Chapter 7
Drug Metabolism Research as Integral Part of Drug Discovery and Development Processes
W. Griffith Humphreys,
W. Griffith Humphreys
Department of Biotransformation, Bristol-Myers Squibb Research and Development, Princeton, New Jersey, USA
Search for more papers by this authorW. Griffith Humphreys,
W. Griffith Humphreys
Department of Biotransformation, Bristol-Myers Squibb Research and Development, Princeton, New Jersey, USA
Search for more papers by this authorBook Editor(s):Mike S. Lee, Mingshe Zhu,
Mingshe Zhu
Department of Biotransformation, Bristol-Myers Squibb Research and Development, Princeton, New Jersey, USA
Search for more papers by this authorSeries Editor(s): Mike S. Lee,
Summary
This chapter contains sections titled:
-
Introduction
-
Metabolic Clearance
-
Metabolite Profiling/Mass Balance Studies
-
Safety Testing of Drug Metabolites
-
Reaction Phenotyping
-
Assessment of Potential Toxicology of Metabolites
-
Assessment of Potential for Active Metabolites
-
Summary
-
References
REFERENCES
- Amacher DE. Reactive intermediates and the pathogenesis of adverse drug reactions: The toxicology perspective. Curr Drug Metab 2006; 7: 219–229.
- Anari MR, Baillie TA. Bridging cheminformatic metabolite prediction and tandem mass spectrometry. Drug Discov Today 2005; 10: 711–717.
- Antoine DJ, Williams DP, Park BK. Understanding the role of reactive metabolites in drug-induced hepatotoxicity: State of the science. Expert Opin Drug Metab Toxicol 2008; 4(11): 1415–1427.
- Argoti D, Liang L, Conteh A, Chen L, Bershas D, Yu CP, Vouros P, Yang E. Cyanide trapping of iminium ion reactive intermediates followed by detection and structure identification using liquid chromatography–tandem mass spectrometry (LC-MS/ MS). Chem Res Toxicol 2005; 18: 1537–1544.
- Baillie TA. Future of toxicology-metabolic activation and drug design: Challenges and opportunities in chemical toxicology. Chem Res Toxicol 2006; 19: 889–893.
- Baillie TA. Approaches to the assessment of stable and chemically reactive drug metabolites in early clinical trials. Chem Res Toxicol 2009; 22(2): 263–266.
- Balani SK, Zhu T, Yang TJ, Liu Z, He B, Lee FW. Effective dosing regimen of 1-aminobenzotriazole for inhibition of antipyrine clearance in rats, dogs, and monkeys. Drug Metab Dispos 2002; 30: 1059–1062.
- Barter ZE, Bayliss MK, Beaune PH, Boobis AR, Carlile DJ, Edwards RJ, Houston JB, Lake BG, Lipscomb JC, Pelkonen OR, Tucker GT, Rostami-Hodjegan A. Scaling factors for the extrapolation of in vivo metabolic drug clearance from in vitro data: Reaching a consensus on values of human microsomal protein and hepatocellularity per gram of liver. Curr Drug Metab 2007; 8(1): 33–45.
- Bateman KP, Kellmann M, Muenster H, Papp R, Taylor L. Quantitative-qualitative data acquisition using a benchtop Orbitrap mass spectrometer. J Am Soc Mass Spectrom 2009; 20(8): 1441–1450.
- Bauman JN, Kelly JM, Tripathy S, Zhao SX, Lam WW, Kalgutkar AS, Obach RS. Can in vitro metabolism-dependent covalent binding data distinguish hepatotoxic from nonhepatotoxic drugs? An analysis using human hepatocytes and liver S-9 fraction. Chem Res Toxicol 2009; 22: 332–340.
- Buch H, Buzello W, Heymann E, Krisch K. Inhibition of phenacetin- and acetanilide-induced methemoglobinemia in the rat by the carboxylesterase inhibitor bis-[p-nitrophenyl] phosphate. Biochem Pharmacol 1969; 18: 801–811.
- Caldwell GW, Yan Z, Tang W, Dasgupta M, Hasting B. ADME optimization and toxicity assessment in early- and late-phase drug discovery. Curr Top Med Chem 2009; 9(11): 965–980.
