkin sisältämistä hiilivedyistä, joita ovat esimerkiksi oktaani ja heptaani. Työn kokeellisessa osassa perehdyttiin seitsemän hydrofobisen ja varauksettoman steroidihormonin erottamiseen mikroemulsioliuoksessa kapillaarielektroforeesitekniikalla. Työssä valmistettiin öljyistä koostuvia mikroemulsioita, joista osan koostumus valittiin kirjallisuuden perusteella. Työssä kokeiltiin myös uusia mikroemulsiokoostumuksia, joissa käytettiin luonnosta peräisin olevia öljyjä: rypsi-, oliivi-, pellavansiemen- ja saksanpähkinäöljyä. Seitsemästä steroidihormonista viisi yhdistettä saatiin erottumaan optimoiduilla menetelmillä. Steroidien erotus perustuu niiden oktanoli-vesi jakautumiskertoimien avulla saatavaan migraatiojärjestykseen. Mikroemulsiossa, jossa käytettiin 1-oktanolia, steroidihormonit erottuivat nopeammin, kuin saksanpähkinäöljyä käytettäessä. Lyhyimmät migraatioajat saatiin mikroemulsiolla, jossa öljyfaasina käytettiin 1-heksanolia ja viidentenä yhdisteenä asetonitriiliä. Selektiivisimmillään menetelmä on, kun erotus tapahtuu liuoksessa, joka koostuu etyyliasetaatista, natriumdodekyylisulfaatista, butanolista, asetonitriilistä ja natriumtetraboraatista. Toteamisrajat tutkituille steroidihormoneille olivat 0,20–0,43 mg/L mikroemulsioissa.