U.S. patent application number 10/044967 was filed with the patent office on 2003-04-17 for high affinity inhibitors for target validation and uses thereof.
This patent application is currently assigned to Princeton University. Invention is credited to Shokat, Kevan M..
Application Number | 20030073218 10/044967 |
Document ID | / |
Family ID | 26813087 |
Filed Date | 2003-04-17 |
United States Patent
Application |
20030073218 |
Kind Code |
A1 |
Shokat, Kevan M. |
April 17, 2003 |
High affinity inhibitors for target validation and uses thereof
Abstract
This invention provides general methods for discovering mutant
inhibitors for any class of enzymes as well as the specific
inhibitors so identified. More specifically, this invention
provides general methods for discovering specific inhibitors for
multi-substrate enzymes. Examples of such multi-substrate enzymes
include, but are not limited to, kinases and transferases. The
mutant inhibitors identified by the methods of this invention can
be used to highly selectively disrupt cell functions such as
oncogenic transformation. In one particular example, this invention
provides a Src protein kinase inhibitor, pharmaceutical
compositions thereof and methods of disrupting transformation in a
cell that expresses the target v-scr comprising contacting the cell
with the protein kinase inhibitor.
Inventors: |
Shokat, Kevan M.; (San
Francisco, CA) |
Correspondence
Address: |
MORGAN LEWIS & BOCKIUS LLP
1111 PENNSYLVANIA AVENUE NW
WASHINGTON
DC
20004
US
|
Assignee: |
Princeton University
|
Family ID: |
26813087 |
Appl. No.: |
10/044967 |
Filed: |
May 29, 2002 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10044967 |
May 29, 2002 |
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09480993 |
Jan 11, 2000 |
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6383790 |
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60115340 |
Jan 11, 1999 |
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60145422 |
Jul 23, 1999 |
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Current U.S.
Class: |
435/184 ;
424/94.1 |
Current CPC
Class: |
G01N 2500/10 20130101;
C07D 487/04 20130101; A61P 25/04 20180101; A61P 43/00 20180101;
A61P 9/10 20180101; G01N 2500/04 20130101; C12Q 1/485 20130101;
A61P 19/02 20180101; G01N 2333/9121 20130101; G01N 33/5011
20130101; A61P 35/00 20180101; G01N 2500/20 20130101; A61P 13/00
20180101 |
Class at
Publication: |
435/184 ;
424/94.1 |
International
Class: |
A61K 038/43; C12N
009/99 |
Goverment Interests
[0002] The research leading to the present invention was supported
in part by the grant NIH(IROIICA70331-01) and
NIH(IROIAI/CA44009-01) from the National Institute of Health. The
government may have certain rights in the present invention.
Claims
What is claimed is:
1. An inhibitor that does not inhibit a catalytic activity of a
wild-type enzyme but inhibits the same catalytic activity of the
corresponding mutant enzyme, wherein the wild-type enzyme and the
mutant enzyme are functionally identical.
2. The inhibitor of claim 1 that inhibits the catalytic activity of
the mutant enzyme with an IC.sub.50 of less than about 200 nM.
3. A method of inhibiting a catalytic activity of a mutant enzyme
comprising contacting the mutant enzyme with an inhibitor of claim
1.
4. An inhibitor that does not inhibit the growth of a cell
expressing a wild-type enzyme but inhibits the growth of a cell
expressing a mutant form of the wild-type enzyme, wherein the
wild-type enzyme and the mutant form of the wild-type enzyme are
functionally identical.
5. The inhibitor of claim 4, wherein the inhibitor is selected from
the group comprising a protein kinase inhibitor and a
methyltransferase inhibitor.
6. A method of inhibiting the growth of a cell expressing a mutant
enzyme comprising contacting the cell with an inhibitor of claim
4.
7. A protein kinase inhibitor represented by the following formula
I: 6wherein R is a 1'-naphthyl, 2'-napthyl; m-phenoxyphenyl;
m-benzyloxyphenyl; m-2', 6'-dichloro, benzyloxyphenyl;
3-piperonylpyrazolo; p-tert-butylphenyl; 1 '-naphthylmethyl;
1'-napthoxymethyl; or 2'-naphthylmethyl.
8. A protein kinase inhibitor of claim 7, wherein R is
1'-naphthyl.
9. A protein kinase inhibitor of claim 7, wherein R is
2'-naphthyl.
10. A protein kinase inhibitor of claim 7, wherein R is
1'-napthylmethyl.
11. A protein kinase inhibitor of claim 7, wherein R is
2'-napthylmethyl.
12. A composition comprising the protein kinase inhibitor of any of
claims 7-11.
13. A method of disrupting transformation in a cell that expresses
a mutant protein kinase of the Src family comprising contacting the
cell with the protein kinase inhibitor of claim 7.
14. The method of claim 13, wherein the mutant protein kinase is
1338G v-Src.
15. The method of claim 13, wherein the mutant protein kinase is
T339G Fyn.
16. A method of disrupting transformation in a cell that expresses
a mutant protein kinase of the Src family comprising contacting the
cell with a composition comprising the protein kinase inhibitor of
claim 7.
17. The method of claim 16, wherein the mutant protein kinase is
1338G v-Src.
18. The method of claim 16, wherein the mutant protein kinase is
T339G Fyn.
19. A method of inhibiting the phosphorylation of a substrate of a
mutant protein kinase comprising incubating a protein kinase
inhibitor of claim 7 with a mixture containing the mutant protein
kinase and its substrate.
20. The method of claim 19, wherein the mutant protein kinase is a
mutant protein kinase of the Src family.
21. The method of claim 20, wherein the mutant protein kinase is a
mutant v-Src.
22. The method of claim 21, wherein the mutant v-Src is I338G
v-Src.
23. The method of claim 19, wherein the mutant protein kinase is a
mutant Fyn.
24. The method of claim 23, wherein the mutant Fyn is T339G
Fyn.
25. The method of claim 19, wherein the mutant protein kinase is a
mutant c-Abl.
26. The method of claim 25, wherein the mutant c-Abl is T315A
Abl.
27. The method of claim 19, wherein the mutant protein kinase is a
mutant CAMK II.alpha..
28. The method of claim 27, wherein the mutant CAMK II.alpha.is
F89G CAMK II.alpha..
29. The method of claim 19, wherein the mutant protein kinase is a
mutant CDK2.
30. The method of claim 29, wherein the mutant CDK2 is F80G
CDK2.
31. The method of claim 19, wherein the mutant protein kinase is a
mutant Cdc28.
32. The method of claim 31, wherein the mutant Cdc28 is
Cdc28-as1.
33. The method of claim 19, wherein the mutant protein kinase is a
mutant Fus3.
34. The method of claim 33, wherein the mutant Fus3 is Fus-as1.
35. A method of inhibiting the catalytic activity of a mutant
enzyme comprising incubating the mutant enzyme with an inhibitor of
claim 7.
36. The method of claim 35, wherein the mutant enzyme is a mutant
protein kinase of the Src family.
37. The method of claim 36, wherein the mutant protein kinase is a
mutant v-Src.
38. The method of claim 37, wherein the mutant v-Src is I338G
v-Src.
39. The method of claim 35, wherein the mutant protein kinase is a
mutant Fyn.
40. The method of claim 39, wherein the mutant Fyn is T339G
Fyn.
41. The method of claim 35, wherein the mutant enzyme is a mutant
c-Abl.
42. The method of claim 41, wherein the mutant c-Abl is T315A
Abl.
43. The method of claim 35, wherein the mutant enzyme is a mutant
CAMK II.alpha..
44. The method of claim 43, wherein the mutant CAMK II.alpha.is
F89G CAMK lI.alpha..
45. The method of claim 38, wherein the mutant enzyme is a mutant
CDK2.
46. The method of claim 45, wherein the mutant CDK2 is F80G
CDK2.
47. The method of claim 35, wherein the mutant protein kinase is a
mutant Cdc28.
48. The method of claim 47, wherein the mutant Cdc28 is
Cdc28-as1.
49. The method of claim 35, wherein the mutant enzyme is a mutant
Fus3.
50. The method of claim 49, wherein the mutant Fus3 is Fus-as1.
51. The method of claim 35, wherein the mutant enzyme is a mutant
methyltransferase.
52. A method of inhibiting the growth of a cell that expresses a
mutant enzyme comprising incubating the cell with a protein kinase
inhibitor of claim 7.
53. The method of claim 52, wherein the mutant enzyme is a mutant
v-Src.
54. The method of claim 53, wherein the mutant v-Src is 1338G
v-Src.
55. The method of claim 52, wherein the mutant enzyme is a mutant
c-Abl.
56. The method of claim 55, wherein the mutant c-Abl is T315A
Abl.
57. The method of claim 52, wherein the mutant enzyme is a mutant
CDK2.
58. The method of claim 57, wherein the mutant CDK2 is F80G
CDK2.
59. The method of claim 52, wherein the mutant enzyme is a mutant
Cdc28
60. The method of claim 52, wherein the mutant Cdc28 is Cdc28-as1.
Description
CROSS REFERENCES TO RELATED APPLICATIONS
[0001] This application claims priority to U.S. Provisional Patent
Application No. 60/115,340, filed on Jan. 11, 1999, and U.S.
Provisional Patent Application No. 60/145,422, filed on Jul. 23,
1999, both applications which are hereby incorporated by reference
in their entirety.
FIELD OF THE INVENTION
[0003] This invention provides general methods for discovering
mutant inhibitors for any class of enzymes as well as the specific
inhibitors so identified. More specifically, this invention
provides general methods for discovering specific inhibitors for
multi-substrate enzymes. Examples of such multi-substrate enzymes
include, but are not limited to, kinases and transferases. The
mutant inhibitors identified by the methods of this invention can
be used to highly selectively disrupt cell functions such as
oncogenic transformation. In one particular example, this invention
provides a Src protein kinase inhibitor, pharmaceutical
compositions thereof and methods of disrupting transformation in a
cell that expresses the target v-Src comprising contacting the cell
with the protein kinase inhibitor.
BACKGROUND OF THE INVENTION
[0004] All publications and patent applications herein are
incorporated by reference to the same extent as if each individual
publication or patent application was specifically and individually
indicated to be incorporated by reference. U.S. patent application
Ser. Nos. 08/797,522 and 601046,727, and PCT/US98/02522 are related
to the present invention and each of these applications is
specifically and individually incorporated by reference in its
entirety.
[0005] The current explosion in the number of newly discovered
genes underscores the need for small molecule ligands which can be
used to elucidate and control gene function. Convergent engineering
of protein/small molecule interfaces has emerged in recent years as
a powerful method for generating novel ligand/receptor pairs with
high specificity. By introducing chemical diversity into the target
protein as well as the small molecule, unique binding interactions
can be designed and exploited more efficiently than through
traditional medicinal chemistry. Such approaches have been used to
chemically explore a number of biological systems. FK506-binding
protein has been engineered to preferentially bind non-natural
FK506 analogues by Schreiber and co-workers, as well as Clackson
and co-workers. This system has been used extensively to
selectively dimerize receptors and control gene expression in a
cellular context. Nuclear hormone receptors have also been shown to
be amendable to chemical genetic design. Corey and co-workers
demonstrated that mutations at two amino acid residues in the
retinoid X receptor are sufficient to create two new classes of
receptors with novel ligand specificities. In a more medicinally
applicable system, Smith and co-workers engineered the protease,
carboxypeptidase Al, to hydrolyze a prodrug of methotrexate which
is resistant to hydrolysis by wild type proteases.
[0006] Protein kinase catalyzed phosphorylation of the hydroxyl
moiety of serine, threonine or tyrosine is the central
post-translational control element in eukaryotic signal
transduction. The phosphorylation state of a given protein can
govern its enzyme activity, protein-protein binding interactions,
and cellular distribution. Phosphorylation and dephosphorylation is
thus a "chemical switch" which allows the cell to transmit signals
from the plasma membrane to the nucleus to ultimately control gene
expression in a highly regulated manner. Highly selective, cell
permeable inhibitors of individual kinases would allow for the
systematic investigation of the cellular function of a kinase in
real time, and thus, would provide invaluable tools for the
deconvolution of phosphorylation dependent processes in signal
transduction cascades.
[0007] The Src family is composed of ten highly homologous
cytosolic kinases which are critical components in an array of cell
signaling pathways ranging from lymphocyte activation to cell
growth and proliferation. Constitutive activation of these enzymes
can lead to oncogenic cell transformation, making-them putative
drug targets for cancer therapies. Because of their importance in
the regulation of these fundamental cellular processes, many
studies have focused on developing inhibitors for the Src family
kinase. However, the potent inhibitors that have been discovered
lack the high selectivity that would be required for probing the
cellular inhibition of an individual target kinase. Conventional
inhibitor screens have produced few if any molecules which can
discriminate between the active sites of the various Src family
kinases.
[0008] Unfortunately, the very features which make kinases so
useful in signal transduction, and which has made them evolve to
become central to almost every cellular function, also makes them
extremely difficult, if not impossible, to study and understand.
Their overlapping protein specificities, their structural and
catalytic similarities, their large number, and their great speed
make the specific identification of their in vivo protein
substrates extremely difficult, if not impossible, using current
genetic and biochemical techniques. This is today the main obstacle
to deciphering the signaling cascades involved in protein
kinase-mediated signal transduction (4,6-8).
[0009] Efforts to dissect the involvement of specific protein
kinases in signal transduction cascades have been frustrated by
their apparent lack of protein substrate specificity in vitro and
in vivo (4,8). The catalytic domains of protein kinases possess
little or no inherent protein substrate specificity, as
demonstrated by domain swapping experiments (18-23). The catalytic
domain from one protein kinase can be substituted into a different
protein kinase with little change in the protein substrate
specificity of the latter (22).
[0010] The poor in vitro specificity of kinases also makes it
difficult, if not impossible, to extrapolate what the in vivo
function of given kinases might be. An isolated protein kinase of
interest will often phosphorylate many test substrates with equal
efficiency (29). This apparently poor substrate specificity is also
found in vivo; for example, many genetic approaches, such as gene
knock out experiments, give no interpretable phenotype due to
compensation by other cellular protein kinases (30,31).
[0011] Another complication is that many protein kinases have been
proposed to phosphorylate downstream and upstream proteins which
are themselves protein kinases; although this appears to make
complex positive feedback loops possible, it also makes dissecting
the cascade even more difficult (1). One important avenue for
deciphering the role and understanding the function of enzymes,
both in vitro and in vivo, is the use of specific enzyme
inhibitors. If one or more compound can be found that will uniquely
inhibit the protein kinase target, the inhibitor can be used to
modulate the enzyme's activity, and the effects of that decrease
can be observed. Whole genome techniques have provided many targets
but their function is unknown. Many methods have been developed to
determine if a given new kinase could be a good target. These
methods, all have in common the lack of a small molecule to inhibit
the enzyme which can lead to confusion.
[0012] For example, the most commonly used state of the art
technique is to knock out the kinase and see a new phenotype.
Typically, deletion of one kinase in the mouse genome (most common
model organism) causes no informative change. This is for two
reasons: 1) either the gene (kinase) is essential during
embryogenesis, thereby causing lethality before birth, or 2) the
gene is absent (knocked out) and its function can be replaced by a
closely related kinase which is still present. The important
difference between the art recognized approach and the invention
herein is that herein small organic molecules are employed to
inhibit the function of the kinase of interest, since it is still
present in the organisms but inactive thus it can cause significant
changes to the organisms and most importantly the changes are
exactly like that which would occur if an inhibitor of wild-type
enzyme was made.
[0013] In addition, such inhibitors are among the most important
pharmaceutical compounds known. For example, aspirin
(acetylsalicylic acid) is such an inhibitor. It inhibits an enzyme
that catalyzes the first step in prostaglandin synthesis, thus
inhibiting the formation of prostaglandins, which are involved in
producing pain (72). Traditional drug discovery can be
characterized as the design and modification of compounds designed
specifically to bind to and inactivate a disease-causing protein;
the relative success of such an effort depends upon the selectivity
of the drug for the target protein and its lack of inhibition of
non-disease associated enzymes with similar enzyme activities. Such
approaches would appear to be promising ways to develop treatments
for cancer, since many human cancers are caused by disregulation of
a normal protein (e.g., when a proto-oncogene is converted to an
oncogene through a gene translocation). And since kinases are key
regulators, they have turned out to be very common proto-oncogenes,
and thus ideal drug design targets.
[0014] The process of designing selective inhibitors is relatively
simple in cases where few similar enzymes are present in the target
organism, for example in cases where inhibitors of a protein unique
to bacteria can be targeted. But unfortunately, the similarities
between the kinases and their large number has almost completely
frustrated the discovery and design of specific inhibitors, and has
blocked most hopes of developing specific pharmaceutical treatments
aimed at the proto-oncogene level. It is expected that the vast
majority of candidate inhibitors will inhibit multiple kinases,
even though they may have initially been identified as inhibiting a
particular, purified kinase.
[0015] These difficulties described above have implications well
beyond the mere frustration of scientists; they have frustrated
efforts to decipher the kinase cascades and the function of
individual kinases in those cascades and other cellular mechanisms.
Such an understanding of kinase activity and function may be
essential before certain human diseases can be effectively treated,
prevented or cured. For example, it has been known for over 30
years that the oncogene bcr-abl is a protein kinase that is
responsible for chronic myelogenous leukemia; but the physiological
substrates that it acts upon to cause oncogenesis, which may be
important drug design targets, have yet to be definitively
identified (11). On the bright side, despite this shortcoming, the
inhibitor CGP 57148 is reportedly now undergoing clinical trials
for use in treating myelogenous leukemia, even though the
substrates it may block phosphorylation of in vivo are not
known.
[0016] The medical significance of these difficulties is further
illustrated by the Rous sarcoma virus (RSV), which has become an
important model system for studying the role of kinases in
oncogenesis. RSV transformation of fibroblasts is controlled by a
single viral gene product, the protein kinase v-src (32). It is the
rapid time course and the dramatic morphological changes during RSV
fibroblast transformation that have made RSV a paradigm for studies
of oncogene activity in all cells. The origin (33), regulation
(3,8,34,35), and structure (25,27,36) of v-Src have been
extensively studied and are well understood (8,37,38). But central
questions about the intensely studied kinase remains unanswered:
what are its direct cellular substrates? Does inhibition of its
catalytic activity effectively inhibit, or even reverse,
transformation? Would such inhibition be an effective therapy for
or prophylactic against RSV transformation? Unfortunately, as
discussed above, the answers to these questions are not
forthcoming, largely because the number of cellular kinases is
enormous (it is estimated that 2% of the mammalian genome encodes
protein kinases (4)) and because protein kinases display
overlapping substrate specificities (8,39) and share catalytic
domains, making the design of specific inhibitors enormously
difficult.
[0017] Although the difficulties are daunting, new methods of
rational drug design and combinatorial organic synthesis make the
design or discovery of kinase-specific inhibitors feasible given
sufficient resources. However, because the kinase networks are
highly degenerate and interconnected in unknown ways, there is
considerable uncertainty with regard to many diseases which kinases
should be targeted for inhibition. Moreover, it is by no means
clear that a specific inhibitor of a given kinase will have any
effect on the disease, either in vitro or in vivo. Because kinases
can be highly promiscuous, there is a significant chance that
inhibiting one kinase will simply force another kinase to "take its
place."
