Clearance mechanism assignment and total clearance prediction in human based upon in silico models

Journal of Medicinal Chemistry

Volumn 57, Issue 10, 2014, Pages 4397-4405

  Lombardo, Franco ^a   Obach, R Scott ^b   Varma, Manthena V ^b   Stringer, Rowan ^a   Berellini, Giuliano ^a  

^a NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

^b PFIZER INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COMPUTER MODEL; DRUG CLEARANCE; HUMAN; IN VITRO STUDY; IN VIVO STUDY; LIVER CLEARANCE; METABOLISM; NONHUMAN; PARTIAL LEAST SQUARES REGRESSION; PREDICTION; PRINCIPAL COMPONENT ANALYSIS; SCIENTIST;

ANIMALS; COMPUTER SIMULATION; HAPLORHINI; HUMANS; LEAST-SQUARES ANALYSIS; METABOLIC CLEARANCE RATE; PRINCIPAL COMPONENT ANALYSIS;

EID: 84901268525     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm500436v     Document Type: Article

References (44)

1. Dedrick, R. L. Animal scale-up J. Pharmacokinet. Biopharm. 1973, 1, 435-461
2. Wajima, T.; Fukumura, K.; Yano, Y.; Oguma, T. Prediction of human clearance from animal data and molecular structural parameters using multivariate regression analysis J. Pharm. Sci. 2002, 91, 2489-2499
3. Ward, K. W.; Smith, B. R. A comprehensive quantitative and qualitative evaluation of extrapolation of intravenous pharmacokinetic parameters from rat, dog, and monkey to humans. I. Clearance Drug Metab. Dispos. 2004, 32, 603-611
4. 1/2 be predicted from in-vivo rat data? Eur. J. Drug Metab. Pharmacokinet. 2004, 29, 133-143
5. Berellini, G.; Waters, N.; Lombardo, F. In silico prediction of total human hlasma clearance J. Chem. Inf. Model. 2012, 52, 2069-2078
6. Nagilla, R.; Ward, K. W. A comprehensive analysis of the role of correction factors in the allometric predictivity of clearance from rat, dog, and monkey to humans J. Pharm. Sci. 2004, 93, 2522-2534
7. Jolivette, L. J.; Ward, K. W. Extrapolation of human pharmacokinetic parameters from rat, dog, and monkey data: molecular properties associated with extrapolative success or failure J. Pharm. Sci. 2005, 94, 1467-1483
8. Tang, H.; Mayersohn, M. A novel model for prediction of human drug clearance by allometric scaling Drug Metab. Dispos. 2005, 33, 1297-1303
9. Evans, C. A.; Jolivette, L. J.; Nagilla, R.; Ward, K. W. Extrapolation of preclinical pharmacokinetics and molecular feature analysis of "discovery-like" molecules to predict human pharmacokinetics Drug Metab. Dispos. 2006, 34, 1255-1265
10. Mahmood, I.; Martinez, M.; Hunter, R. P. Interspecies allometric scaling. Part I: Prediction of clearance in large animals J. Vet. Pharmacol. Ther. 2006, 29, 415-423
11. Martinez, M.; Mahmood, I.; Hunter, R. P. Interspecies allometric scaling: prediction of clearance in large animal species: part II: mathematical considerations J. Vet. Pharmacol. Ther. 2006, 29, 425-432
12. Tang, H.; Mayersohn, M. A global examination of allometric scaling for predicting human drug clearance and the prediction of large vertical allometry J. Pharm. Sci. 2006, 95, 1783-1799
13. Mahmood, I. Role of fixed coefficients and exponents in the prediction of human drug clearance: How accurate are the predictions from one or two species? J. Pharm. Sci. 2009, 98, 2472-2493
14. Lave, T.; Chapman, K.; Goldsmith, P.; Rowland, M. Human clearance prediction: shifting the paradigm Expert Opin. Drug Metab. Toxicol. 2009, 5, 1039-1048
15. Lombardo, F.; Waters, N. J.; Argikar, U.; Dennehy, M. K.; Zhan, J.; Gunduz, M.; Harriman, S. P.; Berellini, G.; Liric Rajlic, I.; Obach, R. S. Comprehensive assessment of human pharmacokinetic prediction based on in vivo animal pharmacokinetic data. Part 2: Clearance J. Clin. Pharmacol. 2013, 52, 178-191
16. Houston, J. B. Utility of in vitro drug metabolism data in predicting in vivo metabolic clearance Biochem. Pharmacol. 1994, 47, 1469-1479
17. Iwatsubo, T.; Hirota, N.; Ooie, T.; Suzuki, H.; Shimada, N.; Chiba, K.; Ishizaki, T.; Green, C. E.; Tyson, C. A.; Sugiyama, Y. Prediction of in vivo drug metabolism in the human liver from in vitro metabolism data Pharmacol. Ther. 1997, 73, 147-171
18. Obach, R. S.; Baxter, J. G.; Liston, T. E.; Silber, B. M.; Jones, B. C.; Macintyre, F.; Rance, D. J.; Wastall, P. The prediction of human pharmacokinetic parameters from preclinical and in vitro metabolism data J. Pharmacol. Exp. Ther. 1997, 283, 46-58
19. Howgate, E. M.; Rowland-Yeo, K.; Proctor, N. J.; Tucker, G. T.; Rostami-Hodjegan, A. Prediction of in vivo drug clearance from in vitro data. I: Impact of inter-individual variability Xenobiotica 2006, 36, 473-497
