Laura Lowe Furge

Cytochrome P450 enzymes in drug metabolism and chemical toxicology: An introduction

Cytochrome P450 (P450) enzymes include a family of related enzymes that are involved in metabolism of vitamins, steroids, fatty acids, and other chemicals. This review presents a brief historical overview of the discovery and characterization of P450 enzymes extending from intermediary metabolism to the fields of drug metabolism and toxicology. Introductions to P450 enzyme structure and function are also presented. The goals of this review are to 1) provide an introduction to a few of the many aspects of P450 research relating to humans, 2) introduce additional ways of thinking about metabolism, 3) provide some basic examples of P450 enzymology, and 4) provide applications to topics widely taught in undergraduate courses in biochemistry.

Annexin VII and Annexin XI Are Tyrosine Phosphorylated in Peroxovanadate-treated Dogs and in Platelet-derived Growth Factor-treated Rat Vascular Smooth Muscle Cells

The intraperitoneal administration of peroxovanadate results in the rapid accumulation of many tyrosine-phosphorylated proteins in the liver and kidney of treated animals. The availability of large pools of tyrosine-phosphorylated proteins derived from normal tissues facilitates the purification and identification of previously unknown targets for cellular tyrosine kinases. Using this procedure, we have thus far identified four proteins in the liver and kidney of peroxovanadate-treated dogs. Two of these, annexin VII and annexin XI, were novel and had not been previously reported to be substrates of tyrosine kinases while the remaining two, ezrin and clathrin, have been reported to be tyrosine phosphorylated in some cell culture systems. In the present study, isolated proteins were identified both by sequence analysis and immunological methods. Annexin VII and annexin XI are present in cultured rat vascular smooth muscle cells and both were tyrosine phosphorylated in response to a physiological ligand, platelet-derived growth factor-BB (PDGF-BB). Furthermore, the extent of tyrosine phosphorylation in response to PDGF-BB was augmented by the co-addition of peroxovanadate to cell cultures. In vitrophosphorylation assays showed that PDGF receptor, calcium-dependent tyrosine kinase (CADTK/Pyk-2), Src kinase, and epidermal growth factor receptor all were able to phosphorylate purified annexin VII and XI on tyrosine residues. These findings confirm the usefulness of phosphatase inhibition by peroxovanadate as a tool for identifying previously unknown physiological targets for cellular protein tyrosine kinases.

Vertical and Horizontal Integration of Bioinformatics Education: A Modular, Interdisciplinary Approach

Bioinformatics education for undergraduates has been approached primarily in two ways: introduction of new courses with largely bioinformatics focus or introduction of bioinformatics experiences into existing courses. For small colleges such as Kalamazoo, creation of new courses within an already resource‐stretched setting has not been an option. Furthermore, we believe that a true interdisciplinary science experience would be best served by introduction of bioinformatics modules within existing courses in biology and chemistry and other complementary departments. To that end, with support from the Howard Hughes Medical Institute, we have developed over a dozen independent bioinformatics modules for our students that are incorporated into courses ranging from general chemistry and biology, advanced specialty courses, and classes in complementary disciplines such as computer science, mathematics, and physics. These activities have largely promoted active learning in our classrooms and have enhanced student understanding of course materials. Herein, we describe our program, the activities we have developed, and assessment of our endeavors in this area.

Molecular Dynamics of CYP2D6 Polymorphisms in the Absence and Presence of a Mechanism-Based Inactivator Reveals Changes in Local Flexibility and Dominant Substrate Access Channels

