Modeling Drug-Induced Liver Toxicity: a Case Study for Pathway Analysis
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FOR PHARMA & LIFE SCIENCES WHITEPAPER Modeling Drug-Induced Liver Toxicity: A Case Study for Pathway Analysis BRINGING NEW, EFFECTIVE AND PROFITABLE DRUGS TO MARKET This case study demonstrates how pathway analysis can be used to create complex, predictive mechanistic models of biological processes, providing novel insights to researchers and helping them direct the course of their studies. Bringing new, effective and profitable drugs to market. EXECUTIVE SUMMARY Liver toxicity is a key reason why new drugs fail in clinical trials, or once they are in broader use. Drug-induced cholestasis is a common form of liver toxicity, yet currently there is no model or test to predict which drugs may induce cholestasis in patients. This case study demonstrates how pathway analysis can be used to create complex, predictive mechanistic models of biological processes, providing novel insights to researchers and helping them direct the course of their studies. INTRODUCTION Drug toxicity is a leading cause for Severe cases, however, may lead to liver dismissing lead compounds during drug failure2. A partial list of medications development and a frequent reason for the known to cause cholestasis includes:iii withdrawal of drugs from clinical trials and subsequently from the market.i, ii Liver • Antibiotics such as ampicillin and toxicity is the major type of drug-induced other penicillins toxicity due to the primary role of the liver • Anabolic steroids in metabolizing foreign chemicals and • Oral contraceptives clearing them from the body. • Chlorpromazine Drug metabolism in liver cells typically • Cimetidine occurs in three phases: oxidation by • Estradiol membrane-associated cytochrome P450 enzymes in hepatocytes, conjugation with • Imipramine various hydrophilic anionic groups causing • Prochlorperazine drug inactivation, and the discharge of conjugated and inactivated forms of • Terbinafine the drug into bile that empties into the • Tolbutamide intestine for excretion from the body1. In this article, we use drug-induced cholestasis as a case study to When a drug or its metabolite inhibits demonstrate how knowledge networks one or more enzymes involved in its composed of drug-target relationships metabolism by the liver, the drug may can be used in combination with accumulate in the liver and cause one or biological association networks to build more types of liver toxicity. Cholestasis a proposed mechanistic model of drug is a common type of liver toxicity toxicity. Such a model might be used characterized by the inability to secrete to predict potential toxicity of a drug bile. Once patients stop taking the drug candidate early in the development causing cholestasis, most will recover pipeline and reduce attrition in the clinical although it can take many months. trial stages, to develop biomarkers of drug toxicity, and even to predict individual risk of drug-induced toxicities. 2 A POWERFUL TOOL FOR PATHWAY ANALYSIS This Underpinning Pathway Studio® A large collection of research articles metabolites that induced cholestasis and is Elsevier’s proprietary text mining on cholestasis already exists, but the manually removed them from the final technology that extracts facts from challenge is sifting through all those result since this model was focused on full-text articles in the more than papers manually to piece together drug-induced cholestasis—an example 2,000 biomedical journals, as well as key results and relationships from the of how researchers can customize search PubMed abstracts. various studies into a single, coherent results based on their own knowledge. disease model for drug induced Armed with Pathway Studio, cholestasis. The process of pathway We hypothesized that drugs induce biologists can rapidly access facts analysis can help researchers make cholestasis through common extracted not only from abstracts, but sense of the vast amount of published mechanisms; therefore, we started also from all the full-text articles in results that are scattered across dozens searching for proteins downstream of the Elsevier corpus. Having access or hundreds of journal articles. Pathway at least two different drugs known to to the full text of articles and an analysis systematically processes induce cholestasis to start the model industry-leading text-mining tool published scientific papers, extracts building process. gives researchers a measurable and gathers relevant information about advantage in terms of rendering a molecular interactions into a database, Pathway Studio enabled us to build complete picture of the genes and and then provides tools to mine that a pathway and apply a filter to hone proteins involved in the biology of a information. This systematic