- Chao P, Maguire T, Novik E, Cheng KC, Yarmush ML. Evaluation of a microfluidic based cell culture platform with primary human hepatocytes for the prediction of hepatic clearance in human. Biochem Pharmacol 2009; 78(6): 625–632.
- Clader JW. The discovery of ezetimibe: A view from outside the receptor. J Med Chem 2004; 47: 1–9.
- Cox KA, White RE, Korfmacher WA. Rapid determination of pharmacokinetic properties of new chemical entities: In vivo approaches. Comb Chem High Throughput Screen 2002; 5: 29–37.
- Daly AK, Day CP. Genetic association studies in drug-induced liver injury. Semin Liver Dis 2009; 29: 400–411.
- Daly AK, Donaldson PT, Bhatnagar P, Shen Y, Pe'er I, Floratos A, Daly MJ, Goldstein DB, John S, Nelson MR, Graham J, Park BK, Dillon JF, Bernal W, Cordell HJ, Pirmohamed M, Aithal GP, Day CP, DILIGEN Study; International SAE Consortium. HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nat Genet 2009; 41: 816–819.
- Dieckhaus CM, Fernandez-Metzler CL, King R, Krolikowski PH, Baillie TA. Negative ion tandem mass spectrometry for the detection of glutathione conjugates. Chem Res Toxicol 2005; 18: 630–638.
- Doss GA, Baillie TA. Addressing metabolic activation as an integral component of drug design. Drug Metab Rev 2006; 38(4): 641–649.
- Evans DC, Watt AP, Nicoll-Griffith DA, Baillie TA. Drug-protein adducts: An industry perspective on minimizing the potential for drug bioactivation in drug discovery and development. Chem Res Toxicol 2004; 17: 3–16.
- Fisher MB, Campanale K, Ackermann BL, VandenBranden M, Wrighton SA. In vitro glucuronidation using human liver microsomes and the pore-forming peptide alamethicin. Drug Metab Dispos 2000; 28: 560–566.
- Fisher MB, Henne KR, Boer J. The complexities inherent in attempts to decrease drug clearance by blocking sites of CYP-mediated metabolism. Curr Opin Drug Discov Devel 2006; 9(1): 101–109.
- Fisher MB, Yoon K, Vaughn ML, Strelevitz TJ, Foti RS. Flavin-containing monooxygenase activity in hepatocytes and microsomes: In vitro characterization and in vivo scaling of benzydamine clearance. Drug Metab Dispos 2002; 30: 1087–1093.
- Fura A. Role of pharmacologically active metabolites in drug discovery and development. Drug Discov Today 2006; 11: 133–142.
- Fura A, Shu YZ, Zhu M, Hanson RL, Roongta V, Humphreys WG. Discovering drugs through biological transformation: Role of pharmacologically active metabolites in drug discovery. J Med Chem 2004; 47: 4339–4351.
- Gan J, Harper TW, Hsueh MM, Qu Q, Humphreys WG. Dansyl glutathione as a trapping agent for the quantitative estimation and identification of reactive metabolites. Chem Res Toxicol 2005; 18: 896–903.
- Gan J, Ruan Q, He B, Zhu M, Shyu WC, Humphreys WG. In vitro screening of 50 highly prescribed drugs for thiol adduct formation—Comparison of potential for drug-induced toxicity and extent of adduct formation. Chem Res Toxicol 2009; 22: 690–698.
- Ghibellini G, Vasist LS, Leslie EM, Heizer WD, Kowalsky RJ, Calvo BF, Brouwer KL. In vitro–in vivo correlation of hepatobiliary drug clearance in humans. Clin Pharmacol Ther 2007; 81(3): 406–413.
- Grime K, Riley RJ. The impact of in vitro binding on in vitro–in vivo extrapolations, projections of metabolic clearance and clinical drug-drug interactions. Curr Drug Metab 2006; 7: 251–264.
- Guengerich FP. Common and uncommon cytochrome P450 reactions related to metabolism and chemical toxicity. Chem Res Toxicol 2001; 14: 611–650.
- Guengerich FP. Cytochrome P450 oxidations in the generation of reactive electrophiles: Epoxidation and related reactions. Arch Biochem Biophys 2003; 409: 59–71.
