Skip to main content

Prediction of Pharmacokinetic Parameters

  • Protocol
  • First Online:
Computational Toxicology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 929))

Abstract

In silico tools specifically developed for prediction of pharmacokinetic parameters are of particular interest to pharmaceutical industry because of the high potential of discarding inappropriate molecules during an early stage of drug development itself with consequent saving of vital resources and valuable time. The ultimate goal of the in silico models of absorption, distribution, metabolism, and excretion (ADME) properties is the accurate prediction of the in vivo pharmacokinetics of a potential drug molecule in man, whilst it exists only as a virtual structure. Various types of in silico models developed for successful prediction of the ADME parameters like oral absorption, bioavailability, plasma protein binding, tissue distribution, clearance, half-life, etc. have been briefly described in this chapter.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Miteva MA, Violas S, Montes M et al (2006) FAF-drugs: free ADME/tox filtering of compound collections. Nucleic Acids Res 34:W738–W744

    Article  PubMed  CAS  Google Scholar 

  2. Boobis A, Gundert-Remy U, Kremers P et al (2002) In silico prediction of ADME and pharmacokinetics: report of an expert meeting organised by COST B15. Eur J Pharm Sci 17:183–193

    Article  PubMed  CAS  Google Scholar 

  3. Huisinga W, Telgmann R, Wulkow M (2006) The virtual lab approach to pharmacokinetics: design principles and concepts. Drug Discov Today 11:800–805

    Article  PubMed  CAS  Google Scholar 

  4. Hodgson J (2001) ADMET—turning chemicals into drugs. Nat Biotechnol 19:722–726

    Article  PubMed  CAS  Google Scholar 

  5. Grass GM, Sinko PJ (2002) Physiologically-based pharmacokinetic simulation modeling. Adv Drug Deliv Rev 54:433–451

    Article  PubMed  CAS  Google Scholar 

  6. Kennedy T (1997) Managing the drug discovery/development interface. Drug Disc Today 2:436–444

    Article  Google Scholar 

  7. Spalding DJM, Harker AJ, Bayliss MK (2000) Combining high-throughput pharmacokinetic screens at the hits-to-leads stage of drug discovery. Drug Disc Today 5:S70–S76

    Article  CAS  Google Scholar 

  8. Butina D, Segall MD, Frankcombe K (2002) Predicting ADME properties in silico: methods and models. Drug Disc Today 7:S83–S88

    Article  CAS  Google Scholar 

  9. van Waterbeemd H, Gifford E (2003) ADMET in silico modelling: towards prediction paradise? Nat Rev Drug Disc 2:192–204

    Article  Google Scholar 

  10. Hou T, Xu X (2004) Recent development and application of virtual screening in drug discovery: an overview. Curr Pharm Des 10:1011–1033

    Article  PubMed  CAS  Google Scholar 

  11. Hou T, Wang J, Zhang W et al (2006) Recent advances in computational prediction of drug absorption and permeability in drug discovery. Curr Med Chem 13:2653–2667

    Article  PubMed  CAS  Google Scholar 

  12. Li AP (2001) Screening for human ADME/Tox drug proteins in drug discovery. Drug Disc Today 6:357–366

    Article  CAS  Google Scholar 

  13. Paul Y, Dhake AS, Singh B (2009) In silico quantitative structure pharmacokinetic relationship modeling of quinolones: apparent volume of distribution. Asian J Pharm 3:202–207

    Article  Google Scholar 

  14. Ekins S, Waller CL, Swaan PW et al (2000) Progress in predicting human ADME parameters in silico. J Pharm Toxicol Methods 44:251–272

    Article  CAS  Google Scholar 

  15. Goodwin JT, Clark DE (2005) In silico predictions of blood–brain barrier penetration: considerations to “keep in mind”. J Pharm Exp Ther 315:477–483

    Article  CAS  Google Scholar 

  16. Linnankoski J, Ranta V-P, Yliperttula M et al (2008) Passive oral drug absorption can be predicted more reliably by experimental than computational models—fact or myth. Eur J Pharm Sci 34:129–139

