Skip to main content
Log in

Improving Early Drug Discovery through ADME Modelling

An Overview

  • Review Article
  • Published:
Drugs in R & D Aims and scope Submit manuscript

Abstract

Drug development is an intrinsically risky business. Like a high stakes poker game the entry costs are high and the probability of winning is low. Indeed, only a tiny percentage of lead compounds ever reach US FDA approval. At any point during the drug development process a prospective drug lead may be terminated owing to lack of efficacy, adverse effects, excessive toxicity, poor absorption or poor clearance. Unfortunately, the more promising a drug lead appears to be, the more costly it is to terminate its development. Typically, the cost of killing a drug grows exponentially as a drug lead moves further down the development pipeline. As a result there is considerable interest in developing either experimental or computational methods that can identify potentially problematic drug leads at the earliest stages in their development. One promising route is through the prediction or modelling of ADME (absorption, distribution, metabolism and excretion). ADME data, whether experimentally measured or computationally predicted, provide key insights into how a drug will ultimately be treated or accepted by the body. So while a drug lead may exhibit phenomenal efficacy in vitro, poor ADME results will almost invariably terminate its development. This review focuses on the use of ADME modelling to reduce late-stage attrition in drug discovery programmes. It also highlights what tools exist today for visualising and predicting ADME data, what tools need to be developed, and the importance of integrating ADME data to aid in compound selection during the earliest phases of drug discovery. In particular, it highlights what tools exist today for visualising and predicting ADME data including: (1) ADME parameter predictors; (2) metabolic fate predictors; (3) metabolic stability predictors; (4) cytochrome P450 substrate predictors; and (5) physiology-based pharmacokinetic (PBPK) modelling software. It also discusses what kinds of tools need to be developed, and the importance of integrating ADME data to aid in compound selection during the earliest phases of drug discovery.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Table I
Table II
Table III
Table IV
Table V

Similar content being viewed by others

References

  1. DiMasi JA, Hansen RW, Grabowski HG. The price of innovation: new estimates of drug development costs. J Health Econ 2003; 22: 151–85

    Article  PubMed  Google Scholar 

  2. Bains W. Failure rates in drug discovery and development: will we ever get any better? Drug Disc World 2004; Fall: 9–17

    Google Scholar 

  3. Horton R. Vioxx, the implosion of Merck and aftershocks at the FDA. Lancet 2004; 364: 1995–6

    Article  PubMed  Google Scholar 

  4. Lang, L. Valdecoxib (Bextra) withdrawal leaves pain relief treatment gap. Gastroenterology 2005; 128: 1769–70

    Article  PubMed  Google Scholar 

  5. Lazarou J, Pomeranz BH, Corey PN. Incidence of adverse drug reactions in hospitalized patients: a meta-analysis of prospetive studies. JAMA 1998; 279: 1200–5

    Article  PubMed  CAS  Google Scholar 

  6. Glick M, Klon AE, Acklin P, et al. Enriching extremely noisy high-throughput screening data using a naive Bayes classifier. J Biomol Screening 2004; 9: 32–6

    Article  CAS  Google Scholar 

  7. Rogers D, Brown RD, Hahn M. Using extended-connectivity fingerprints with Laplacian-modified Bayesian analysis in high-throughput screening follow-up. J Biomol Screening 2005; 10: 682–6

    Article  CAS  Google Scholar 

  8. Klon AE, Glick M, Thoma M, et al. Finding more needles in the haystack: a simple and efficient method for improving high-throughput docking results. J Med Chem 2004; 47: 2743–9

    Article  PubMed  CAS  Google Scholar 

  9. Li AP. Screening for human ADME/Tox drug properties in drug discovery. Drug Discov Today 2001; 6: 357–66

    Article  PubMed  CAS  Google Scholar 

  10. Dalvie D. Recent advances in the applications of radioisotopes in drug metabolism, toxicology and pharmacokinetics. Curr Pharm Des 2000; 6: 1009–28

    Article  PubMed  CAS  Google Scholar 

  11. Marathe PH, Shyu WC, Humphreys WG. The use of radiolabeled compounds for ADME studies in discovery and exploratory development. Curr Pharm Des 2004; 10: 2991–3008

    Article  PubMed  CAS  Google Scholar 

  12. Chu I, Nomeir AA. Utility of mass spectrometry for in-vitro ADME assays. Curr Drug Metab 2006; 7: 467–77

    Article  PubMed  CAS  Google Scholar 

  13. Nicholson JK, Connelly J, Lindon JC, et al. Metabonomics: a platform for studying drug toxicity and gene function. Nat Rev Drug Discov 2002; 1: 153–61

    Article  PubMed  CAS  Google Scholar 

  14. Van de Waterbeemd H. From in vivo to in vitro/in silico ADME: progress and challenges. Expert Opin Drug Metab Toxicol 2005; 1: 1–4

