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Predicting the Risks of Drug-Induced Liver Injury in Humans Utilizing Computational Modeling

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Advances in Computational Toxicology

Abstract

Drug-induced liver injury (DILI ) is a significant challenge to clinicians, drug developers, as well as regulators. There is an unmet need to reliably predict risk for DILI . Developing a risk management plan to improve the prediction of a drug’s hepatotoxic potential is a long-term effort of the research community. Robust predictive models or biomarkers are essential for assessing the risk for DILI in humans, while an improved DILI annotation is vital and largely affects the accuracy and utility of the developed predictive models . In this chapter, we will focus on the DILI research efforts at the National Center for Toxicological Research of the US Food and Drug Administration . We will first introduce our drug label-based approach to annotate the DILI risk associated with individual drugs and then upon these annotations we developed a series of predictive models that could be used to assess the potential of DILI risk, including the “rule-of-two ” model , DILI score model , and conventional and modified Quantitative structure–activity relationship (QSAR ) models.

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Abbreviations

DF:

Decision Forest

DILI:

Drug-Induced Liver Injury

DILIN:

Drug-Induced Liver Injury Network

EMA:

European Medicines Agency

FDA:

Food and Drug Administration

LTKB:

Liver Toxicity Knowledge Base

MOA:

Mode of Action

QSAR:

Quantitative Structure–Activity Relationship

RM:

Reactive Metabolites

References

  1. Chen M et al (2011) FDA-approved drug labeling for the study of drug-induced liver injury. Drug Discov Today 16(15–16):697–703

    Article  Google Scholar 

  2. Avigan MI, Muñoz MA (2018) Perspectives on the regulatory and clinical science of drug-induced liver injury (DILI). In: Drug-induced liver toxicity. Springer, Berlin, pp 367–393

    Google Scholar 

  3. Noureddin N, Kaplowitz N (2018) Overview of mechanisms of drug-induced liver injury (DILI) and key challenges in DILI research. In: Drug-induced liver toxicity. Springer, Berlin, pp 3–18

    Google Scholar 

  4. Fielden MR, Kolaja KL (2008) The role of early in vivo toxicity testing in drug discovery toxicology. Expert Opin Drug Saf 7(2):107–110

    Article  CAS  Google Scholar 

  5. Zhang M, Chen M, Tong W (2012) Is toxicogenomics a more reliable and sensitive biomarker than conventional indicators from rats to predict drug-induced liver injury in humans? Chem Res Toxicol 25(1):122–129

    Article  CAS  Google Scholar 

  6. Khan I, Hausner E (2018) Regulatory toxicological studies: identifying drug-induced liver injury using nonclinical studies. In: Drug-induced liver toxicity. Springer, Berlin, pp 395–410

    Google Scholar 

  7. Olson H et al (2000) Concordance of the toxicity of pharmaceuticals in humans and in animals. Regul Toxicol Pharmacol 32(1):56–67

    Article  CAS  Google Scholar 

  8. Lewis W et al (1996) Fialuridine and its metabolites inhibit DNA polymerase gamma at sites of multiple adjacent analog incorporation, decrease mtDNA abundance, and cause mitochondrial structural defects in cultured hepatoblasts. Proc Natl Acad Sci 93(8):3592–3597

    Article  CAS  Google Scholar 

  9. Chen M et al (2013) Liver Toxicity Knowledge Base (LTKB)—a systems approach to a complex end point. Clin Pharmacol Ther 95(5):409–412

    Article  Google Scholar 

  10. Chen M et al (2014) Toward predictive models for drug-induced liver injury in humans: are we there yet? Biomark Med 8(2):201–213

    Article  CAS  Google Scholar 

  11. Chen M, Borlak J, Tong W (2013) High lipophilicity and high daily dose of oral medications are associated with significant risk for drug-induced liver injury. Hepatology 58(1):388–396

    Article  CAS  Google Scholar 

  12. Chen M, Borlak J, Tong W (2016) A model to predict severity of drug-induced liver injury in humans. Hepatology 64(3):931–940

    Article  CAS  Google Scholar 

  13. Chen M et al (2013) Quantitative structure-activity relationship models for predicting drug-induced liver injury based on FDA-approved drug labeling annotation and using a large collection of drugs. Toxicol Sci 136(1):242–249

    Article  CAS  Google Scholar 

  14. Chen M et al (2015) Drug-induced liver injury: interactions between drug properties and host factors. J Hepatol 63(2):503–514

    Article  CAS  Google Scholar 

  15. Chen M et al (2016) DILIrank—the largest reference drug list ranked by the risk for developing drug-induced liver injury in humans. Drug Discov Today 21(4):648–653