    Article  PubMed  CAS  Google Scholar 

  17. Modi S (2004) Positioning ADMET in silico tools in drug discovery. Drug Disc Today 9:14–15

    Article  Google Scholar 

  18. Mager DE (2006) Quantitative structure–pharmacokinetic/pharmacodynamic relationships. Adv Drug Del Rev 58:1326–1356

    Article  CAS  Google Scholar 

  19. Gunaratna C (2001) Drug metabolism and pharmacokinetics in drug discovery: a primer for bioanalytical chemists, part II. Curr Sep 19:87–92

    CAS  Google Scholar 

  20. Hansch C (1972) Quantitative relationships between lipophilic character and drug metabolism. Drug Metab Rev 1:1–14

    Article  Google Scholar 

  21. Lipinski CA, Lombardo F, Dominy BW et al (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 23:3–25

    Article  CAS  Google Scholar 

  22. Lipinski CA (2000) Druglike properties and the causes of poor solubility and poor permeability. J Pharm Toxicol Methods 44:235–249

    Article  CAS  Google Scholar 

  23. Ghose AK, Viswanadhan VN, Wendoloski JJ (1999) A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. J Comb Chem 1:55–68

    Article  PubMed  CAS  Google Scholar 

  24. Wenlock MC, Austin RP, Barton P, Davis AM, Leeson PD (2003) A comparison of physiochemical property profiles of development and marketed oral drugs. J Med Chem 46:1250–1256

    Article  PubMed  CAS  Google Scholar 

  25. Norinder U, Bergstrçm CAS (2006) Prediction of ADMET properties. ChemMedChem 1:920–937

    Article  PubMed  CAS  Google Scholar 

  26. Hirono S, Nakagome I, Hirano H et al (1994) Non-congeneric structure–pharmacokinetic property correlation studies using fuzzy adaptive least-squares: oral bioavailability. Biol Pharm Bull 17:306–309

    Article  PubMed  CAS  Google Scholar 

  27. Palm K, Luthman K, Ungel AL et al (1996) Correlation of drug absorption with molecular surface properties. J Pharm Sci 85:32–39

    Article  PubMed  CAS  Google Scholar 

  28. Wessel MD, Jurs PC, Tolan JW et al (1998) Prediction of human intestinal absorption of drug compounds from molecular structure. J Chem Inf Comput Sci 38:726–735

    Article  PubMed  CAS  Google Scholar 

  29. Nestorov I, Aarons L, Rowland M (1998) Quantitative structure-pharmacokinetics relationships II. Mechanistically based model for the relationship between the tissue distribution parameters and the lipophilicity of the compounds. J Pharmacokinet Biopharm 26:521–545

    PubMed  CAS  Google Scholar 

  30. Winiwarter S, Bonham NM, Ax F et al (1998) Correlation of human jejunal permeability (in vivo) of drugs with experimentally and theoretically derived parameters. A multivariate data analysis approach. J Med Chem 41:4939–4949

    Article  PubMed  CAS  Google Scholar 

  31. Clark DE (1999) Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena. 1. Prediction of intestinal absorption. J Pharm Sci 88:807–814

    Article  PubMed  CAS  Google Scholar 

  32. Stenberg P, Luthman K, Ellens H et al (1999) Prediction of the intestinal absorption of endothelin receptor antagonists using three theoretical methods of increasing complexity. Pharm Res 16:1520–1526

    Article  PubMed  CAS  Google Scholar 

  33. Ghuloum AM, Sage CR, Jain AN (1999) Molecular hashkeys: a novel method for molecular characterization and its application for predicting important pharmaceutical properties of molecules. J Med Chem 42:1739–1748

    Article  PubMed  CAS  Google Scholar 

  34. Egan WJ, Merz KM, Baldwin JJ (2000) Prediction of drug absorption using multivariate statistics. J Med Chem 43:3867–3877