Cytochrome P450 enzymes (CYPs) represent an important enzyme superfamily involved in metabolism of many endogenous and exogenous small molecules. CYP2D6 is responsible for ∼15% of CYP-mediated drug metabolism and exhibits large phenotypic diversity within CYPs with over 100 different allelic variants. Many of these variants lead to functional changes in enzyme activity and substrate selectivity. Herein, a molecular dynamics comparative analysis of four different variants of CYP2D6 was performed. The comparative analysis included simulations with and without SCH 66712, a ligand that is also a mechanism-based inactivator, in order to investigate the possible structural basis of CYP2D6 inactivation. Analysis of protein stability highlighted significantly altered flexibility in both proximal and distal residues from the variant residues. In the absence of SCH 66712, *34, *17-2, and *17-3 displayed more flexibility than *1, and *53 displayed more rigidity. SCH 66712 binding reversed flexibility in *17-2 and *17-3, through *53 remained largely rigid. Throughout simulations with docked SCH 66712, ligand orientation within the heme-binding pocket was consistent with previously identified sites of metabolism and measured binding energies. Subsequent tunnel analysis of substrate access, egress, and solvent channels displayed varied bottle-neck radii. Taken together, our results indicate that SCH 66712 should inactivate these allelic variants, although varied flexibility and substrate binding-pocket accessibility may alter its interaction abilities.

Metoclopramide is metabolized by CYP2D6 and is a reversible inhibitor, but not inactivator, of CYP2D6

Abstract 1. Metoclopramide is a widely used clinical drug in a variety of medical settings with rare acute dystonic events reported. The aim of this study was to assess a previous report of inactivation of CYP2D6 by metoclopramide, to determine the contribution of various CYPs to metoclopramide metabolism, and to identify the mono-oxygenated products of metoclopramide metabolism. 2. Metoclopramide interacted with CYP2D6 with Type I binding and a Ks value of 9.56 ± 1.09 µM. CYP2D6 was the major metabolizer of metoclopramide and the two major products were N-deethylation of the diethyl amine and N-hydroxylation on the phenyl ring amine. CYPs 1A2, 2C9, 2C19, and 3A4 also metabolized metoclopramide. 3. While reversible inhibition of CYP2D6 was noted, CYP2D6 inactivation by metoclopramide was not observed under conditions of varying concentration or varying time using SupersomesTM or pooled human liver microsomes. 4. The major metabolites of metoclopramide were N-hydroxylation and N-deethylation formed most efficiently by CYP2D6 but also formed by all CYPs examined. Also, while metoclopramide is metabolized primarily by CYP2D6, it is not a mechanism-based inactivator of CYP2D6 in vitro.

Molecular Analysis and Modeling of Inactivation of Human CYP2D6 by Four Mechanism Based Inactivators

Human cytochrome P450 2D6 (CYP2D6) is involved in metabolism of approximately 25% of pharmaceutical drugs. Inactivation of CYP2D6 can lead to adverse drug interactions. Four inactivators of CYP2D6 have previously been identified: 5-Fluoro-2-[4-[(2-phenyl-1H-imidazol-5-yl)methyl]-1-piperazinyl]pyrimidine(SCH66712), (1-[(2-ethyl- 4-methyl-1H-imidazol-5-yl)-methyl]-4-[4-(trifluoromethyl)-2-pyridinyl]piperazine(EMTPP), paroxetine, and 3,4- methylenedioxymethamphetamine (MDMA). All four contain planar, aromatic groups as well as basic nitrogens common to CYP2D6 substrates. SCH66712 and EMTPP also contain piperazine groups and substituted imidazole rings that are common in pharmaceutical agents, though neither of these compounds is clinically relevant. Paroxetine and MDMA contain methylenedioxyphenyls. SCH66712 and EMTPP are both known protein adductors while paroxetine and MDMA are probable heme modifiers. The current study shows that each inactivator displays Type I binding with Ks values that vary by 2-orders of magnitude with lower Ks values associated with greater inactivation. Comparison of KI, kinact, and partition ratio values shows SCH66712 is the most potent inactivator. Molecular modeling experiments using AutoDock identify Phe120 as a key interaction for all four inactivators with face-to-face and edge-to-face pi interactions apparent. Distance between the ligand and heme iron correlates with potency of inhibition. Ligand conformations were scored according to their binding energies as calculated by AutoDock and correlation was observed between molecular models and Ks values.