20. Shiran, M. R.; Proctor, N. J.; Howgate, E. M.; Rowland-Yeo, K.; Tucker, G. T.; Rostami-Hodjegan, A. Prediction of metabolic drug clearance in humans: in vitro-in vivo extrapolation vs allometric scaling Xenobiotica 2006, 36, 567-580
21. Obach, R. S. Predicting clearance in humans from in vitro data Curr. Top. Med. Chem. 2011, 11, 334-339
22. Nikolic, K.; Agababa, D. Prediction of hepatic microsomal intrinsic clearance and human clearance values for drugs J. Mol. Graphics Modell. 2009, 28, 245-252
23. Li, H.; Sun, J.; Sui, X.; Liu, J.; Yan, Z.; Liu, X.; Sun, Y.; He, Z. First principle, structure-based prediction of hepatic metabolic clearance values in human Eur. J. Med. Chem. 2009, 44, 1600-1606
24. Yang, X.; Gandhi, Y. A.; Duignan, D. B.; Morris, M. E. Prediction of biliary excretion in rats and humans using molecular weight and quantitative structure-pharmacokinetic relationships AAPS J. 2009, 11, 511-525
25. Varma, M. V. S.; Feng, B.; Obach, R. S.; Troutman, M. D.; Chupka, J.; Miller, H. R.; El-Kattan, A. Physicochemical determinants of human renal clearance J. Med. Chem. 2009, 52, 4844-4852
26. Paixao, P.; Gouveia, L. F.; Morais, J. A. G. Prediction of the in vitro intrinsic clearance determined in suspensions of human hepatocytes by using artificial neural networks Eur. J. Pharm. Sci. 2010, 39, 310-321
27. Yap, C. W.; Li, Z. R.; Chen, Y. Z. Quantitative structure-pharmacokinetic relationships for drug clearance by using statistical learning methods J. Mol. Graphics Modell. 2006, 24, 383-395
28. Yu, M. J. Predicting total clearance in humans from chemical structure J. Chem. Inf. Model. 2010, 50, 1284-1295
29. Demir-Kavuk, O.; Bentzien, J.; Muegge, I.; Knapp, E.-W. DemQSAR: predicting human volume of distribution and clearance of drugs J. Comput.-Aided Mol. Des. 2011, 25, 1121-1133
30. Gombar, V. K.; Hall, S. D. Quantitative structure activity relationship models of clinical pharmacokinetics: clearance and volume of distribution J. Chem. Inf. Model. 2013, 53, 948-957
31. Manga, N.; Duffy, J. C.; Rowe, P. H.; Cronin, M. T. D. Hierarchical QSAR model for urinary excretion of drugs in humans as predictive tool for biotransformation QSAR Comb. Sci. 2003, 22, 263-273
32. Obach, R. S.; Lombardo, F.; Waters, N. J. Trend analysis of a database of intravenous pharmacokinetic parameters in humans for 670 compounds Drug Metab. Dispos. 2008, 36, 1385-1405
33. Svetnik, V.; Liaw, A.; Tong, C.; Culberson, J. C.; Sheridan, R. P.; Feuston, B. P. Random forest: a classification and regression tool for compound classification and QSAR modeling J. Chem. Inf. Comput. Sci. 2003, 43, 1947-1958
34. Shitara, Y.; Sugiyama, Y. Pharmacokinetic and pharmacodynamic alterations of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors: drug-drug interactions and interindividual differences in transporter and metabolic enzyme functions J. Pharmacol. Ther. 2006, 112, 71-105
35. Varma, M. V.; Chang, G.; Lai, Y.; Feng, B.; El-Kattan, A. F.; Litchfield, J.; Goosen, T. C. Physicochemical property space of hepatobiliary transport and computational models for predicting rat biliary excretion Drug Metab. Dispos. 2012, 40, 1527-1537
36. Maeda, K.; Ikeda, Y.; Fujita, T.; Yoshida, K.; Azuma, Y.; Haruyama, Y.; Yamane, N.; Kumagai, Y.; Sugiyama, Y. Identification of the rate-determining process in the hepatic clearance of atorvastatin in a clinical cassette microdosing study Clin. Pharmacol. Ther. 2011, 90, 575-581
37. VolSurf+. http://www.moldiscovery.com/soft-vsplus.php (accessed April 16 2014).
38. Fortuna, C. G.; Barresi, V.; Berellini, G.; Musumarra, G. Design and synthesis of trans 2-(furan-2-yl)vinyl heteroaromatic iodides with antitumour activity Bioorg. Med. Chem. 2008, 16, 4150-4159
39. SMARTS - a language for describing molecular patterns. http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html (accessed April 16 2014).
40. SMILES - a simplified chemical language. http://www.daylight.com/dayhtml/ doc/theory/theory.smiles.html (accessed April 16, 2014).
41. Wold, S.; Albano, C.; Dunn, W. J., III; Edlund, U.; Esbensen, K.; Geladi, P.; Hellberg, S.; Johansson, E.; Lindberg, W.; Sjöström, M. Multivariate data analysis in chemistry. In Chemometrics; Kowalski, B. R., Ed.; Springer: Dordrecht, The Netherlands, 1984; pp 17-95.
42. Westerhuis, J. A.; Kourti, T.; MacGregor, F. Analysis of multiblock and hierarchical PCA and PLS models J. Chemom. 1998, 12, 301-321
43. SIMCA. http://www.umetrics.com/simca (accessed April 16, 2014).
44. Efron, B. Bootstrap methods: another look at the jackknife Ann. Stat. 1979, 1, 1-26