    Article  PubMed  CAS  Google Scholar 

  35. Andrews CW, Bennett L, Yu LX (2000) Predicting human oral bioavailability of a compound: development of a novel quantitative structure–bioavailability relationship. Pharm Res 17:639–644

    Article  PubMed  CAS  Google Scholar 

  36. Zhao YH, Le J, Abraham MH et al (2001) Evaluation of human intestinal absorption data and subsequent derivation of a quantitative structure–activity relationship (QSAR) with the Abraham descriptors. J Pharm Sci 90:749–784

    Article  PubMed  CAS  Google Scholar 

  37. Colmenarejo G, Alvarez-Pedraglio A, Lavandera JL (2001) Chemoinformatic models to predict binding affinities to human serum albumin. J Med Chem 44:4370–4378

    Article  PubMed  CAS  Google Scholar 

  38. Mandagere AK, Thompson TN, Hwang KK (2002) A graphical model for estimating oral bioavailability of drugs in humans and other species from their Caco-2 permeability and in vitro liver enzyme metabolic stability rates. J Med Chem 45:304–311

    Article  PubMed  CAS  Google Scholar 

  39. Veber DF, Johnson SR, Cheng H-Y et al (2002) Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem 45:2615–2623

    Article  PubMed  CAS  Google Scholar 

  40. Karalis V, Tsantili-Kakoulidou A, Macheras P (2002) Multivariate statistics of disposition pharmacokinetic parameters for structurally unrelated drugs used in therapeutics. Pharm Res 19:1827–1834

    Article  PubMed  CAS  Google Scholar 

  41. Wajima T, Fukumura K, Yano Y et al (2002) Prediction of human clearance from animal data and molecular structural parameters using multivariate regression analysis. J Pharm Sci 91:2489–2499

    Article  PubMed  CAS  Google Scholar 

  42. Doniger S, Hofmann T, Yeh J (2002) Predicting CNS permeability of drug molecules: comparison of neural network and support vector machine algorithms. J Comput Biol 9:849–864

    Article  PubMed  CAS  Google Scholar 

  43. Shen M, Xiao YD, Golbraikh A et al (2003) Development and validation of k-nearest-neighbor QSPR models of metabolic stability of drug candidates. J Med Chem 46:3013–3020

    Article  PubMed  CAS  Google Scholar 

  44. Zmuidinavicius D, Didziapetris R, Japertas P et al (2003) Classification structure–activity relations (C-SAR) in prediction of human intestinal absorption. J Pharm Sci 92:621–633

    Article  PubMed  CAS  Google Scholar 

  45. Lobell M, Sivarajah V (2003) In silico prediction of aqueous solubility, human plasma protein binding and volume of distribution of compounds from calculated pKa and AlogP98 values. Mol Divers 7:69–87

    Article  PubMed  CAS  Google Scholar 

  46. Wajima T, Fukumura K, Yano Y et al (2003) Prediction of human pharmacokinetics from animal data and molecular structural parameters using multivariate regression analysis: oral clearance. J Pharm Sci 92:2427–2440

    Article  PubMed  CAS  Google Scholar 

  47. Turner JV, Maddalena DJ, Cutler DJ et al (2003) Multiple pharmacokinetic parameter prediction for a series of cephalosporins. J Pharm Sci 92:552–559

    Article  PubMed  CAS  Google Scholar 

  48. Pérez MA, Sanz MB, Torres LR et al (2004) A topological sub-structural approach for predicting human intestinal absorption of drugs. Eur J Med Chem 39:905–916

    Article  PubMed  Google Scholar 

  49. Turner JV, Maddalena DJ, Cutler DJ (2004) Pharmacokinetic parameter prediction from drug structure using artificial neural networks. Int J Pharm 270:209–219

    Article  PubMed  CAS  Google Scholar 

  50. Pan D, Iyer M, Liu J et al (2004) Constructing optimum blood brain barrier QSAR models using a combination of 4D-molecular similarity measures and cluster analysis. J Chem Inf Comput Sci 44:2083–2098

