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.

Towards the validation of "in silico" models and physicochemical filters to identify and characterize new chemical entities

Summary: Lipophilicity plays an important role in the determination and the comprehension of the pharmacokinetic behavior of drugs. It is usually expressed by the partition coefficient (log P) in the n-octanol/water system. The use of an additional solvent system (1,2-dichlorethane/water) is necessary to obtain complementary information, as the log Poct values alone are not sufficient to explain ail biological properties. The aim of this thesis is to develop tools allowing to predict lipophilicity of new drugs and to analyze the information yielded by those log P values. Part I presents the development of theoretical models used to predict lipophilicity. Chapter 2 shows the necessity to extend the existing solvatochromic analyses in order to predict correctly the lipophilicity of new and complex neutral compounds. In Chapter 3, solvatochromic analyses are used to develop a model for the prediction of the lipophilicity of ions. A global model was obtained allowing to estimate the lipophilicity of neutral, anionic and cationic solutes. Part II presents the detailed study of two physicochemical filters. Chapter 4 shows that the Discovery RP Amide C16 stationary phase allows to estimate lipophilicity of the neutral form of basic and acidic solutes, except of lipophilic acidic solutes. Those solutes present additional interactions with this particular stationary phase. In Chapter 5, 4 different IANI stationary phases are investigated. For neutral solutes, linear data are obtained whatever the IANI column used. For the ionized solutes, their retention is due to a balance of electrostatic and hydrophobie interactions. Thus no discrimination is observed between different series of solutes bearing the same charge, from one column to an other. Part III presents two examples illustrating the information obtained thanks to Structure-Properties Relationships (SPR). Comparing graphically lipophilicity values obtained in two different solvent systems allows to reveal the presence of intramolecular effects .such as internai H-bond (Chapter 6). SPR is used to study the partitioning of ionizable groups encountered in Medicinal Chemistry (Chapter7). Résumé La lipophilie joue un .rôle important dans la détermination et la compréhension du comportement pharmacocinétique des médicaments. Elle est généralement exprimée par le coefficient de partage (log P) d'un composé dans le système de solvants n-octanol/eau. L'utilisation d'un deuxième système de solvants (1,2-dichloroéthane/eau) s'est avérée nécessaire afin d'obtenir des informations complémentaires, les valeurs de log Poct seules n'étant pas suffisantes pour expliquer toutes les propriétés biologiques. Le but de cette thèse est de développer des outils permettant de prédire la lipophilie de nouveaux candidats médicaments et d'analyser l'information fournie par les valeurs de log P. La Partie I présente le développement de modèles théoriques utilisés pour prédire la lipophilie. Le chapitre 2 montre la nécessité de mettre à jour les analyses solvatochromiques existantes mais inadaptées à la prédiction de la lipophilie de nouveaux composés neutres. Dans le chapitre 3, la même méthodologie des analyses solvatochromiques est utilisée pour développer un modèle permettant de prédire la lipophilie des ions. Le modèle global obtenu permet la prédiction de la lipophilie de composés neutres, anioniques et cationiques. La Partie II présente l'étude approfondie de deux filtres physicochimiques. Le Chapitre 4 montre que la phase stationnaire Discovery RP Amide C16 permet la détermination de la lipophilie de la forme neutre de composés basiques et acides, à l'exception des acides très lipophiles. Ces derniers présentent des interactions supplémentaires avec cette phase stationnaire. Dans le Chapitre 5, 4 phases stationnaires IAM sont étudiées. Pour les composés neutres étudiés, des valeurs de rétention linéaires sont obtenues, quelque que soit la colonne IAM utilisée. Pour les composés ionisables, leur rétention est due à une balance entre des interactions électrostatiques et hydrophobes. Donc aucune discrimination n'est observée entre les différentes séries de composés portant la même charge d'une colonne à l'autre. La Partie III présente deux exemples illustrant les informations obtenues par l'utilisation des relations structures-propriétés. Comparer graphiquement la lipophilie mesurée dans deux différents systèmes de solvants permet de mettre en évidence la présence d'effets intramoléculaires tels que les liaisons hydrogène intramoléculaires (Chapitre 6). Cette approche des relations structures-propriétés est aussi appliquée à l'étude du partage de fonctions ionisables rencontrées en Chimie Thérapeutique (Chapitre 7) Résumé large public Pour exercer son effet thérapeutique, un médicament doit atteindre son site d'action en quantité suffisante. La quantité effective de médicament atteignant le site d'action dépend du nombre d'interactions entre le médicament et de nombreux constituants de l'organisme comme, par exemple, les enzymes du métabolisme ou les membranes biologiques. Le passage du médicament à travers ces membranes, appelé perméation, est un paramètre important à optimiser pour développer des médicaments plus puissants. La lipophilie joue un rôle clé dans la compréhension de la perméation passive des médicaments. La lipophilie est généralement exprimée par le coefficient de partage (log P) dans le système de solvants (non miscibles) n-octanol/eau. Les valeurs de log Poct seules se sont avérées insuffisantes pour expliquer la perméation à travers toutes les différentes membranes biologiques du corps humain. L'utilisation d'un système de solvants additionnel (le système 1,2-dichloroéthane/eau) a permis d'obtenir les informations complémentaires indispensables à une bonne compréhension du processus de perméation. Un grand nombre d'outils expérimentaux et théoriques sont à disposition pour étudier la lipophilie. Ce travail de thèse se focalise principalement sur le développement ou l'amélioration de certains de ces outils pour permettre leur application à un champ plus large de composés. Voici une brève description de deux de ces outils: 1)La factorisation de la lipophilie en fonction de certaines propriétés structurelles (telle que le volume) propres aux composés permet de développer des modèles théoriques utilisables pour la prédiction de la lipophilie de nouveaux composés ou médicaments. Cette approche est appliquée à l'analyse de la lipophilie de composés neutres ainsi qu'à la lipophilie de composés chargés. 2)La chromatographie liquide à haute pression sur phase inverse (RP-HPLC) est une méthode couramment utilisée pour la détermination expérimentale des valeurs de log Poct.