Substituted Imidazole of 5-Fluoro-2-[4-[(2-phenyl-1H-imidazol-5-yl)methyl]-1-piperazinyl]pyrimidine Inactivates Cytochrome P450 2D6 by Protein Adduction

5-Fluoro-2-[4-[(2-phenyl-1H-imidazol-5-yl)methyl]-1-piperazinyl]pyrimidine (SCH 66712) is a potent mechanism-based inactivator of human cytochrome P450 2D6 that displays type I binding spectra with a Ks of 0.39 ± 0.10 μM. The partition ratio is ∼3, indicating potent inactivation that addition of exogenous nucleophiles does not prevent. Within 15 min of incubation with SCH 66712 and NADPH, ∼90% of CYP2D6 activity is lost with only ∼20% loss in ability to bind CO and ∼25% loss of native heme over the same time. The stoichiometry of binding to the protein was 1.2:1. SDS-polyacrylamide gel electrophoresis with Western blotting and autoradiography analyses of CYP2D6 after incubations with radiolabeled SCH 66712 further support the presence of a protein adduct. Metabolites of SCH 66712 detected by mass spectrometry indicate that the phenyl group on the imidazole ring of SCH 66712 is one site of oxidation by CYP2D6 and could lead to methylene quinone formation. Three other metabolites were also observed. For understanding the metabolic pathway that leads to CYP2D6 inactivation, metabolism studies with CYP2C9 and CYP2C19 were performed because neither of these enzymes is significantly inhibited by SCH 66712. The metabolites formed by CYP2C9 and CYP2C19 are the same as those seen with CYP2D6, although in different abundance. Modeling studies with CYP2D6 revealed potential roles of various active site residues in the oxidation of SCH 66712 and inactivation of CYP2D6 and showed that the phenyl group of SCH 66712 is positioned at 2.2 Å from the heme iron.

Innovation in the Biochemistry/Molecular biology laboratory

For 2015, the special series on Innovation in the Biochemistry/Molecular Biology Lab focuses on the teaching of ethics in the laboratory. The timeless and expansive nature of this topic may cause some readers to question how it is innovative. However, while there seem to be reminders of ethics in short essays and in informal settings, we have found that the literature is short on examples of how it is being taught and integrated within laboratory coursework. BMB lab educators often do not feel proficient in teaching ethics if they have had minimal or no training in the field. Rather than bringing ethics into their classrooms, they may suggest that their students read books [1–3] or enroll in an ethics course on campus. Many colleges and universities now offer a science-based ethics course [4–7]. However, a survey of BMB faculty carried out in 2008 for the Teagle project, “Biochemistry/Molecular Biology and Liberal Education,” indicated that only about half of them taught ethics in the context of scientific research [8]. Ethics is becoming a prominent theme among research scientists and student members of scientific organizations. BAMBEd is published for the International Union for Biochemistry and Molecular Biology (IUBMB). The IUBMB mission includes a Code of Ethics for Members that encompasses seven specific guiding principles [9]. The items on the list range from “high ethical, professional and scientific standards in both conducting and reporting their research activities” to “protection and sustainability of the environment.” Perhaps the most widely used ethics issues in teaching relate to integrity in data handling and reporting, while issues of sustainability in biomedical research and good stewardship with resources are also gaining attention. Young research scientists are encountering and identifying issues of ethics in their work and are engaging in larger conversations about ethics. Issues identified in recent Science magazine publications include scientific communication, ownership of graduate school projects, healthy research environments that foster integrity, use of animal models, junk science, and protection of the environment, among others [10, 11]. The American Society for Biochemistry and Molecular Biology has recently begun accreditation for Biochemistry and Molecular Biology undergraduate programs. As part of the application process, programs must describe how they incorporate “the teaching of responsible conduct of research/professional code of conduct” [12] in order to fulfill the necessary skill of “awareness of the ethical issues in the molecular life sciences”[13]. The Council on Undergraduate Research (CUR) is planning to focus on ethics in the Fall 2015 CUR Quarterly [14]. BAMBEd has recently published laboratory activities that contain ethics components [15–19], some of these in the context of personalized medicine [15, 16] or biotechnology [17]. Other publications, including books and websites reviewed in this journal and elsewhere focus heavily on teaching ethics as a philosophical issue to be presented to students in a didactic setting and typically as a separate course. However, teaching of ethics as a topic separate from the scientific and laboratory setting does not have the same impact on student understanding, appreciation, and application of ethics in their research experiences [18]. Compartmentalization of ethics, as noted by Smith et al. [18] can lead students to think of ethics separately from their research, whereas inclusion of ethics in the laboratory setting encourages students to see that their laboratory work has an ethical component. Arkwright-Keeler and Stapleton have collated many resources to assist faculty in designing modules or stand-alone courses [19]. An interesting direction taken by some institutions is to include ethics in courses that prepare students for the transition to graduate school [20–23]. One area that seems to need further attention is development of assessment tools for ethics modules. The articles selected for the 2015 series provide examples or theoretical frameworks for integration of ethics into the undergraduate laboratory. They include: *Address for correspondence to: Department of Chemistry, Kalamazoo College, Kalamazoo, MI 49006. E-mail: Laura.Furge@kzoo.edu. Received 7 January 2015; Accepted 18 January 2015 DOI 10.1002/bmb.20853 Published online 25 February 2015 in Wiley Online Library (wileyonlinelibrary.com) Innovation in the Biochemistry/Molecular Biology Laboratory