    Article  CAS  Google Scholar 

  16. Chen M et al (2014) An improved testing strategy to predict risk for drug-induced liver injury in humans using high-content screening assays and the ‘Rule-of-two’ model. Arch Toxicol 88(7):1439–1449

    Article  CAS  Google Scholar 

  17. Liu Z et al (2011) Translating clinical findings into knowledge in drug safety evaluation–drug induced liver injury prediction system (DILIps). PLoS Comput Biol 7(12):e1002310

    Article  CAS  Google Scholar 

  18. Mishra P, Chen M (2017) Application of “Rule-of-two” model to direct-acting antivirals for treatment of chronic hepatitis C: can it predict potential for hepatotoxicity? Gastroenterology 152(6):1270–1274

    Article  Google Scholar 

  19. Wang Y et al (2013) A unifying ontology to integrate histological and clinical observations for drug-induced liver injury. Am J Pathol 182(4):1180–1187

    Article  CAS  Google Scholar 

  20. Yu K et al (2014) High daily dose and being a substrate of cytochrome P450 enzymes are two important predictors of drug-induced liver injury. Drug Metab Dispos 42(4):744–750

    Article  Google Scholar 

  21. Yu K et al (2014) Mining hidden knowledge for drug safety assessment: topic modeling of LiverTox as a case study. BMC Bioinform 15(Suppl 17):S6

    Article  Google Scholar 

  22. Przybylak KR, Cronin MT (2012) In silico models for drug-induced liver injury—current status. Expert Opin Drug Metab Toxicol 8(2):201–217

    Article  CAS  Google Scholar 

  23. Abboud G, Kaplowitz N (2007) Drug-induced liver injury. Drug Saf 30(4):277–294

    Article  CAS  Google Scholar 

  24. Greene N et al (2010) Developing structure-activity relationships for the prediction of hepatotoxicity. Chem Res Toxicol 23(7):1215–1222

    Article  CAS  Google Scholar 

  25. Gustafsson F et al (2013) A correlation between the in vitro drug toxicity of drugs to cell lines which express human P450s and their propensity to cause liver injury in humans. Toxicol Sci 137(1):189–211

    Article  Google Scholar 

  26. Suzuki A et al (2010) Drugs associated with hepatotoxicity and their reporting frequency of liver adverse events in VigiBase: unified list based on international collaborative work. Drug Saf 33(6):503–522

    Article  CAS  Google Scholar 

  27. Ursem CJ et al (2009) Identification of structure-activity relationships for adverse effects of pharmaceuticals in humans. Part A: use of FDA post-market reports to create a database of hepatobiliary and urinary tract toxicities. Regul Toxicol Pharmacol 54(1):1–22

    Article  CAS  Google Scholar 

  28. Rodgers AD et al (2010) Modeling liver-related adverse effects of drugs using k nearest neighbor quantitative structure-activity relationship method. Chem Res Toxicol 23(4):724–732

    Article  CAS  Google Scholar 

  29. Zhu X, Kruhlak NL (2014) Construction and analysis of a human hepatotoxicity database suitable for QSAR modeling using post-market safety data. Toxicology 321:62–72

    Article  CAS  Google Scholar 

  30. Sakatis MZ et al (2012) Preclinical strategy to reduce clinical hepatotoxicity using in vitro bioactivation data for >200 compounds. Chem Res Toxicol 25(10):2067–2082

    Article  CAS  Google Scholar 

  31. Lammert C et al (2008) Relationship between daily dose of oral medications and idiosyncratic drug-induced liver injury: search for signals. Hepatology 47(6):2003–2009

    Article  CAS  Google Scholar 

  32. Weng Z et al (2015) A comprehensive study of the association between drug hepatotoxicity and daily dose, liver metabolism, and lipophilicity using 975 oral medications. Oncotarget 6(19):17031–17038

    Article  Google Scholar 

  33. Xu JJ et al (2008) Cellular imaging predictions of clinical drug-induced liver injury. Toxicol Sci 105(1):97–105

    Article  CAS  Google Scholar 

  34. Atienzar FA, Nicolas J-M (2018) Prediction of human liver toxicity using in vitro assays: limitations and opportunities. In: Drug-induced liver toxicity. Springer, Berlin, pp 125–150

    Google Scholar 

  35. Thakkar S et al (2018) The Liver Toxicity Knowledge Base (LKTB) and drug-induced liver injury (DILI) classification for assessment of human liver injury. Expert Rev Gastroenterol Hepatol 12(1):31–38

    Article  CAS  Google Scholar 

  36. Chen M et al (2014) Toward predictive models for drug-induced liver injury in humans: are we there yet? Biomark Med 8(2):201–213