[0018] The present invention provides a strategy (i.e.,
methodology) of combining chemical and genetic approaches to enable
the rapid generation of highly selective small molecule inhibitors
for one engineered enzymes, such as kinases and methyltransferases,
in vitro and in whole cells. The invention disclosed herein
involves using a specific point mutation to create a unique pocket
in the substrate binding pocket or site of the enzyme of interest
which does not occur in any other enzyme in the genome. A specific
inhibitor of the engineered enzyme is then synthesized by
derivatizing an enzyme inhibitor with a bulky group designed to fit
the novel active site pocket. By using genetic manipulation to
introduce a unique structural difference into the conserved enzyme
active site, highly selective inhibitors can be identified from
very small panels (10 compounds) of putative inhibitors as
explained herein. The inhibitors of the present invention are
useful for studying the function of enzymes in biochemical pathways
as well as for therapeutic purposes.
SUMMARY OF THE INVENTION
[0019] This invention provides inhibitors that do not inhibit a
catalytic activity of a wild-type enzyme but do inhibit the same
catalytic activity of the corresponding mutant enzyme, wherein the
wild-type enzyme and the mutant enzyme are functionally identical.
More specifically, the inhibitors of the present invention inhibit
the catalytic activity of a mutant enzyme with an IC.sub.50 of less
than about 200 nM. The present invention further provides methods
of inhibiting a catalytic activity of a mutant enzyme by contacting
the mutant enzyme with the inhibitors of this invention.
[0020] The present invention provides inhibitors that do not
inhibit the growth of a cell expressing a wild-type enzyme but do
inhibit the growth of a cell expressing a mutant form of the
wild-type enzyme, wherein the wild-type enzyme and the mutant form
of the wild-type enzyme are functionally identical. Examples of
inhibitors provided by the present invention include, but are not
limited to, protein kinase inhibitors, lipid kinase inhibitors,
aminoglycoside kinase inhibitors and transferase inhibitors, such
as methyltransferase inhibitors. The present invention also
provides methods of inhibiting the growth of a cell expressing a
mutant enzyme by contacting a cell with the inhibitors of the
present invention.
[0021] The present invention further provides protein kinase
inhibitors represented by the following formula I: 1
[0022] wherein R is a 1'-naphthyl, 2'-napthyl; m-phenoxyphenyl;
m-benzyloxyphenyl; m-2',6'-dichloro, benzyloxyphenyl;
3-piperonylpyrazolo; p-tert-butylphenyl; 1'-naphthylmethyl;
1'-napthoxymethyl; or 2'-naphthylmethyl. More specifically, the
present invention provides such protein kinase inhibitors where R
is 1'-naphthyl; 2'-naphthyl or 1'-napthylmethyl; 2'-napthylmethyl.
The present invention also provides compositions which include the
protein kinase inhibitors of the present invention.
[0023] The present invention provides methods of disrupting
transformation in a cell that expresses a mutant protein kinase of
the Src family by contacting the cell with the protein kinase
inhibitors of the present invention. More specifically, the present
invention provides methods of disrupting transformation in a cell
that expresses I338G v-Src or T339G Fyn by contacting the cell with
the protein kinase inhibitors of the present invention.
[0024] The present invention further provides methods of disrupting
transformation in a cell that expresses a mutant protein kinase of
the Src family by contacting the cell with a composition comprising
the protein kinase inhibitors of the present invention. More
specifically, the present invention provides methods of disrupting
transformation in a cell that expresses I338G v-Src or T339G Fyn by
contacting the cell with a composition comprising the protein
kinase inhibitors of the present invention.
[0025] The present invention also provides methods of inhibiting
the phosphorylation of a substrate of a mutant protein kinase by
incubating a protein kinase inhibitor of the present invention with
a mixture containing the mutant protein kinase and its
substrate.
[0026] The present invention also provides methods of inhibiting
the catalytic activity of a mutant enzyme by incubating the mutant
enzyme with an inhibitor of the present invention.
[0027] The present invention also provides methods of inhibiting
the growth of a cell by incubating the cell with an inhibitor of
the present invention.
[0028] Mutant protein kinases used in the methods of the present
invention include, but are not limited to the following: i) mutant
protein kinases of the Src family, such as mutant v-Src; ii) mutant
Fyn; iii) mutant c-Abl; iv) mutant CAMK II.alpha.; v) mutant CDK2;
vi) mutant Cdc28 and vii) mutant Fus3. Specific examples of mutant
protein kinases used in the methods of the present invention
include, but are not limited to the following: i) I338G v-Src; ii)
T339G Fyn; iii) T315A Ab1; iv) F89G CAMK II.alpha.; v) F80G CDK2;
vi) Cdc28-as1 and vii) Fus-as1.
[0029] This invention further provides a general approach for
sensitizing protein kinases to cell permeable molecules which do
not inhibit any wild-type protein kinases. Using this approach,
potent and specific inhibitors from two structural classes of
putative inhibitors are identified for seven protein kinases from
five distinct sub-families. This approach can be used in vivo to
systematically generate conditional alleles of protein kinases.
[0030] This invention also provides mutant kinase, Cdc28-as1
(analog-specific 1), that is uniquely sensitive to the
cell-permeable inhibitor
4-amino-1-(tert-butyl)-3-(1'-naphthylmethyl)pyrazolo[3,4-d]pyri-
midine (1-NM-PP1). In cdc28-as1 cells, entry into mitosis is
inhibited by low concentrations of 1-NM-PP1, whereas higher
concentrations of inhibitor are required to induce the G1 arrest
that is typically observed in temperature-sensitive cdc28 mutants.
Genome-wide transcriptional analysis confirms that 1-NM-PP1
treatment of cdc28-as1 cells leads to inhibition of G2/M-specific
gene expression, whereas treatment of wild-type cells has no
significant effects. The generation of the analog-specific
cdc28-as1 mutant thus provides a highly specific method for
inhibiting Cdc28 activity in the cell, and demonstrates the general
utility of this method in the analysis of protein kinases.
BRIEF DESCRIPTION OF THE FIGURES
[0031] FIG. 1 is a schematic representation of the protein domain
structures of v-Src, of XD4 (which has a deletion of residues
77-225), of the glutathione S-transferase (GST)-XD4 fusion protein,
and of the GST-XD4 fusion protein double mutant (V323A, I338A).
[0032] FIG. 2 is a schematic representation of adenosine
triphosphate (ATP), with an "X" bound to the N.sup.6 position; and
in the box below, schematic representations are provided for the
twelve side chains that take the place of "X" in each of the
orthogonal ATP analogs described in the examples (which are always
referred to by the numbers 1-12 set forth in bold typeface).
[0033] These analogs are:
1 1-N.sup.6(methoxy)ATP 7-N.sup.6-(pyrolidino)ATP
2-N.sup.6(ethoxy)ATP 8-N.sup.6(cyclopenty)ATP 3-N.sup.6(acetyl)ATP
9-N.sup.6(cyclopentyloxy)ATP 4-N.sup.6(i-propoxy)ATP
10-N.sup.6-(pipperidino)ATP 5-N.sup.6-(benzyl)ATP
11-N.sup.6-(cyclohexyl)ATP
[0034] FIG. 3 is an anti-phosphotyrosine immunoblot showing the
level of protein tyrosine phosphorylation following treatment of a
murine lymphocyte cell lysate with ATP or one of the ATP analogs
(A*TPs).
[0035] FIG. 4 provides a close-up view of the X-ray model showing
the ATP binding domain in cAMP dependent protein kinase (1ATP).
[0036] FIGS. 5A-C: FIG. 5A shows an anti-phosphotyrosine blot of
cell lysates expressing XD4 and GST-XD4(V323A, I338A). FIG. 5B
shows an autoradiogram showing levels of phosphorylation when cell
lysates are provided only radiolabeled ATP or only radiolabeled
N.sup.6 (cyclopentyl) ATP. FIG. 5C shows an autoradiogram showing
autophosphorylation of GST-XD4 and GST-XD4(V323A, I338A) by
radiolabeled ATP and radiolabeled
N.sup.6(cyclopentyl)ATP(A*TP(8)).
[0037] FIG. 6 is a bar chart showing the relative degree to which
ATP and each of the twelve ATP analogs inhibits GST-XD4 and
GST-XD4(V323A, I338A) catalyzed phosphorylation by radiolabeled
ATP.
[0038] FIG. 7 shows autoradiograms indicating the levels of
autophosphorylation by several v-Src position 338 single mutants
when provided with either radiolabeled ATP and radiolabeled N.sup.6
(cyclopentyl)ATP as phosphate donor substrate.
[0039] FIG. 8 is a schematic diagram of a method of the present
invention for determining which phosphorylated substrates in cells
were phosphorylated by a particular kinase. Here v-src.
[0040] FIGS. 9A-C show the chemical structures for three known
kinase inhibitors, Damnacanthal (A), PP1 (B) and CGP 57148 (C),
along with summaries of their inhibition constants (IC.sub.50) for
several kinases.
[0041] FIGS. 10A-C: FIGS. 10A and 10B show the structures of a
variety of bulky substituents which, when added to either N-4 of
PP3 or to N.sup.6 of adenosine diphosphate, or to N.sup.6 of
adenosine monophosphate, or to N.sup.6 of adenosine (specifically
N.sup.6 cyclopentyloxy adenosine) to produce inhibitors of the
mutant kinase v-Src(T120G), which is an engineered kinase of the
present invention; the synthesis and inhibition constants (FIG.
10C) for these inhibitors are discussed in Example 12 below.
[0042] FIGS. 11A-11B shows the chemical structure of N-4
cyclopentoyl PP3, and autogradiograms of electrophoresed proteins
which have become radiolabeled in the presence of N-4 cyclopentoyl
PP3 in the presence of either wild-type v-Src or the mutant
(I338G).
[0043] FIGS. 12A-F: FIGS. 12A-F disclose a chart presenting
additional inhibitor analogs prepared and tested in accordance with
the present invention.
[0044] Names corresponding to FIGS. 12A-12F:
[0045] a. 1-tert-Butyl-3-phenyl-1H-indazol-4-ylamine
[0046] b. (1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-ethyl-amine
[0047] c. (1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-propyl-amine
[0048] d.
(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-isobutyl-amine
[0049] e.
(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-cyclopentylmethyl-amine
[0050] f.
(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-furan-2-ylmethyl-amine
[0051] g. Benzyl-(1-tert-butyl-3-phenyl-1H-indazol-4-yl)-amine
[0052] h. N-(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-acetamide
[0053] i.
N-(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-propionamide
[0054] j.
N-(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-isobutyramide
[0055] k.
N-(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-2-phenyl-acetamide
[0056] l. Cyclobutanecarboxylic acid
(1-tert-butyl-3-phenyl-1H-indazol-4-y- l)-amide
[0057] m. Cyclopentanecarboxylic acid
(1-tert-butyl-3-phenyl-1H-indazol-4-- yl)-amide
[0058] n. Cyclohexanecarboxylic acid
(1-tert-butyl-3-phenyl-1H-indazol-4-y- l)-amide
[0059] o. Furan-2-carboxylic acid
(1-tert-butyl-3-phenyl-1H-indazol-4-yl)-- amide
[0060] p. N-(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-benzamide
[0061] q.
N-(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-4-methyl-benzamide
[0062] r.
N-(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-4-ethyl-benzamide
[0063] s.
N-(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-4-isopropyl-benzamide
[0064] t
N-(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-4-propyl-benzamide
[0065] u.
4-tert-Butyl-N-(1-tert-butyl-3-phenyl-1H-indazol-4-yl)-benzamide
[0066] v. Biphenyl-4-carboxylic acid
(1-tert-butyl-3-phenyl-1H-indazol-4-y- l)-amide
[0067] w.
N-(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-4-chloro-benzamide
[0068] x.
N-(1-tert-Butyl-3-phenyl-1H-indazol-4yl)-3,4-dichloro-benzamide
[0069] y. 1-tert-Butyl-3-p-tolyl-1H-indazol-4-ylamine
[0070] z.
(1-tert-Butyl-3-p-tolyl-1H-indazol-4-yl)-cyclopentylmethyl-amine
[0071] aa. N-(1-tert-Butyl-3-p-tolyl-1H-indazol-4-yl)-acetamide
[0072] bb.
N-(1-tert-Butyl-3-phenyl-1H-indazol-4-yl)-2,2-dimethyl-propiona-
mide
[0073] cc. 1-Methyl-3-phenyl-1H-indazol-4-ylamine
[0074] dd. sec-Butyl-(1-methyl-3-phenyl-1H-indazol-4-yl)-amine
[0075] ee.
(1-Ethyl-propyl)-(1-methyl-3-phenyl-1H-indazol-4-yl)-amine
[0076] ff.
(2-Methyl-butyl)-(1-methyl-3-phenyl-1H-indazol-4-yI)-amine
[0077] gg.
(3-Methyl-butyl)-(1-methyl-3-phenyl-1H-indazol-4-yl)-amine
[0078] hh.
Cyclopentyl-(1-methyl-3-phenyl-1H-indazol-4-yl)-amine
[0079] ii. Cyclohexyl-(1-methyl-3-phenyl-1H-indazol-4-yl)-amine
[0080] jj. (1-Methyl-3-phenyl-1H-indazol-4-yl)-phenyl-amine
[0081] kk.
(3-chloro-phenyl)-(1-methyl-3-phenyl-1H-indazol-4-yl-amine
[0082] ll. Benzyl-(1-methyl-3-phenyl-1H-indazol-4-yl)-amine
[0083] mm. 4-Chloro-1,3-diphenyl-1H-indazole
[0084] mn. 1,3-Diphenyl-1H-indazol-4-ylamine
[0085] oo. (1,3-Diphenyl-1H-indazol-4-yl)-propyl-amine
[0086] pp. sec-Butyl-(1,3-diphenyl-1H-indazol-4-yl)-amine
[0087] qq.
(1,3-Diphenyl-1H-indazol-4-yl)-(1-ethyl-propyl)-amine
[0088] rr.
(1,3-Diphenyl-1H-indazol-4-yl)-(2-methyl-butyl)-amine
[0089] ss.
(1,3-Dimethyl-butyl)-(1,3-diphenyl-1H-indazol-4-yl)-amine
[0090] tt.
(3,3-Dimethyl-butyl)-(1,3-diphenyl-1H-indazol-4-yl)-amine
[0091] uu. (1,3-Diphenyl-1H-indazol-4-yl)-diethyl-amine
[0092] vv. Cyclopentyl-(1,3-diphenyl-1H-indazol-4-yl)-amine
[0093] ww. Cyclohexyl-(1,3-diphenyl-1H-indazol-4-yl)-amine
[0094] xx. (1,3-Diphenyl-1H-indazol-4-yl)-phenyl-amine
[0095] yy. 1-Benzyl-4-chloro-3-phenyl-1H-indazole
[0096] zz. 1-Benzyl-3-phenyl-1H-indazol-4-ylamine
[0097] aaa.
(1-Benzyl-3-phenyl-1H-indazol-4-yl)-(1-ethyl-propyl)-amine
[0098] bbb.
(1-Benzyl-3-phenyl-1H-indazol-4-yl)-(1,3-dimethyl-butyl)-amine
[0099] ccc. (1-Benzyl-3-phenyl-1H-indazol-4-yl)-diethyl-amine
[0100] ddd.
(1-Benzyl-3-phenyl-1H-indazol-4-yl)-cyclopentyl-amine
[0101] eee.
(1-Benzyl-3-phenyl-1H-indazol-4-yl)-cyclohexyl-amine
[0102] fff. (1-Benzyl-3-phenyl-1H-indazol-4-yl)-phenyl-amine
[0103] FIGS. 13A-13B: FIG. 13A sets forth a schematic
representation of the specificity problems associated with using
small molecule protein kinase inhibitors to deconvolute cell
signaling. Kinase catalytic domains (red ovals) are highly
conserved. Thus, the majority of potent inhibitors block the
activity of closely related kinases and broadly down regulate
pathways mediated by kinase activity. FIG. 13B sets forth a
schematic representation of the approach toward selective protein
kinase inhibition described here. A space creating mutation is
introduced into the ATP binding site of the kinase of choice (Src).
This mutation creates an active site pocket (notch) in Src which
can be uniquely recognized by a rationally designed small molecule
inhibitor. This inhibitor contains a bulky chemical group (bump)
which makes it orthogonal to wild type protein kinases. Design of
the complementary kinase/inhibitor pair allows for highly selective
inhibition of the target kinase in the context of whole cell.
[0104] FIGS. 14A-14B: FIG. 14A sets forth a structure of N-6
cyclopentyloxyadenosine (1). FIG. 14B sets forth the synthesis of
pyrazolo[3,4-d] pyrimidine inhibitor and analogues. 2 was
synthesized according to Hanefeld, et al. (i) RCOCI (10 equiv.),
pyridine, 5(C, 1 h; then warm to 22(c, 11 h; (ii) LiAlH.sub.4 (3.0
equiv), dry THF under argon, 0(C, 30 min; then heat to reflux for
30 min. All compounds were characterized by .sup.1H NMR (300 MHz)
and high resolution mass spectrometry (EI).
[0105] FIGS. 15A-15C: FIG. 15A sets forth the chemical structures
of quercetin (5) and AMP PNP (6). FIG. 15B shows the predicted
binding orientation of 2 in src family kinase active sites. The
crystal structures of Hck bound to AMP PNP (red) and Hck bound to
quercetin (blue) were superimposed according to the HcK protein
backbone (white). The structure of 2 (yellow) was subsequently
docked into the kinase active site by superimposing the
pyrazolo[3,4-d]pyrimidine ring system of 2 onto the adenine ring of
AMP PNP. FIG. 15C shows the predicted close contact between N-4 of
2 and the side chain of residue 338 in src family kinases. Molecule
2 has been docked into the ATP binding site of the src family
kinase, Hck, as in FIG. 3. The atoms of the threonine 338 side
chain and 2 are colored according to their element makeup
(green=carbon, blue=nitrogen, red=oxygen, white=hydrogen) and the
Hck backbone is shown in purple. The methyl hydrogens of the
threonine side chain are now shown. Images were generated using the
program InsightII.
[0106] FIG. 16 shows the inhibitor 3 g (FIG. 14) blocks p36
phosphorylation in I338G v-Src, but not WT v-Src transformed NIH3T3
fibroblasts. Non-transformed NIH3T3 cells (lane 1). WT v-Src
transformed NIH3T3 cells (lanes 2-3), and I338G v-Src transformed
NIH3T3 cells (lanes 4-5) were incubated with 1.1% DMSO (lanes 1, 2
and 4) or 100 mM 3 g in 1.1% DMSO (lanes 3 and 5). After 12 hours,
the cells were lysed. Phosphorylation levels were determined as in
FIG. 4.
[0107] FIGS. 17A-J show the I338G v-Src transformed fibroblasts
selectively acquire a flattened morphology and selectively regain
Actin stress fibers upon incubation with 3 g (FIG. 14).
Non-transformed (a., b.), WT v-Src transformed (c., d., g., h.),
and I338G v-Src transformed (e., f., i., j.). NIH3T3 fibroblasts
were treated with either 1.1% DMSO (a., c., e., g., i.) or 100 mM
analog 3 g in 1% DMSO (d., f., h., j.). After 48 hours cells were
photographed (a., c., f.), stained with phalloidin-FITC, and
visualized (b., g., j.) by fluorescence microscopy.
[0108] FIG. 18 sets forth the synthesis of C.sup.3 Derivatized PP1
Analogues. Conditions: (i.) 2 equiv NaH, 1 equiv malonitrile, THF,
RT, 0.5 h; (ii.) 5 equiv NaHcO.sub.3, 5 equiv dimethyl sulfate,
dioxane/H.sub.2O(6/1), 80.degree. C., 1 h; (iii.) 1 equiv
triethylamine, 1 equiv tert-butylhydrazine hydrochloride, EtOH,
reflux, 1 h; (iv.) formamide, 180.degree. C., 12 h.
