Gut Microbiome Integration in Drug Discovery and Development of Small Molecules.

Human microbiomes, particularly in the gut, could have a major impact on the efficacy and toxicity of drugs. However, gut microbial metabolism is often neglected in the drug discovery and development process. Medicen, a Paris-based human health innovation cluster, has gathered more than 30 international leading experts from pharma, academia, biotech, clinical research organizations, and regulatory science to develop proposals to facilitate the integration of microbiome science into drug discovery and development.

Peripheral tryptophan, serotonin, kynurenine, and their metabolites in major depression: A case-control study.

Aim: Tryptophan is the sole precursor of both peripherally and centrally produced serotonin and kynurenine. In depressed patients, tryptophan, serotonin, kynurenine, and their metabolite levels remain unclear. Therefore, peripheral tryptophan and metabolites of serotonin and kynurenine were investigated extensively in 173 patients suffering from a current major depressive episode (MDE) and compared to 214 healthy controls (HC).

Direct and quantitative evaluation of the major human CYP contribution (fmCYP) to drug clearance using the in vitro Silensomes™ model.

1. We have applied the concept of using MBIs to produce CYP-Silensomes to quantify the contribution of the major CYPs to drug metabolism (fmCYP). 2.

The human plasma-metabolome: Reference values in 800 French healthy volunteers; impact of cholesterol, gender and age.

Metabolomic approaches are increasingly used to identify new disease biomarkers, yet normal values of many plasma metabolites remain poorly defined. The aim of this study was to define the "normal" metabolome in healthy volunteers. We included 800 French volunteers aged between 18 and 86, equally distributed according to sex, free of any medication and considered healthy on the basis of their medical history, clinical examination and standard laboratory tests.

Direct and quantitative evaluation of the human CYP3A4 contribution (f) to drug clearance using the in vitro SILENSOMES model.

1. Among the different in vitro studies recommended by the regulatory agencies, no gold-standard model can easily and directly measure the quantitative CYP450 contributions to drug biotransformation. In this article, we propose an original strategy, called Silensomes, to produce human liver microsomes silenced for one specific CYP450, thanks to specific mechanism-based inhibitors (MBI).

Amyotrophic lateral sclerosis and denervation alter sphingolipids and up-regulate glucosylceramide synthase.

Amyotrophic lateral sclerosis (ALS) is a fatal adult-onset disease characterized by upper and lower motor neuron degeneration, muscle wasting and paralysis. Growing evidence suggests a link between changes in lipid metabolism and ALS. Here, we used UPLC/TOF-MS to survey the lipidome in SOD1(G86R) mice, a model of ALS.

Ultra performance liquid chromatography - mass spectrometry studies of formalin-induced alterations of human brain lipidome.

The development of 'omics' sciences offers new opportunities for the study of neurodegenerative diseases but increases at the same time the sample demand on brain banks that collect and store valuable human post-mortem tissue. Our study aims to evaluate in lipidomics the potential of formalin-fixed tissue compared with the cryopreservation method, considered as the gold standard for biochemical research. Two complementary liquid chromatography/mass spectrometry analytical platforms were used on the basis of hybrid quadrupole time-of-flight and triple quadrupole mass spectrometers.

Comparing translational population-PBPK modelling of brain microdialysis with bottom-up prediction of brain-to-plasma distribution in rat and human.

The prediction of brain extracellular fluid (ECF) concentrations in human is a potentially valuable asset during drug development as it can provide the pharmacokinetic input for pharmacokinetic-pharmacodynamic models. This study aimed to compare two translational modelling approaches that can be applied at the preclinical stage of development in order to simulate human brain ECF concentrations. A population-PBPK model of the central nervous system was developed based on brain microdialysis data, and the model parameters were translated to their corresponding human values to simulate ECF and brain tissue concentration profiles.

A physiologically based modeling strategy during preclinical CNS drug development.

Physiologically based pharmacokinetic (PBPK) modeling of the central nervous system (CNS) provides the opportunity to predict the relevant drug concentrations at the therapeutic target site during preclinical and clinical development. In order to successfully interpret model results, and to provide confidence in the subsequent human predictions, it is essential that an appropriate model structure is chosen at the preclinical stage which takes into account both physiological and drug-specific knowledge. However, the models published to date in the literature show significant variation in the approaches applied by different authors, which can lead to difficulties in the interpretation of model parameter estimates.

Physiologically based pharmacokinetic modelling of drug penetration across the blood-brain barrier--towards a mechanistic IVIVE-based approach.

Predicting the penetration of drugs across the human blood-brain barrier (BBB) is a significant challenge during their development. A variety of in vitro systems representing the BBB have been described, but the optimal use of these data in terms of extrapolation to human unbound brain concentration profiles remains to be fully exploited. Physiologically based pharmacokinetic (PBPK) modelling of drug disposition in the central nervous system (CNS) currently consists of fitting preclinical in vivo data to compartmental models in order to estimate the permeability and efflux of drugs across the BBB.

Development of a physiologically based pharmacokinetic model for the rat central nervous system and determination of an in vitro-in vivo scaling methodology for the blood-brain barrier permeability of two transporter substrates, morphine and oxycodone.

