Pharmacokinetic-based drug design tool and method

• US 6,542,858 B1
• Filed: 05/26/1999
• Issued: 04/01/2003
• Est. Priority Date: 09/14/1998
• Status: Expired due to Fees

• Current Assignee: Lion Bioscience AG (2invest AG)
• Original Assignee: Lion Bioscience AG (2invest AG)
• Inventors: Sinko, Patrick J., Norris, Daniel A., Grass, George M., Wehrli, John E., Leesman, Glen D.
• Primary Examiner(s): Brusca, John S.
• Assistant Examiner(s): Moran, Marjorie A.
• Application Number:
  US09/320,545
• Time in Patent Office: 1,406 Days
• Field of Search: 395/500.32, 702/19, 702/100, 703/2, 703/11
• US Class Current: 703/2
• CPC Class Codes: A61P 31/12 Antivirals
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry
• CPC Class Codes: G16C 20/62 Design of libraries
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

The present invention relates to a pharmacokinetic-based design and selection tool (PK tool) and methods for predicting absorption of an administered compound of interest. The methods utilize the tool, and optionally a separately operable component or subsystem thereof. The PK tool includes as computer-readable components: (1) input/output system; (2) physiologic-based simulation model of one or more segments of a mammalian system of interest having one or more physiological barriers to absorption that is based on the selected route of administration; and (3) simulation engine having a differential equation solver: The invention also provides methods for optimizing as well as enabling minimal input requirements a physiologic-based simulation model for predicting in vivo absorption, and optionally one or more additional properties, from either in vitro or in vivo data. The PK tool of the invention may be provided as a computer system, as an article of manufacture in the form of a computer-readable medium, or a computer program product and the like. Subsystems and individual components of the PK tool also can be utilized and adapted in a variety of disparate applications for predicting the fate of an administered compound. The PK tool and methods of the invention can be used to screen and design compound libraries, select and design drugs, as well as predict drug efficacy in mammals from in vitro and/or in vivo data of one or more compounds of interest. The PK tool and methods of the invention also finds use in selecting, designing, and preparing drug compounds, and multi-compound drugs and drug formulations (i.e., drug delivery system) for preparation of medicaments for use in treating mammalian disorders.

Claims

1. A method of predicting a pharmacokinetic property of a compound in a first anatomical segment of a mammalian system from a pharmacokinetic property of the compound in a second anatomical segment of the mammalian system, the method comprising:

providing a model, the model comprising at least one regional correlation parameter, wherein the at least one regional correlation parameter comprises a value obtained by;

(i) assigning an initial value to the at least one regional correlation parameter of the model;

(ii) inputting first data for a plurality of compounds in the second anatomical segment of the mammalian system into the model and running the model to generate output data;

(iii) comparing the output data with second data for the plurality of compounds in the first anatomical segment of a mammalian system;

(iv) selecting a new value for the at least one regional correlation parameter such that deviation of the comparison in step (iii) is reduced; and

(v) replacing the value for the at least one regional correlation parameter in the model with the new value selected in step (iv); and

using the model to predict the pharmacokinetic property of the compound in the first anatomical segment of the mammalian system from the pharmacokinetic property of the compound in the second anatomical segment of the mammalian system.

2. The method of claim 1, wherein the value is further obtained by repeating steps (ii)-(v) one or more times until a difference between the output data and the second data source is less than the largest of the experimental error in the first or second data for a particular compound in the plurality of compounds or the inter-day variation in the first or second data for a particular compound in the plurality of compounds.

3. The method of claim 2, wherein the difference is determined by one of the following:

normalized difference, collective regression coefficient, normalized arithmetic mean, normalized median, normalized geometric mean, normalized harmonic mean, variance, standard deviation, and coefficient of variation.

4. The method of claim 1, wherein the model determines a change in one or more physiological parameters of the first and second segments and movement and disposition of the compound in the first and second segments as a function of time.

5. The method of claim 4, wherein the model further comprises a regional correlation estimation algorithm.

6. The method of claim 5, wherein the algorithm is selected from the group consisting of a polynomial, exponential, and logarithm.

7. The method of claim 5, wherein the algorithm is selected from the group consisting of equations for fluid transit, fluid absorption, mass transit, mass dissolution, mass solubility, and mass absorption.

8. The method of claim 1, wherein the pharmacokinetic property is selected from the group consisting of absorption, distribution, metabolism, elimination and toxicity.

9. The method of claim 1, wherein the pharmacokinetic property is selected from the group consisting of permeability, solubility, dissolution rate and transport mechanism.

10. The method of claim 1, further comprising:

reversibly storing the estimated value for the pharmacokinetic parameter of the compound in the first segment in a database.

11. The method of claim 1, further comprising:

reversibly storing in a computer-implemented database an output value generated by the model corresponding to the pharmacokinetic property of the compound in a segment of the mammalian system.

12. The method of claim 1, wherein the mammalian system is selected from the group consisting of gastrointestinal tract, liver, heart, kidney, eye, nose, lung, skin and brain.

13. The method of claim 1, wherein the mammalian system is human.

14. The method of claim 1, wherein the first data comprises in vitro data.

15. The method of claim 14, wherein the in vitro data is derived from testing of the compound in an assay that generates data selected from the group consisting of cell, tissue, physicochemical, structure-activity relationship (SAR) SAR, and quantitative structure-activity relationship (QSAR) QSAR data.

16. The method of claim 1, wherein the model is provided on a computer system having a data processor, a memory and a display.

17. The method of claim 16, wherein the computer system is a standalone computer having a data processor, a memory and a display.

18. The method of claim 1, wherein the model is provided as readable program code embodied in a computer readable medium.

19. The method of claim 1, wherein the first and second data are stored in the same data source.

20. The method of claim 1, wherein the first data is stored in a first data source and the second data is stored in a second data source.

21. The method of claim 1, wherein the at least one regional correlation parameter is a plurality of regional correlation parameters, and wherein step (i) assigns an initial value to each of the plurality of regional correlation parameters, step (iv) selects a new value for one or more of the plurality of regional correlation parameters, and step (v) replaces the value of the one or more of the plurality of regional correlation parameters with the new value selected in step (iv).

22. A method for optimizing at least one regional correlation parameter in a model for predicting a pharmacokinetic property of a compound in a first anatomical segment of a mammalian system from a pharmacokinetic property of the compound in a second anatomical segment of the mammalian system, the method comprising:

(i) assigning an initial value to the at least one regional correlation parameter of the model;

(ii) inputting first data for a plurality of compounds in the second anatomical segment of the mammalian system into the model and running the model to generate output data;

(iii) comparing the output data with second data for the plurality of compounds In the first anatomical segment of a mammalian system;

(iv) selecting a new value for the at least one regional correlation parameter such that deviation of the comparison in step (iii) is reduced; and

(v) replacing the value for the at least one regional correlation parameter with the new value selected in step (iv).

23. The method of claim 22, wherein the value is further obtained be repeating steps (ii)-(v) one or more times until a difference between the output obtained using the first data source as input data into the model and the second data source is less than the largest of the experimental error in the first or second data for a particular compound in the plurality of compounds or the inter-day variation in the first or second data for a particular compound in the plurality of compounds.

24. The method of claim 23, wherein the difference is determined by one of the following:

normalized difference, collective regression coefficient, normalized arithmetic mean, normalized median, normalized geometric mean, normalized harmonic mean, variance, standard deviation, and coefficient of variation.

25. The method of claim 22, wherein the model determines the change in one or more physiological parameters of the first and second segments and the movement and disposition of the compound in the first and second segments as a function of time.

26. The method of claim 25, wherein the model further comprises a regional correlation estimation algorithm.

27. The method of claim 26, wherein the algorithm is selected from the group consisting of a polynomial, exponential, and logarithm.

28. The method of claim 26, wherein the algorithm is selected from the group consisting of equations for fluid transit, fluid absorption, mass transit, mass dissolution, mass solubility, and mass absorption.

29. The method of claim 22, wherein the pharmacokinetic property is selected from the group consisting of absorption, distribution, metabolism, elimination and toxicity.

30. The method of claim 22, wherein the pharmacokinetic property is selected from the group consisting of permeability, solubility, dissolution rate and transport mechanism.

31. The method of claim 22, wherein the model further comprises:

database for reversibly storing the estimated value for the pharmacokinetic parameter of the compound in the first segment.

32. The method of claim 22, wherein the model further comprises:

a computer-implemented database for reversibly storing an output value generated by the model corresponding to the pharmacokinetic property of the compound in a segment of the mammalian system.

33. The method of claim 22, wherein the mammalian system is selected from the group consisting of gastrointestinal tract, liver, heart, kidney, eye, nose, lung, skin and brain.