[0109] FIG. 19 sets forth a schematic representation of the
predicted binding orientation of two classes of derivatized
pyrazolo[3,4-d) pyrimidines. Analogues that were derivatized at
N.sup.4 may have lost potency due to an interruption of the
ATP-like hydrogen bonding network. This network is presumably
intact in the C.sup.3 derivatized inhibitors.
[0110] FIGS. 20A-20B: FIG. 20A shows the effect of 6a (FIG. 18) on
tyrosine phosphorylation in NIH3T3 fibroblasts expressing either
wild type v-Src (lanes 1, 2) or I338G v-Src (lanes 3-8). Cells were
treated with the indicated amount of 6a (FIG. 18) in 0.5% DMSO for
30 min and immediately lysed. Cellular proteins were separated by
polyacrylamide gel electrophoresis (10%) and transferred to
nitrocellulose. Tyrosine phosphorylated proteins were visualized by
immunoblotting with a monoclonal anti-phosphotyrosine antibody
(4G10). FIG. 20B shows the effect of 6a (FIG. 18) on tyrosine
phosphorylation in wild type Jurkat cells. 10.sup.6 Jurkat cells
were incubated at 37.degree. C. for 30 min in the presence of 0.5%
DMSO (lanes 9,10), 500 nM 6a (lane 11), or 10 .mu.M PPI (lane 12).
Cells in lanes 10-12 were subsequently treated with 0.5 mM
pervanadate for 10 min before lysis. Tyrosine phosphorylated
proteins were visualized as in FIG. 20A.
[0111] FIGS. 21A-21B: FIGS. 21A and B show 338G v-Src transformed
fibroblasts selectively acquire a flattened morphology and
selectively regain actin stress upon incubation with 6a (FIG. 18).
FIG. 21A show non-transformed NIH3T3 cells. FIG. 21B show cells
transformed by either wild type v-Src or I338G v-Src were treated
with 0.5% DMSO or 250 nM 6a in 0.5% DMSO for 16 hours. All cells
were fixed, stained with phalloidin-rhodamine, and visualized by
confocal microscopy.
[0112] FIGS. 22A-22B: FIG. 22A shows chemical structures of
(+)-K252a (1) and (+)-Staurosporine (2). FIG. 22B shows crystal
structure of 2 bound to CDK2 (28). CDK2 is shown in magenta with
the peptide backbone illustrated as a ribbon and the F80 side chain
as sticks. Staurosporine is shown with CPK coloring as follows:
carbon (green), nitrogen (blue), oxygen (red). Hydrogens are not
shown.
[0113] FIGS. 23A-C: FIG. 23A sets forth a schematic diagram of
mating assay used to test for Fus3 function. FIGS. 23B and C show
selective disruption of fus3-as1 yeast mating by 10 (FIG. 28) and
11 (FIG. 28). Haploid URA3 his3 S. cerevisiae expressing either
wild-type Fus3, Fus3-as1, or no Fus3 at OD.sub.600=0.5 were mated
with an equal number of ura3 HIS3fus1.DELTA.fus2.DELTA. cells and
pipetted onto a nitrocellulose disk. The disk was placed on a YPD
plate containing the indicated amounts of inhibitor for 5 hours at
30.degree. C. Cells were liberated from the disks and serial
dilutions of the resulting cultures were plated on media lacking
uracil and histidine and grown for two days at 30.degree. C. and
the colonies were counted. To ensure that 10 and 11 (FIG. 28) were
not non-selectively cytotoxic, all cultures were also plated on
YPD. No significant decrease in cfu/mL on YPD plates was observed
for any of the three strains in the presence of 10 or 11 (FIG. 28).
FIG. 23B sets forth Photograph of plates lacking histidine and
uracil which were inoculated with 0.1 mL of the mating cultures
from the following strains (from top): fus3.DELTA., fus3, fus3+5
.mu.M 10, fus3-as1, fus3-as1+5 .mu.M 10. FIG. 23C shows disruption
of Fus3 dependent mating is selective and dose dependent. Red bars
indicate the cfu/mL.times.10.sup.-3 for wild-type Fus3 expressing
yeast at the indicted inhibitor concentrations. Green bars indicate
the cfu/mL.times.10.sup.-3 for Fus3-as1 expressing yeast at the
indicted inhibitor concentrations. Experimental conditions are as
described above.
[0114] FIG. 24 shows the structure of
4-amino-1-(tert-butyl)-3-(2'-napthyl-
methyl)pyrazolo[3,4-d]pyrimidine (6j).
[0115] FIGS. 25A-D set forth 500 nM 1-NM-PP1 addition causes a drop
in G2/M transcription. FIGS. 25A-C show an asynchronous population
of cdc28-as1 cells was treated with 1-NM-PP1 for 120 minutes.
Genome-wide transcriptional differences in the absence and presence
of inhibitor were measured by oligonucleotide microarray analysis
of cellular mRNA (127). For comparison, FIG. 25A shows the
percentage of genes whose transcription is known to be regulated
during the cell cycle (150). FIG. 25B shows transcripts that
decreased over 2.5-fold following inhibitor treatment. FIG. 25C
shows transcripts that increase after inhibitor treatment.
Transcripts are grouped in the lists and pie charts according to
their known cell cycle regulation (150). FIG. 25D shows genome-wide
changes in gene expression were assessed in four comparisons as
follows: 1. cdc28-as1 cells+500 nM 1-NM-PP1 compared to untreated
cdc28-as1 cells (as1+500/asl); 2. drug-treated cdc28-as1 cells
compared to drug-treated wild-type cells (as1+500/wt+500); 3.
untreated cdc28-as1 cells compared to wild-type cells (as1/wt); and
4. drug-treated wild-type cells compared to untreated wild-type
cells (wt+500/wt). For each comparison, the ratio of gene
expression under the two conditions was converted to its natural
logarithm. The mean logarithmic change in expression of all genes
in each of the major cell cycle clusters (G1, S, S/G2, G2/M, M/G1),
as well as that of genes whose expression is not
cell-cycle-regulated (Unreg.), was calculated. Error bars represent
standard errors of the means.
[0116] FIGS. 26A and 26B: (a.) Classification, substrate
specificities, and cellular functions of the protein kinases
utilized in this report. (b.) Sequence alignment of the residues
surrounding position 338 (v-Src numbering) for the protein kinases
listed in (a).
[0117] FIG. 27: 50% inhibitory concentrations (IC.sub.50, .mu.M)
for K252a and C(7) derivatized K252a analogs against a panel of
wild-type and rationally engineered protein kinases. The
derivatized portion of the inhibitors are highlighted in red.
IC.sub.50 values for the best K252a derivative/engineered kinase
pair are shown in blue. Kinase purification and measurement of
IC.sub.50 values were performed essentially as described (86).
[0118] FIG. 28: 50% inhibitory concentrations (IC.sub.50, .mu.M)
for PP1 and C(3)-phenyl derivatized PP1 analogs against a panel of
wild-type and rationally engineered protein kinases. The
derivatized portion of the inhibitors are highlighted in red.
IC.sub.50 values for the best PP1 derivative/engineered kinase pair
are shown in blue. Kinase purification and measurement of IC.sub.50
values were performed essentially as described (86).
DETAILED DESCRIPTION OF THE INVENTION
I. Definitions
[0119] As is generally the case in biotechnology, the description
of the present invention herein has required the use of a
substantial number of terms of art. Although it is not practical to
do so exhaustively, definitions for some of these terms are
provided here for ease of reference. Definitions for other terms
also appear elsewhere herein, and those are not repeated here. It
is important to note that it is not intended that the terms defined
here or elsewhere herein be given a meaning other than that which
those skilled in the art would understand them to have when used in
the field, and it is therefore urged that other sources also be
consulted in interpreting the meaning of these terms and those
defined elsewhere herein. However, the definitions provided here
and elsewhere herein should always be considered in determining the
scope and meaning of the defined terms.
[0120] As used herein, the term "enzyme" means any naturally
occurring or synthetic macromolecular substance composed wholly or
largely of protein, that catalyzes, more or less specifically, one
or more (bio)chemical reactions. The substances upon which the
enzymes act are known as "substrates", for which the enzyme
possesses a specific binding or "active site". Enzymes can also act
on macromolecular structures such as muscle fibers and more "cargo"
such as intracellular vesicles. Such proteins are called motor
proteins, two classes of which are myosins and kinesins.
[0121] As used herein, the term "catalytic activity of an enzyme"
is defined as the property measured by the increase in the rate of
conversion of a specified chemical reaction that the enzyme
produces in an assay system.
[0122] As used herein, the term "kinase" means any
phosphotransferase enzyme that transfers a phosphate group.
[0123] As used herein, the term "protein kinase" means any enzyme
that phosphorylates one or more hydroxyl or phenolic groups in
proteins, ATP being the phosphoryl-group donor.
[0124] As used herein, the term "phosphorylase" means any enzyme
that catalyzes the phosphorolytic removal of the nonreducing
terminal glucose residue from a glucan.
[0125] As used herein, the term "phosphorylase kinase" is
synonymous with the term "protein phosphorylase kinase" and means
any phosphorylase enzyme that converts phosphorylase b to
phosphorylase a.
[0126] As used herein, the term "phosphorylase phosphatase" is
synonymous with "protein phosphorylase phosphatase" means any
phosphorylase enzyme that converts phosphorylase a to phosphorylase
b.
[0127] As used herein, the term "tyrosine kinase" is synonymous
with the term "protein tyrosine kinase" and means an enzyme that
transfers the terminal phosphate of ATP to a specific tyrosine
residue on its target protein.
[0128] As used herein, the term "transferase" means any enzyme that
catalyzes the transfer of a group--e.g., the methyl group, glycosyl
group, acyl group, phosphorus-containing, or other groups.
[0129] As used herein, the term "methyltransferase" is synonymous
with the term "transmethylase" and means any of the enzymes which
catalyze the transfer of a methyl group.
[0130] The term "low affinity inhibitor" refers to a small molecule
which has a binding constant (IC.sub.50) for the target enzyme of
greater than about 200 nM, and thus would need to be used at a high
concentrations in a cell based or whole animal based assay ( a
concentration of greater than 50 .mu.M). Such high concentrations
might induce non-specific drug affects that could mask the specific
role of the desired target of the inhibitor.
[0131] As used herein, the term "mutant specific inhibitor" is
defined as an inhibitor that inhibits a specific type of mutant
enzyme.
[0132] As used herein, the term "monospecific inhibitor" means an
inhibitor that is only able to react with a single specified
enzyme.
[0133] The term "high affinity inhibitor" refers to a small
molecule which has a binding constant (IC.sub.50) for the target
enzyme of less than about 200 nM, and thus allowing ti to be used
at "low" concentrations in a cell based or whole animal based assay
(a concentration less than 50 .mu.M). At lower concentrations, the
non-specific effects of the small molecule would be lessened, thus
allowing a more true response to inhibition of the target kinase to
be assessed.
[0134] The term "orthogonal" is used here to mean a compound that
is similar, structurally and/or geometrically, to the natural
substrate for a given enzyme, or to an inhibitor of the wild-type
form of the enzyme, but has differences in chemical structure which
make that compound less able to bind to the wild-type form of the
enzyme than is the natural substrate. By "natural" substrate it is
meant that the substrate which is utilized by the wild-type form of
that enzyme. The orthogonal inhibitors of the present invention may
be referred to in different ways herein; for example, sometimes
they are referred to as "modified substrates," "modified
inhibitors," "analogs," "derivatives," just as "substrates," or
"inhibitors," and perhaps by other terms as well. However, in each
instance, the same meaning is intended. Of course, the meaning of
"orthogonal" and its synonyms are further explained in the
descriptions of the invention provided below.
[0135] The putative orthogonal substrates and inhibitors of the
embodiments of the invention described herein were made by adding
bulky substituents to an atom on the natural substrate of known
kinase inhibitor, respectively. However, the present invention is
not so limited. For example, it is possible to make an orthogonal
substrate that is smaller than a known inhibitor or the natural
substrate, e.g., by preparing an analog that is missing one or more
atoms or substituents that are present in the natural substrate.
With such putative orthogonal substrates or inhibitors, one could
mutate the enzyme to contain one or more amino acids having more
bulky side chains than those found in the wild-type amino acid
sequence, so that when the orthogonal substrate or inhibitor binds,
those more bulky amino acid side chains fill or partially fill the
extra space created by the missing atoms or substituents. In this
way, it would be expected that the mutant would bind to and/or be
inhibited by the orthogonal substrate or inhibitor but would not
substantially utilize the normal substrate, because the added bulky
amino acids present a steric hindrance to its binding. Such an
approach would allow for highly selective control of the resulting
mutant.
[0136] It is important to keep in mind that even though the
substrates and inhibitors of the examples herein are of the
non-competitive type, this should not be viewed as a limitation of
the scope of the present invention. Many different types of enzyme
substrates and inhibitors are known, e.g., competitive,
non-competitive, uncompetitive, "suicide" inhibitors, etc.
Competitive inhibitors compete with a substrate for its binding
site, but since the inhibitor cannot participate in the catalytic
reaction which that enzyme carries out, it slows down catalysis.
Non-competitive inhibitors bind to the active site, but then become
covalently or ironically bound to the protein structure of the
enzyme, such that they cannot come off. Thus, they inhibit
catalysis by taking molecules of enzyme out of the reaction
altogether. More detailed descriptions of these and other
competitive mechanisms can be found in a. variety of sources (e.g.,
72). By applying the understanding of the art regarding such
mechanisms to the design of inhibitors of the present invention,
all such types of inhibitors could be made.
[0137] For example, an analog which can bind, but not react, would
provide a competitive inhibition, and an analog which becomes
covalently attached to the enzyme upon binding, would be a
non-competitive inhibitor, i.e,, a poison. All such types of
inhibitors are within the scope of the present invention.
[0138] The term "homologous to" has been used to describe how
information about how to modify one enzyme can be deducted from
information regarding the three-dimensional structure of other,
related enzymes. As those in the field well know, a part of one
enzyme which is "homologous" to part of a second enzyme has a
protein sequence which is related to that of the second enzyme.
This relationship is that they have a number of amino acids in the
same relative location to one another. For example, the imaginary
sequence Asp-Met-Phe-Arg-Asp-Lys-Glu (SEQ ID NO: 10) and the
imaginary sequence Asp-Met-Ile-Arg-Glu-Lys-Asp (SEQ ID NO: 11) have
four amino acids in the same relative location, and three which are
different, and they would be said to have homologous sequences.
Note that the three amino acids that are different between the
chains are "conservative" differences, in that the substitutions in
the second sequence relative to the first are with amino acids that
have similar functionalities on their side chains. For example, Glu
and Arg both have charged groups and both Phe and Ile are
hydrophobic. Although this is often the case with homologous
protein sequences, it need not be the case, and these two imaginary
sequences would still be considered homologous even if the
differences were not conservative. Reference 71 gives a good
overview of which domains of the known kinases are considered by
the art to be "homologous." In addition, although the art may not
generally agree, it is intended hee that sequences that are
identical to one another also be considered to be "homologous" to
one another.
[0139] The term "domain" is also one well known in the art, and it
refers to a region in a protein which has been identified as having
a particular functionality. For example, the three domains in
protein kinases have been discussed elsewhere herein, and their
functional roles have been discussed. Often, as is the case with
the kinases, different enzymes of the same family will have the
same number of domains with each serving the same function, and
they are often (but probably not always) arranged in the same order
along the protein sequence. Interestingly, as is the case for the
kinases, one enzyme may have a different length of protein sequence
between its domains than does another. However, since the domains
of two related enzymes are generally (but probably not always)
homologous to one another, this does not generally hamper the
identification of corresponding domains.
[0140] In describing the broader aspects of the present invention,
the terms "multi-substrate" or "multi-substrate enzyme" are used.
These terms are synonymous and are intended to mean enzymes which
bind two or more substrates. Those multi-substrate enzymes of most
interest here are those which catalytically attach at least part of
one substrate to at least one other substrate. The kinases and the
transferases are but two families of such multi-substrate enzymes,
and those of skill in the art will readily recognize that there are
other such enzymes and enzyme families.
[0141] The term "recognize" is sometimes used here to describe the
ability of a substrate to specifically bind to the active site on
an enzyme. This simply refers to the fact that an enzyme's
substrate (or sometimes substrate derivatives or even completely
different compounds that mimic the substrate) can contact and bind
to the enzyme's active site, but other compounds will not. This
concept is well known in the art. Enzymologists often say that the
enzyme has an affinity for its substrate, or that the substrate has
an affinity for the enzyme. They also say that an enzyme has
"substrate specificity," These all really describe the same
phenomenon.
[0142] A related term is the term "bind." An inhibitor generally
binds, or sticks to, to an active site through one or more
hydrophobic, hydrophilic, hydrogen, and/or ionic bonds, or, in the
case of non-competitive inhibitors, through covalent bonds.
Although the complex understanding in the art regarding inhibitor
binding and the reasons for inhibition may be of interest, such an
understanding is not essential to understanding the present
invention.
[0143] It is sufficient to simply note that binding by an inhibitor
causes inhibition of the catalytic reaction.
[0144] The terms "mutant" and "engineered form," when used to
describe the enzymes of the present invention, simply mean that
they have sequences that have a different amino acid at one or more
position when compared to the sequence of the wild-type enzyme. In
describing such mutants, two letters separated by a number indicate
the amino acid mutations made. The letters are single-letter amino
acid codes, and the numbers are the amino acid residue positions in
the intact, wild-type enzyme. For example, GST-XD4 is a fusion
protein containing a fragment, XD4, that has the same sequence as a
specific part of the wild-type v-Src. In the designation
GST-XD4(V323A, I338A), the valine in the sequence of v-Src fragment
XD4 that represents position 323 in the compete wild-type v-Src
sequence has been replaced by alanine, and the isoleucine in the
XD4 fragment that represents position 338 in the complete wild type
v-Src sequence has also been replaced with alanine. Thus, the terms
"mutant" and "engineered form" encompass portions of the wild-type
enzyme containing the mutated amino acid or amino acids.
[0145] The term "A*TP" refers to a form of ATP in which additional
atoms or groups of atoms are added to one or more positions of the
ATP structure. In addition, A*TP means an analog of ATP which has
one or more of its atoms removed to form a molecule which is
smaller than ATP itself. A*TP does not necessarily mean a
non-natural analog of ATP, for example GTP could be considered an
analog of ATP for the purposes of this definition.
[0146] The phrase "functionally silent active site mutation" means
that the mutation does not disrupt the normal cellular role of the
protein. In other words, the "functionally silent" mutant should be
able to completely, or at least significantly, be able to replace
the biological role of the wild-type protein. For example, if a
cell or organism is created in which the wild-type form of the
protein is absent and then the "functionally silent" form of the
enzyme is added into that cell or organism, this "mutant
containing" cell or organism should be very similar if not
identical in behavior (by any appropriate assay) to the original
unmodified form of the cell or organism.
II. General Description
[0147] This invention provides specific protein kinase inhibitors.
Selective protein kinase inhibitors are highly sought after as
tools for studying cellular signal transduction cascades, yet few
have been discovered due to the highly conserved fold of kinase
catalytic domains. Through a combination of small molecule
synthesis and protein mutagenesis a highly potent (IC.sub.50=1.5 nM
and uniquely specific inhibitor (4-amino-1
-tert-butyl)-3-(1'-naphthyl)pyrazolo [3,4-d]pyrimidine) of a
rationally engineered v-Src protein kinase (Ile338Gly v-Src) has
been identified. Both the potency and specificity of this compound
surpass those of amy known Src family protein kinase inhibitors.