    Article  PubMed  CAS  Google Scholar 

  51. Bai JP, Utis A, Crippen G et al (2004) Use of classification regression tree in predicting oral absorption in humans. J Chem Inf Comput Sci 44:2061–2069

    Article  PubMed  CAS  Google Scholar 

  52. Li H, Yap CW, Ung CY et al (2005) Effect of selection of molecular descriptors on the prediction of blood–brain barrier penetrating and nonpenetrating agents by statistical learning methods. J Chem Inf Model 45:1376–1384

    Article  PubMed  CAS  Google Scholar 

  53. Aureli L, Cruciani G, Cesta MC et al (2005) Predicting human serum albumin affinity of interleukin-8 (CXCL8) inhibitors by 3D-QSPR approach. J Med Chem 48:2469–2479

    Article  PubMed  CAS  Google Scholar 

  54. Rahnasto M, Raunio H, Poso A et al (2005) Quantitative structure–activity relationship analysis of inhibitors of the nicotine metabolizing CYP2A6 enzyme. J Med Chem 48:440–449

    Article  PubMed  CAS  Google Scholar 

  55. Zhou XF, Shao Q, Coburn RA et al (2005) Quantitative structure–activity relationship and quantitative structure–pharmacokinetics relationship of 1,4-dihydropyridines and pyridines as multidrug resistance modulators. Pharm Res 22:1989–1996

    Article  PubMed  CAS  Google Scholar 

  56. Jung SJ, Choi SO, Um SY et al (2006) Prediction of the permeability of drugs through study on quantitative structure–permeability relationship. J Pharm Biomed Anal 41:469–475

    Article  PubMed  CAS  Google Scholar 

  57. Gleeson MP, Waters NJ, Paine SW et al (2006) In silico human and rat Vss quantitative structure–activity relationship models. J Med Chem 49:1953–1963

    Article  PubMed  CAS  Google Scholar 

  58. Linnankoski J, Mäkelä JM, Ranta VP et al (2006) Computational prediction of oral drug absorption based on absorption rate constants in humans. J Med Chem 49:3674–3681

    Article  PubMed  CAS  Google Scholar 

  59. Garg P, Verma J (2006) In silico prediction of blood–brain barrier permeability: an artificial neural network model. J Chem Inf Model 46:289–297

    Article  PubMed  CAS  Google Scholar 

  60. Doddareddy MR, Cho YS, Koh HY et al (2006) In silico renal clearance model using classical Volsurf approach. J Chem Inf Model 46:1312–1320

    Article  PubMed  CAS  Google Scholar 

  61. Yap CW, Li ZR, Chen YZ (2006) Quantitative structure–pharmacokinetic relationships for drug clearance by using statistical learning methods. J Mol Graph Model 24:383–395

    Article  PubMed  CAS  Google Scholar 

  62. Dureja H, Madan AK (2006) Topochemical models for the prediction of permeability through blood brain barrier. Int J Pharm 323:27–33

    Article  PubMed  CAS  Google Scholar 

  63. Dureja H, Madan AK (2007) Validation of topochemical models for the prediction of permeability through blood brain barrier. Acta Pharm 57:451–467

    Article  PubMed  CAS  Google Scholar 

  64. Hou T, Wang J, Li Y (2007) ADME evaluation in drug discovery. 8. The prediction of human intestinal absorption by a support vector machine. J Chem Inf Model 47:2408–2415

    Article  PubMed  CAS  Google Scholar 

  65. Iyer M, Tseng YJ, Senese CL et al (2007) Prediction and mechanistic interpretation of human oral drug absorption using MI-QSAR analysis. Mol Pharm 4:218–231

    Article  PubMed  CAS  Google Scholar 

  66. Cuadrado MU, Ruiz IL, Gómez-Nieto MA (2007) QSAR models based on isomorphic and nonisomorphic data fusion for predicting the blood brain barrier permeability. J Comput Chem 28:1252–1260