    Article  PubMed  Google Scholar 

  15. Jain KK. Applications of AmpliChip CYP450. Mol Diagn 2005; 9: 119–27

    Article  PubMed  Google Scholar 

  16. Garg P, Verma J. In silico prediction of blood brain barrier permeability: an artificial neural network model. J Chem Inf Model 2006; 46: 289–97

    Article  PubMed  CAS  Google Scholar 

  17. Zhao YH, Le J, Abraham MH, et al. Evaluation of human intestinal absorption data and subsequent derivation of a quantitative structure-activity relationship (QSAR) with the Abraham descriptors. J Pharm Sci 2001; 90 (6): 749–84

    Article  PubMed  CAS  Google Scholar 

  18. Iyer M, Tseng YJ, Senese CL, et al. Prediction and mechanistic interpretation of human oral drug absorption using MI-QSAR analysis. Mol Pharmaceutics 2007; 4: 218–31

    Article  CAS  Google Scholar 

  19. Lombardo F, Obach RS, Shalaeva MY, et al. Prediction of human volume of distribution values for neutral and basic drugs: 2. Extended data set and leave-class-out statistics. J Med Chem 2004; 47 (5): 1242–50

    Article  PubMed  CAS  Google Scholar 

  20. Klon AE, Lowrie JF, Diller DJ. Improved naïve Bayesian modeling of numerical data for absorption, distribution, metabolism and excretion (ADME) property prediction. J Chem Inf Model 2006; 46: 1945–56

    Article  PubMed  CAS  Google Scholar 

  21. Chiou WL. The rate and extent of oral bioavailability versus the rate and extent of oral absorption: clarification and recommendation of terminology. J Pharmacokinet Pharmacodyn 2001; 28: 3–6

    Article  PubMed  CAS  Google Scholar 

  22. Tetko IV. The WWW as a tool to obtain molecular parameters. Mini Rev Med Chem 2003; 3: 809–20

    Article  PubMed  CAS  Google Scholar 

  23. Selassie CD, Mekapati SB, Verma RP. QSAR: then and now. Curr Top Med Chem. 2002; 2: 1357–79

    Article  PubMed  CAS  Google Scholar 

  24. Weininger D. SMILES, a chemical language and information system: 1. Introduction to methodology and encoding rules. J Chem Inf Comput Sci 1988; 28: 31–6

    Article  CAS  Google Scholar 

  25. Miteva MA, Violas S, Montes M, et al. FAF-Drugs: free ADME/tox filtering of compound collections. Nucleic Acids Res 2006; 34: W738–44

    Article  PubMed  CAS  Google Scholar 

  26. Geldenhuys WJ, Gaasch KE, Watson M, et al. Optimizing the use of open-source software applications in drug discovery. Drug Discov Today 2006; 11: 127–32

    Article  PubMed  CAS  Google Scholar 

  27. Lipinski CA. Drug-like properties and the causes of poor solubility and poor permeability. J Pharmacol Toxicol Methods 2000; 44: 235–49

    Article  PubMed  CAS  Google Scholar 

  28. Andrews CW, Bennett L, Yu LX. Predicting human oral bioavailability of a compound: development of a novel quantitative structure-bioavailability relationship. Pharm Res 2000; 17: 639–44

    Article  PubMed  CAS  Google Scholar 

  29. Yoshida F, Topliss JG. QSAR model for drug human oral bioavailability. J Med Chem 2000; 43: 2575–85

    Article  PubMed  CAS  Google Scholar 

  30. Hou T, Wang J, Zhang W, et al. ADME evaluation in drug discovery: 6. Can oral bioavailability in humans be effectively predicted by simple property-based rules? J Chem Inf Model 2007; 47: 460–3

    Article  PubMed  CAS  Google Scholar 

  31. Mitchell T. Machine learning. New York: McGraw Hill, 1997

    Google Scholar 

  32. Cruz JA, Wishart DS. Applications of machine learning in cancer prediction and prognosis. Cancer Informatics 2006; 2: 59–67

    Google Scholar 

  33. Rodvold DM, McLeod DG, Brandt JM, et al. Introduction to artificial neural networks for physicians: taking the lid off the black box. Prostate 2001; 46: 39–44

    Article  PubMed  CAS  Google Scholar 

  34. Hou T, Wang J, Zhang W. Recent advances in computational prediction of drug absorption and permeability in drug discovery. Curr Medicinal Chem 2006; 13: 2653–67

    Article  CAS  Google Scholar 

  35. Stouch TR, Kenyon JR, Johnson SR, et al. In silico ADME/Tox: models fail. J Comput Aided Mol Des 2003; 17: 83–92

    Article  PubMed  CAS  Google Scholar 

  36. Lombardo F, Gifford E, Shalaeva MY. In silico ADME prediction: data, models, facts and myths. Mini Rev Med Chem 2003; 3: 861–75