The molecule strongly inhibits the engineered v-Src in whole cells
but does not inhibit tyrosine phosphorylation in cells, that
express only wild type protein kinases. In addition, the inhibitor
selectively disrupts transformation in cells that express the
target v-Src. The structural degeneracy of kinase active site
should allow the same complementary inhibitor/protein design
strategy to be widely applicable across this entire enzyme
super-family. Thus, this invention provides mutant tyrosine and
ser/thr kinases.
[0148] This invention provides mutant protein kinases that are
sensitive to the disclosed cell permeable inhibitors. The mutant
protein kinases belong to the following sub-families: Src family
(v-Src, Fyn), Abl family (c-Abl), Ca.sup.+2/Calmodulin dependent
family (CAMK II.alpha.), and cyclin dependent family (CDK2 and
Cdc28).
III. Protein Kinase Inhibiitor
[0149] The present invention provides a protein kinase inhibitor
represented by the following formula I: 2
[0150] wherein R is a 1'-naphthyl, 2'-naphthyl; m-phenoxyphenyl;
m-benzyloxphenyl; m-2', 6'-dichloro,benzyloxyphenyl;
3-piperonylpyrazolo; p-tert-butylphenyl; 1'-naphthylmethyl;
1'-naphthoxymethyl; or 2'-naphthylmethyl.
[0151] In one embodiment the naphthyl is a naphthylpyrazolo,
pyrimidine. In another embodiment the protein kinase inhibitor is
represented by the formula 6a as set forth in FIG. 18. In another
embodiment the protein kinase inhibitor is represented by the
formula 6b as set forth in FIG. 18. In another embodiment the
m-phenoxyphenyl is a m-phenoxphenyl, pyrazolopyrimidine. In another
embodiment the protein kinase inhibitor is represented by the
formula 6c as set forth in FIG. 18. In another embodiment the
m-benzyloxphenyl is a m-benzyloxyphenyl, pyrazolopyrimidine. In
another embodiment the protein kinase inhibitor is represented by
the formula 6d as set forth in FIG. 18. In another embodiment the
m-dichloro, benzyloxphenyl is a m-dichloro, benzyloxyphenyl,
pyrazolopyrimidine. In another embodiment the protein kinase
inhibitor is represented by the formula 6e as set forth in FIG. 18.
In another embodiment the 3-piperonyl is a 3-piperonyl,
pyrazolopyrimidine. In another embodiment the protein kinase
inhibitor is represented by the formula 6f as set forth in FIG. 18.
In another embodiment the p-tert-butylphenyl is a
p-tert-butylphenyl, pyrazolopyrimidine. In another embodiment the
protein kinase inhibitor is represented by the formula 6g as set
forth in FIG. 18. In another embodiment the naphthylmethyl is a
naphthylmethyl, pyrazolopyrimidine. In another embodiment the
protein kinase inhibitor is represented by the formula 6h as set
forth in FIG. 18. In another embodiment the protein kinase
inhibitor is represented by the formula 6j as set forth in FIG. 24.
In another embodiment the naphthoxyethyl is a naphthoxylmethyl,
pyrazolopyrimidine. In another embodiment the protein kinase
inhibitor is represented by the formula 6i as set forth in FIG.
24.
[0152] This invention provides a src family kinase inhibitor, where
the inhibitor is
[0153]
4-amino-1-(tert-butyl)-3-(1'-naphthyl)pyrazolo[3,4-d]pyrimidine
(6a);
[0154]
4-amino-1-(tert-butyl)-3-(2'-naphthyl)pyrazolo[3,4-d]pyrimidine
(6b);
[0155]
4-amino-1-(tert-butyl)-3-(m-phenoxyphenyl)pyrazolo[3,4-d]pyrimidine
(6c);
[0156]
4-amino-1-(tert-butyl)-3-(m-beizyloxyphenyl)pyrazolo[3,4-d]pyrimidi-
ne (6d);
[0157] 4-amino-1-(tert-butyl)-3-(m-(2',6'-dichloro)benzyloxyphenyl)
pyrazolo[3,4-d]pyrimidine (6e);
[0158] 4-amino-1-(tert-butyl)-3-piperonylpyrazolo[3,4-d]pyrimidine
(6f);
[0159] 4-amino-1-(tert-butyl)-3-(p-tert-butylphenyl)pyrazolo[3,4
d]pyrimidine (6g);
[0160]
4-amino-1-(tert-butyl)-3-(1'-naphthylmethyl)pyrazolo[3,4-d]pyrimidi-
ne (6h);
[0161]
4-amino-1(tert-butyl)-3-(1'-naphthoxymethyl)pyrazolo[3,4-d]pyrimidi-
ne (6i); or
[0162]
4-amino-1-(tert-butyl)-3-(2'-naphthylmethyl)pyrazolo[3,4-d]pyrimidi-
ne (6j).
[0163] As demonstrated herein all starting materials and synthetic
reagents were purchased from commercial suppliers unless otherwise
noted. Acid chlorides that were not readily commercially available
(3c, 3d, 3e, 3h, 3i) were synthesized by treating the corresponding
carboxylic acids with excess oxalyl chloride and catalytic DMF in
diethyl ether. All PP 1 analogues were synthesized according to
Henefeld, et al. The group of modified inhibitors was screened
against the catalytic domain of the target kinase, I338G v-Src,
which was expressed in bacteria and purified as a
gluthathione-S-transferase (GST) fusion protein. All of the C.sup.3
derivatized analogues are more potent inhibitors of I338G v-Src
than the most potent molecule (compound 3g, IC.sub.50=430 nM, FIG.
15) identified from the first generation panel of N.sup.4
derivatized compounds (see FIG. 15). Four of the molecules (6a, 6b,
6d, 6h) inhibit the target kinase at low nM concentrations with the
two naphthyl isomers (6a, 6b) exhibiting the greatest potency
(IC.sub.50=1.5 nM). Under the conditions of our assay the parent
molecule, PP1, inhibited its optimal target, Fyn, at only
IC.sub.50=30 nM. This data shows that an inhibitor design strategy
combining enzyme engineering with directed small molecule synthesis
can not only match the potency of molecules identified through
screening of large libraries, but can lead to a significant
increase (20 fold in the case of 6a, 6b) in affinity over
previously optimized inhibitors of wild type kinase. Compounds
having the formula of 6a and 6b are the most potent inhibitors of
any Src family protein kinase that have been reported to date.
Compound 6h and 6j are more orthogonal to wild-type kinases and is
of medium potency. They are not as potent as 6a and 6b, but since
they bind very poorly to wild-type kinases, they are ultimately
very useful for inhibiting mutant kinases.
[0164] The present invention provides a pharmaceutical composition
comprising a protein kinase inhibitor represented by the following
formula I: 3
[0165] where R is a 1'-napthyl, 2'-naphthyl;
m-phenoxyphenyl;m-benzyloxyph- enyl; m-2',6'-dichloro,
benzyloxyphenyl; 3-peronylpyrazolo; p-tert-butylphenyl;
1'-naphthylmethyl; 1'-naphthoxymethyl; or 2'-naphthylmethyl; and a
suitable diluent or carrier.
[0166] In one embodiment the naphthyl is a naphthylpyrazolo,
pyrimidine. In another embodiment the protein kinase inhibitor is
represented by the formula 6a as set forth in FIG. 18. In another
embodiment the protein kinase inhibitor is represented by the
formula 6b as set forth in FIG. 18. In another embodiment the
protein kinase inhibitor is represented by the formula 6c as set
forth in FIG. 18. In another embodiment the m-benzyloxphenyl is a
m-benzyloxyphenyl, pyrazolopyrimidine. In another embodiment the
protein kinase inhibitor is represented by the formula 6d as set in
FIG. 18. In another embodiment the m-dichloro, benzyloxyphenyl is a
m-dichloro, benzyloxyphenyl, pyrazolopyrimidine. In another
embodiment the protein kinase inhibitor is represented by the
formula 6e as set forth in FIG. 18. In another embodiment the
3-piperonyl is a 3-piperonyl, pyrazolopyrimidine. In another
embodiment the protein kinase inhibitor is represented by the
formula 6f as set forth in FIG. 18. In another embodiment the
p-tert-butylphenyl is a p-tert-butylphenyl,pyrazol- opyrimidine. In
another embodiment the protein kinase inhibitor is represented by
the formula 6g as set forth in FIG. 18. In another embodiment the
naphthylmethyl is a naphthylmethyl, pyrazolopyrimidine. In another
embodiment the protein kinase inhibitor is represented by the
formula 6h as set forth in FIG. 18. In another embodiment the
protein kinase inhibitor is represented by the formula 6j as set
forth in FIG. 24. In another embodiment the naphthoxyethyl is a
naphthoxylmethyl, pyrazolopyrimidine. In another embodiment the
protein kinase inhibitor is represented by the formula 6i as set
forth in FIG. 20.
[0167] This invention provides a pharmaceutical composition
comprising a src family protein kinase inhibitor, wherein the
inhibitor is
[0168]
4-amino-1-(tert-butyl)-3-(1'-naphthyl)pyrazolo[3,4-d]pyrimidine
(6a);
[0169]
4-amino-1-(tert-butyl)-3-(2'-naphthyl)pyrazolo[3,4-d]pyrimidine
(6b);
[0170]
4-amino-1-(tert-butyl)-3-(m-phenoxyphenyl)pyrazolo[3,4-d]pyrimidine
(6c);
[0171]
4-amino-1-(tert-butyl)-3-(m-benzyloxyphenyl)pyrazolo[3,4-d]pyrimidi-
ne (6d);
[0172] 4-amino-1-(tert-butyl)-3-(m-(2',6'-dichloro)benzyloxyphenyl)
pyrazolo[3,4-d]pyrimidine (6e);
[0173] 4-amino-1-(tert-butyl)-3-piperonylpyrazolo[3,4-d]pyrimidine
(6f);
[0174] 4-amino-1-(tert-butyl)-3-(p-tert-butylphenyl)pyrazolo[3,4
d]pyrimidine (6g);
[0175]
4-amino-1-(tert-butyl)-3-(1'-naphthylmethyl)pyrazolo[3,4-d]pyrimidi-
ne (6h);
[0176]
4-amino-1(tert-butyl)-3-(1'-naphthoxymethyl)pyrazolo[3,4-d]pyrimidi-
ne (6i); or
[0177]
4-amino-1(tert-butyl)-3-(2'-naphthylmethyl)pyrazolo[3,4-d]pyrimidin-
e (6j); and a suitable carrier or diluent.
[0178] This invention provides a method of disrupting
transformation in a cell that express the target mutant v-Src
comprising contacting the cell with a protein kinase inhibitor
represented by the following formula I: 4
[0179] wherein R is a 1'-naphthyl, 2'-naphthyl; m-phenoxyphenyl;
m-benzyloxyphenyl; m-2',6'-dichloro, benzyloxyphenyl;
3-piperonylpyrazolo; p-tert-butylphenyl; 1'-napthylmethyl;
1-naphthoxymethyl; or 2'-napthylmethyl.
[0180] In one embodiment the naphthyl is a naphthylpyrazolo,
pyrimidine. In another embodiment the protein kinase inhibitor is
represented by the formula 6a as set forth in FIG. 18. In another
embodiment the protein kinase inhibitor is represented by the
formula 6b as set forth in FIG. 18. In another embodiment the
m-phenoxyphenyl is a m-phenoxyphenyl, pyrazolopyrimidine. In
another embodiment the protein kinase inhibitor is represented by
the formula 6c as set forth in FIG. 18. In another embodiment the
m-benzyloxyphenyl is a m-benzyloxyphenyl,pyrazolopyrimidin- e. In
another embodiment the protein kinase inhibitor is represented by
the formula 6d as set forth in FIG. 18. In another embodiment the
m-dichloro, benzyloxyphenyl is a m-dichloro,
benzyloxyphenyl,pyrazolopyri- midine. In another embodiment the
protein kinase inhibitor the 3-piperonyl is a 3-piperonyl,
pyrazolopyrimidine. In another embodiment the protein kinase
inhibitor is represented by the formula 6f as set forth in FIG. 18.
In another embodiment the p-tert-butylphenyl is a
p-tert-butylphenyl,pyrazolopyrimidine. In another embodiment the
protein kinase inhibitor is represented by the formula 6g as set
forth in FIG. 18. In another embodiment the naphthylmethyl is a
naphthylmethyl,pyrazolo- pyrimidine. In another embodiment the
protein kinase inhibitor is represented by the formula 6h as set
forth in FIG. 18. In another embodiment the protein kinase
inhibitor is represented by the formula 6j as set forth in FIG. 24.
In another embodiment the naphthoxyethyl is a naphthoxylmethyl,
pyrazolopyrimidine. In another embodiment the protein kinase
inhibitor is represented by the formula 6i as set forth in FIG.
18.
[0181] This invention provides a method of disrupting
transformation in a cell that expresses the target mutant v-Src
comprising contacting the cell with a pharmaceutical composition
comprising a protein kinase inhibitor represented by the following
formula I: 5
[0182] wherein R is a 1'-naphthyl, 2'-naphthyl; m-phenoxyphenyl;
m-benzyloxyphenyl; m-2', 6'-dichloro, benzyloxyphenyl;
3-piperonylpyrazolo; p-tert-butylphenyl; 1'-naphthylmethyl;
1'-naphthoxymethyl; 2'-naphthylmethyl; and a suitable diluent or
carrier.
[0183] In one embodiment the naphthyl is a
naphthylpyrazolo,pyrimidine. In another embodiment the protein
kinase inhibitor is represented by the formula 6a as set forth in
FIG. 18. In another embodiment the protein kinase inhibitor is
represented by the formula 6b as set forth in FIG. 18. In another
embodiment the m-phenoxyphenyl is a m-phenoxyphenyl,
pyrazolopyrimidine. In another embodiment the protein kinase
inhibitor is represented by the formula 5c as set forth in FIG. 18.
In another embodiment the protein kinase inhibitor is represented
by the formula 6d as set forth in FIG. 18. In another embodiment
the m-dichloro,benzloxyphenyl is a m-dichloro,
benzyloxyphenyl,pyrazolopyrimi- dine. In another embodiment the
protein kinase inhibitor is represented by the formula 6e as set
forth in FIG. 18. In another embodiment the 3-piperonyl is a
3-piperonyl, pyrazolopyrimidine. In another embodiment the protein
kinase inhibitor is represented by the formula 6f as set forth in
FIG. 18. In another embodiment the p-tert-butylphenyl is a
p-tert-butylphenyl, pyrazolopyrimidine. In another embodiment the
protein kinase inhibitor is represented by the formula 6g as set
forth in FIG. 18. In another embodiment the naphthylmethyl is a
naphthylmethyl,pyrazolo- pyrimidine. In another embodiment the
protein kinase inhibitor is represented by the formula 6h as set
forth in FIG. 18. In another embodiment the protein kinase
inhibitor is represented by the formula 6j as set forth in FIG. 24.
In another embodiment the naphthoxyethyl is a naphthoxylmethyl,
pyrazolopyrimidine. In another embodiment the protein kinase
inhibitor is represented by the formula 6i as set forth in FIG.
18.
[0184] As demonstrated herein, wild type v-Src expressing cells
that are treated with 6a appear indistinguishable from untreated
wild type cells suggesting that 6a has no effect on this non-mutant
cell line. However, cells expressing the target kinase have clear
actin fibers and appear indistinguishable from normal NIH3T3
fibroblasts when incubated with 250 nM 6a for 16 hours. From this
data it is clear that small molecule inhibition of v-Src's
catalytic activity is sufficient to block its role in
onocogenesis.
[0185] The lower alkyl groups on the compound represented by
formula I which may be included contain 1-6 carbon atoms and
iinclude methyl, ethyl, propyl, butyl, pentyl, hexyl, and the
corresponding branched-chain isomers thereof. These groups are
optionally substituted by one or more halo hydroxy, amino or lower
alkylamino groups. Where the possibility exists for substitution of
a phenyl or aryl ring, the position of the substituents may be
ortho, meta, orpara to the point of attachment of the phenyl or
aryl ring to the nitrogen of the hydrazine group. Preferably, the
substituents are para or meta to the point of attachment, and where
more than one is present on the same ring, they are preferably in
the para and meta positions. The halo atoms in the above formula
may be fluoro, chloro, bromo or iodo. The lower alkoxy groups
contain 1-6, and preferably 1-3, carbon atoms and are illustrated
by methoxy, ethoxy, n-propoxy, isopropoxy and the like. Further, as
contemplated herein the t-butyl group may be substituted or
modified with any of the above.
[0186] The compounds of the instant invention may include labels or
markers such as fluorescent dyes in a range of blue, red, green,
yellow, colors, and especially blue and green colors. The color of
fluorescence may be different from the absorption color.
Fluorescent pigments possess high luminenscence and advantageous
application properties, for example, high light fastness and a low
migration tendency. The possession of fluorescent properties
further enables the use of the compounds of the instant invention
in a variety of medical, pharmaceutical and diagnostic
applications. The compounds of the instant invention can also be
utilized to label various therapeutic agents to enable their
disposition in the body. As such, therapy with such labeled
therapeutic agents can be closely monitored with respect to target
organs and tissues. This is particularly useful in the treatment of
various cancers, especially those of a solid tumor type, where
localization of the chemotherapeutic agent is extremely important
and dosage due to the possibility of side-effects, must be closely
monitored.
[0187] The inhibitors of the present invention belong to the family
of pyrazolopyrimidines. Pyrazolopyrimidines are useful in the
treatment and prevention of respiratory diseases represented by
asthma (U.S. Pat. No. 5,942,515). Moreover,
amino-pyrazolopyrimidine derivatives have been used as protein
kinase inhibitors for inhibiting cell proliferation and are thus
useful in the treating tumors and hyperproliferative diseases (WO
9631510). This family of inhibitors has also been shown to be
useful in the treatment of cardiovascular and urogenital diseases
(DE 19709126 A) and for treating ischaemia, arthritis and pain (WO
9640707). Thus, the inhibitors of the present invention are also
expected to have therapeutic applications.
[0188] In addition, the present invention provides a solution to
the above-described problems by providing materials and methods by
which a single protein kinase can be specifically inhibited without
the simultaneous inhibition of another protein kinase.
IV. Engineered Kinase and Engineered Multi-Substrate Enzymes
[0189] In a first aspect, the present invention involves the
engineering of kinase and other multi-substrate enzymes such that
they can utilize modified substrates which are not as readily used
by their wild-type forms. The invention further provides such
chemically modified nucleotide triphosphate substrates, methods of
making them, and methods of using them. The methods of the present
invention include methods for using the modified substrates along
with the engineered kinase to identify which protein substrates the
kinase act upon, to measure the extent of such action, and to
determine if test compounds can modulate such action.
[0190] In a further aspect, the invention provides engineered
protein kinase which can bind inhibitors that are not as readily
bound by the wild-type forms of those enzymes. Methods of making
and using all such engineered kinase are also provided. The
invention further provides such inhibitors, methods of making them,
and methods of using them. The methods of the present invention
include methods for using the inhibitors along with the engineered
kinase to identify which protein substrates the kinase act upon, to
measure the kinetics of such action, and to determine the
biochemical and cellular effects of such inhibition. They also
relate to the use of such inhibitors and engineered kinase to
elucidate which kinase may be involved in disease; these kinase can
then become the subject to efforts to design or discover more
traditional specific inhibitors of their wild-type forms, which may
prove to be valuable in treating the kinase-related disease or
disorder.
[0191] Furthermore, methods are provided for inserting the
engineered kinase into cells or whole animals, preferably in place
of the corresponding wild-type kinase, and then using the inhibitor
to which it has been adapted as a tool for study of the
disease-kinase relationship, and ultimately, as a drug for the
treatment of the disease.
