Claims
- 1. A method of inducing apoptosis in a eukaryotic cell, the method comprising contacting the cell with an agent that is a RabGGT inhibitor.
- 2. The method of claim 1, wherein the RabGGT inhibitor reduces the level of RabGGT mRNA in the cell.
- 3. The method of claim 1, wherein the RabGGT inhibitor is an interfering RNA.
- 4. The method of claim 1, wherein the RabGGT inhibitor reduces the level of RabGGT protein in the cell.
- 5. The method of claim 1, wherein the RabGGT inhibitor inhibits RabGGT enzymatic activity.
- 6. The method of claim 5, wherein the RabGGT inhibitor is a benzodiazapine compound.
- 7. The method of claim 5, wherein the RabGGT inhibitor is a tetrahydroquinoline compound.
- 8. The method of claim 1, wherein the agent does not substantially inhibit farnesyl transferase activity.
- 9. A method of inhibiting tumor growth in an individual having a tumor, the method comprising:
identifying a compound that is a RabGGT inhibitor; testing the ability of the compound to modulate farnesyl transferase (FT) activity; modifying the compound, wherein the modified compound exhibits reduced modulation of FT activity compared to the unmodified compound, wherein inhibition of RabGGT is retained; and administering to the individual an effective amount of an agent that is a RabGGT inhibitor.
- 10. The method of claim 9, wherein the RabGGT inhibitor reduces the level of RabGGT mRNA in the tumor.
- 11. The method of claim 9, wherein the RabGGT inhibitor is an interfering RNA.
- 12. The method of claim 9, wherein the RabGGT inhibitor reduces the level of RabGGT protein in the tumor.
- 13. The method of claim 9, wherein the RabGGT inhibitor inhibits RabGGT enzymatic activity.
- 14. The method of claim 13, wherein the RabGGT inhibitor is a benzodiazapine compound.
- 15. The method of claim 13, wherein the RabGGT inhibitor is a tetrahydroquinoline compound.
- 16. The method of claim 9, wherein the agent does not substantially inhibit famesyl transferase activity.
- 17. A method of determining the susceptibility of a tumor to treatment with a RabGGT inhibitor, the method comprising detecting a level of RabGGT in the tumor, wherein a level of RabGGT that is elevated compared to a normal cell of the same tissue type indicates that the tumor is susceptible to treatment with a RabGGT inhibitor.
- 18. A method of identifying an agent that selectively modulates RabGGT enzymatic activity, the method comprising;
determining the effect, if any, of the agent on enzymatic activity of RabGGT; and determining the effect, if any, of the agent on enzymatic activity of farnesyl transferase; wherein an increase or decrease of enzymatic activity of RabGGT of at least about 15% compared to the enzymatic activity of RabGGT in the absence of the agent, and a reduction of enzymatic activity of farnesyl transferase of less than about 10% compared to the enzymatic activity of famesyl transferase in the absence of the agent, indicates that the agent is a selective modulator of RabGGT enzymatic activity.
- 19. An agent identified by the method of claim 18.
- 20. A method of identifying an agent that modulates RabGGT enzymatic activity and modulates apoptosis, the method comprising:
determining the effect, if any, of the agent on RabGGT enzymatic activity; and determining the effect, if any, of the agent on apoptosis in a eukaryotic cell, wherein an increase or decrease of enzymatic activity of RabGGT of at least about 15% compared to the enzymatic activity of RabGGT in the absence of the agent, and wherein an increase or decrease in apoptosis of at least about 15% compared to the level of apoptosis in the absence of the agent indicates that the agent modulates RabGGT enzymatic activity and apoptosis.
- 21. A database comprising:
a machine-readable data storage medium comprising a data storage material encoded with machine-readable data, wherein said data comprises the three-dimensional coordinates of a subset of the atoms in a RabGGT polypeptide.