    Article  PubMed  CAS  Google Scholar 

  37. Filliponi E, Cruciani G, Tabarrini O, et al. QSAR study and Volsurf characterization of anti-HIV quinolone library. J Comput Aided Mol Des 1001; 15: 203–7

    Article  Google Scholar 

  38. Liao C, Liu B, Shi L, et al. Construction of a virtual combinatorial library using SMILES strings to discover potential structure-diverse PPAR modulators. Eur J Med Chem 2005; 40: 632–40

    Article  PubMed  CAS  Google Scholar 

  39. Ulven T, Receveur JM, Grimstrup M, et al. Novel selective orally active CRTH2 antagonists for allergic inflammation from in silico derived hits. J Med Chem 2006; 49: 6638–41

    Article  PubMed  Google Scholar 

  40. Samiulla DS, Vaidyanathan VV, Arun PC, et al. Rational selection of structurally diverse natural product scaffolds with favorable ADME properties for drug discovery. Mol Divers 2005; 9: 131–9

    Article  PubMed  CAS  Google Scholar 

  41. Baranczewski P, Stanczak A, Sundberg K, et al. Introduction to in vitro estimation of metabolic stability and drug interactions of new chemical entities in drug discovery and development. Pharmacol Rep 2006; 58: 453–72

    PubMed  CAS  Google Scholar 

  42. Yap CW, Xue Y, Li ZR, et al. Application of support vector machines to in silico prediction of cytochrome p450 enzyme substrates and inhibitors. Curr Top Med Chem 2006; 6: 1593–607

    Article  PubMed  CAS  Google Scholar 

  43. Fox T, Kriegl JM. Machine learning techniques for in silico modeling of drug metabolism. Curr Top Med Chem 2006; 6: 1579–91

    Article  PubMed  CAS  Google Scholar 

  44. Pelkonen O, Raunio H. In vitro screening of drug metabolism during drug development: can we trust the predictions? Expert Opin Drug Metab Toxicol 2005; 1: 49–59

    Article  PubMed  CAS  Google Scholar 

  45. Gerlowski LE, Jain PK. Physiologically based pharmacokinetic modelling: principles and applications. J Pharm Sci 1983; 72: 1103–127

    Article  PubMed  CAS  Google Scholar 

  46. Theil FP, Guentert TW, Haddad S, et al. Utility of physiologically based pharmacokinetic models to drug development and rational drug discovery candidate selection. Toxicol Lett 2003; 138: 29–49

    Article  PubMed  CAS  Google Scholar 

  47. Norris DA, Leesman GD, Sinko PJ, et al. Development of predictive pharmacokinetic simulation models for drug discovery. J Control Release 2000; 65: 55–62

    Article  PubMed  CAS  Google Scholar 

  48. Agoram B, Woltosz WS, Bolger MB. Predicting the impact of physiological and biochemical processes on oral drug bioavailability. Adv Drug Deliv Rev 2001; 50 Suppl. 1: S41–67

    Article  PubMed  CAS  Google Scholar 

  49. Kuentz M, Nick S, Parrott N, et al. A strategy for preclinical formulation development using GastroPlus as pharmacokinetic simulation tool and a statistical screening design applied to a dog study. Eur J Pharm Sci 2006; 27: 91–9

    Article  PubMed  CAS  Google Scholar 

  50. Qin LX, Beyer RP, Hudson FN, et al. Evaluation of methods for oligonucleotide array data via quantitative real-time PCR. BMC Bioinformatics 2006; 7: 23

    Article  PubMed  Google Scholar 

  51. Hou TJ, Xia K, Zhang W, et al. ADME evaluation in drug discovery: 4. Prediction of aqueous solubility based on atom contribution approach. J Chem Inf Comp Sci 2004; 44: 266–75

    Article  CAS  Google Scholar 

  52. Green DV. Virtual screening of virtual libraries. Prog Med Chem 2003; 41: 61–97

    Article  PubMed  CAS  Google Scholar 

  53. Stoner CL, Gifford E, Stankovic C, et al. Implementation of an ADME enabling selection and visualization tool for drug dicovery. J Pharm Sci 2004; 93: 1131–41

    Article  PubMed  CAS  Google Scholar 

  54. Turinsky A, Sensen CW. On the way to building an integrated computational environment for the study of developmental patterns and genetic diseases. Int J Nanomed 2006; 1: 89–96

    Article  Google Scholar 

Download references

Acknowledgements

The author acknowledges Genome Canada, Genome Alberta and the National Institute for Nanotechnology (NRC) for their financial support in the preparation of this review. The author has no conflicts of interest that are directly relevant to the content of this review.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to David S. Wishart.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wishart, D.S. Improving Early Drug Discovery through ADME Modelling. Drugs R D 8, 349–362 (2007). https://doi.org/10.2165/00126839-200708060-00003

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.2165/00126839-200708060-00003

Keywords

Navigation