[0192] The present invention also more generally relates to
engineered forms of multi-substrate enzymes which covalently attach
part or all of at least one (donor) substrate to at least one other
(recipient) substrate. These engineered forms will accept modified
substrates and inhibitors that are not as readily bound by the
wild-type forms of those enzymes.
[0193] The invention also relates to methods for making and using
such engineered enzymes as well as modified donor substrates. The
methods of the present invention include methods for using the
modified substrates and inhibitors along with the engineered
enzymes to identify which substrates the enzymes act upon, to
measure the kinetics of such action, and in the instance of the
modified substrates, to determine the recipient substrates to which
part or all of the donor substrate becomes attached, to measure the
extent of such action, and to identify and measure the extent of
modulation thereof by test compounds.
[0194] In the instance of inhibitors, the methods seek to determine
the biochemical and cellular effects of such inhibition. The
methods also extend to the use of such inhibitors and engineered
enzymes to elucidate which enzymes may be involved in disease;
these enzymes can then become the subject of efforts to design or
discover specific inhibitors of their wild-type forms, which may
prove to be valuable in treating the enzyme-related disease or
disorder. Furthermore, methods are provided for inserting the
engineered enzyme into cells or whole animals, preferably in place
of the corresponding wild-type enzyme, and then using the inhibitor
to which it has been adapted as a tool for study of the
disease-enzyme relationship, and ultimately, as a drug for the
treatment of the disease.
[0195] According to the present invention, through enzyme
engineering a structural distinction can be made between the
nucleotide binding site of a protein kinase of interest, and the
nucleotide binding sites of other kinase. This distinction allows
the engineered kinase to use a nucleotide triphosphate or an
inhibitor that is not as readily bound by the wild-type form of
that kinase, or by other kinase. In a preferred embodiment with
respect to the inhibitor, the inhibitor used is one that is
"orthogonal" to the "natural" nucleotide triphosphate substrate for
that kinase, or is orthogonal to a less specific inhibitor (e.g.,
one which is readily bound by the wild-type form of that kinase).
The term "orthogonal," as discussed above, means that the substrate
or inhibitor is similar in structure (including those that are
geometrically similar but not chemically similar, as described
below), but differs in a way that limits its ability to bind to the
wild-type form.
V. Orthogonal Nucleotide Triphosphate
[0196] An engineered kinase made according to the present invention
will be able to use an orthogonal nucleotide triphosphate substrate
that is not as readily used by other, non-engineered kinase present
in cells. Preferably, it will be able to use an orthogonal
nucleotide triphosphate that is riot substantially used by other
kinase; and most preferably, it will be able to use an orthogonal
nucleotide triphosphate substrate that cannot be used at all by
other kinase. By labeling the phosphate on the orthogonal
substrate, e.g., by using radioactive phosphorous (p.sup.32), and
then adding that labeled substrate to permeabilized cells or cell
extracts, the protein substrates of the engineered kinase will
become labeled, whereas the protein substrates of other kinase will
be at least labeled to a lesser degree; preferably, the protein
substrates of the other kinase will not be substantially labeled,
and most preferably, they will not be labeled at all.
[0197] The detailed description and examples provided below
describe the use of this strategy to uniquely tag the direct
substrates of the prototypical protein kinase, v-Src. Through
protein engineering a chemical difference has been made in the
amino acid sequence which imparts a structural distinction between
the nucleotide binding site of the modified v-Src and that of all
other kinase. The v-Src kinase was engineered to recognize an ATP
analog (A*TP), N.sup.6-(cyclopentyl)ATP, which is orthogonal to the
nucleotide substrate of wild-type kinase. The generation of a v-Src
mutant with specificity for an orthogonal A*TP substrate allows for
the direct substrates of v-Src to be uniquely radiolabeled using
[y-.sup.32P] N.sup.6-(cyclopentyl)ATP, because it is able to serve
as substrate to the engineered v-Src kinase, but is not
substantially able to serve as substrate for other cellular
kinase.
[0198] The detailed description and examples provided below
describe the use of this strategy to uniquely identify the direct
substrates of the prototypical protein kinase, v-Src. Through
protein engineering a chemical difference has been made in the
amino acid sequence which imparts a new structural distinction
between the nucleotide binding site of the modified v-Src and that
of all other kinase. The engineered v-Src kinase that have been
made and presented herein bind to an orthogonal analog of the more
general kinase inhibitor PP3: the compound N-4 cyclopentyl PP3
(FIG. 11A). The generation of a v-Src mutant with specificity for
such an inhibitor allows for the mutant to be inhibited, whereas
other kinase in the same test system are not substantially
inhibited, not even the wild-type form of that same kinase.
VI. Mutant Protein Kinase
[0199] As is apparent from the foregoing, it is one object of the
present invention to provide a mutant protein kinase which accepts
an orthogonal nucleotide triphosphate analog as a phosphate donor
substrate. Another object of the present invention is to provide a
nucleotide sequence which encodes such a mutant protein kinase; and
it is a further object to provide a method for producing such a
nucleic acid sequence. It is also an object of the invention to
provide methods for producing such a mutant protein kinase, for
example, by expressing such a nucleic acid sequence. It is also an
object of the present invention to provide such orthogonal
nucleotide triphosphates and methods for their synthesis, including
N.sup.6-(cyclopentyl)ATP, N.sup.6-(cyclopentyloxy)ATP,
N.sup.6-(cyclohexyl)ATP, N.sup.6-(cyclohexyloxy) ATP,
N.sup.6-(benzyl)ATP, N.sup.6-(benzyloxy)ATP,
N.sup.6-(pyrolidino)ATP, and N.sup.6-(piperidino) ATP, (27).
[0200] It is yet another object of the invention to provide a
method for determining whether a test compound positively or
negatively modulates the activity of a protein kinase with respect
to one or more protein substrates. More particularly, and in
accordance with the further aspect of the invention, it is a
primary object to provide a mutant protein kinase which binds to
and is inhibited by an inhibitor, which inhibitor less readily
binds to or inhibits the corresponding wild-type kinase.
[0201] A further object of the present invention is to provide a
nucleotide sequence which encodes such a mutant protein Ikinase;
and it is a further object to provide a method for producing such a
nucleic acid sequence. It is also an object of the invention to
provide methods for producing such a mutant protein kinase, for
example, by expressing such a nucleic acid sequence. It is another
object of the present invention to provide such inhibitors, such as
the compound N-4 cyclopentyl PP3, and methods for their synthesis.
Another object is to provide a method for determining what are the
substrates for a given protein kinase. It is yet another object of
the invention to provide a method for determining whether specific
inhibition of a particular kinase produces a biochemical or
phenotypic effect in a test systems such as a cell-free extracts,
cell cultures, or living multicellular organisms. It is a further
object of the invention to provide a method to determine whether
inhibition of a particular kinase might have therapeutic value in
treating disease. It is yet another object to provide methods for
the study of the activity, kinetics, and catalytic mechanisms of a
kinase by studying the inhibition of the corresponding mutant of
the present invention. A further object is to provide methods of
preventing and treating kinase-mediated diseases by introducing an
inhibitor-adapted mutant kinase of the present invention into a
diseased organism, and preferably diminishing or, most preferably,
depleting the organism of the wild-type enzyme; and then
administering the inhibitor to regulate the activity of the now
disease-mediating mutant kinase so as to diminish or eliminate the
cause or symptoms of the disease.
VII. Multi-Substrate Enzymes
[0202] Based upon the foregoing and the detailed description of the
present invention provided below, one of ordinary skill in the art
will readily recognize that the present invention can be used more
generally to study multi-substrate enzymes which covalently
transfer a donor substrate or portion thereof to a recipient
substrate, as do the kinase, and enzymes which do not bind two
substrates or transfer a group. Such applications of the present
invention are also further described in the detailed description
which follows. Accordingly, it is yet a further object of the
present invention to provide a mutant multi-substrate enzyme which
binds to an inhibitor, which inhibitor is less readily bound to the
wild-type enzyme or to other enzymes with similar activity.
[0203] It is another object of the invention to provide a
nucleotide sequence which encodes such a mutant multi-substrate
enzyme; and it is a further object to provide a method for
producing such a nucleic acid sequence. It is also an object of the
invention to provide methods for producing such a mutant
multi-substrate enzyme, for example, by expressing such a nucleic
acid sequence. It is also an object of the present invention to
provide such inhibitors and methods for their synthesis. Another
object is to provide a method for determining what are the
substrates for a given multi-substrate enzyme. It is yet another
object of the invention to provide a method for determining whether
specific inhibition of a particular multi-substrate enzyme produces
a biochemical or phenotypic effect in a test systems such as a
cell-free extracts, cell cultures, or living multicellular
organisms. It is a further object of the invention to provide a
method to determine whether inhibition of a particular
multi-substrate enzyme might have therapeutic value in treating
disease.
[0204] The present invention involves the engineering of kinase and
other multi-substrate enzymes such that they can become bound by
inhibitors which are not as readily bound by their wild-type forms.
Modified substrates and mutant enzymes that can bind them have been
used to study an elongation factor (41) and a receptor for
cyclophilin A (42). However, prior to the present invention, it was
not known how, or even if, multi-substrate enzymes which covalently
attach part or all of a donor substrate onto a recipient substrate
could be engineered to bind to an inhibitor, yet still retain at
least some catalytic activity and at least some specificity for the
recipient substrate in the absence of the inhibitor. The present
invention is that this can be done, as explained below; and this
invention for the first time opens the door to the selective
inhibition of individual kinase, which are not only important tools
for understanding of the kinase cascades and other complex
catalytic cellular mechanisms, but also may provide avenues for
therapeutic intervention in diseases where those mechanisms come
into play.
[0205] It is yet another object to provide methods for the study of
the activity, kinetics, and catalytic mechanisms of a
multi-substrate enzyme by studying the inhibition of the
corresponding mutant of the present invention. A further object is
to provide a method of preventing and treating multi-substrate
enzyme-mediated diseases by introducing an inhibitor-adapted
multi-substrate enzyme of the present invention into a diseased
organism, and preferably diminishing or, most preferably, depleting
the organism of the wild-type enzyme; and then administering the
inhibitor to regulate the now disease-mediating mutant enzyme so as
to diminish or eliminate the cause or symptoms of the disease.
[0206] As mentioned above, the present invention is not limited to
mutant kinase, orthogonal inhibitors, and their synthesis and use.
The present invention will work just as well for other
multi-substrate enzymes which covalently transfer part or all of
one substrate, here called the donor, to another substrate, here
called the recipient; and there are surely more such enzymes yet to
be discovered. In any such instance, one of skill in the art who
has studied the present specification will well appreciate the
applicability of the present invention to such enzymes. The tasks
at hand in such an instance are quite similar to those described in
detail here for the kinase. First, it is necessary to identify what
the donor substrate is, and/or to identify compounds which can
inhibit that kinase, even if it is not specific for that
kinase.
[0207] Second, it is necessary to consider where a bulky
substituent might be added to the substrate of the inhibitor such
that it will not bind as readily to the wild-type kinase, or
preferably will not bind substantially to the wild-type kinase, and
preferably, will not bind at all. Of course, it is not really
necessary, in the case of kinase or in other multi-substrate
enzymes as described above, to be restrictive with respect to which
analogs of these to make; one can make a variety of them, even
including some that seem unlikely to be ideal, and determine by
screening which one or ones are the best. Further guidance
regarding how to do this can be gained from the examples below. The
inhibition assay, the results of which are shown in FIG. 6, is a
non-limiting example of an assay particularly well suited to such
screening.
[0208] The third step is to engineer the kinase such that one or
more amino acid in the three-dimensional location where the bulky
group would be expected to be if the analog did bind are replaced
with amino acids having less bulky side chains, thus "making room"
for the bulky moiety of the inhibitor. Steps two and three can, of
course, be carried out in the reverse order.
[0209] For example, transferase enzymes would be most interesting
candidates for study using the present invention. One could,
following the teachings provided herein, prepare mutant
transferases which will accept orthogonal inhibitors, and these
could be used together in order to identify the direct substrates
of one particular transferase in a large gamily of homologous
transferases, by the methods described above for the kinase. The
family of methyl-transferases would be of clear interest, and could
quite easily be studied using the methods provided herein. These
enzymes all use the same nucleotide based cofactor,
S-adenosylmethionine (AdoMet), as a methyl (CH3) group donor. The
different members of the family can transfer the methyl group of
AdoMet to a wide variety of cellular components such as proteins
(in which case the methyl group is added to arginine, aspartate,
and glutamate side chains), DNA (in which case the methyl group is
added to the C-5 position of cytosine, or the N-7 of guanine), to
components of cell membrane components such as phospholipids, and
also to a number of small amine containing hormones. Many new
targets are also being identified for this diverse family of
enzymes. The present invention provides the opportunity to decipher
the tremendously complex cellular mechanisms that these enzymes are
carrying out.
[0210] For example, one could synthesize a set of AdoMet analogs
that contain additional bulky hydrophobic groups at the N-6
position, or at other ring positions, which would make the analogs
orthogonal, and thus not be accepted as readily by wild-type
methyltransferases as is the natural substrate; and the structure
int eh region of the transferred methyl group might be altered such
that the methyl group is more chemically resistant to transfer; or,
for example, S-adenosylcysteine might be used as the starting
compound instead. Using the crystal structures of DNA
methyltransferase M.Hhal and the catechol methyltransferase
catechol O-methyl-transferase (COMT), one can identify those amino
acids in the adenine binding pocket which are candidates for
mutation as was done herein for the protein kinase; and one of
ordinary skill in the art should readily be able to identify a set
of residues to mutate in order to accommodate the bulky hydrophobic
groups of one or more of the orthogonal substrates.
[0211] For example, one might mutate large hydrophobic groups to
smaller alanine or glycine residues, or replace hydrogen bonding
amino acids with others that compliment the orthogonal purine
analogs of AdoMet. Of course, a myriad of other possible mutations
may work as well, and all would be within the scope of the present
invention. In addition, from sequence alignments and crystal
structures of methyltransferases, it is known that they have a
common catalytic domain structure (70); so this approach is not
limited to M.Hhal and COMT, but should be equally applicable to
other methyl transferases.
[0212] After a methyltransferase mutant is identified which accepts
an orthogonal inhibitor, radiolabeled AdoMet can then be
synthesized which contains a C-14 labeled methyl group attached to
the sulfur atom of AdoMet. When this radiolabeled analog is added
to cells expressing one mutant methyltransferase, the direct
substrates (e.g., protein or DNA, or polyamines) of all
methyltransferases in the sample will be specifically radiolabeled
with the C-14 methyl group. But when this is done in the presence
of the orthogonal inhibitor, the specific substrates for the
methyltransferase of interest will be less labeled in comparison to
the sample not containing the inhibitor; preferably, they will not
be substantially labeled, and most preferably, will not be labeled
at all. In this way, or through the use of other methods described
herein for the study of the kinase, direct substrates of
methyltransferases can be identified which are important in cancer,
embryonic development, chemotaxis of poly morphonuclear leukocytes,
or in neurological disorders. In addition, the methods of the
present invention can then be used to determining whether compounds
can be identified that modulate the activity of the enzyme. The
several other aspects of the present invention, although perhaps
not described here, could also be applied to the methyl
transferases, and also to other multi-substrate enzymes.
[0213] The foregoing discussion of the application of the present
invention to the methyl transferases is not intended to limit the
scope of the present invention, but to illustrate of the
applicability of the present invention to multi-substrate enzymes
other than the protein kinase. As will be appreciated by those in
the art, the present invention could be applied similarly to other
multi-substrale enzymes using similar approaches.
[0214] As described in the examples below, using the present
invention the utility of a v-Src kinase which shows high
specificity for a synthetic inhibitor while maintaining its
wild-type specificity for tyrosine containing peptides and proteins
was demonstrated and made, thus satisfying the initial research
goals. By exploiting the highly conserved nature of the ATP binding
site across the kinase superfamily and the availability of
structural information from other protein kinase, novel inhibition
specificity for v-Src was engineered without any detailed
structural information about v-Src itself. That an unrelated kinase
was used as a blueprint for designing orthogonal ATP analogs to tag
the direct cellular substrates of v-Src, and have prepared
inhibitors from like origins, demonstrates that this approach
should work for other kinase as well.
VIII. Modified Inhibitors and Substrates
[0215] The inhibitors contemplated by this invention may be useful
in studies directed towards developing other useful mutants of this
and other kinase, and for the several methods described elsewhere
herein. However, the scope of the present invention is not limited
to the use of these particular inhibitors, and those of ordinary
skill in the art will recognize that many other possible structures
could be substituted for or supplement those described herein. For
example, different, simpler, and even more complex aliphatic or
aromatic groups could be added to the N.sup.6 position of ADP or to
the N.sub.4 position of PP3. In addition, the inhibitors of the
present invention are not limited to modifications of nucleotides
at the N.sup.6 position or modifications of PP3 at the N.sub.4
position. Chemical means to modify various positions on such
compounds are known, and any of the resulting derivatives would be
within the scope of the present invention; it is even possible to
make changes or substitutions in their ring structures. Exemplary
variants are presented herein, and particular reference is made to
FIG. 12 where both analogs and data relating to their activity is
set forth. Of course, the use of such inhibitors may require that
different positions in the protein sequence of the kinase be
modified in order to make an engineered kinase that will bind to
them, but such different modifications are well within the scope of
the present invention.
[0216] In addition, it is important to note that the inhibitors of
the present invention are not limited to ADP and PP3 derivatives.
For example, it should be possible to utilize derivatives of other
natural nucleotide phosphate donor substrate as such inhibitors.
For studying some kinase, different analog bases may in fact be
preferred. For example, it is know that some kinase utilize GTP as
phosphate donor substrate and energy source; to make inhibitors for
engineered firms of such kinase, analogs of guanosine diphosphate
would be suitable. Furthermore, it is well known that related
compounds (e.g., other bases) and compounds chemically unrelated to
the natural substrate can sometimes nevertheless bind to an active
site, and can (but for the purposes of this invention need not), be
acted upon or act upon other substrates through chemical catalysis
by the enzyme. Sometimes they participate in the catalyzed reaction
in the same way as the natural substrate, sometimes in different
ways. Such compounds and their derivatives would be suitable
starting points for the design of inhibitors that are orthogonal to
them, and which would be within the scope of the present invention.
Similarly, other known kinase inhibitors can be used as a starting
point for synthesis of inhibitors of the present invention, such as
those whose structures appear in FIG. 9. Of course, even
derivatives of inhibitors that are currently unknown would, once
identified, be suitable core structures for the design of
inhibitors of the present invention, as illustrated herein and made
a part hereof.
[0217] Furthermore, the inhibitors of the present invention are not
limited to those made by chemical synthetic means, but also include
compounds which may be found in nature, and which can serve that
role, some of which are discussed above. In addition, those of
ordinary skill in the art will appreciate that there are other
variations besides those set forth here, and that these are all
within the scope of the present invention.
[0218] The inhibitors that are candidates for use in accordance
with the present invention can conveniently be screened to
determine the extent to which they are accepted by wild-type
kinase, using a screening procedure such as that set forth in
Example 13 below, or by a screening procedure involving the use of
a cell or cells which are rich in protein kinase activity as set
forth in Example 9 herein. By such an assay, one can determine
whether each inhibitor is bound by wild-type kinase to a lesser
degree than the engineered kinase, or preferably, if the wild-type
kinase do not substantially bind to that inhibitor, or most
preferably, do not bind the inhibitor at all. For those substrates
that are less readily bound, it may be worthwhile to try to
engineer the kinase of interest so that it will more readily bind
to them. Of course, one could make the engineered kinase first and
then assay it along side the wild-type enzyme to determine whether
it uses a given orthogonal substrate better than the wild-type
kinase; this was the approach used in Example 13. However, under
most circumstances, pre-screening as described above will be
preferred. Of course, other assay approaches will be apparent to
those in the field, and the use of such assays would be within the
scope of the present invention.