    Article  PubMed  CAS  Google Scholar 

  67. Gleeson MP (2007) Plasma protein binding affinity and its relationship to molecular structure: an in-silico analysis. J Med Chem 50:101–112

    Article  PubMed  CAS  Google Scholar 

  68. Li C, Liu T, Cui X et al (2007) Development of in vitro pharmacokinetic screens using Caco-2, human hepatocyte, and Caco-2/human hepatocyte hybrid systems for the prediction of oral bioavailability in humans. J Biomol Screen 12:1084–1091

    Article  PubMed  CAS  Google Scholar 

  69. Hou T, Wang J, Zhang W et al (2007) ADME evaluation in drug discovery. 6. Can oral bioavailability in humans be effectively predicted by simple molecular property-based rules? J Chem Inf Model 47:460–463

    Article  PubMed  CAS  Google Scholar 

  70. Moda TL, Montanari CA, Andricopulo AD (2007) Hologram QSAR model for the prediction of human oral bioavailability. Bioorg Med Chem 15:7738–7745

    Article  PubMed  CAS  Google Scholar 

  71. De Buck SS, Sinha VK, Fenu LA et al (2007) The prediction of drug metabolism, tissue distribution, and bioavailability of 50 structurally diverse compounds in rat using mechanism-based absorption, distribution, and metabolism prediction tools. Drug Metab Dispos 35:649–659

    Article  PubMed  Google Scholar 

  72. Hou T, Wang J, Zhang W et al (2007) ADME evaluation in drug discovery. 7. Prediction of oral absorption by correlation and classification. J Chem Inf Model 47:208–218

    Article  PubMed  CAS  Google Scholar 

  73. Fu XC, Wang GP, Shan HL et al (2008) Predicting blood–brain barrier penetration from molecular weight and number of polar atoms. Eur J Pharm Biopharm 70:462–466

    Article  PubMed  CAS  Google Scholar 

  74. Zhang L, Zhu H, Oprea TI et al (2008) QSAR modeling of the blood–brain barrier permeability for diverse organic compounds. Pharm Res 25:1902–1914

    Article  PubMed  CAS  Google Scholar 

  75. Sinha VK, De Buck SS, Fenu LA et al (2008) Predicting oral clearance in humans: how close can we get with allometry? Clin Pharmacokinet 47:35–45

    Article  PubMed  CAS  Google Scholar 

  76. Ma CY, Yang SY, Zhang H et al (2008) Prediction models of human plasma protein binding rate and oral bioavailability derived by using GA-CG-SVM method. J Pharm Biomed Anal 47:677–682

    Article  PubMed  CAS  Google Scholar 

  77. Dureja H, Gupta S, Madan AK (2008) Topological models for prediction of pharmacokinetic parameters of cephalosporins using random forest, decision tree and moving average analysis. Sci Pharm 76:377–394

    Article  CAS  Google Scholar 

  78. Dureja H, Gupta S, Madan AK (2009) Decision tree derived topological models for prediction of physico-chemical, pharmacokinetic and toxicological properties of antihistaminic drugs. Int J Comput Biol Drug Des 2:353–370

    Article  PubMed  CAS  Google Scholar 

  79. Lanevskij K, Japertas P, Didziapetris R et al (2009) Ionization-specific prediction of blood–brain permeability. J Pharm Sci 98:122–134

    Article  PubMed  CAS  Google Scholar 

  80. Kokate A, Li X, Williams PJ et al (2009) In silico prediction of drug permeability across buccal mucosa. Pharm Res 26:1130–1139

    Article  PubMed  CAS  Google Scholar 

  81. Berellini G, Springer C, Waters NJ et al (2009) In silico prediction of volume of distribution in human using linear and nonlinear models on a 669 compound data set. J Med Chem 52:4488–4495