- Guengerich FP. Principles of covalent binding of reactive metabolites and examples of activation of bis-electrophiles by conjugation. Arch Biochem Biophys 2005; 433: 369–378.
- Guengerich FP. Cytochrome P450S and other enzymes in drug metabolism and toxicity. AAPS J 2006; 8: E101–111.
- Hallifax D, Houston JB. Methodological uncertainty in quantitative prediction of human hepatic clearance from in vitro experimental systems. Curr Drug Metab 2009; 10(3): 307–321.
- Harper TW, Brassil PJ. Reaction phenotyping: Current industry efforts to identify enzymes responsible for metabolizing drug candidates. AAPS J 2008; 10(1): 200–207.
- Harrill AH, Watkins PB, Su S, Ross PK, Harbourt DE, Stylianou IM, Boorman GA, Russo MW, Sackler RS, Harris SC, Smith PC, Tennant R, Bogue M, Paigen K, Harris C, Contractor T, Wiltshire T, Rusyn I, Threadgill DW. Mouse population-guided resequencing reveals that variants in CD44 contribute to acetaminophen-induced liver injury in humans. Genome Res 2009; 19: 1507–1515.
- Hawkins DR. Use and value of metabolism databases. Drug Discov Today 1999; 4: 466–471.
- Hellriegel ET, Bjornsson TD, Hauck WW. Interpatient variability in bioavailability is related to the extent of absorption: Implications for bioavailability and bioequivalence studies. Clin Pharmacol Ther 1996; 60: 601–607.
- Houston JB, Galetin A. Methods for predicting in vivo pharmacokinetics using data from in vitro assays. Curr Drug Metab 2008; 9(9): 940–951.
- Hsieh Y, Korfmacher W. The role of hyphenated chromatography–mass spectrometry techniques in exploratory drug metabolism and pharmacokinetics. Curr Pharm Des 2009; 15(19): 2251–2261.
- Huang C, Zheng M, Yang Z, Rodrigues AD, Marathe P. Projection of exposure and efficacious dose prior to first-in-human studies: How successful have we been? Pharm Res 2008; 25(4): 713–726.
- Hughes AR, Spreen WR, Mosteller M, Warren LL, Lai EH, Brothers CH, Cox C, Nelsen AJ, Hughes S, Thorborn DE, Stancil B, Hetherington SV, Burns DK, Roses AD. Pharmacogenetics of hypersensitivity to abacavir: From PGx hypothesis to confirmation to clinical utility. Pharmacogenom J 2008; 28: 365–374.
- Humphreys WG, Unger SE. Safety assessment of drug metabolites: Characterization of chemically stable metabolites. Chem Res Toxicol 2006; 19(12): 1564–1569.
- International Conference on Harmonisation. Non-Clinical Safety Studies for the Conduct of Human Clinical Trials for Pharmaceuticals, ICH Guidance M3(R2), 2009, available: http://www.emea.europa.eu/pdfs/human/ich028695en.pdf.
- Kalgutkar AS, Didiuk MT. Structural alerts, reactive metabolites, and protein covalent binding: How reliable are these attributes as predictors of drug toxicity? Chem Biodivers 2009; 6(11): 2115–2137.
- Kaplowitz N. Idiosyncratic drug hepatotoxicity. Nat Rev Drug Discov 2005; 4: 489–499.
- Kilford PJ, Stringer R, Sohal B, Houston JB, Galetin A. Prediction of drug clearance by glucuronidation from in vitro data: Use of combined cytochrome P450 and UDPglucuronosyltransferase cofactors in alamethicin-activated human liver microsomes. Drug Metab Dispos 2009; 37(1): 82–89.
- Kim HJ, Cho JH, Klaassen CD. Depletion of hepatic 3'-phosphoadenosine 5'-phosphosulfate (PAPS) and sulfate in rats by xenobiotics that are sulfated. J Pharmacol Exp Ther 1995; 275: 654–658.
- Kindmark A, Jawaid A, Harbron CG, Barratt BJ, Bengtsson OF, Andersson TB, Carlsson S, Cederbrant KE, Gibson NJ, Armstrong M, Lagerström-Ferm ér ME, Dells én A, Brown EM, Thornton M, Dukes C, Jenkins SC, Firth MA, Harrod GO, Pinel TH, Billing-Clason SM, Cardon LR, March RE. Genome-wide pharmacogenetic investigation of a hepatic adverse event without clinical signs of immunopathology suggests an underlying immune pathogenesis. Pharmacogenomics J 2008; 8: 186–195.
- Klopf W, Worboys P. Scaling in vivo pharmacokinetics from in vitro metabolic stability data in drug discovery. Comb Chem High Throughput Screen. 2010; 13(2): 159–69.
- Kramer MA, Tracy TS. Studying cytochrome P450 kinetics in drug metabolism. Expert Opin Drug Metab Toxicol 2008; 4(5): 591–603.
- Kumar S, Mitra K, Kassahun K, Baillie TA. Approaches for minimizing metabolic activation of new drug candidates in drug discovery. Handb Exp Pharmacol 2010; (196): 511–544.
- Lave T, Coassolo P, Reigner B. Prediction of hepatic metabolic clearance based on interspecies allometric scaling techniques and in vitro–in vivo correlations. Clin Pharmacokinet 1999; 36: 211–231.
- Liebler DC, Guengerich FP. Elucidating mechanisms of drug-induced toxicity. Nat Rev Drug Discov 2005; 4: 410–420.
- Lin JH, Wong BK. Complexities of glucuronidation affecting in vitro in vivo extrapolation. Curr Drug Metab 2002; 3: 623–646.
- Masubuchi N, Makino C, Murayama N. Prediction of in vivo potential for metabolic activation of drugs into chemically reactive intermediate: Correlation of in vitro and in vivo generation of reactive intermediates and in vitro glutathione conjugate formation in rats and humans. Chem Res Toxicol 2007; 20: 455–464.
- McGinnity DF, Soars MG, Urbanowicz RA, Riley RJ. Evaluation of fresh and cryopreserved hepatocytes as in vitro drug metabolism tools for the prediction of metabolic clearance. Drug Metab Dispos 2004; 32(11): 1247–1253.
- Miners JO, Mackenzie PI, Knights KM. The prediction of drug-glucuronidation parameters in humans: UDP-glucuronosyltransferase enzyme-selective substrate and inhibitor probes for reaction phenotyping and in vitro–in vivo extrapolation of drug clearance and drug-drug interaction potential. Drug Metab Rev 2010; 42(1): 189–201.
- Mutlib A, Lam W, Atherton J, Chen H, Galatsis P, Stolle W. Application of stable isotope labeled glutathione and rapid scanning mass spectrometers in detecting and characterizing reactive metabolites. Rapid Commun Mass Spectrom 2005; 19: 3482–3492.
- Nakayama S, Atsumi R, Takakusa H, Kobayashi Y, Kurihara A, Nagai Y, Nakai D, Okazaki O. A zone classification system for risk assessment of idiosyncratic drug toxicity using daily dose and covalent binding. Drug Metab Dispos 2009; 37: 1956–1962.
- Nassar AE, Kamel AM, Clarimont C. Improving the decision-making process in the structural modification of drug candidates: Enhancing metabolic stability. Drug Discov Today 2004; 9(23): 1020–1028.
- Obach RS. Prediction of human clearance of twenty-nine drugs from hepatic micro-somal intrinsic clearance data: An examination of in vitro half-life approach and nonspecific binding to microsomes. Drug Metab Dispos 1999; 27: 1350–1359.
- Obach RS, Kalgutkar AS, Soglia JR, Zhao SX. Can in vitro metabolism-dependent covalent binding data in liver microsomes distinguish hepatotoxic from nonhepatotoxic drugs? An analysis of 18 drugs with consideration of intrinsic clearance and daily dose. Chem Res Toxicol 2008; 21: 1814–1822.
- Pelkonen O, Turpeinen M. In vitro–in vivo extrapolation of hepatic clearance: Biological tools, scaling factors, model assumptions and correct concentrations. Xenobiotica 2007; 37(10–11): 1066–1089.
- Rane A, Wilkinson GR, Shand DG. Prediction of hepatic extraction ratio from in vitro measurement of intrinsic clearance. J Pharmacol Exp Ther 1977; 200: 420–424.
- Roffey SJ, Obach RS, Gedge JI, Smith DA. What is the objective of the mass balance study? A retrospective analysis of data in animal and human excretion studies employing radiolabeled drugs. Drug Metab Rev 2007; 39(1): 17–43.
- Ruan Q, Peterman S, Szewc MA, Ma L, Cui D, Humphreys WG, Zhu M. An integrated method for metabolite detection and identification using a linear ion trap/Orbitrap mass spectrometer and multiple data processing techniques: Application to indinavir metabolite detection. J Mass Spectrom 2008; 43(2): 251–261.
- Shou M, Lu AY. Antibodies as a probe in cytochrome P450 research. Drug Metab Dispos 2009; 37(5): 925–931.
- Shu YZ, Johnson BM, Yang TJ. Role of biotransformation studies in minimizing metabolism-related liabilities in drug discovery. AAPS J 2008; 10(1): 178–192.
- Smith DA, Obach RS. Seeing through the mist: Abundance versus percentage. Commentary on metabolites in safety testing. Drug Metab Dispos 2005; 33: 1409–1417.
- Smith DA, Obach RS. Metabolites in safety testing (MIST): Considerations of mechanisms of toxicity with dose, abundance, and duration of treatment. Chem Res Toxicol 2009; 22: 267–279.
- Smith DA, Obach RS, Williams DP, Park BK. Clearing the MIST (metabolites in safety testing) of time: The impact of duration of administration on drug metabolite toxicity. Chem Biol Interact 2009; 179(1): 60–67.
- Soars MG, Burchell B, Riley RJ. In vitro analysis of human drug glucuronidation and prediction of in vivo metabolic clearance. J Pharmacol Exp Ther 2002; 301: 382–390.
- Soars MG, Grime K, Sproston JL, Webborn PJ, Riley RJ. Use of hepatocytes to assess the contribution of hepatic uptake to clearance in vivo. Drug Metab Dispos 2007a; 35 (6): 859–865.
- Soars MG, McGinnity DF, Grime K, Riley RJ. The pivotal role of hepatocytes in drug discovery. Chem Biol Interact 2007b; 168(1): 2–15.
- Srivastava A, Maggs JL, Antoine DJ, Williams DP, Smith DA, Park BK. Role of reactive metabolites in drug-induced hepatotoxicity. Handb Exp Pharmacol 2010; (196): 165–194.
- Stringer RA, Strain-Damerell C, Nicklin P, Houston JB. Evaluation of recombinant cytochrome P450 enzymes as an in vitro system for metabolic clearance predictions. Drug Metab Dispos 2009; 37(5): 1025–1034.
- Sun H, Scott DO. Structure-based drug metabolism predictions for drug design. Chem Biol Drug Des 2010; 75(1): 3–17.
- Takakusa H, Masumoto H, Yukinaga H, Makino C, Nakayama S, Okazaki O, Sudo K. Covalent binding and tissue distribution/retention assessment of drugs associated with idiosyncratic drug toxicity. Drug Metab Dispos 2008; 36: 1770–1779.
- Tang W, Lu AY. Drug metabolism and pharmacokinetics in support of drug design. Curr Pharm Des 2009; 15(19): 2170–2183.
- Thompson TN. Optimization of metabolic stability as a goal of modern drug design. Med Res Rev 2001; 21: 412–449.
- Tiller PR, Yu S, Bateman KP, Castro-Perez J, McIntosh IS, Kuo Y, Baillie TA. Fractional mass filtering as a means to assess circulating metabolites in early human clinical studies. Rapid Commun Mass Spectrom 2008a; 22(22): 3510–3516.
- Tiller PR, Yu S, Castro-Perez J, Fillgrove KL, Baillie TA. High-throughput, accurate mass liquid chromatography/tandem mass spectrometry on a quadrupole time-offlight system as a “first-line” approach for metabolite identification studies. Rapid Commun Mass Spectrom 2008b; 22(7): 1053–1061.