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.).

Involvement of connexin 43 in meiotic maturation of bovine oocytes.

In ovarian follicles, cumulus cells provide the oocyte with small molecules that permit growth and control maturation. These nutrients reach the germinal cell through gap junction channels, which are present between the cumulus cells and the oocyte, and between the cumulus cells. In this study the involvement of intercellular communication mediated by gap junction channels on oocyte maturation of in vitro cultured bovine cumulus-oocyte complexes (COCs) was investigated. The stages of oocyte maturation were determined by Hoechst 33342 staining, which showed that 90% of COCs placed in the maturation medium for 24 h progress to the metaphase II stage. Bovine COC gap junction communication was disrupted initially using n-alkanols, which inhibit any passage through gap junctions. In the presence of 1-heptanol (3 mmol l(-1)) or octanol (3.0 mmol l(-1) and 0.3 mmol l(-1)), only 29% of the COCs reached metaphase II. Removal of the uncoupling agent was associated with restoration of oocyte maturation, indicating that treatment with n-alkanols was neither cytotoxic nor irreversible. Concentrations of connexin 43 (Cx43), the major gap junction protein expressed in the COCs, were decreased specifically using a recombinant adenovirus expressing the antisense Cx43 cDNA (Ad-asCx43). The efficacy of adenoviral infection was > 95% in cumulus cells evaluated after infection with recombinant adenoviruses expressing the green fluorescence protein. RT-PCR performed on total RNA isolated from Ad-asCx43-infected COCs showed that the rat Cx43 cDNA was transcribed. Western blot analysis revealed a three-fold decrease in Cx43 expression in COCs expressing the antisense RNA for Cx43. Injection of cumulus cells with Lucifer yellow demonstrated further that the resulting lower amount of Cx43 in infected COCs is associated with a two-fold decrease in the extent of coupling between cumulus cells. In addition, oocyte maturation was decreased by 50% in the infected COC cultures. These results indicate that Cx43-mediated communication between cumulus cells plays a crucial role in maturation of bovine oocytes.

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.

Effect of water velocity on the uptake of polychlorinatedd biphenyls (PCBs) by silicone rubber (SR) and low-density polyethylene (LDPE) passive samplers: an assessment of the efficiency of performance reference compounds (PRCs) in river-like flow conditions

One aim of this study is to determine the impact of water velocity on the uptake of indicator polychlorinated biphenyls (iPCBs) by silicone rubber (SR) and low-density polyethylene (LDPE) passive samplers. A second aim is to assess the efficiency of performance reference compounds (PRCs) to correct for the impact of water velocity. SR and LDPE samplers were spiked with 11 or 12 PRCs and exposed for 6 weeks to four different velocities (in the range of 1.6 to 37.7 cm s−1) in river-like flow conditions using a channel system supplied with river water. A relationship between velocity and the uptakewas found for each iPCB and enables to determine expected changes in the uptake due to velocity variations. For both samplers, velocity increases from 2 to 10 cm s−1, 30 cm s−1 (interpolated data) and 100 cm s−1 (extrapolated data) lead to increases of the uptake which do not exceed a factor of 2, 3 and 4.5, respectively. Results also showed that the influence of velocity decreased with increasing the octanol-water coefficient partition (log Kow) of iPCBs when SR is used whereas the opposite effect was observed for LDPE. Time-weighted average (TWA) concentrations of iPCBs in water were calculated from iPCB uptake and PRC release. These calculations were performed using either a single PRC or all the PRCs. The efficiency of PRCs to correct the impact of velocity was assessed by comparing the TWA concentrations obtained at the four tested velocities. For SR, a good agreement was found among the four TWA concentrations with both methods (average RSD b 10%). Also for LDPE, PRCs offered a good correction of the impact of water velocity (average RSD of about 10 to 20%). These results contribute to the process of acceptance of passive sampling in routine regulatory monitoring programs.