The impact of the intestine in determining the oral bioavailability of drugs has been extensively studied. Its large surface area, metabolic content and positioning at the first site of exposure for orally ingested xenobiotics means its contribution can be significant for certain drugs. However, prediction of the exact metabolic component of the intestine is limited, in part due to limitations in validation of in vitro tools as well as in vitro-in vivo extrapolation scaling factors. Microsomes are a well established in vitro tool for extrapolating hepatic metabolism, however standardised methodologies for preparation in the intestine are limited, in light of complexities in preparation (e.g. presence of multiple non-metabolic cells, proteases and mucus). Therefore, the aims of this study were to establish an optimised method of intestinal microsome preparation via elution in the proximal rat intestine, and to determine microsomal scaling factors by correcting for protein losses during preparation. In addition, to assess species in another preclinical species (dog) and human as well as assessing and regional differences in scaling factors and metabolism. Following optimisation of a reproducible intestinal microsome preparation method in the rat, the importance of heparin in limiting mucosal contamination was established. These microsomes were characterised for total cytochrome P450 (CYP) content, and CYP and uridine 5′-diphosphate glucuronosyltransferase (UGT) activities using maker probes of testosterone and 4-nitrophenol. Loss corrected microsomal scaling factors between two pools of n=9 rats was 9.6±3.5 (recovery 33%). A broad range of compounds (n=25) in terms of metabolic activity and physicochemical properties were screened in rat intestinal microsomes. The prediction accuracy relative to in house generated or literature in vivo estimates of the fraction escaping intestinal metabolism (FG) through in vitro-in vivo extrapolation of observed metabolism and the derived scaling factors and either Caco-2 permeability of physicochemical permeability estimates utilising the Qgut model. In the dog, regional differences in intestinal scaling factors and metabolic activities were explored, as well as relationships between the proximal intestine and liver in matched donors. Positive correlations in both hepatic activity and microsomal scalars were observed. Robust scaling factors were established using the 3 microsomal markers. A total of 24 compounds were screened for hepatic and intestinal metabolism in order to make in vivo estimates of FG, the fraction escaping hepatic metabolism (FH) and oral bioavailability (F). Estimates based on Caco-2 and physicochemical based scaling, as well as utilising a commercial PBPK software platform (ADAM model, Simcyp® v12) were broadly similar with generally reduced prediction accuracy in proximal physicochemical based Qgut scaling, and improved predictions using Caco-2 Qgut or PBPK approaches. Worse predictions were observed for compounds with high protein binding, transporter substrates and/or CYP3A inhibitors. Regional metabolism demonstrated peak metabolism in the proximal intestine, before declining distally. Human intestinal microsomes were prepared for jejunum and ileum tissue. Although samples were limited, regional differences in metabolic activities and scaling factors were also assessed, using correction markers and activity in 23 compounds. In all, 20 compounds overlapped between all three species. Comparison in Fa.FG between rat and human CYP3A substrates showed a modest relationship, however relationships between species and human were generally poor given the observed differing metabolic contributions of testosterone and 4-NP metabolite formation between species limited the observed relationships between species. However, within species, good estimates of oral bioavailability were observed. This is the largest know interspecies comparison of intestinal metabolism and scaling factors with microsomes prepared within the same lab.

The majority of drugs available on the market are intended to be administered through the oral route. To achieve the desired therapeutic effect, an orally administered drug must first reach the systemic circulation and then its site of action. The fraction of the administered drug that reaches the systemic circulation is known as oral bioavailability and it is the product of the absorption and first-pass metabolism processes occurring in both the GI tract and the liver. The factors controlling bioavailability are manifold –both drug and physiologically related - and their complex interplay is key to defining a drug’s oral bioavailability. In drug discovery and development it is therefore pivotal to anticipate and understand the bioavailability of a drug candidate; a far from simple task, considering the multifactorial nature of the process. For that reason, the overall aim of this thesis was to provide different modelling and simulation (M&S) strategies that can be used for the prediction of oral bioavailability that can be of use in drug discovery and development. The first part of this thesis was focused on the evaluation of the use of bioavailability data obtained from pre-clinical species as a predictor of the human value, in a more traditional approach. In particular, the aim was to evaluate models that can quantitatively and qualitatively provide a relationship between animal and human bioavailability, by analysing trends in a large bioavailability dataset. This section demonstrated that although pre-clinical species cannot quantitatively predict bioavailability, the data obtained from them can be used for qualitative prediction of the human value. Nevertheless, such a modelling approach does not provide a mechanistic rationale of the factors affecting the bioavailability differences. Consequently, the second part of this thesis was focused on such mechanistic predictions. Particularly, we investigated the impact that drug release patterns can have on drug absorption and intestinal first pass metabolism, taking into account the physiological differences observed across the length of the human gastrointestinal (GI) tract. These release patterns are suspected to lead to bioavailability differences due to changes in the first-pass metabolism, especially for CYP3A substrates. Therefore we investigated this phenomenon applying a physiologically-based pharmacokinetic (PBPK) M&S approach: firstly, from the discovery point of view, using PBPK models in a prospective fashion to investigating the drug-related factors that might lead to such differences and secondly, from the development point of view, to predict the mechanistic differences in absorption and metabolism of oxybutynin, a drug known for its higher bioavailability when formulated as a modified release (MR) product. The latter was done by developing and applying a novel simplified PBPK model to predict such differences. The results of this work showed that the intestinal metabolism can be significantly reduced when having MR formulations of CYP3A substrates which, in some cases, can lead to higher relative bioavailability. Additionally, this thesis provided novel methods and models that have the potential to improve bioavailability predictions when using PBPK models, in particular for drugs formulated as MR.