HPLC Determination of Caffeine and Paraxanthine in Urine: An Assay for Cytochrome P450 1A2 Activity.

Cytochrome P450 enzymes are a family of heme‐containing proteins located throughout the body with roles in metabolism of endogenous and exogenous compounds. Among exogenous compounds, clinically relevant pharmaceutical agents are nearly all metabolized by P450 enzymes. However, the activity of the different cytochrome P450 enzymes varies among individuals and, therefore, so does drug efficacy as well as susceptibility to side effects and toxicity. Thus, assessing P450 activity is of great interest in drug development and clinical pharmacology. This study investigates the phenotyping of a single P450 activity by analyzing urine samples using isocratic reverse‐phase HPLC. Specifically, the activity of human P450 1A2, which converts caffeine into paraxanthine, can be investigated by measuring the change in caffeine and paraxanthine concentrations in urine over time following a single dose of caffeine. There is an observable relationship between caffeine intake and paraxanthine formation that varies among individuals. This laboratory exercise provides a means for simple assessment of P450 1A2 metabolic activity using an HPLC method without additional extraction or purification steps and introduces students to the complexities of individualized medicine as well as the basic biochemical techniques of sample preparation and quantitative HPLC. Furthermore, students may design and test their own hypothesis using these methods.

Mechanism-based Inactivation of Human Cytochrome P450 3A4 by Two Piperazine-containing Compounds

Human cytochrome P450 3A4 (CYP3A4) is responsible for the metabolism of more than half of pharmaceutic drugs, and inactivation of CYP3A4 can lead to adverse drug-drug interactions. The substituted imidazole compounds 5-fluoro-2-[4-[(2-phenyl-1H-imidazol-5-yl)methyl]-1-piperazinyl]pyrimidine (SCH 66712) and 1-[(2-ethyl-4-methyl-1H-imidazol-5-yl)methyl]-4-[4-(trifluoromethyl)-2-pyridinyl]piperazine (EMTPP) have been previously identified as mechanism-based inactivators (MBI) of CYP2D6. The present study shows that both SCH 66712 and EMTPP are also MBIs of CYP3A4. Inhibition of CYP3A4 by SCH 66712 and EMTPP was determined to be concentration, time, and NADPH dependent. In addition, inactivation of CYP3A4 by SCH 66712 was shown to be unaffected by the presence of electrophile scavengers. SCH 66712 displays type I binding to CYP3A4 with a spectral binding constant (Ks) of 42.9 ± 2.9 µM. The partition ratios for SCH 66712 and EMTPP were 11 and 94, respectively. Whole protein mass spectrum analysis revealed 1:1 binding stoichiometry of SCH 66712 and EMTPP to CYP3A4 and a mass increase consistent with adduction by the inactivators without addition of oxygen. Heme adduction was not apparent. Multiple mono-oxygenation products with each inactivator were observed; no other products were apparent. These are the first MBIs to be shown to be potent inactivators of both CYP2D6 and CYP3A4.