IX. Reengineering a Kinase
[0219] There are several criteria that should be satisfied in
reengineering a kinase in order to uniquely tag its authentic
substrates in the presence of wild-type tyrosine and
serine/threonine kinase. The engineered kinase should: (1) accept
an ATP analog (A*TP) that is utilized less readily by wild-type
protein kinase; preferably, accept an A*TP that is not
substantially utilized by wild-type kinase; and most preferably,
accept an A*TP that is not utilized by wild-type kinase at all; (2)
preferably, use the A*TP analog with high catalytic efficiency; and
(3) preferably, have reduced catalytic efficiency for the natural
nucleotide substrate (ATP) so that in the presence of cellular
levels of ATP (1-2 mM) the mutated kinase would preferenitially
utilize A*TP as the phosphodonor. If such engineered kinase are to
be used to study the protein substrate specificity of the wild-type
kinase, then these criteria must be met without substantially
altering the protein target specificity of the kinase.
[0220] Likewise several criteria should be satisfied in
reengineering a kinase in order that it will be inhibited by the
inhibitors of the present invention. The engineered kinase should:
(1) bind to an inhibitor which is bound less readily by wild-type
protein kinase; preferably, the inhibitor will not substantially
bind to wild-type kinase; and most preferably, will not bind at all
to wild-type kinase; (2) preferably, the engineered kinase will
bind the inhibitor with high affinity (i.e., low IC.sub.50). It is
not generally of particular importance whether the inhibitor binds
to the wild-type form of the kinase that corresponds to the
engineered kinase, as such binding and the resulting inhibition
would augment that of the engineered kinase. However, it is most
likely that the wild-type form of that kinase will not bind the
inhibitor any better than other wild-type kinase. If an inhibitable
engineered kinase is to be used to study the protein substrate
specificity of the wild-type kinase, or to replace the wild-type
form of that kinase through gene therapy or other means, as further
discussed below, then a further concern is that the above-described
criteria must preferably be met without substantially altering the
protein target specificity of the engineered kinase when compared
with the corresponding wild-type form.
[0221] When viewed from the perspective of the state of the art
when the present invention was made, it was not predictable whether
it would be possible to satisfy all of these criteria
simultaneously; in fact, it was doubtful, because the ATP binding
site that is engineered is very close to the second substrate
binding site, i.e., the peptide binding site. However, as shown by
the examples below, all of these criteria, including the preferred
criteria, were in fact met simultaneously when the described v-Src
mutants were made, provided them with N.sup.6(cyclopentyl)ATP and
inhibited them using N4-cyclopentyl PP3.
[0222] Example 1 describes the twelve ATP analogs which were used
in the studies on mutant v-Src, which are described in the further
examples which follow. These orthogonal ATP analogs may be useful
in studies directed towards developing other useful mutants of this
and other kinase, and for the several methods described elsewhere
herein. However, the scope of the present invention is not limited
to the use of these particular ATP analogs, and those of ordinary
skill in the art will recognize that many other possible orthogonal
substrates could be substituted for or supplement those described
herein. For example, different and even more complex aliphatic or
aromatic groups could be added to the N.sup.6 position of ATP. In
addition, the orthogonal substrates of the present invention are
not limited to modifications of nucleotides at the N.sup.6
position. Chemical means to modify various positions on adenosine
are known, and any of these would be within the scope of the
present invention; and it is even possible to make changes or
substitutions in the ring structures of nucleotides. Of course, the
use of such orthogonal substrates may require that different
positions in the protein sequence of the kinase be modified in
order to make an engineered kinase that will bind to them, but such
different modifications are well within the scope of the present
invention.
[0223] In addition, it is important to note that the orthogonal
substrates of the present invention are not limited to ATP
derivatives. For studying different kinases, different analog bases
may in fact be preferred. For example, it is known that some kinase
utilize GTP as phosphate donor substrate and energy source; for
studies of such kinase, analogs of guanosine triphosphate would be
preferred. It is well known that compounds chemically unrelated to
the natural substrate can sometimes nevertheless bind to an active
site, and can even be acted upon or act upon other substrates
through chemical catalysis by the enzyme. Sometimes they
participate in the catalyzed reaction in the same way as the
natural substrate, sometimes in different ways. Such compounds and
their derivatives would also be within the scope of the terms
"natural substrate" and "orthogonal substrate" as used herein.
[0224] Furthermore, the orthogonal substrates of the present
invention are not limited to those made by chemical synthetic
means, but also include compounds which may be found in nature, and
which can serve that role. Those of ordinary skill in the art will
appreciate that there are other variations besides those set forth
here, and that these are all within the scope of the present
invention.
[0225] The orthogonal nucleotides that are candidates for use in
accordance with the present invention can conveniently be screened
to determine the extent to which they are accepted by a wild-type
kinase, using a screening procedure such as that set forth in
Example 2 below. By such an assay, one can determine whether each
orthogonal substrate is accepted by wild-type kinase to a lesser
degree than the normal substrate for such kinase, or preferably, do
not substantially accept that substrate, or most preferably, do not
accept it at all. For those substrates that are least less readily
accepted, it may be worthwhile to try to engineer the kinase of
interest so that it will more readily accept them. Of course, one
could make the engineered kinase first and then assay it along side
the wild-type enzyme to determine whether it uses a given
orthogonal substrate better than the wild-type kinase. However,
under most circumstances, pre-screening such as is described in
Example 2 will be preferred. Of course, other assay approaches will
be apparent to those in the field, and the use of such assays would
be within the scope of the present invention.
[0226] The design of an engineered v-Src is described in Example 3
below. As is described, the engineered form was designed by
reference to the crystal structures of other kinases which have
domains that are homologous to those found in most if not all
kinase. As will be seen, the example mutant kinase described herein
have been constructed as fragments of protein kinase, rather than
as containing the entire sequences; but it was found there is no
substantial difference in performance when the entire sequence is
used. Of course, the concepts and the practicalities are the same
whether fragments or whole kinase are used, and both are within the
scope of the present invention. As such, the term "kinase" should
be viewed as including the whole enzyme or a fragment of one,
including when interpreting the claims.
[0227] Using this approach, it is possible to design similar
mutants of virtually any other kinase, such as a protein kinase, a
lipid kinase, or an aminoglycoside kinase. The method of doing this
comprises the steps of: (a) identifying, from the amino acid the
alignment of a kinase of interest with a kinase having a known
kinase inhibitor (which may be non-specific for that kinase,
specific for kinases generally but not for that kinase, or specific
for that kinase), one or more amino acids which are close enough to
a substituent on the bound phosphate donor substrate or inhibitor
that would sterically restrict entry of a bulky substituent
attached to that position in a putative orthogonal inhibitor; and
(b) mutating a nucleotide sequence which encodes the wild-type
protein kinase such that the nucleotide triplets encoding one or
more of the identified amino acids, are converted to nucleotide
triplets that encode amino acids having side chains that are
sterically less bulky than the identified amino acids. The
above-described method uses steric restriction of entry or
exclusion as the criteria for deciding which amino acid(s) to
change, and how to change them. However, the present invention is
not so limited. It is also possible to engineer a kinase to change
its ability to bind to an orthogonal substrate by considering other
factors, such as hydrophobicity, hydrophilicity, ionic binding or
repulsion, hydrogen bonding, forming covalent bonds between the
enzyme and electrophilic groups on orthogonal substrates, etc.
[0228] The study of protein kinase using the present invention will
be greatly facilitated by the vast knowledge regarding the domain
structure of many different kinase, and their generally homologous
sequences. The Protein Kinase Facts Book (71) provides protein
sequence data for the three functional domains in literally
hundreds of protein kinase, and this along with sequence
information available in the primary literature, should greatly
facilitate the further application of the present invention to the
kinase. Similar information is available regarding other
multi-substrate enzymes, which should facilitate their study and
use according to the present invention.
[0229] Although the preferred method of the present invention
involves the rational design of substrate analogs and mutant
protein kinase, both could alternatively be made by use of methods
known as combinatorial methods. There are many combinatorial
methods of synthesizing organic compounds. Using one such method,
one could synthesize nucleoside analogs on resin beads using
sequential chemical steps, and then release them from the resin
prior to phosphoirylation to make the nucleotide triphosphates.
After using such a method to make a collection or library of
putative orthogonal substrates for mutants of v-Src kinase, other
protein kinase, or other multi-substrate enzymes, the collection or
library could be screened for particularly favorable binding or
catalytic properties. This may allow for the more thorough search
of structural, conformational, and electronic features of such
putative orthogonal substrates. Moreover, it is often found that
when larger numbers of analogs of a given substrate are
investigated, and unexpectedly efficient substrate or inhibitor can
be found Furthermore, sometimes the compounds which are the most
desirable would not have been chosen if only well understood
parameters were used to specifically design the best compound.
[0230] There are also many combinatorial methods known in the art
for making protein mutants. These include "error prone" polymerase
chain reaction (PCR), "sexual" PCR, or PCR using primers with
random nucleotides as fixed positions in the protein sequence.
Other sequence randomization methods might include using chemical
mutagens of cDNA or plasmid DNA, or MutD type strains of bacteria,
which are known to introduce mutations randomly in proteins that
they express. It would be possible to carry out the present
invention by exploiting such methods for making randomly mutated
protein kinase or other multi-substrate enzymes, and then screening
for one with particularly high activity with a particular
orthogonal substrate, or with some or all of the putative
orthogonal substrates made using combinatorial synthesis, as
described in the paragraph above. The assay methods described in
the examples below would be suitable for this purpose, and those in
the art would be readily able to design alternative approaches.
[0231] These methods and other methods which are or may be
developed to explore protein sequence space and the structural
space of small organic molecules might be particularly useful for
the technological application described here, where changing or
altering both the protein and the putative inhibitor in order to
find the best possible non=natural (i.e., orthogonal) fit. The use
of any of these or any of the other methods described herein would
be within the scope of the present invention.
[0232] The synthesis of one engineered kinase is described in
Example 4. The focus of this effort was on amino acid side chains
that were within about 4.ANG. of the N.sup.6 of ATP; but there is
nothing magical about that distance. Residues with side chains that
are within about 1.ANG., 2.ANG., 3.ANG., 5.ANG., 6.ANG., 7.ANG.,
8.ANG., 9.ANG., 10.ANG., or lesser, greater or intermediate
distances should also be considered as targets for modification.
Amino acids with side chains that are within about 3.ANG. to about
6.ANG. would be preferred targets. Generally those amino acids with
the closer side chains will be preferred over those with more
distant side chains, as they would be expected to cause the
greatest steric or other interference with the orthogonal
substituent on the inhibitor; and those with the very closest side
chains wold be the most preferred.
[0233] Of course, there are many other ways to modify and express
genetic sequences today then those used in the examples, such as
site-directed mutagenesis. The use of any or all of these would be
within the scope of the present invention. In addition, although
the use of genetic engineering is today probably the preferred
method to prepare such mutants, it is not the only way. For
example, one could design an engineered kinase and then synthesize
that protein by known methods of chemical peptide synthesis. Or, it
may be possible to chemically modify a given enzyme in a specific
location such that one or more side chain changes in size,
hydrophobicity, or other characteristic, such that it can more
readily utilize an orthogonal substrate. The use of all such
methods are within the scope of the invention.
[0234] Example 7 describes testing which could be done to determine
whether the engineered kinase had retained its protein substrate
specificity. It is preferred that the wild-type protein substrate
specificity be substantially retained if, as in the examples, the
goal is to use the engineered kinase to study what substrates the
kinase acts upon and to what degree it does so, or it is to be used
to replace or supplement the corresponding wild-type kinase in
vivo, e.g., through genetic engineering. However, although for such
purposes it is important that the kinase still recognize the same
substrates as the wild-type, it is not critical that it do so with
the same kinetics; i.e., if it does so slower or faster, or to a
greater or lesser degree, the engineered kinase may still have
substantial value for such purposes. If the engineered kinase does
not recognize the same protein substrates as the wild-type enzyme,
it may have less value in studying the wild-type enzyme, but may
still have substantial value in studying protein phosphorylation
and kinase in general, and would still be within the scope of the
invention.
[0235] Of course, the particular assays used in Example 7, although
useful, need not be used. Those of skill in the art will readily be
able to develop or adopt other assays that can provide comparable
information.
[0236] Once a mutant kinase has been made which accepts a given
orthogonal substrate analog, or which is inhibited by a given
inhibitor, it can be characterized using classical enzyme kinetic
analysis, as illustrated in Examples 5 and 6. Also, as shown in
Example 8, one can study the degree to which the mutant can utilize
or be inhibited by the analog, and 0whether the analog is a "dead"
(i.e., wholly ineffective) inhibitor for the wild-type enzyme. Of
course, the methods used in the examples are not the only ways
these studies can be done, and those of skill in the rt can easily
design alternate approaches.
[0237] As illustrated in Example 10, it is not necessary to make
multiple amino acid substitutions to provide a mutant that will be
inhibited by an inhibitor of the present invention. It may only be
necessary to make a single amino acid change, as is the case with
the mutants GST-XD4(I338A) and GST-XD4 (I338G).
X. Assay to Identify Kinase Substrates
[0238] One embodiment of the present invention is as follows.
First, the orthogonal inhibitor is added to two samples of the cell
of interest which either express an added gene for the engineered
kinase or express the normal copy of the kinase of interest. The
inhibitor can be added before after or during the activation of a
signaling cascade (such as permeabilized cells, cell extracts, or
cells that are naturally permeable to them). Then a method which
allows detection of all phosphorylated proteins in a cell or cell
fraction, e.g., by using radioactive phosphorous [y-.sup.32P]ATP or
by using monoclonal antibodies specific for phosphorylated amino
acids is used to reveal the result of specifically inhibition of
the kinase of interest. In the cells expressing the normal copy of
the kinase of interest, the protein substrates of the native kinase
will become labeled, even in the presence of the inhibitor, whereas
the protein substrates of the engineered kinase will at least be
labeled to a lesser degree; preferably, the protein substrates of
the engineered kinase will not be substantially labeled, and most
preferably, they will not be labeled at all.
[0239] It is also preferable if the wild-type kinase corresponding
to the mutant has been removed from the cells, e.g., by "knock-out"
of the cellular gene(s) for it. If the labeled proteins of such an
assay are examined in tandem with control samples containing the
wild-type kinase but not the mutant kinase, certain bands will be
diminished in intensity in the mutant-treated sample relative to
the control. Preferably, the difference in intensity will be high;
most preferably, there will be bands which are missing in the
mutant-containing samples treated with the inhibitor. This wold
indicate that the wild-type form of that kinase phosphorylates
those differentially labeled proteins; when the kinase is
inhibited, those bands do not get labeled.
[0240] Example 10 provides one example of a method of using a
mutant kinase of the present invention, along with its orthogonal
substrate analog or its inhibitor, as the case may be, to detect
which are the intracellular protein substrates for that protein
kinase. Developing such a test was primary goal of the research
that led to the present invention.
[0241] Generally, the method described in Example 10 and in FIG. 8
would appear to be generally applicable; however, there are many
other possible approaches that could be used, once a mutant that
accepts an orthogonal substrate analog or inhibitor has been
prepared. The natural phosphate donor substrate is first prepared
to contain a labeled moiety on the terminal phosphate, for example,
by replacing the phosphate with [y-.sup.32 P] phosphate. This
substrate, along with the analog or inhibitor, is then added to a
sample of lysed cells, cell extracts, permeabilized cells, or cells
which are naturally permeable to the orthogonal nucleotide
triphosphate substrate analog or to the inhibitor, and which
express the mutant kinase, or to which the mutant kinase has been
exogenously added (e.g., by microinjection). After incubation under
conditions that will allow the mutant kinase to become inhibited,
and/or to phosphorylate its protein substrates to the extent not
inhibited, the labeled products are then extracted and analyzed in
comparison with those produced by a control sample, which was
treated substantially the same way, but without the addition of the
analog or inhibitor, respectively. Methods for the detection of
labeled proteins are well known, and include both quantitative and
qualitative methods. In addition, all methods for characterizing
and identifying proteins can be used to determine with specificity
what the protein substrates are, and what their functions are.
Ultimately, it should be possible to develop an understanding of
what protein substrates each of the various protein kinase act
upon, and reveal in great detail the mysteries of cellular signal
transduction.
[0242] Once one or more cellular protein substrate has been
identified, similar assays can be used to identify drugs or other
compounds that can modulate the activity of a given protein kinase
on one or more substrates. For example, one could add small amounts
of solutions of a variety of such compounds to test samples
containing cell-free extract, mutant kinase, along with a labeled
orthogonal substrate analog and/or inhibitor. The labeled proteins
can then be identified, e.g., by gel electrophoresis followed by
autoradiography, and compared with a duplicate test sample treated
the same way, but to which no drug or other compound was added.
[0243] If a protein is not labeled in a sample having an added
compound plus substrate analog and/or inhibitor that does get
labeled in a sample treated with the analog and/or the inhibitor,
this indicates that the added compound has caused the kinase to
phosphorylate a protein that it does not act on in the absence of
the compound, i.e., the compound upwardly modulates the activity of
the kinase for that protein. Alternatively, if a labeled protein
appears in a test sample to which the compound or drug was added,
but does not appear in a test sample not having the compound or
drug added, this indicates that the added compound has prevented
the kinase from phosphorylating a protein that it does act on in
the absence of the compound, i.e., the compound downwardly
modulates the activity of the kinase for that protein
substrate.
[0244] Furthermore, if quantitative measurements are made for each
labeled protein, e.g., by scanning autoradiograms and integrating
the data, more subtle effect on kinase activity can be detected.
For example, it may be found that a protein is more fully or less
fully phosphorylated in the presence or absence of a given compound
(i.e., has been less dramatically modulated). It can also be
expected that some compounds will upwardly modulate kinase activity
for some proteins and downwardly modulate activity for others at
the same time.
XI. Use in Screening for Drug Design Target Kinase
[0245] As mentioned above, because kinase play key roles in various
diseases, it is of great interest to develop inhibitors which can
specifically inhibit a single wild-type kinase or group of
wild-type kinase. By down-modulating the activity of these
disease-involved kinase, it should be possible to reduce the
disease symptoms, or even cure the disease. However, the great
difficulty which has been experienced in making such inhibitors of
wild-type kinase, as briefly described above, limits the potential
of that approach. The primary difficulty is finding inhibitors
which are specific, and do not inhibit other kinase than the
intended target. The reasons for such non-specificity are (i) the
nucleotide triphosphate binding sites of kinase are highly
conserved in evolution, and (ii) many kinase are "degenerate," that
is, they have sufficiently similar activities and specificities
that they can substitute for other kinase that because of gene
deletion or other reason are absent or diminished in concentration
in the cells. The problem of binding site similarities can in many
instances be overcome, e.g., by careful rational inhibitor design,
or by selection of inhibitors from combinatorial libraries on the
basis of specificity. However, efforts to do so with a kinase that
is truly degenerate with another kinase will likely be unfruitful,
either all of the co-degenerate kinase will be inhibited by even
the best candidate compounds, or even if the target is inhibited,
it will be impossible to tell, because a degenerate kinase will
"take over" the activity of the inhibited one.
[0246] Because of this, there is a need for a way to screen kinases
to determine which wild-type kinase are degenerate, and thus
probably poor candidates for specific inhibition, and which are not
degenerate, and therefor preferred candidates for specific
inhibition. The present invention provides such a method. The
present invention provides a means to generate a specific, unique
kinase inhibitor for any kinase of interest, by making a mutant of
the kinase that is specifically designed to be inhibited by
candidate inhibitors selected, and then studying the effects of
that inhibition.