- Tolonen A, Turpeinen M, Pelkonen O. Liquid chromatography–mass spectrometry in in vitro drug metabolite screening. Drug Discov Today 2009; 14 (3–4): 120–133.
- Uetrecht J. Screening for the potential of a drug candidate to cause idiosyncratic drug reactions. Drug Discov Today 2003; 8: 832–837.
- Uetrecht J. Immune-mediated adverse drug reactions. Chem Res Toxicol 2009; 22(1): 24–34.
- U.S. Food and Drug Administration (FDA). Guidance for Industry: Safety Testing of Drug Metabolites, 2008, available: http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/ucm79266.pdf.
- Usui T, Mise M, Hashizume T, Yabuki M, Komuro S. Evaluation of the potential for drug-induced liver injury based on in vitro covalent binding to human liver proteins. Drug Metab Dispos 2009; 37: 2383–2392.
- Van Heek M, France CF, Compton DS, McLeod RL, Yumibe NP, Alton KB, Sybertz EJ, Davis HR, Jr. In vivo metabolism-based discovery of a potent cholesterol absorption inhibitor, SCH58235, in the rat and rhesus monkey through the identification of the active metabolites of SCH48461. J Pharmacol Exp Ther 1997; 283: 157–163.
- Walgren JL, Mitchell MD, Thompson DC. Role of metabolism in drug-induced idiosyncratic hepatotoxicity. Crit Rev Toxicol 2005; 35: 325–361.
- Walker D, Brady J, Dalvie D, Davis J, Dowty M, Duncan JN, Nedderman A, Obach RS, Wright P. A holistic strategy for characterizing the safety of metabolites through drug discovery and development. Chem Res Toxicol 2009; 22(10): 1653–1662.
- White RE. High-throughput screening in drug metabolism and pharmacokinetic support of drug discovery. Annu Rev Pharmacol Toxicol 2000; 40: 133–157.
- Wrona M, Mauriala T, Bateman KP, Mortishire-Smith RJ, O'Connor D. “All-in-one” analysis for metabolite identification using liquid chromatography/hybrid quadrupole time-of-flight mass spectrometry with collision energy switching. Rapid Commun Mass Spectrom 2005; 19(18): 2597–2602.
- Yamamoto T, Itoga H, Kohno Y, Nagata K, Yamazoe Y. Prediction of oral clearance from in vitro metabolic data using recombinant CYPs: Comparison among well-stirred, parallel-tube, distributed and dispersion models. Xenobiotica 2005; 35: 627–646.
- Yan Z, Maher N, Torres R, Caldwell GW, Huebert N. Rapid detection and characterization of minor reactive metabolites using stable-isotope trapping in combination with tandem mass spectrometry. Rapid Commun Mass Spectrom 2005; 19: 3322–3330.
- Yao M, Ma L, Duchoslav E, Zhu M. Rapid screening and characterization of drug metabolites using multiple ion monitoring dependent product ion scan and post-acquisition data mining on a hybrid triple quadrupole-linear ion trap mass spectrometer. Rapid Commun Mass Spectrom 2009; 23(11): 1683–1693.
- Zhang H, Davis CD, Sinz MW, Rodrigues AD. Cytochrome P450 reaction-phenotyping: An industrial perspective. Expert Opin Drug Metab Toxicol 2007; 3(5): 667–687.
- Zhang NR, Yu S, Tiller P, Yeh S, Mahan E, Emary WB. Quantitation of small molecules using high-resolution accurate mass spectrometers — A different approach for analysis of biological samples. Rapid Commun Mass Spectrom 2009a; 23(7): 1085–1094.
- Zhang Z, Zhu M, Tang W. Metabolite identification and profiling in drug design: Current practice and future directions. Curr Pharm Des 2009b; 15(19): 2220–2235.
- Zhang H, Zhang D, Ray K, Zhu M. Mass defect filter technique and its applications to drug metabolite identification by high-resolution mass spectrometry. J Mass Spec-trom 2009c 44(7): 999–1016.
- Zhu M, Zhang D, Zhang H, Shyu WC. Integrated strategies for assessment of metabolite exposure in humans during drug development: Analytical challenges and clinical development considerations. Biopharm Drug Dispos 2009; 30 (4): 163–184.
