Effects of oral administration of S-1 on the pharmacokinetics of SN-38, irinotecan active metabolite, in patients with advanced colorectal cancer

XenoMet: A Corpus of Texts to Extract Data on Metabolites of Xenobiotics

Understanding the biotransformation of xenobiotics in the human body is critical for a comprehensive assessment of drug effects since pharmacologically active drug metabolites may exhibit a range of biological effects that often differ from those of the original pharmaceutical agent. Studies of the biotransformation mechanisms of xenobiotics have resulted in numerous publications. Extracting information about the parent compounds (substrates) and their metabolites from the texts allows retrieval of information on their biological activities, molecular mechanisms of action, and toxicity. Manual curation of the names of xenobiotics, their metabolites, and biotransformation reactions in the text is a challenging task due to the large number of publications related to studies of pharmaceutical agents metabolism. Our aim is to create an annotated corpus of texts that can be used for automated extraction of the names of xenobiotics, including pharmaceutical agents that undergo biotransformation and their metabolites. Prior to manual annotation of the corpus, semiautomatic annotation was carried out based on the earlier developed rule-based method for parent compounds and their metabolites extraction. To create XenoMet, we automatically extracted relevant texts from PubMed using a query based on MeSH terms. The names of biotransformation reactions were recognized by using an in-house-developed dictionary. Then, we manually verified the extracted data by correcting errors in the named entity annotation and identified the associations between substrates and metabolites. We tested the applicability of XenoMet for the reconstruction of a metabolic tree and for the automated extraction of the chemical names of substrates, metabolites, and reactions of biotransformation. Classification of the named entities of metabolites, substrates, and biotransformation reactions by a conditional random fields approach using XenoMet as the training set provides an F1-score of 0.79.

Impact of liver diseases and pharmacological interactions on the transportome involved in hepatic drug disposition

The liver plays a pivotal role in drug disposition owing to the expression of transporters accounting for the uptake at the sinusoidal membrane and the efflux across the basolateral and canalicular membranes of hepatocytes of many different compounds. Moreover, intracellular mechanisms of phases I and II biotransformation generate, in general, inactive compounds that are more polar and easier to eliminate into bile or refluxed back toward the blood for their elimination by the kidneys, which becomes crucial when the biliary route is hampered. The set of transporters expressed at a given time, i.e., the so-called transportome, is encoded by genes belonging to two gene superfamilies named Solute Carriers (SLC) and ATP-Binding Cassette (ABC), which account mainly, but not exclusively, for the uptake and efflux of endogenous substances and xenobiotics, which include many different drugs. Besides the existence of genetic variants, which determines a marked interindividual heterogeneity regarding liver drug disposition among patients, prevalent diseases, such as cirrhosis, non-alcoholic steatohepatitis, primary sclerosing cholangitis, primary biliary cirrhosis, viral hepatitis, hepatocellular carcinoma, cholangiocarcinoma, and several cholestatic liver diseases, can alter the transportome and hence affect the pharmacokinetics of drugs used to treat these patients. Moreover, hepatic drug transporters are involved in many drug-drug interactions (DDI) that challenge the safety of using a combination of agents handled by these proteins. Updated information on these questions has been organized in this article by superfamilies and families of members of the transportome involved in hepatic drug disposition.

Individualization of Irinotecan Treatment: A Review of Pharmacokinetics, Pharmacodynamics, and Pharmacogenetics

Since its clinical introduction in 1998, the topoisomerase I inhibitor irinotecan has been widely used in the treatment of solid tumors, including colorectal, pancreatic, and lung cancer. Irinotecan therapy is characterized by several dose-limiting toxicities and large interindividual pharmacokinetic variability. Irinotecan has a highly complex metabolism, including hydrolyzation by carboxylesterases to its active metabolite SN-38, which is 100- to 1000-fold more active compared with irinotecan itself. Several phase I and II enzymes, including cytochrome P450 (CYP) 3A4 and uridine diphosphate glucuronosyltransferase (UGT) 1A, are involved in the formation of inactive metabolites, making its metabolism prone to environmental and genetic influences. Genetic variants in the DNA of these enzymes and transporters could predict a part of the drug-related toxicity and efficacy of treatment, which has been shown in retrospective and prospective trials and meta-analyses. Patient characteristics, lifestyle and comedication also influence irinotecan pharmacokinetics. Other factors, including dietary restriction, are currently being studied. Meanwhile, a more tailored approach to prevent excessive toxicity and optimize efficacy is warranted. This review provides an updated overview on today’s literature on irinotecan pharmacokinetics, pharmacodynamics, and pharmacogenetics.