    Article  CAS  Google Scholar 

  37. Chen M et al (2016) DILIrank: the largest reference drug list ranked by the risk for developing drug-induced liver injury in humans. Drug Discov Today 21(4):648–653

    Article  CAS  Google Scholar 

  38. Thakkar S et al (2018) Drug-induced liver injury (DILI) classification and its application on human DILI risk prediction. In: Drug-induced liver toxicity. Springer, Berlin, pp 45–59

    Google Scholar 

  39. Regev A (2014) Drug-induced liver injury and drug development: industry perspective. Semin Liver Dis 34(02):227–239

    Article  CAS  Google Scholar 

  40. García-Cortés M et al (2011) Causality assessment methods in drug induced liver injury: strengths and weaknesses. J Hepatol 55(3):683–691

    Article  Google Scholar 

  41. Light DS, Aleo MD, Kenna JG (2018) Interpretation, integration, and implementation of in vitro assay data: the predictive toxicity challenge. In: Drug-induced liver toxicity. Springer, Berlin, pp 345–364

    Google Scholar 

  42. Ballet F (2010) Back to basics for idiosyncratic drug-induced liver injury: dose and metabolism make the poison. Gastroenterol Clin Biol 34(6–7):348–350

    Article  CAS  Google Scholar 

  43. Walgren JL, Mitchell MD, Thompson DC (2005) Role of metabolism in drug-induced idiosyncratic hepatotoxicity. Crit Rev Toxicol 35(4):325–361

    Article  CAS  Google Scholar 

  44. Uetrecht JP (1999) New concepts in immunology relevant to idiosyncratic drug reactions: the “danger hypothesis” and innate immune system. Chem Res Toxicol 12(5):387–395

    Article  CAS  Google Scholar 

  45. Senior JR (2008) What is idiosyncratic hepatotoxicity? What is it not? Hepatology 47(6):1813–1815

    Article  Google Scholar 

  46. Uetrecht J (2001) Prediction of a new drug’s potential to cause idiosyncratic reactions. Curr Opin Drug Discov Dev 4(1):55–59

    CAS  Google Scholar 

  47. Lammert C et al (2010) Oral medications with significant hepatic metabolism at higher risk for hepatic adverse events. Hepatology 51(2):615–620

    Article  CAS  Google Scholar 

  48. Leeson PD, Springthorpe B (2007) The influence of drug-like concepts on decision-making in medicinal chemistry. Nat Rev Drug Discov 6(11):881–890

    Article  CAS  Google Scholar 

  49. Waring MJ (2010) Lipophilicity in drug discovery. Expert Opin Drug Discov 5(3):235–248

    Article  CAS  Google Scholar 

  50. Leeson PD (2018) Impact of physicochemical properties on dose and hepatotoxicity of oral drugs. Chem Res Toxicol 31(6):494–505

    Article  CAS  Google Scholar 

  51. Shah F et al (2015) Setting clinical exposure levels of concern for drug-induced liver injury (DILI) using mechanistic in vitro assays. Toxicol Sci 147(2):500–514

    Article  CAS  Google Scholar 

  52. Mishra P, Chen M (2017) Direct-acting antivirals for chronic hepatitis C: can drug properties signal potential for liver injury? Gastroenterology 152(6):1270–1274

    Article  Google Scholar 

  53. Kaplowitz N (2013) Avoiding idiosyncratic DILI: two is better than one. Hepatology 58(1):15–17

    Article  Google Scholar 

  54. Lewis JH (2014) Drug-induced liver injury, dosage, and drug disposition: is idiosyncrasy really unpredictable? Clin Gastroenterol Hepatol 4(1):4–8

    Google Scholar 

  55. Aleo MD et al (2014) Human drug-induced liver injury severity is highly associated to dual inhibition of liver mitochondrial function and bile salt export pump. Hepatology 60(3):1015–1022

    Article  CAS  Google Scholar 

  56. Stephens C, Andrade RJ, Lucena MI (2014) Mechanisms of drug-induced liver injury. Curr Opin Allergy Clin Immunol 14(4):286–292

    Article  CAS  Google Scholar 

  57. Park BK et al (2011) Managing the challenge of chemically reactive metabolites in drug development. Nat Rev Drug Discov 10(4):292–306

    Article  CAS  Google Scholar 

  58. Stepan AF et al (2011) Structural alert/reactive metabolite concept as applied in medicinal chemistry to mitigate the risk of idiosyncratic drug toxicity: a perspective based on the critical examination of trends in the top 200 drugs marketed in the United States. Chem Res Toxicol 24(9):1345–1410

    Article  CAS  Google Scholar 

  59. Smith DA, Obach RS (2006) Metabolites and safety: what are the concerns, and how should we address them? Chem Res Toxicol 19(12):1570–1579