Le développement de méthodes in vitro fiables et prédictives représente à l’heure actuelle un véritable défi. En effet, la demande en méthodes alternatives à l’expérimentation animale n’a cessé de croître ces dernières années du fait de la mise en place de législations limitant par considérations éthiques l’utilisation de ces modèles in vivo. De plus, ce besoin a été renforcé par le règlement européen REACH (Registration, Evaluation, Authorization and Restriction of Chemicals) imposant aux industriels de valider l’innocuité de nombreuses substances déjà commercialisées. Toutefois, les modèles in vitro classiques consistant en la culture simple de cellules en monocouche dans des boîtes de Petri ne permettent pas de conserver les propriétés initiales de ces cellules et de retranscrire les conditions et l’environnement cellulaire des organes in vivo. Le développement de méthodes alternatives in vitro prédictives s’avèrent donc crucial en particulier pour mimer le fonctionnement de deux organes : l’intestin et le foie. En effet, ces deux organes sont largement impliqués dans les processus d’Absorption, Distribution, Métabolisme et Excrétion (ADME) de la plupart des xénobiotiques ingérés. C’est pour ces raisons que nous avons testé la faisabilité de l’une de ces méthodes in vitro alternative permettant d’associer une barrière intestinale à la culture dynamique de cellules hépatiques au sein de microsystèmes dans le cadre de ce doctorat. Cette coculture est effectuée au sein du dispositif appelé IIDMP (Integrated Insert in a Dynamic Microfluidic Platform). Nous avons décidé de tester d’une part l’influence de la culture dynamique et d’autre part d’éventuelles interactions entre les cellules intestinales et hépatiques sur la fonctionnalité et l’activité métabolique de ces deux types cellulaires. Les résultats obtenus durant ce doctorat ont permis d’atteindre 4 objectifs :- Développer un dispositif fiable en termes de fonctionnalité (fluidique, robustesse…).- Mettre en évidence l’innocuité du dispositif lorsque des cellules de lignée et primaires y étaient cultivées.- Démontrer les avantages de l’utilisation de ce dispositif comparativement à l’utilisation de modèles classiques in vitro, en particulier avec des cellules de lignée.- Démontrer que l’utilisation de ce dispositif permettait de mettre en évidence des phénomènes d’interactions entre cellules intestinales et hépatiques notamment sur l’activité du CYP1A2 des hépatocytes qu’ils soient issus d’une lignée ou de cultures primaires. / The development of reliable and predictive in vitro methods is a real challenge. Indeed, the demand for alternative methods to animal experimentation has been growing in recent years due to the introduction of legislation limiting the use of these models in vivo by ethical considerations. Moreover, this need was amplified by regulations such as the European REACH (Registration, Evaluation, Authorization and Restriction of Chemicals) requiring the safety validation of many substances. However, the conventional in vitro model consisting in a simple cell culture monolayer in Petri dishes does not preserve the initial properties of these cells and does not mimic the conditions of the cellular environment and organs in vivo. The development of alternative in vitro predictive methods is crucial especially to mimic the working of two organs: the intestine and liver. Indeed, these two organs are involved in the process of Absorption, Distribution, Metabolism and Excretion (ADME) of most xenobiotics ingested.We propose in this thesis to test the feasibility of one of these in vitro alternative methods allowing the association between an intestinal barrier and the dynamic culture of hepatic cells in microsystems in a device called IIDMP (Integrated Dynamic Insert in a Microfluidic Platform). We tested the influence of the flow of culture and possible interactions between intestinal and liver cells on the function and metabolic activity of these two cell types.Then, we demonstrated that : - This device is reliable in terms of global functionality (fluid, robustness ...).- This device did not injury the integrity of the cell line and primary cells.- The use of this device has many advantages when compared with the use of conventional in vitro models, especially with cells line.- The use of this device highlights phenomena of interaction between hepatic and intestinal cells as an increase of the CYP1A2 activity of HepG2 C3A and human primary hepatocytes.