- 22. A computer for producing a three-dimensional representation of a RabGGT protein, wherein said computer comprises:
a machine-readable data storage medium comprising a data storage material encoded with machine-readable data, wherein said data comprises the three-dimensional coordinates of a subset of the atoms in RabGGT polypeptide; a working memory for storing instructions for processing said machine-readable data; a central-processing unit coupled to said working memory and to said machine-readable data storage medium for processing said machine readable data into said three-dimensional representation; and a display coupled to said central-processing unit for displaying said three-dimensional representation.
- 23. The computer of claim 22, wherein said RabGGT polypeptide is complexed with a Rab protein.
- 24. The computer of claim 22, wherein said RabGGT polypeptide is bound to an agent.
- 25. The computer of claim 24, wherein said agent is an inhibitor of RabGGT enzymatic activity.
- 26. A computer-assisted method for identifying potential modulators of apoptosis, using a programmed computer comprising a processor, a data storage system, an input device, and an output device, comprising the steps of:
(a) inputting into the programmed computer through said input device data comprising the three-dimensional coordinates of a subset of the atoms in a RabGGT enzyme, thereby generating a criteria data set; (b) comparing, using said processor, said criteria data set to a computer database of chemical structures stored in said computer data storage system; (c) selecting from said database, using computer methods, chemical structures having a portion that is structurally similar to said criteria data set; (d) outputting to said output device the selected chemical structures having a portion similar to said criteria data set.
- 27. A compound having a chemical structure selected using the method of claim 26.
- 28. A method of identifying an agent that modulates a binding event between a RabGGT polypeptide and a second polypeptide or polypeptide complex, the method comprising:
contacting the agent with a sample comprising a RabGGT polypeptide and a second polypeptide; and determining the effect, if any, of the test agent on the binding between the RabGGT polyeptide and the second polypeptide or polypeptide complex.
- 29. The method of claim 28, wherein the second polypeptide is a Rab polypeptide.
- 30. The method of claim 28, wherein the polypeptide complex is a Rab/REP complex.
- 31. The method of claim 28, wherein said determining is performed using a method selected from a FRET assay, a BRET assay, a fluorescence quenching assay; a fluorescence anisotropy assay; an immunological assay; and an assay involving binding of a detectably labeled protein to an immobilized protein.
- 32. A method of identifying an agent that induces apoptosis and/or inhibits cell proliferation comprising:
a) screening a test agent in an assay system that detects changes in RabGGT level or activity, b) identifying a test agent that reduces RabGGT levels or activity in said assay system, and c) determining whether the test agent identified in (b) induces apoptosis in a cell and/or inhibits cell proliferation.
- 33. The method of claim 32 wherein the assay system is a high-throughput screening (HTS) system that detects changes in RabGGT enzymatic activity.
- 34. A method of identifying a clinical compound for treatment of disorders associated with undesired or uncontrolled cell proliferation comprising:
a) performing the method of claim 32 to identify an agent that induces apoptosis and/or inhibits cell proliferation, b) using said agent as a lead compound to design and synthesize analog compounds, and c) selecting an analog compound having favorable properties for use as a clinical compound.
- 35. A kit comprising a clinical compound identified according to the method of claim 34 and instructions for administering the clinical compound to a patient afflicted with a disorder associated with undesired or uncontrolled cell proliferation.
- 36. A method of inducing apoptosis in a cell comprising contacting the cell with the clinical compound identified by the method of claim 34.
- 37. The method of claim 1, wherein the RabGGT inhibitor is an antibody.
Parent Case Info
[0001] This application claims benefit to provisional application U.S. Serial No. 60/401,604 filed Aug. 7, 2002; and U.S. Serial No. 60/476,722 filed Jun. 6, 2003; under 35 U.S.C. 119(e). The entire teachings of the referenced applications are incorporated herein by reference.
Provisional Applications (2)
|
Number |
Date |
Country |
|
60476722 |
Jun 2003 |
US |
|
60401604 |
Aug 2002 |
US |