    Article  CAS  Google Scholar 

  60. Uetrecht J (2006) Evaluation of which reactive metabolite, if any, is responsible for a specific idiosyncratic reaction*. Drug Metab Rev 38(4):745–753

    Article  CAS  Google Scholar 

  61. Srivastava A et al (2010) Role of reactive metabolites in drug-induced hepatotoxicity. In: Adverse drug reactions. Springer, Berlin, pp 165–194

    Google Scholar 

  62. Park B et al (2011) Drug bioactivation and protein adduct formation in the pathogenesis of drug-induced toxicity. Chem Biol Interact 192(1):30–36

    Article  CAS  Google Scholar 

  63. Kalgutkar AS et al (2005) A comprehensive listing of bioactivation pathways of organic functional groups. Curr Drug Metab 6(3):161–225

    Article  CAS  Google Scholar 

  64. Evans DC et al (2004) Drug-protein adducts: an industry perspective on minimizing the potential for drug bioactivation in drug discovery and development. Chem Res Toxicol 17(1):3–16

    Article  CAS  Google Scholar 

  65. Chen M et al (2012) A decade of toxicogenomic research and its contribution to toxicological science. Toxicol Sci 130(2):217–228

    Article  CAS  Google Scholar 

  66. Hong H et al (2018) Quantitative structure–activity relationship models for predicting risk of drug-induced liver injury in humans. In: Drug-induced liver toxicity. Springer, Berlin, pp 77–100

    Google Scholar 

  67. Fisk L, Greene N, Naven R (2018) Physicochemical properties and structural alerts. In: Drug-induced liver toxicity. Springer, pp 61–76

    Google Scholar 

  68. Hong H et al (2017) Development of decision forest models for prediction of drug-induced liver injury in humans using a large set of FDA-approved drugs. Sci Rep 7(1):17311

    Article  Google Scholar 

  69. Wu L et al (2017) Integrating drug’s mode of action into quantitative structure-activity relationships for improved prediction of drug-induced liver injury. J Chem Inf Model 57(4):1000–1006

    Article  CAS  Google Scholar 

  70. Tice RR et al (2013) Improving the human hazard characterization of chemicals: a Tox21 update. Environ Health Perspect 121(7):756

    Article  Google Scholar 

  71. Hong H et al (2008) Mold2, molecular descriptors from 2D structures for chemoinformatics and toxicoinformatics. J Chem Inf Model 48(7):1337–1344

    Article  CAS  Google Scholar 

  72. Liu Z et al (2011) Translating clinical findings into knowledge in drug safety evaluation—drug induced liver injury prediction system (DILIps). PLoS Comput Biol 7(12):e1002310

    Article  CAS  Google Scholar 

  73. Kuhn M et al (2010) A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol 6:343

    Article  Google Scholar 

  74. Wong MW et al (2018) Status and use of Induced Pluripotent Stem Cells (iPSCs) in toxicity testing. In: Drug-induced liver toxicity. Springer, Berlin, pp 199–212

    Google Scholar 

  75. Monckton CP, Khetani SR (2018) Engineered human liver cocultures for investigating drug-induced liver injury. In: Drug-induced liver toxicity. Springer, Berlin, pp 213–248

    Google Scholar 

  76. Otieno MA, Gan J, Proctor W (2018) Status and future of 3D cell culture in toxicity testing. In: Drug-induced liver toxicity. Springer, Berlin, pp 249–261

    Google Scholar 

  77. Persson M (2018) High content screening for prediction of human drug-induced liver injury. In: Drug-induced liver toxicity. Springer, Berlin, pp 331–343

    Google Scholar 

  78. Porceddu M et al (2018) In vitro assessment of mitochondrial toxicity to predict drug-induced liver injury. In: Drug-induced liver toxicity. Springer, Berlin, pp 283–300

    Google Scholar 

  79. Chen M et al (2015) Drug-induced liver injury: Interactions between drug properties and host factors. J Hepatol 63(2):503–514

    Article  CAS  Google Scholar 

  80. Stephens C, Lucena MI, Andrade RJ (2018) Host risk modifiers in idiosyncratic drug-induced liver injury (DILI) and its interplay with drug properties. In: Drug-induced liver toxicity. Springer, Berlin, pp 477–496

    Google Scholar 

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Chen, M. et al. (2019). Predicting the Risks of Drug-Induced Liver Injury in Humans Utilizing Computational Modeling. In: Hong, H. (eds) Advances in Computational Toxicology. Challenges and Advances in Computational Chemistry and Physics, vol 30. Springer, Cham. https://doi.org/10.1007/978-3-030-16443-0_13

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