A whole-body physiologically based pharmacokinetic (PBPK) model was developed for the prediction of unbound drug concentration-time profiles in the rat brain, in which drug transfer across the blood-brain barrier (BBB) was treated mechanistically by separating the parameters governing the rate (permeability) of BBB transfer from brain binding. An in vitro-in vivo scaling strategy based on Caco-2 cell permeability was proposed to extrapolate the active transporter-driven component of this permeability, in which a relative activity factor, RAF, was estimated by fitting the model to rat in vivo profiles. This scaling factor could be interpreted as the ratio of transporter activity between the in vitro system and the in vivo BBB, for a given drug in a given in vitro system.

Pharmacometabonomic investigation of dynamic metabolic phenotypes associated with variability in response to galactosamine hepatotoxicity.

Galactosamine (galN) is widely used as an in vivo model of acute liver injury. We have applied an integrative approach, combining histopathology, clinical chemistry, cytokine analysis, and nuclear magnetic resonance (NMR) spectroscopic metabolic profiling of biofluids and tissues, to study variability in response to galactosamine following successive dosing. On re-challenge with galN, primary non-responders displayed galN-induced hepatotoxicity (induced response), whereas primary responders exhibited a less marked response (adaptive response).

Physiologically based pharmacokinetic (PBPK) modelling tools: how to fit with our needs?

In 2005, a survey compared a number of commercial PBPK software available at the time, mainly focusing on 'ready to use' modelling tools. Since then, these tools and software have been further developed and improved to allow modellers to perform WB-PBPK modelling including ADME processes at a high level of sophistication. This review presents a comparison of the features, values and limitations of both the 'ready to use' software and of the traditional user customizable software that are frequently used for the building and use of PBPK models, as well as the challenges associated with the various modelling approaches regarding their current and future use.

Optimized preprocessing of ultra-performance liquid chromatography/mass spectrometry urinary metabolic profiles for improved information recovery.

Ultra-performance liquid chromatography coupled to mass spectrometry (UPLC/MS) has been used increasingly for measuring changes of low molecular weight metabolites in biofluids/tissues in response to biological challenges such as drug toxicity and disease processes. Typically samples show high variability in concentration, and the derived metabolic profiles have a heteroscedastic noise structure characterized by increasing variance as a function of increased signal intensity. These sources of experimental and instrumental noise substantially complicate information recovery when statistical tools are used.

Metabonomic studies on human hepatocyte in primary culture.

Mechanisms involved in induction processes have been investigated using fresh human hepatocytes in culture as a cellular model and using mass spectrometry-based metabonomics as a global investigation tool. Sample preparation to data analysis have been detailed in an approach enabling to separate drug-induced (endogenous metabolites) and drug-related (drug metabolites) biomarkers for reference inducers. Rifampicin, a nuclear pregnane X receptor (PXR) ligand; CITCO, a nuclear constitutive androstane receptor (CAR) ligand; and phenobarbital, which activates both CAR and PXR, have been used.

[Chemoinformatics and virtual screening of molecules for therapeutic use].

Successful identification of new chemical entities with drug-like properties in pharmaceutical and academic research groups involves an early screen and the use of a large number of public and proprietary chemical libraries. Before applying high-throughput experimental screening approaches, virtual screening strategies have been put in place in order to sort and filter this massive amount of compounds and data available at these very early stages. Chemoinformatic tools have a crucial role in this selection process and enable therapeutic chemists to focus very early on promising candidates.

Integrated comparison of drug-related and drug-induced ultra performance liquid chromatography/mass spectrometry metabonomic profiles using human hepatocyte cultures.

The biochemical variations induced in human primary hepatocyte cultures by reference activators of xenoreceptor CAR (NR1I3) and PXR (NR1I2), i.e., rifampicin, phenobarbital, and 6-(4-chlorophenyl)imidazo[2,1-b] [1,3]thiazole-5-carbaldehyde O-3,4-dichlorobenzyl) oxime (CITCO), were investigated using a global metabonomics approach.

[Biomarkers: "Found in translation"].

Despite continued increase in global Pharma R & D expenditure, the number of innovative drugs obtaining market approval has declined since 1994. The pharmaceutical industry is now entering a crucial juncture where increasing rates of attrition in clinical drug development as well as increasing development timelines are impacted by external factors such as intense regulatory pricing and safety pressures, increasing sales erosion due to generics, as well as exponential increases in the costs of bringing a drug to market. Despite these difficulties, numerous opportunities exist such as multiple unmet medical needs, the increasing incidence of certain diseases such as Alzheimer's disease, cancer, diabetes and obesity due to demographic changes, as well as the emergence of evolving markets such as China, India, and Eastern Europe.

Development of an in vitro rat intestine segmental perfusion model to investigate permeability and predict oral fraction absorbed.

Purpose: The aims of the study are to develop and evaluate an in vitro rat intestine segmental perfusion model for the prediction of the oral fraction absorbed of compounds and to assess the ability of the model to study intestinal metabolism.

Methods: The system consisted of a perfusion cell with a rat intestinal segment and three perfusion circulations (donor, receiver, and rinsing circulation). Lucifer yellow (LY) was applied as internal standard together with test compounds in the donor circulation.

Characterization of microsomal cytochrome P450-dependent monooxygenases in the rat olfactory mucosa.

Nasal administration of a drug ensures therapeutic action by rapid systemic absorption and/or the entry of some molecules into the brain through different routes. Many recent studies have pointed out the presence of xenobiotic-metabolizing enzymes in rat olfactory mucosa (OM). Nevertheless, very little is known about the precise identity of isoforms of cytochrome P450 (P450)-dependent monooxygenases (P450) and their metabolic function in this tissue.