2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes

Cytochrome P450 (CYP) 3A4, 2D6, 2C9, 2C19, and 1A2 are the most important drug-metabolizing enzymes in the human liver. Knowledge of which parts of a drug molecule are subject to metabolic reactions catalyzed by these enzymes is crucial for rational drug design to mitigate ADME/toxicity issues. SMARTCyp, a recently developed 2D ligand structure-based method, is able to predict site-specific metabolic reactivity of CYP3A4 and CYP2D6 substrates with an accuracy that rivals the best and more computationally demanding 3D structure-based methods. In this article, the SMARTCyp approach was extended to predict the metabolic hotspots for CYP2C9, CYP2C19, and CYP1A2 substrates. This was accomplished by taking into account the impact of a key substrate-receptor recognition feature of each enzyme as a correction term to the SMARTCyp reactivity. The corrected reactivity was then used to rank order the likely sites of CYP-mediated metabolic reactions. For 60 CYP1A2 substrates, the observed major sites of CYP1A2 catalyzed metabolic reactions were among the top-ranked 1, 2, and 3 positions in 67%, 80%, and 83% of the cases, respectively. The results were similar to those obtained by MetaSite and the reactivity + docking approach. For 70 CYP2C9 substrates, the observed sites of CYP2C9 metabolism were among the top-ranked 1, 2, and 3 positions in 66%, 86%, and 87% of the cases, respectively. These results were better than the corresponding results of StarDrop version 5.0, which were 61%, 73%, and 77%, respectively. For 36 compounds metabolized by CYP2C19, the observed sites of metabolism were found to be among the top-ranked 1, 2, and 3 sites in 78%, 89%, and 94% of the cases, respectively. The computational procedure was implemented as an extension to the program SMARTCyp 2.0. With the extension, the program can now predict the site of metabolism for all five major drug-metabolizing enzymes with an accuracy similar to or better than that achieved by the best 3D structure-based methods. Both the Java source code and the binary executable of the program are freely available to interested users

Role of cytochrome P450 enzymes on alcohol/nicotine-mediated oxidative stress and cytotoxicity in monocytes/astrocytes: Implications for HIV-infected alcohol/tobacco users

Title from PDF of title page, viewed on March 13, 2013Dissertation advisor: Santosh KumarVitaIncludes bibliographic references (p. 124-143)Thesis (Ph.D.)--School of Pharmacy. University of Missouri--Kansas City, 2012Alcohol abuse is known to induce liver diseases and neurodegeneration. Chronic alcohol use during medication is known to decrease drug efficacy and increase toxicity. In addition, alcohol is known to interact with other substances of abuse, such as tobacco. Cytochrome P450 2E1 (CYP2E1), which is induced by alcohol, is mainly involved in alcohol metabolism in the liver and extra-hepatic cells in chronic users. As a result of alcohol metabolism, CYP2E1 produces reactive oxygen species (ROS), which in turn inhibits acetaldehyde dehydrogenase leading to accumulation of acetaldehyde, both of which are known to damage DNA, protein, and lipids. In addition, nicotine-metabolizing enzyme CYP2A6 and a major drug-metabolizing enzyme CYP3A4 are induced by alcohol, suggesting their role in unexpected alcohol-drug-tobacco interactions. Our central hypothesis is that CYP2A6, CYP2E1, and CYP3A4 play important role in alcohol, nicotine, and antiretroviral therapeutic (ART) drug metabolism, respectively, in monocytes/macrophages and astrocytes, leading to oxidative stress-mediated toxicity and alcohol-ART interactions. Monocytes/macrophages and astrocytes are important cell types in studying HIV-1 pathogenesis and AIDS/neuroAIDS development. Our results showed that 1) CYP2A6, CYP2E1 and CYP3A4 are induced by alcohol in U937 monocytes/macrophages, while only CYP2E1 is induced by alcohol at both mRNA and protein levels in SVGA astrocytes, 2) CYP2A6 metabolizes nicotine in U937 macrophages and SVGA astrocytes, leading to increased production of ROS, 3) CYP3A4 binds nelfinavir and other protease inhibitors (PI) and is inhibited by these PIs, 4) In both U937 monocytes and SVGA astrocytes, CYP2A6 is regulated by alcohol through oxidative stress-induced PKC/MEK/Nrf2 pathway, while CYP2E1 is regulated by oxidative stress-induced PKC/JNK/SP1 pathway, 5) In human monocytes/macrophages, CYP2E1 is induced in alcoholic as well as HIV-infected individuals. In conclusions, our findings suggested that alcohol-mediated induction of CYP2A6, CYP2E1, and CYP3A4 is responsible for increased oxidative stress, increased cytotoxicity, and decreased efficacy of ART in monocytes/macrophages and astrocytes. Since alcohol abuse and co-abuse of alcohol and tobacco are 3 times higher among HIV+ patients than that of the general population, our findings have implications in HIV-1 pathogenesis, AIDS and neuroAIDS. Our subsequent findings would help optimize ART medication and help develop alternative interventions in alcohol and tobacco-consuming HIV-infected individuals.General introduction -- General materials and methods -- Evaluation of the role of ethanol on cytochrome P450 expression -- Evaluation of the role of CYP2A6, CYP2E1 and CYP3A4 in monocytes/macrophages and astrocytes -- Mechanistic study of ethanol-mediated CYP2A6 expression: PKC-MEK-NRF2 pathway -- Mechanistic study of ethanol-induced CYP2E1 expression: PKC/JNK/SP1 pathway -- Effect of alcohol consumption on expressions of CYP2E1 and ALDH in humans -- General discussion -- Appendi