    Article  PubMed  CAS  Google Scholar 

  82. McIntyre TA, Han C, Davis CB (2009) Prediction of animal clearance using naïve Bayesian classification and extended connectivity fingerprints. Xenobiotica 39:487–494

    Article  PubMed  CAS  Google Scholar 

  83. Li H, Sun J, Sui X, Yan Z et al (2009) Structure-based prediction of the nonspecific binding of drugs to hepatic microsomes. AAPS J 11:364–370

    Article  PubMed  CAS  Google Scholar 

  84. Emoto C, Murayama N, Rostami-Hodjegan A et al (2009) Utilization of estimated physicochemical properties as an integrated part of predicting hepatic clearance in the early drug-discovery stage: impact of plasma and microsomal binding. Xenobiotica 39:227–235

    Article  PubMed  CAS  Google Scholar 

  85. Paixão P, Gouveia LF, Morais JA (2009) Prediction of drug distribution within blood. Eur J Pharm Sci 36:544–554

    Article  PubMed  Google Scholar 

  86. Chang C, Duignan DB, Johnson KD (2009) The development and validation of a computational model to predict rat liver microsomal clearance. J Pharm Sci 98:2857–2867

    Article  PubMed  CAS  Google Scholar 

  87. Li H, Sun J, Sui X et al (2009) First-principle, structure-based prediction of hepatic metabolic clearance values in human. Eur J Med Chem 44:1600–1606

    Article  PubMed  CAS  Google Scholar 

  88. Grabowski T, Jaroszewski JJ (2009) Bioavailability of veterinary drugs in vivo and in silico. J Vet Pharmacol Ther 32:249–257

    Article  PubMed  CAS  Google Scholar 

  89. Fan Y, Unwalla R, Denny RA et al (2010) Insights for predicting blood–brain barrier penetration of CNS targeted molecules using QSPR approaches. J Chem Inf Model 50:1123–1133

    Article  PubMed  CAS  Google Scholar 

  90. Shen J, Cheng F, Xu Y et al (2010) Estimation of ADME properties with substructure pattern recognition. Chem Inf Model 50:1034–1041

    Article  CAS  Google Scholar 

  91. Yu MJ (2010) Predicting total clearance in humans from chemical structure. J Chem Inf Model 50:1284–1295

    Article  PubMed  CAS  Google Scholar 

  92. Paixão P, Gouveia LF, Morais JA (2010) Prediction of the in vitro intrinsic clearance determined in suspensions of human hepatocytes by using artificial neural networks. Eur J Pharm Sci 39:310–321

    Article  PubMed  Google Scholar 

  93. Kharkar PS (2010) Two-dimensional (2D) in silico models for absorption, distribution, metabolism, excretion and toxicity (ADME/T) in drug discovery. Curr Top Med Chem 10:116–126

    Article  CAS  Google Scholar 

  94. Lombardo F, Gifford E, Shalaeva MY (2003) In silico ADME prediction: data, models, facts and myths. Mini Rev Med Chem 3:861–875

    Article  PubMed  CAS  Google Scholar 

  95. Liu X, Tu M, Kelly RS et al (2004) Development of a computational approach to predict blood–brain barrier permeability. Drug Metab Dispos 32:132–139

    Article  PubMed  CAS  Google Scholar 

  96. Sui X, Sun J, Wu X et al (2008) Predicting the volume of distribution of drugs in humans. Curr Drug Metab 9:574–580

    Article  PubMed  CAS  Google Scholar 

  97. Ekins S, Boulanger B, Swaan PW et al (2002) Towards a new age of virtual ADME/TOX and multidimensional drug discovery. J Comput Aided Mol Des 16:381–401

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to A. K. Madan .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Madan, A.K., Dureja, H. (2012). Prediction of Pharmacokinetic Parameters. In: Reisfeld, B., Mayeno, A. (eds) Computational Toxicology. Methods in Molecular Biology, vol 929. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-050-2_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-050-2_14

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-049-6

  • Online ISBN: 978-1-62703-050-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics