CLASSIFICATION OF KINASE INHIBITORS USING NONLINEAR OPTICAL TECHNIQUES

• US 20140113312A1
• Filed: 03/21/2012
• Published: 04/24/2014
• Est. Priority Date: 03/21/2011
• Status: Active Grant

• Current Assignee: BlueLight Therapeutics, Inc.
• Original Assignee: Biodesy, Inc.
• Inventors: Salafsky, Joshua S., McGuinness, Ryan
• Granted Patent: US 9,428,789 B2
• Time in Patent Office: Days
• US Class Current: 435/7.8
• CPC Class Codes: C12Q 1/485 involving kinase
• CPC Class Codes: G01N 2500/00 Screening for compounds of potential therapeutic value
• CPC Class Codes: G01N 33/58 involving labelled substances G01N33/53 takes precedence
• CPC Class Codes: G01N 33/6803 General methods of protein analysis not limited to specific proteins or families of proteins

Abstract

A method is disclosed for classifying and distinguishing between type I and type II kinase inhibitors. The method involves the use of non-linear optical techniques, in particular second-harmonic generation (SHG) to identify conformational changes in kinase proteins obtained from known type I or type II inhibitors. The method further involves deducing the manner of binding of unknown inhibitors by comparison with the signal changes produced by known ligands. The method is also applied to comparing the conformational changes induced by the binding of generic and branded kinase inhibitor drugs to a target kinase.

Claims

1. A method for classifying a kinase inhibitor as a type I or type II kinase inhibitor based on a conformational change that the kinase inhibitor induces in the structure of a kinase labeled with a second harmonic-active label, wherein the label has a net orientation at an interface, the method comprising:

a. contacting the kinase with a kinase inhibitor, wherein the kinase specifically interacts with said kinase inhibitor;

b. detecting an interaction between the kinase and said kinase inhibitor by measuring a first signal or signal change generated by the second harmonic-active label using a surface-selective technique, wherein the first signal or signal change indicates a conformational change in the structure of the kinase that is specific for the kinase inhibitor; and

c. classifying the kinase inhibitor as a type I or type II kinase inhibitor by comparing the first signal or signal change of (b) with a second signal or signal change detected by an interaction between the kinase and a known type I or type II inhibitor of the kinase, wherein the second signal or signal change indicates a conformational change in the structure of the kinase that is specific for the known type I or type II inhibitor of the kinase.

8. The method of any of claim 1, wherein the kinase comprises an affinity tag.

9. The method of claim 1, wherein the conformational change in the structure of the kinase is detected in real time.

10. The method of claim 1, wherein the kinase inhibitor is a small molecule chemical compound, a non-antibody inhibitory peptide, an antibody, or any combination thereof.

11. The method of claim 1, wherein the second harmonic-active label is bound to the kinase by one or more sulfhydryl groups on the surface of the kinase.

12. The method of claim 11, wherein said one or more sulfhydryl groups are native sulfhydryl groups.

13. The method of claim 11, wherein said one or more sulfhydryl groups are engineered sulfhydryl groups.

14. The method of claim 1, wherein said one or more sulfhydryl groups are not located within the kinase activation loop.

16. The method of claim 1, wherein the second harmonic-active label is an unnatural amino acid.

2-7. -7. (canceled)

15. (canceled)

17-18. -18. (canceled)

19. A method for comparing the conformational changes induced by a generic drug and a a.branded drug in the structure of a kinase labeled with a second harmonic-active label, wherein the label has a net orientation at an interface, and wherein the branded drug is a type I or type II kinase inhibitor, the method comprising:

a. contacting the kinase with the branded drug, wherein the kinase specifically interacts with the branded drug;

b. detecting an interaction between the kinase and the branded drug by measuring a first signal or signal change generated by the second harmonic-active label using a surface-selective technique, wherein the first signal change indicates a conformational change in the structure of the kinase that is specific for the branded drug;

c. contacting the kinase with the generic drug, wherein the kinase specifically interacts with the generic drug; and

d. detecting an interaction between the kinase and the generic drug by measuring a second signal or signal change generated by the second harmonic-active label using a surface-selective technique, wherein the second signal or signal change indicates a conformational change in the structure of the kinase that is specific for the generic drug and wherein the second signal or signal change is compared to the first signal or signal change to determine whether the conformational change induced in the kinase by the generic drug is identical to the change induced by the branded drug.

20-36. -36. (canceled)

37. A method for classifying an unknown candidate kinase inhibitor as a type I or type II kinase inhibitor based on a conformational change that the candidate kinase inhibitor induces in the structure of a kinase labeled with a second harmonic-active label, wherein the label has a net orientation at an interface, and wherein the kinase has no known type I or type II inhibitors, the method comprising:

a. contacting the kinase with the candidate kinase inhibitor, wherein the kinase specifically interacts with said candidate kinase inhibitor;

b. detecting an interaction between the kinase and said candidate kinase inhibitor by measuring a signal or signal change generated by the second harmonic-active label using a surface-selective technique, wherein the signal or signal change indicates a conformational change in the structure of the kinase that is specific for the candidate kinase inhibitor;

c. comparing the signal or signal change detected in (b) with a signal or signal change produced by the interaction between a known type I or type II kinase inhibitor and a kinase known to be inhibited by said known type I or type II kinase inhibitor to classify the candidate kinase inhibitor based on the conformational change it induces in the structure of the kinase.

38-55. -55. (canceled)

56. A method for classifying a first kinase inhibitor as a type I or type II kinase inhibitor based on a conformational change that the first kinase inhibitor induces in the structure of a first kinase labeled with a second harmonic-active label, wherein the label has a net orientation at an interface, the method comprising:

a. contacting the first kinase with a first kinase inhibitor, wherein the first kinase specifically interacts with said first kinase inhibitor;

b. detecting an interaction between the first kinase and said first kinase inhibitor by measuring a first signal or signal change generated by the second harmonic-active label using a surface-selective technique, wherein the first signal or signal change indicates a conformational change in the structure of the first kinase that is specific for the first kinase inhibitor; and

c. classifying the first kinase inhibitor as a type I or type II kinase inhibitor by comparing the first signal or signal change of (b) with a second signal or signal change detected by an interaction between a second kinase and a known type I or type II inhibitor of the second kinase, wherein the second signal or signal change indicates a conformational change in the structure of the second kinase that is specific for the known type I or type II inhibitor of the second kinase.

57. The method of claim 56, wherein the first kinase has no other known kinase inhibitors.

58. The method of claim 56, further comprising comparing a profile of the first signal or signal change to a profile of the second signal or signal change.

59. The method of claim 56, wherein (c) further comprises utilizing structurally conserved homology of kinases across a kinome.

60. The method of claim 56, wherein the kinase is attached to a surface.

61. The method of claim 60, further comprising contacting the kinase attached to the surface with imidazole.

62. The method of claim 61, further comprising measuring a signal or signal change generated by the second harmonic-active label using the surface-selective technique, wherein the signal or signal change indicates a specific interaction of the kinase with the surface.

63. The method of claim 56, further comprising mass-spectrometrically confirming that a residue in the kinase is labeled by the second harmonic-active label.

64. The method of claim 56, wherein the kinase is labeled with an additional second harmonic-active label that is distinguishable from the second harmonic-active label.