34. The method of claim 22, wherein the mammalian system is human.

35. The method of claim 22, wherein the first data comprises in vitro data.

36. The method of claim 35, wherein the in vitro data is derived from testing of the compound in an assay that generates data selected from the group consisting of cell, tissue, physicochemical, structure-activity relationship (SAR) SAR, and quantitative structure-activity relationship (QSAR) QSAR data.

37. The method of claim 22, wherein the model is provided on a computer system having a data processor, a memory and a display.

38. The method of claim 22, wherein the computer system is a standalone computer having a data processor, a memory and a display.

39. The method of claim 22, wherein the model is provided as readable program code embodied in a computer readable medium.

40. The method of claim 22, wherein the first and second data are stored in the same data source.

41. The method of claim 22, wherein the first data is stored in a first data source and the second data is stored in a second data source.

42. The method of claim 22, wherein the at least one regional correlation parameter is a plurality of regional correlation parameters, and wherein step (i) assigns an initial value to each of the plurality of regional correlation parameters, step (iv) selects a new value for one or more of the plurality of regional correlation parameters, and step (v) replaces the value of the one or more of the plurality of regional correlation parameters with the new value selected in step (iv).

43. A computer readable device comprising:

a computer readable medium; and

a program generating a data structure on the computer readable medium containing a model for predicting a pharmacokinetic property of a compound in a first anatomical segment of a mammalian system from a pharmacokinetic property of the compound in a second anatomical segment of the mammalian system, the model comprising at least one regional correlation parameter, wherein the at least one regional correlation parameter comprises a value obtained by;

(i) assigning an initial value to the at least one regional correlation parameter of the model;

(ii) inputting data from a first data source into the model and running the model to generate output data, the first data source containing first data for a plurality of compounds in the second anatomical segment of the mammalian system;

(iii) comparing the output data with a second data source, the second data source containing second data for the plurality of compounds in the first anatomical segment of a mammalian system;

(iv) selecting a new value for the at least one regional correlation parameter such that deviation of the comparison in step (iii) is reduced; and

(v) replacing the value for the at least one regional correlation parameter in the model with the new value selected in step (iv).

44. The device of claim 43, wherein the value is further obtained by repeating steps (ii)-(v) one or more times until a difference between the output obtained using the first data source as input data into the model and the second data source is less than the largest of the experimental error in the first or second data for a particular compound in the plurality of compounds or the inter-day variation in the first or second data for a particular compound in the plurality of compounds.

45. The device of claim 44, wherein the difference is determined by one of the following:

normalized difference, collective regression coefficient, normalized arithmetic mean, normalized median, normalized geometric mean, normalized harmonic mean, variance, standard deviation, and coefficient of variation.

46. The device of claim 43, wherein the model determines the change in one or more physiological parameters of the first and second segments and the movement and disposition of the compound in the first and second segments as a function of time.

47. The device of claim 46, wherein the model further comprises a regional correlation estimation algorithm.

48. The device of claim 47, wherein the algorithm is selected from the group consisting of a polynomial, exponential, and logarithm.

49. The device of claim 47, wherein the algorithm is selected from the group consisting of equations for fluid transit, fluid absorption, mass transit, mass dissolution, mass solubility, and mass absorption.

50. The device of claim 43, wherein the pharmacokinetic property is selected from the group consisting of absorption, distribution, metabolism, elimination and toxicity.

51. The device of claim 43, wherein the pharmacokinetic property is selected from the group consisting of permeability, solubility, dissolution rate and transport mechanism.

52. The device of claim 43, further comprising:

a database contained in the data structure for reversibly storing the estimated value for the pharmacokinetic parameter of the compound in the first segment.

53. The device of claim 43, further comprising:

a computer-implemented database for reversibly storing an output value generated by the model corresponding to the pharmacokinetic property of the compound in a segment of the mammalian system.

54. The device of claim 43, wherein the mammalian system is selected from the group consisting of gastrointestinal tract, liver, heart, kidney, eye, nose, lung, skin and brain.

55. The device of claim 43, wherein the mammalian system is human.

56. The device of claim 43, wherein the first data comprises in vitro data.

57. The device of claim 56, wherein the in vitro data is derived from testing of the compound in an assay that generates data selected from the group consisting of cell, tissue, physicochemical, structure-activity relationship (SAR) SAR, and quantitative structure-activity relationship (QSAR) QSAR data.

58. The device of claim 43, wherein the device is provided in a computer system having a data processor, a memory and a display.