[0247] Another, preferred method of such screening would be to
produce animal models for the disease of interest, and then "knock
out" the wild-type gene, and then, by genetic engineering, insert
into the genome a gene encoding a mutant kinase of the present
invention "knock-in". Then, an inhibitor of the present invention,
preferably one which has been shown in vitro to inhibit the mutant,
can be used to down-regulate the mutant kinase. If down regulation
leads to a decrease in the symptoms or morbidity of the disease in
the model animal, or eliminates the disease, then that kinase is a
preferred candidate for the development of a specific inhibitor of
the wild-type form.
XII. Gene Therapy Applications
[0248] The mutant kinase and inhibitors of the present invention
can also be used directly to treat diseases in humans and animals.
Just as described above for the animal model systems, gene
substitution could be used on patients with diseases which are
mediated by those kinase. The wild-type for one or more such
wild-type kinase would be deleted, e.g., by "knock-out" methods
known in the art, and then specifically inhibitable mutants of
those one or more kinase would be added to the animal's genome,
e.g.., by "knock-in" or gene therapy methods which are known in the
art. Then, the inhibitor could be used as a drug to down-modulate
those one or more mutant kinase, such that the disease is
ameliorated to at lest some degree, but the degree of activity of
those kinase which may be found to be necessary for normal cellular
function could be maintained. Of course, the kinase could also be
essentially "turned off" by strong inhibition, if that proved to be
therapeutically effective. Furthermore, if it is found that the
disease is greatly improved or cured by a period of down-regulation
or being turned off, then administration of the inhibitor could be
discontinued, and the disease well might not return or exacerbate.
If not, then inhibition could be discontinued on a long term or
even permanent basis, and the mutants could be left to function in
the place of the wild-type kinase for the remainder of that
patient's life. Since the specific inhibitors of the present
invention are not present in the environment, the mutant kinase
should behave just like the wild-type (except to the extent that
the engineering may have changed their activity or kinetics). And
if the disease should recur or flare up again int eh future, the
patient could again be treated with the inhibitor, without the need
to repeat the gene exchange.
XIII. Development of a Molecular Switch for Inhibitor Sensitive
Alleles of any Protein Kinase
[0249] The present invention provides a general approach for
sensitizing protein kinases to cell permeable molecules which do
not inhibit any wild-type protein kinases. Using a chemical switch
to design a unique protein/small molecule interface, protein
kinases with unique sensitivity to cell permeable inhibitors were
engineered. Seven protein kinases from five distinct families were
selected in a semi-random fashion. Inhibitors were identified for
every kinase. It is demonstrated that this approach can be
successful even for protein kinases which are not potently
inhibited by the chosen "lead" inhibitor. It has been shown that
divergent scaffolds can be used to generate very different analogs
which are specific for the same target. In addition, specific in
vivo inhibition of a target kinase without the need to carry out an
in vitro screen has been shown. The data suggests that a majority
of protein kinases will be susceptible to this target specific
inhibition strategy. For organisms that readily undergo homologous
recombination (such as Saccharomyces cerevisiae, Dictyostelium
discoideum, DT40 chicken B cells, and embryonic stem cells) this
approach opens up the possibility of rapidly generating conditional
allelic strains for every protein kinase in the genome, even those
without visible null phenotypes. A library of such strains would
represent a significant step forward in realizing the
pharmacogenomic vision of identifying small molecule ligands for
every gene product in the cell.
XIV. Cdc28 Mutant Kinase Sensitive to Cell-Permeable Chemical
Inhibitor
[0250] The cyclin-dependent protein kinases (Cdks) drive and
coordinate the events of the eukaryotic cell division cycle (112).
In the budding yeast Saccharomyces cerevisiae, the cell cycle is
regulated by Cdc28(Cdkl) (reviewed in (113)), whose function has
been studied primarily by the analysis of temperature-sensitive
(ts) mutant alleles (114). At 37.degree. C., most of these mutants
arrest in G1, suggesting that progression through START is uniquely
sensitive to inhibition of Cdc28 activity. Interestingly, analysis
of ts mutants has not provided clear evidence that Cdc28 plays a
role in the G2/M transition, despite abundant evidence that Cdkl is
required for mitotic entry in other eukaryotes (115-117).
[0251] Temperature-sensitive mutants are powerful tools in the
analysis of gene function, but analysis of ts phenotypes can
sometimes be complicated by the effects of heat shock. In addition,
the mechanism of ts protein inactivation is rarely understood in
molecular detail. For example, the kinase activity of Cdc28 is
decreased in certain cdc28 ts mutants at high temperature (118),
but it is not clear if the cell cycle arrest is due to an effect on
the catalytic function of the enzyme or due to defects in protein
folding, stability, or interactions with other proteins.
[0252] Chemical genetics provides an alternative approach to the
generation of conditional defects in gene function (119-121). In
this approach, the function of a previously identified gene product
is determined through the use of a highly specific chemical
inhibitor identified by rational design or screening of chemical
libraries. Unfortunately, this approach has had only limited
success in the study of protein kinases, whose highly conserved
active sites make it difficult to identify mutant specific
inhibitors (121, 122).
[0253] A highly specific chemical genetic approach that involves
the design of a mutated target kinase that is uniquely sensitive to
a cell-permeable chemical inhibitor was developed (123-125). Based
on mutation of the corresponding residue in the Src family of
kinases (126), phenylalanine 88 in Cdc28 was replaced with a
glycine, resulting in the formation of a new pocket in the
ATP-binding site. This mutant kinase, Cdc28-as1 (analog-specific
1), was predicted to be sensitive to
4-amino-1-(tert-butyl)-3-(1'-naphthylmethyl)pyrazolo[3,4-d]pyrimidine
(1-NM-PP1), an analog of the kinase inhibitor PP 1 that carries a
modification that should occupy the engineered pocket in the ATP
binding site.
[0254] This invention demonstrates that an allele-specific chemical
inhibitor can be used to study Cdc28 activity in vivo. At low
concentrations of 1-NM-PP1, cdc28-as1 strains delay or arrest in
G2/M with hyperpolarized buds. This phenotype is similar to that
observed in cells lacking the mitotic cyclins Clb1-4 (139). The
phenotype in cdc28-as1 cells is due to a reduction in Cdc28
activity below some threshold required for mitotic entry and for
the switch from apical to isotropic bud growth. Apparently, the
activity of G1/S cyclin-Cdk complexes in these cells is still
sufficient to trigger budding and DNA replication. Only at higher
concentrations of inhibitor is the activity of these complexes
reduced below the threshold required for passage through START.
These data are generally consistent with the notion that different
cell cycle events are triggered by specific threshold levels of CDK
activity, and that later events require higher amounts of activity
(140). However, the differences in the substrate specificity of
different cyclins also contribute to the ordering of cell cycle
events (141-143).
[0255] The evidence that G2/M progression is most sensitive to
Cdc28 inhibition seems to contradict previous results with
temperature-sensitive cdc28 mutants, most of which arrest as
unbudded cells in G 1. Perhaps the G1 arrest at high temperature is
explained by differences in the temperature sensitivity of
different forms of Cdc28. For example, a GI arrest might result if
Cdc28-Clb complexes in S phase or G2/M are more heat-resistant than
the monomeric Cdc28 that predominates in G1. The use of
allele-specific chemical inhibition provides a powerful alternative
method that avoids these and other problems with
temperature-sensitive mutants.
[0256] The structure of the ATP binding site is highly conserved
among protein kinases, and therefore our approach should be
applicable to the analysis of any protein kinase (thus far, we have
successfully identified specific inhibitors of engineered Src, Fyn,
Cdk2, CaMKII.alpha., c-Ab1, Fus3, Lck, p38, and Pho85 (123-125,
144). This method also provides an approach to the generation of
conditional alleles that is more rapid than traditional methods for
the isolation of temperature sensitive alleles. In addition, the
availability of a new class of conditional alleles will allow
straightforward epistasis analysis to order gene products in linear
signaling pathways: reciprocal shift experiments between an
analog-specific allele and any other temperature-sensitive or cold
sensitive gene product of interest can now be performed. The
results also suggest that the strength of the mutant allele can be
controlled by varying the concentration of inhibitor: thus,
cdc28-as1 behaves as a weak allele at moderate inhibitor
concentrations and a virtual null allele at high concentrations.
The application of this method to other protein kinases should
therefore allow the identification of gene functions with different
requirements for catalytic activity. Similarly, in cases where a
protein kinase is thought to have both kinase-dependent and
-independent functions (145), the use of an analog-specific allele
would inhibit only those functions that require kinase activity.
Finally, the same kinase mutation that generates the
analog-specific allele also allows the kinase to use radiolabeled
ATP analogs that are modified to complement the engineered ATP
binding site (126, 146). Addition of these ATP analogs and the
mutant kinase to cell lysates should lead to the labeling and
identification of direct kinase targets. This approach can also be
used to identify specific Cdc28 substrates.
XV. Cell Lines
[0257] As explained elsewhere herein, engineered expression vectors
containing the nucleic acid encoding the mutant enzyme may be used
to transform an appropriate host cell. A number of mammalian cell
lines are known in the art and include immortalized cell lines
available from the American Type Culture Collection (ATCC), such
as, but not limited to, Chinese hamster ovary (CHO) cells, HeLa
cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS),
human hepatocellular carcinoma cells (e.g., Hep G2), Madin-Darby
bovine kidney ("MDBK") cells NIH/3T3, 293 cells (ATCC #CRL
1573),COS-7, 293, BHK, CHO, TM4, CV1, VERO-76, HELA, MDCK, BRL 3A,
W138, Hep G2, MMT 060562, TRI cells, as well as others. A well
known example of an avian cell line is the chicken B cell line
"DT-40". Examples of vectors useful for transforming such cell
lines include, but are not limited to, retroviral vectors, vaccinia
virus vectors, adenovirus vectors, herpes virus vector, fowl pox
virus vector, bacterial expression vectors, plasmids, such as
pcDNA3 (Invitrogen, San Diego, Calif.) or the baculovirus transfer
vectors.
[0258] Insect cells for use with baculovirus expression vectors
include, inter alia, Aedes aegypti, Autographa californica, Bombyx
mori, Drosophila melanogaster, Spodoptera frugiperda, and
Trichoplusia ni.
[0259] In another embodiment, genes of the invention are cloned
downstream of a C. elegans constitutive or inducible promoter, such
as the heat-shock promoter element in an expression vector such as
pPD,69.78 hsp 16.2 or pPD69.3 hsp 16-41, which are public domain
vectors for creating C. elegans transgenic lines in which the gene
of interest is under the control of an inducible heat shock
promoter element. Transgenic C. elegans may then be obtained by
microinjection of oocytes.
[0260] In another embodiment, Drosophila cells may be transfected
with commonly available vectors (156, 157).
[0261] Streptococcus spp. and other lower eukaryotic cells will
find use with the present expression constructs. Yeast hosts useful
in the present invention include inter alia, Saccharomyces
cerevisiae, Candida albicans, Candida maltosa, Hansenula
polymorpha, Kluyveromyces fragilis, Kluyveromyces lactis, Pichia
guillerimondii, Pichia pastoris, Schizosaccharomyces pombe and
Yarrowia lipolytica.
[0262] The following examples are provided to describe and
illustrate the present invention. As such, they should not be
construed to limit the scope of the invention. Those in the art
will well appreciate that many other embodiments also fall within
the scope of the invention, as it is described hereinabove and in
the claims.
EXPERIMENTAL DETAILS SECTION
EXAMPLE 1
[0263] Synthesis of ATP analogs: Twelve different orthogonal ATP
analogs were synthesized. FIG. 2 is a schematic representation of
their structure. The Figure shows adenosine triphosphate (ATP),
with an "X" bound to the 6 position; and in the box below,
schematic representations are provided for the twelve side chains
that take the place of "X" in each of the orthogonal ATP analogs
described int eh examples (which are always referred to by the
numbers 1-12 set forth n bold typeface). Those analogs are:
2 1-N.sup.6(methoxy)ATP 7-N.sup.6-(pyrolidino)ATP
2-N.sup.6(ethoxy)ATP 8-N.sup.6(cyclopentyl)ATP 3-N.sup.6(acetyl)ATP
9-N.sup.6(cyclopentyloxy)ATP 4-N.sup.6(i-propoxy)ATP
10-N.sup.6-(pipperidino)ATP 5-N.sup.6-(benzyl)ATP
11-N.sup.6-(cyclohexyl)ATP 6-N.sup.6-(benxyloxy)ATP
12-N.sup.6-(cyclohexyloxy)ATP
[0264] Analogs 1, 2, 4, 6, 9, and 12 were synthesized via Dimroth
rearrangement of the corresponding N.sup.1 alkoxy adenine
derivatives in four steps starting from adenosine, according to the
procedure of Fujii et al (43). Analog 5 was synthesized similarly
via Dimroth rearrangement of N.sup.1 beizyladenosine (44). Analog 3
was prepared via in situ protection of the adenosine hydroxyl
groups as trimethylsilyl ethers and subsequent treatment with
acetyl chloride, according to McLaughlin et. al. (45). Analogs 7,
8, 10 & 11 ere synthesized via treatment of 6-chloropurine
riboside (Aldrich) with pyrrolidine, cyclopentylamine, piperidine
& cyclohexylamine, respectively (46).
[0265] Triphosphate synthesis was carried out according to the
method of Ludwig (47) with the exception of the preparation of
pyrophosphate. Accordingly, bis-tri-N-butyl ammonium pyrophosphate
was prepared by mixing 1 equivalent of pyrophosphoric acid with 2
equivalents of tributylamine in a (1:1) water: ethanol mixture
until a homogenous solution was obtained. Solvent was removed under
vacuum to dryness and the pyrophosphate was stored over
P.sub.2O.sub.5 overnight. All non-radioactive nucleotides ere
characterized by .sup.1H--NMR, mass spectral analysis and strong
anion exchange (SAX) HPLC (Rainin # 83-EO3-ETI).
[0266] [y-.sup.32P] N.sup.6-(cyclopentyl)ATP was synthesized
according the method of Hecht and Kozarich (48). The radiolabeled
analog was purified by DEAE (A-25) Sephadex (Pharmacia) column
chromatography and the triphosphate was identified by co-injection
of the radiolabeled material with an authentic sample of
N.sup.6-(cyclopentyl) ATP on an SAX-anion exchange HPLC column
(Rainin) (linear gradient of 5-750 mM ammonium phosphate pH 3.9 in
10 min. At 0.5 mL/min). The chemical yield of the reaction varied
from 70% to 80%.
EXAMPLE 2
[0267] Screening of Nucleotide Analogs: To identify compounds that
would not be accepted as substrates by any existing cellular kinase
(53), a panel of synthetic A*TP analogs were screened in a murine
lymphocyte lysate (CF) rich in protein tyrosine kinase (13). The
assays were performed using spleenocytes (8-30 week old male and
female C57/B6 mice from the Princeton University Animal Facility)
which were isolated and washed in RPMI-1640 medium containing 5%
Bovine Calf Serum (BCS), 1% Hepes and DNAseI (1 .mu.g/ml). Red
cells were lysed at 4.degree. C. by treatment with 17 mM tris
ammonium chloride pH 7.2. The cells were hypotonically lysed on ice
for 10 min. In 1 mM Hepes pH 7.4, 5 mM MgCl.sub.2, leupeptin (10
.mu.g/ml), aprotinin (10 .mu.g/ml) and 100 uM PMSF according to the
method of Fukazawa et. al. (51). After vortexing and
centrifuigation at 500 xg, the supernatant was collected. Cells
were stored at 4.degree. C. for 20 min. To attenuate the basal
protein phosphorylation level, after which the buffer was adjusted
to 20 mM Hepes pH 7.4, 10 mM MgCl.sub.2 and 1 mM NaF. Sodium
vanadate (100 uM) was then added to inhibit the activity of
phosphotyrosine phosphatases.
[0268] Each nucleotide triphosphate was added to a final
concentration of 100 uM to 5.times.10.sup.6 cell equivalents and
incubated at 37.degree. C. for 5 min. after which 4X Laemmli gel
loading buffer was added to the cell lysate to quench the reaction.
Proteins were separated by 12.5% SDS-PAGE and transferred to
Protran BA85 (Schleicher-Schuell). The blot was probed with the
anti-phosphotyrosine monoclonal antibody 4G10 (Upstate
Biotechnology) and the bound antibody was detected via enhanced
chemiluminescence (cat. 34080, Pierce) following treatment with
HRP- coupled goat-anti-mouse antibody (VWR cat. 7101332) according
to the manufacturer's instructions.
[0269] The results are shown in FIG. 3, which is an
anti-phosphotyrosine protein immunoblot showing the level of
protein tyriosine phosphorylation following treatment of a murine
lymphocyte cell lysate (CF) with 100 uM of ATP or A*TPs (1-12). The
cell lysate used includes the protein tyrosine kinase Src, Fyn,
Lck, Lyn, Yes, Fgr, Hck, Zap, Syk, Btk, Blk, and other protein
tyrosine kinase present in B and T lymphocytes, macrophages, and
follicular dendritic cells (13). Molecular size standards (in
kilodaltons) are indicated. The A*TPs containing the smallest
N.sup.6 substituents, 1 (methoxy), 2 (ethoxy), and 3 (acetyl)
showed some ability to serve as cellular protein tyrosine kinase
substrates (FIG. 3, lanes 3-5). The A*TPs with sterically demanding
N.sup.6 substituents, 4 (I-propoxy), 5 (benzyl), and 6 (benzyloxy),
and all analogs containing cyclic aliphatic substituents (7-12)
showed little or no protein phosphorylation (FIG. 3, lanes 6-8,
11-16).
[0270] To test for possible metathesis of orthogonal A*TPs (7-12)
with cellular ADP to give A*DP and ATP, 1 mM ADP was added to cell
lysate kinase reactions identical to those shown in FIG. 3; the
pattern of phosphoproteins was the same, indicating that no
significant metathesis of A*TP occurs in a complete cell lysate
system.
[0271] Based upon these results, it appears that analogs (7-12) are
"dead substrates" for wild-type protein tyrosine kinase, i.e., the
wild-type substrates do not substantially, or at all, accept these
as phosphate donor substrate. These analogs thus were chosen as the
most preferred targets for reengineering the nucleotide binding
site of v-Src.
EXAMPLE 3
[0272] Designing the Mutant v-Src: No crystal structures of any
protein tyrosine kinase in an active conformation have been solved
to date although several structures of inactive kinase have been
solved (54,55). However, two crystal structures of catalytically
active ser/thr kinase have been solved (56,57). There is a high
degree of functional homology between the ser/thr and the protein
tyrosine kinase catalytic domains as shown by affinity labeling of
the identical catalytically active lysine residue in both kinase
families (K72 in cAMP dependent kinase (PKA), K295 in v-Src)
(58,58). Inspection of the PKA (56) and cyclin dependent kinase-2
(CDK2)-cyclinA (57) crystal structures revealed two amino acid side
chains within a 4 A sphere of the N.sup.6 amino group of bound ATP.
V104/M120 (PKA) and V64/F80 (CDK2) (60).
[0273] FIG. 4 shows a close-up view of the ATP binding site in cAMP
dependent protein kinase (PKA), which is bound to ATP. Three
residues within a 4 A sphere of the N.sup.6 amine of ATP (Val104,
Met120, and Glu121) and the catalytically essential lysine residue
(Lys72) are shown in ball-and-stick representation. The remainder
of the protein is shown in ribbon format. This figure was created
by feeding the output of Molscript into the Raster3D rendering
program (68,69). Note that in the model, the side chain of Glu121
is pointed away from the adenine ring binding region, and therefore
Glu121 was not a candidate for alteration.
