Drug interaction with UDP-Glucuronosyltransferase (UGT) enzymes is a predictor of drug-induced liver injury.

BACKGROUND AND AIMS: DILI frequently contributes to the attrition of new drug candidates and is a common cause for the withdrawal of approved drugs from the market. Although some noncytochrome P450 (non-CYP) metabolism enzymes have been implicated in DILI development, their association with DILI outcomes has not been systematically evaluated. APPROACH AND RESULTS: In this study, we analyzed a large data set comprising 317 drugs and their interactions in vitro with 42 non-CYP enzymes as substrates, inducers, and/or inhibitors retrieved from historical regulatory documents using multivariate logistic regression. We examined how these in vitro drug-enzyme interactions are correlated with the drugs' potential for DILI concern, as classified in the Liver Toxicity Knowledge Base database. Our study revealed that drugs that inhibit non-CYP enzymes are significantly associated with high DILI concern. Particularly, interaction with UDP-glucuronosyltransferases (UGT) enzymes is an important predictor of DILI outcomes. Further analysis indicated that only pure UGT inhibitors and dual substrate inhibitors, but not pure UGT substrates, are significantly associated with high DILI concern. CONCLUSIONS: Drug interactions with UGT enzymes may independently predict DILI, and their combined use with the rule-of-two model further improves overall predictive performance. These findings could expand the currently available tools for assessing the potential for DILI in humans.

Metabolic-based drug-drug interactions prediction, recent approaches for risk assessment along drug development.

Prediction of in vivo drug-drug interactions (DDIs) from in vitro and in vivo data, also named in vitro in vivo extrapolation (IVIVE), is of interest to scientists involved in the discovery and development of drugs. To avoid detrimental DDIs in humans, new drug candidates should be evaluated for their possible interaction with other drugs as soon as possible, not only as an inhibitor or inducer (perpetrator) but also as a substrate (victim). DDI risk assessment is addressed along the drug development program through an iterative process as the features of the new compound entity are revealed. Both in vitro and preclinical/clinical outcomes are taken into account to better understand the behavior of the developed compound and to refine DDI predictions. During the last decades, several equations have been proposed in the literature to predict DDIs, from a quantitative point of view, showing a substantial improvement in the ability to predict metabolism-based in vivo DDIs. Mechanistic and dynamic approaches have been proposed to predict the magnitude of metabolic-based DDIs. The purpose of this article is to provide an overview of the current equations and methods, the pros and cons of each method, the required input data for each of them, as well as the mechanisms (i.e., reversible inhibition, mechanism-based inhibition, induction) underlying metabolic-based DDIs. In particular, this review outlines how the methods (static and dynamic) can be used in a complementary manner during drug development. The discussion of the limitations and advantages associated with the various approaches, as well as regulatory requirements in that field, can give the reader a helpful overview of this growing area.

Recursive partitioning for the prediction of cytochromes P450 2D6 and 1A2 inhibition: importance of the quality of the dataset.

The purpose of this study was to explore the use of detailed biological data in combination with a statistical learning method for predicting the CYP1A2 and CYP2D6 inhibition. Data were extracted from the Aureus-Pharma highly structured databases which contain precise measures and detailed experimental protocol concerning the inhibition of the two cytochromes. The methodology used was Recursive Partitioning, an easy and quick method to implement. The building of models was preceded by the evaluation of the chemical space covered by the datasets. The descriptors used are available in the MOE software suite. The models reached at least 80% of Accuracy and often exceeded this percentage for the Sensitivity (Recall), Specificity, and Precision parameters. CYP2D6 datasets provided 11 models with Accuracy over 80%, while CYP1A2 datasets counted 5 high-accuracy models. Our models can be useful to predict the ADME properties during the drug discovery process and are indicated for high-throughput screening.

Knowledge-based analysis of multi-potent G-protein coupled receptors ligands.

A large number of chemical structures that interact with G-protein coupled receptors (GPCRs) have been disclosed in patents or published papers. Most of these compounds are selective for a given protein target; however, it is well recognized that some GPCR-drugs interact with multiple targets. Using a literature database, we have identified compounds that act on different GPCRs. These protein targets are usually divided in three main classes, A, B and C, based on sequence similarity, but they can also be grouped pharmacologically based on endogenous ligand characteristics. In this paper, we specifically focus on compounds able to recognize two different classes or different pharmacological clusters within the same class. Despite the large number of GPCR ligands described in the literature, we identified a limited number of molecules acting on both classes A and B, only few acting on classes A and C and none acting on class B and C receptors. A search for bi- or multi-potent compounds exhibiting activities on different pharmacological clusters of class A receptors revealed cases of cross reactivity, the most frequent concerning amine and peptide receptor clusters.

Drug repositioning using in silico compound profiling.

BACKGROUND: Drug repositioning is a current strategy to find new uses for existing drugs, patented or not, and for late-stage candidates that failed for lack of efficacy. RESULTS: In silico profiling of several marketed drugs (methadone, rapamycin, saquinavir and telmisartan) was performed, exploiting a vast amount of published information. Similar compounds were assessed in terms of target-activity profiles for major drug-target families. In silico profiles were visualized within an interactive heat map and detailed analysis was performed associated with the accessible current knowledge. CONCLUSION: Based on a basic principle assuming that similar molecules share similar target activity, new potential targets and, therefore, opportunities of potential new indications have been identified and discussed.

Assessing potency of c-Jun N-terminal kinase 3 (JNK3) inhibitors using 2D molecular descriptors and binary QSAR methodology.

JNK3 signaling pathway is gaining interest due to its involvement in many neurological disorders. The purpose of this study was to explore for the first time the use of a large and diverse dataset in combination with binary QSAR methodology for predicting JNK3 activity class. Data were extracted from Aureus Pharma' AurSCOPE Kinase knowledge database and active or inactive classes were assigned to ligands based on IC50 biological activity. Two sets of 2D molecular descriptors (P_VSA and BCUT) were used to build models using different biological activity thresholds. The design of the models was preceded by the evaluation of the chemical space covered by the datasets and an assessment of its chemical diversity. The best model was found using a 100 nM IC50 threshold with surface-based P_VSA descriptors. This binary QSAR model reached an overall accuracy of 98% and a leave-one-out cross-validated accuracy of 94%. Most relevant descriptors were found to encode size and hydrophobic interactions. These derived models can be useful for screening chemical libraries in the search for new JNK3 inhibitors.

Development of an ADME and drug-drug interactions knowledge database for the acceleration of drug discovery and development.

It is widely recognised that predicting or determining the absorption, distribution, metabolism and excretion (ADME) properties of a compound as early as possible in the drug discovery process helps to prevent costly late-stage failures. Although in recent years high-throughput in vitro absorption distribution metabolism excretion toxicity (ADMET) screens have been implemented, more efficient in silico filters are still highly needed to predict and model the most relevant metabolic and pharmacokinetic end points, and thereby accelerate drug discovery and development. The usefulness of the data generated and published for the chemist, biologist or project manager who ultimately wants to understand and optimise the ADME properties of lead compounds cannot be argued with. Collecting and comparing data is an overwhelming task for the time-pressed scientist. Aureus Pharma provides a uniquely specialised solution for knowledge generation in drug discovery. AurSCOPE(®) ADME/DDI (drug-drug interaction) is a fully annotated, structured knowledge database containing all the pertinent biological and chemical information on the metabolic properties of drugs. This Aureus knowledge database has proven to be highly useful in designing predictive models and identifying potential drug-drug interactions.