59. The device of claim 58, wherein the computer system is a standalone computer having a data processor, a memory and a display.

60. The method of claim 43, wherein the first and second data are stored in the same data source.

61. The method of claim 43, wherein the first data is stored in a first data source and the second data is stored in a second data source.

62. The method of claim 43, wherein the at least one regional correlation parameter is a plurality of regional correlation parameters, and wherein step (i) assigns an initial value to each of the plurality of regional correlation parameters, step (iv) selects a new value for one or more of the plurality of regional correlation parameters, and step (v) replaces the value of the one or more of the plurality of regional correlation parameters with the new value selected in step (iv).

63. A computer system for predicting a pharmacokinetic property of a compound in a first anatomical segment of a mammalian system from a pharmacokinetic property of the compound in a second anatomical segment of the mammalian system, the computer system comprising:

a computer; and

a model running on the computer, the model comprising at least one regional correlation parameter, the at least one regional correlation parameter comprises a value obtained by;

(i) assigning an initial value to the at least one regional correlation parameter of the model;

(ii) inputting data from a first data source into the model and running the model to generate output data, the first data source containing first data for a plurality of compounds in the second anatomical segment of the mammalian system;

(iii) comparing the output data with a second data source, the second data source containing second data for the plurality of compounds in the first anatomical segment of a mammalian system;

(iv) selecting a new value for the at least one regional correlation parameter such that deviation of the comparison in step (iii) is reduced; and

(v) replacing the value for at least one regional correlation parameter in the model with the new value selected in step (iv).

64. The system of claim 63, wherein the value is further obtained by repeating steps (ii)-(v) one or more times until a difference between the output obtained using the first data source as input data into the model and the second data source is less than the largest of the experimental error in the first or second data for a particular compound in the plurality of compounds or the inter-day variation in the first or second data for a particular compound in the plurality of compounds.

65. The system of claim 64, wherein the difference is determined by one of the following:

normalized difference, collective regression coefficient, normalized arithmetic mean, normalized median, normalized geometric mean, normalized harmonic mean, variance, standard deviation, and coefficient of variation.

66. The system of claim 63, wherein the model determines the change in one or more physiological parameters of the first and second segments and the movement and disposition of the compound in the first and second segments as a function of time.

67. The system of claim 66, wherein the model further comprises a regional correlation estimation algorithm.

68. The system of claim 67, wherein the algorithm is selected from the group consisting of a polynomial, exponential, and logarithm.

69. The system of claim 67, wherein the algorithm is selected from the group consisting of equations for fluid transit, fluid absorption, mass transit, mass dissolution, mass solubility, and mass absorption.

70. The system of claim 63, wherein the pharmacokinetic property is selected from the group consisting of absorption, distribution, metabolism, elimination and toxicity.

71. The system of claim 63, wherein the pharmacokinetic property is selected from the group consisting of permeability, solubility, dissolution rate and transport mechanism.

72. The system of claim 63, further comprising:

a database on the computer for reversibly storing the estimated value for the pharmacokinetic parameter of the compound in the first segment.

73. The system of claim 63, further comprising:

a database on the computer for reversibly storing an output value generated by the model corresponding to the pharmacokinetic property of the compound in a segment of the mammalian system.

74. The system of claim 63, wherein the mammalian system is selected from the group consisting of gastrointestinal tract, liver, heart, kidney, eye, nose, lung, skin and brain.

75. The system of claim 63, wherein the mammalian system is human.

76. The system of claim 63, wherein the first data comprises in vitro data.

77. The system of claim 76, wherein the in vitro data is derived from testing of the compound in an assay that generates data selected from the group consisting of cell, tissue, physicochemical, structure-activity relationship (SAR) SAR, and quantitative structure-activity relationship (QSAR) QSAR data.

78. The system of claim 63, wherein the computer comprises a data processor, a memory and a display.

79. The system of claim 78, wherein the computer system is a standalone computer having a data processor, a memory and a display.

80. The method of claim 63, wherein the first and second data are stored in the same data source.

81. The method of claim 63, wherein the first data is stored in a first data source and the second data is stored in a second data source.

82. The method of claim 63, wherein the at least one regional correlation parameter is a plurality of regional correlation parameters, and wherein step (i) assigns an initial value to each of the plurality of regional correlation parameters, step (iv) selects a new value for one or more of the plurality of regional correlation parameters, and step (v) replaces the value of the one or more of the plurality of regional correlation parameters with the new value selected in step (iv).