approach in on individual proteins, complexes, disease or response to a drug. helps researchers ensure a more and protein functional-classes. We also comprehensive survey of the published hypothesized that drugs might cause information, which in turn gives them cholestasis by inhibiting off-target greater confidence in the interpretation proteins and, therefore, we filtered for of their experimental data. For this relationships with negative regulatory case study, we used Elsevier’s Pathway effects. Manual inspection of the result- Studio to review virtually all of the ing drug-target relationships revealed published information about the process that many cholestasis-inducing drugs of cholestasis, find common features were anticancer drugs that shared com- among cholestasis-inducing drugs, and mon therapeutic targets irrelevant to by applying knowledge of the biology, cholestasis. To identify off-target proteins we could propose an in-silico model for potentially relevant to cholestasis, we drug-induced cholestasis. extended the search to capture proteins linked to all types of cholestasis – rather Creating a draft model of drug-Induced than only drug-induced cholestasis - with cholestasis positive or unknown regulatory effects. We began by selecting the term “cholestasis” in Pathway Studio’s knowledgebase and searched for small molecule entities associated with positive regulation upstream of the cholestasis starting point. By inspecting the sentences extracted from the literature by Pathway Studio for some of these upstream entities, we identified several 3 The set of identified proteins linked We then began building a cholestasis to cholestasis in the literature was model from 21 proteins directly involved compared to the set of common targets in bile acid metabolism, irrespective of cholestatic drugs, and the proteins at of their method of regulation. The the intersection of those groups were proteins in the model could be classified chosen for further analysis. After manual as hepatocyte bile acid importers or curation and removing highly generic exporters, or enzymes for bile acid and uninformative functional classes synthesis and conjugation (Figure 1). The (e.g., cytokines and monooxygenases), model is consistent with the current view we identified 58 proteins linked to of bile acid circulation that postulates cholestasis and inhibited by at least two that hepatocytes preferentially import cholestatic drugs. damaged, unconjugated bile acids and export repaired conjugated bile acids3, while maintaining levels of circulating bile by synthesizing it from cholesterol. lipid transport cholesterol metabolism cholesterol cholesterol export ABCA1 BA import BA export Slco1a1 ABCB11 SLC22A8 BA conjugation ABCB1 acetate- Slco1a4 HMGCR HSD11B1 CYP3A4 UGT1A1 CoA ... CYP7A1 CYP27A1 ABCC4 SLCO1B1 ABCC1 BA synthesis SLC10A1 xenobiotic -transp... SLC22A1 ABCG2 SLCO1B3 bile acid transpor t bile acids bile acid metabolism Figure 1. A screenshot of the pathway generated by Pathway Studio showing 21 proteins (red ovals and amber hexagons) chosen for a draft of the drug-induced cholestasis model. (See Figure 2.) 4 Expanding the draft model by bile acids5, 7. FXR and PXR activate Sub-network enrichment analysis The next step was to find transcription the expression of proteins involved in (SNEA)4 is a statistical method factors upstream from the proteins bile acid conjugation and secretion, but developed for Pathway Studio to in the model using another function at the same time repress expression of identify sub-networks in the global of Pathway Studio. The top seven genes involved in bile acid import and knowledge network that are enriched sub-network enrichment (SNE) seeds synthesis (Figure 2). If there is an excess with entities selected by the user. The included six nuclear receptors and of bile, FXR and PXR induce conjugation biological interpretation of SNEA hepatic nuclear factor-1 (HNF1A) of bile acids, thereby increasing their results depends on the type of the in the following order of statistical secretion while suppressing bile acid global knowledge chosen for analysis. significance: PXR, FXR, CAR, PPARA, synthesis and import. If there is a deficit We used the option “Expression RXR, HNF1A, and SHP. HNF1A of bile, decreased FXR and PXR activities targets” that allows for identification functions in liver growth and derepress synthesis and import of bile of major expression regulators differentiation and, therefore, we acids, while down-regulating conjugation upstream of the userselected proteins. excluded it from the list of bile acid and secretion. Based on this regulation homeostasis regulators. Reviews of the profile, FXR and PXR likely act as principal supporting evidence revealed that only internal sensors and regulators of bile FXR and PXR could be directly activated