[0274] The sequence alignment of the ATP binding regions of PKA
(SEQ. ID. No. 1), CDK2 (SEQ. ID>NO. 2), and v-Src (SEQ. ID. NO.
3) are shown below. The residues shown in bold correspond to the
amino acids with side chains in a 5.ANG. sphere of the N.sup.6
amino group of kinase bound ATP.
3 (SEQ ID NO:1) Subdomain IV V PKA (99) NFPFLVKLEFSFKDNSNLYMVMEYVPG
(125) (SEQ ID NO:2) CDK2 (59) NHPNIVKLLDVIHTENKLYLVFEFLHQ (85) (SEQ
ID NO:3) v-Src (318) RHEKLVQLYAVVSE-EPIYIVIEYMSK (343)
[0275] Based on the functional similarity between the
above-described kinase, positions V323 and I338 in the v-Src
catalytic domain were mutated, which correspond to V104/M120 in PKA
& V64/F80 in CDK2. By mutating these residues to alanine, it
was hoped to create an additional "pocket" in the nucleotide
binding site of v-Src to allow binding of one of the preferred
orthogonal A*TPs (4-12).
EXAMPLE 4
[0276] Mutant Synthesis, Expression and Purification: The mutant
(V323A, 1338A) was made as described below. Both the wild-type and
the double alanine mutant of the v-Src catalytic domain, (the XD4
fragment) were made as glutathione S-transferase (GST) fusion
proteins (GST-XD4) (61,62). These were made in E. coli, which is an
good expression host because it lacks any endogenous protein
tyrosine kinase, as described in the following Example. The XD4
fragment of v-Src was used because it contains and intact SH1
catalytic domain but lacks the non-catalytic regulatory SH3 and SH2
domains, and exhibits higher specific activity than full-length
v-Src.
[0277] Overlap extension PCR was used to make GST-XD4 (V323A,
I338A) (49). Pfu polymerase (Stratagene) was used in the PCR
reactions according to the manufacturer's protocol. Six synthetic
oligonucleotides were used:
4 (5'-TTTGGATCCATGGGGAGTAGCAAGAGCAAG), SEQ ID NO:4
(5'-TTTGAATTCCTACTCAGCGACCTCCAACAC). SEQ ID NO:5
(5'-TGAGAAGCTGGCTCAACTGTACGCAG). SEQ ID NO:6
(5'-CTGCGTACAGTTGAGCCAGCTTCTCA). SEQ ID NO:7
(5'-CTACATCGTCGCTGAGTACATGAG). SEQ ID NO:8
(5'-CTCATGTACTCAGCGACGATGTAG). SEQ ID NO:9
[0278] Primer SEQ ID No. 4 contains a BamH1 site and primer SEQ. ID
No. 5 contains and EcoR1 site (shown in italics). Primers SEQ ID
NO.: 6 and SEQ ID NO.: 7 contain the nucleotide sequence changes to
introduce the V323A mutation (nucleotides encoding mutations are
shown in bold). Primers SEQ ID NO. 8 and SEQ ID NO. 9 contain the
I338A mismatch.
[0279] The XD4 gene from Yep51-XD4 plasmid (a gift of B. Cochran at
Tufts Medical School) was amplified with primers SEQ. ID NO. 4 and
SEQ. ID. NO. 5. The PCR product was digested with BamH1 and EcoR1
and ligated into BamH1 and EcoR1-digested pGEX-KT and then
transformed into the E. coli strain DH5a. BOSC 23(6) and viral
particles harvested after 2 days as desciibed(6). NIH 3T3 cells
were infected as described (7) with these viral particles and
stable transfectants were selected in puromycin containing media as
described (5). Stable transfectants were maintained in media
containing puromycin to ensure no loss of expression of v-Src.
[0280] The final results are shown in FIG. 1, which is a diagram
showing the domain structure of v-Src including the Src-homology
3,2, and 1 (SH3, SH2 & SH1) domains, with the domain boundaries
indicated by the amino acid residue numbers listed above each boxed
domain. The domain structure of XD4 is also represented, which
contains a deletion of residues 77-225 (.DELTA.77-225). Domain
organizations of the glutathione S-transferase (GST) fusion with
XD4 (numbering from v-Src), and the doubly mutated GST-XD4
(representing both V323A, I338A and I338G) are also shown
schematically.
EXAMPLE 5
[0281] Testing the Mutant v-Src For Ability to Bind Orthogonal ATP
Analogs: The ability of the N.sup.6 substituted ATP analogs (1-12,
FIG. 2) to differentially inhibit wild-type and mutant kinase
phosphorylation of RR-Src with [.gamma.-.sup.32P] ATP, which is a
measure of their ability to bind to the respective ATP binding
sites was evaluated. Assays were carried out in triplicate at
37.degree. C. in a final volume of 30 .mu.L buffered at pH 8.0
containing 50 mM Tris, 10 mM MgCl.sub.2, 1.6 mM glutathione, 1
mg/ml BSA, 1 mM RR-Src peptide with either GST-XD4 (100 nM) or
GST-XD4(V323A, I338A) (100 nM) and 10 .mu.M [.gamma.-.sup.32P] ATP
(1000 cpm/pmol) [Dupont NEN]. Cold ATP or ATP analogs (100 .mu.M)
(1-12) were added prior to addition of the kinase. After 30 minutes
the reactions were quenched by spotting 25 .mu.L of the reaction
volume onto p81 phosphocellulose disks (Whattman) and these were
immersed in 250 mL of 10% acetic acid for >30 minutes followed
by washing and scintillation counting according to standard methods
(52).
[0282] The results are shown in FIG. 6. Relative inhibition of
GST-XD4 is shown by solid bars, and relative inhibition by
GST-XD4(V323A, I338A) is represented by the diagonal filled bars.
Percent inhibition (1-v.sub.I/v.sub.0) is reported as a ratio of
v.sub.I (cpm in the presence of 100 .mu.M of the indicated
triphosphate and 10 .mu.M [.gamma.-.sup.32P] ATP (1000
cpm/pmol)/v.sub.0 (cpm in the presence of 10 .mu.M
[.gamma.-.sup.32P] ATP (1000 cpm/pmol) alone--background cpm due to
non-specific 10 .mu.M [.gamma.-.sup.32P] ATP binding to the
phosphocellulose disks (<0.1% of total input counts)). Error
bars represent the S.D. determined from four separate experiments
with three replicates.
[0283] The wild-type kinase GST-XD4 displays poor binding affinity
for most ATP analogs (FIG. 6, solid bars) as expected from the
lymphocyte kinase assay (FIG. 3). In contrast, the doubly mutated
GST-XD4(V323A, I338A) shows excellent inhibition by more sterically
demanding N.sup.6 substituted ATP analogs (FIG. 6, shaded bars).
Most significantly, the GST-XD4(V323A, I338A) mutant is inhibited
by ATP analogs 5, 8, 9, and 11 almost as well as the wild-type
kinase, GST-XD4, is inhibited by its natural substrate ATP. It was
confirmed that GST-XD4(V323A, I338A) and the full length
GST-v-Src(V323A, I338A) display the same inhibition pattern with
ATPs (1-12).
[0284] Four of the nine "dead" substrates identified in the screen
of wild-type kinase specificity (FIG. 3) bind well to the mutant
kinase. This high success rate in identifying new substrates for a
mutant v-Src which are not accepted by wild-type kinase suggests
that a key feature of the v-Src nucleotide binding site was
identified, namely the residues which make a close fit around the
N.sup.6 amino group of ATP. It is worth noting that no wild-type
protein kinase is known which contain an alanine at the position
corresponding to I338 in v-Src (position 120 in PKA). If a
sterically demanding amino acid side chain at this position also
plays a critical role in determining the specificity of other
kinase, it should well be possible to engineer them to accept
orthogonal substrates using an approach very similar to the one
described here, and such engineered kinase would be well within the
scope of the present invention.
EXAMPLE 6
[0285] Determining Catalytic Efficiency of Mutant v-Src with the
Most Preferred Orthogonal ATP Analog: The ability of
N.sup.6-(cyclopentyl) ATP, 8, to serve as a catalytically competent
substrate of both wild-type GST-XD4 and the GST-XD4(V323A, I338A)
mutant over the other three ATP analogs 5, 9, and 11 because analog
8 exhibited a slightly lower level of phosphorylation with
wild-type kinase was tested (FIG. 3, lane 12).
[0286] ATP and N.sup.6-(cyclopentyl) ATP dependent RR-Src
phosphorylation (1 mM) by GST-XD4 (V323A, I338A) and GST-XD4 were
carried out at low substrate conversion (<5%) in triplicate.
Kinetic constants were determined by analysis of Lineweaver-Burk
plots of the rate data (64). Assays were carried out in triplicate
at 37.degree. C. in a final volume of 30 .mu.L buffered at pH 8.0
containing 50 mM Tris, 10 mM MgCl.sub.2, 1.6 mM glutathione, 1
mg/mL BSA, 1 mM RR-Src peptide with either GST-XD4 (100 nM) or
GST-XD4(V323A, I338A) (100 nM) and 10 .mu.M
[0287] [.gamma.-.sup.32P] ATP (1000 cpm/pmol) or [.gamma.-.sup.32P]
N.sup.6-(cyclopentyl)ATP (5000 cpm/pmol) as indicated.
5TABLE 1 Kinetics for Phosphate Donor Substrates GST-XD4 GST-XD4
(V323A, I338A) k.sub.cat K.sub.M k.sub.cat/K.sub.M K.sub.cat
K.sub.M K.sub.cat/K.sub.M Nucleotide (min.sup.-1) .mu.M
(min.sup.-1M.sup.-1) (min.sup.-1) .mu.M (min.sup.-1M.sup.-1) ATP 2
.+-. 0.5 12 .+-. 3 1.6 .times. 10.sup.5 0.8 .+-. 0.2 150 .+-. 20
5.3 .times. 10.sup.3 N.sup.6-(cyclo- 2000(K.sub.I) (5 .+-. 2)
.times. 10.sup.2 15 .+-. 3 3.3 .times. 10.sup.3 pentyl)ATP
[0288] As shown in Table 1 above, the wild-type kinase GST-XD4 did
not substantially phosphorylate the RR-Src peptiide with
[.gamma.-.sup.32P] N.sup.6-(cyclopentyl)ATP, confirming the
previous observations that this analog is not a significant
substrate for the wild-type kinase. In contrast, GST-XD4(V323A,
I338A) displayed Michaelis-Menten kinetics with the orthogonal ATP,
[.gamma.-.sup.32P] N.sup.6-cyclopenyl)ATP. The K.sub.M of the
mutant for the orthogonal substrate is quite close to the K.sub.M
of GST-XD4 for ATP. On the other hand, the mutant has a K.sub.M for
ATP which is more than 10-fold higher than the K.sub.M of GST-YXD4
for ATP.
[0289] The parameter used to rank catalysts for competing
substrates is the ratio of the turnover number to the
Michaelis-Menten constant, k.sub.cat/K.sub.M (the "specificity
constant") (64). The k.sub.cat/K.sub.M of the engineered mutant
GST-XD4(V323A, I338A) with the orthogonal substrate
[.gamma.-.sup.32P] N.sup.6-(cyclopentyl)ATP is, only 50-fold lower
than the k.sub.cat/K.sub.M value of the wild-type kinase with its
natural substrate, ATP. This catalytic efficiency with the
orthogonal ATP substrate, coupled with the mutant kinase's lower
catalytic efficiency with ATP when compared to the wild-type,
satisfy two of the design criteria discussed above.
[0290] It is even more significant that the new substrate,
[.gamma.-.sup.32P] N.sup.6-(cyclopentyl)ATP, is not substantially
utilized by wild-type GST-XD4, as demonstrated by the apparent
complete inability of GST-XD4 to use this analog as a phosphodonor
for autophosphorylation; this is illustrated in FIG. 5C, lane 3.
FIG. 5C is an autoradiogram showing [.gamma.-.sup.32P] ATP
dependent autophosphorylation of GST-XD4, lane 1, or GST-XD4(V323A,
I338A), lane 2; and [.gamma.-.sup.32P] N.sup.6-(cyclopentyl)ATP
dependent phosphorylation of GST-XD4, lane 3, or GST-XD4(V323A,
I338A) phosphorylation, lane 4. Note that in contrast to GST-XD4,
the engineered kinase is efficiently autophosphorylated with
[.gamma.-.sup.32P] N.sup.6-(cyclopentyl)ATP (FIG. 5C, lane 4).
EXAMPLE 7
[0291] Confirming Retention of Protein Substrate Specificity: As
shown in Table 2 below, it was discovered that the wild-type
GST-XD4 kinase phosphorylated to a well characterized peptide
substrate of v-Src, RR-Src, with kinetics consistent with
literature reports (63). This indicates that the sequence
engineering had not substantially affected the catalytic activity
of the enzyme with respect to its protein substrates.
6TABLE 2 Kinetics for Protein Substrate RR-Src GST-XD4
GST-XD4(V323A, I338A) Nucleotide K.sub.M (mM) K.sub.M (mM)
(Saturated) ATP 2.6 .+-. 0.9 3.1 .+-. 0.9 N.sup.6-(cyclo- -- 2.1
.+-. 0.9 pentyl)ATP
[0292] Assays of GST-XD4 and GST-XD4(V323A, I338A) phosphorylation
of RR-Src were carried out in triplicate at 37.degree. C. in a
final volume of 30 .mu.L buffered at pH 8.0 containing 50 mM Tris,
10 mM MgCl.sub.2, 1.6 mM glutathione, 1 mg/ml BSA, 1 mM RR-Src
peptide with either GST-XD4 (100 nM) or GST-XD4(V323A, I338A) (100
nM) and 10 .mu.M [.gamma.-.sup.32P] ATP (1000 cpm/pmol) [Dupont
NEN].
[0293] To determine whether the alanine mutations have any effect
on the protein substrate specificity, the K.sub.M of both the
wild-type and the mutant fusion proteins for the RR-Src peptide was
measured. At saturating concentrations of [.gamma.-.sup.32P] ATP
the wild-type and the mutant display essentially the same K.sub.M
for RR-Src, 2.6.+-.0.9 mM, respectively (63). In addition, the K of
the mutant for the protein substrate in the presence of saturating
amounts of the orthogonal substrate was also essentially the same,
2.1.+-.0.9 mM. These findings suggest that the alanine mutations in
the ATP binding pocket, which is proximal to the adjacent
phospho-acceptor binding site, do not affect the protein target
specificity.
[0294] In support of this, the engineered kinase phosphorylates the
same broad set of proteins that are phosphorylated by wild-type XD4
when each is expressed in Sf9 insect cells. This is shown in the
FIG. 5(a), which shows an anti-phosphotyrosine protein blot of cell
lysates (10.sup.8 cell equivalents/land) from Sf9 insect cells
expressing 6-His-XD4, lane 2, or 6-His-XD4 (V323A, I338A) lane 3.
These blots were carried out following lysis of 10.sup.6 cells in a
buffer containing 0.1% Triton-X-100, 50 mM Tris, pH 8.0, using a
procedure similar to that of the blots of Example 2.
[0295] The Sf9 insect cell system is a good host for expressing
small amounts of protein tyrosine kinase because these cells
contain most of the same machinery necessary to carry out
post-translational modifications to proteins resulting in kinase
which are more similar in activity to those found in mammalian
cells. Furthermore, uninfected Sf9 cells lack endogenous protein
tyrosine kinase activity, as shown in Figure 5A, lane 1, and thus
the phosphotyrosine containing proteins in lanes 2 and 3 of FIG. 5A
are substrates of the expressed 6-His-XD4 or mutant 6-His-XD4
kinase. The small differences in phosphorylation level of
particular proteins in attributed to the lower catalytic activity
of the mutant XD4 (V323A, I338A) compared to the wild-type kinase.
Taken together, these data show that the peptide specificity of the
engineered kinase is virtually identical to that of wild-type
v-Src.
EXAMPLE 8
[0296] Confirmation that the Engineered Kinase Accepts the
Preferred Orthogonal Substrate, but the Wild-Type Kinase Does Not
Substantially Accept It: The ultimate goal of this work is to use
mutant kinase specific for synthetic substrate analogs to tag the
direct protein substrates in whole cells or cell lysates. For this
it is preferably that no wild-type kinase, including ser/thr
specific kinase (which carry out the bulk of cellular
phosphorylation, as only 0.03% of all phosphoamino acids are
tyrosine) (65), substantially accept the synthetic substrate. To
establish that [.gamma.-.sup.32P] N.sup.6-(cyclopentyl)ATP is
essentially a "dead substrate" for all wild-type cellular kinase,
in vitro kinase reactions with [.gamma.-.sup.32P] ATP or
[.gamma.-.sup.32P] N.sup.6-(cyclopentyl)ATP were performed with
murine lymphocyte lysates.
[0297] These assays were performed in a manner similar to the
procedure set forth in Example 2, with the exception of the use of
radiolabeled [.gamma.-.sup.32P] ATP or [.gamma.-.sup.32P]
N.sup.6-(cyclopentyl)ATP (5000 cpm/pmole) added to a final
concentration of 100 ,.mu.M with 5.times.10.sup.6 cell equivalents
and incubated at 37.degree. C. for 10 min., after which 4X Laemmli
gel loading buffer was added to the cell lysate to quench the
reaction. Proteins were separate by 12.5% SDS-PAGE. The gel was
soaked in 10% acetic acid, 10% isopropanol for 1 h. after which it
was dried in a gel dryer and exposed to Biomax MS film (Kodak #
111-1681) for 1 h.
[0298] The results are shown in FIG. 5(b), which is an
autoradiogram showing the level of phosphorylation in hypotonicaily
lysed murine lymphocytes with [.gamma.-.sup.32P] ATP, lane 1 or
[.gamma.-.sup.32P] N.sup.6-(cyclopentyl)ATP, lane 2. There are no
radiolabeled phosphoproteins in the cell lysate following addition
of [.gamma.-.sup.32P] N.sup.6-(cyclopentyl)ATP, confirming the true
orthogonal nature of N.sup.6-(cyclolpentyl)ATP with respect to all
wild type protein kinase. The same result was found when in vitro
kinase reactions with [.gamma.-.sup.32P] ATP or [.gamma.-.sup.32P]
N.sup.6-(cyclopentyl)ATP and NIH 3T3 cell lysates were used instead
of freshly isolated murine lymphocytes. In principle, the ability
to follow one protein kinase's activity in the presence of all
other cellular kinase would allow for the identification of the
direct kinase targets in a particular cell type by using membrane
permeabilization (66) and a cell permeable form of A*TP to
introduce [.gamma.-.sup.32P] A*TP into cells (67).
EXAMPLE 9
[0299] Construction and Analysis of Single Mutation v-Src Mutants:
In order to determine whether a single mutation might be sufficient
to allow N.sup.6 (cyclopentyl)ATP to be efficiently used as a
substrate, three additional v-Src derived mutants were prepared,
using methods comparable to those of Example 4. However, these had
only single mutations, at position 338. These were again expressed
as GST-XD fusion proteins. These mutants, GIST-XD(I338A),
GST-XD(I338G), were then tested as described in Example 8.
[0300] The results are shown in FIG. 7. The gel lanes shown on the
top left of FIG. 7 shown that the mutant with alanine at the 338
position was able to utilize the natural substrate, ATP, more
readily than the mutant with serine at that same position. The gel
lanes shown on the bottom left of FIG. 7 show that the mutant with
alanine in position 338 is also better able to use ATP as a
substrate than is the mutant with glycine at that position. The
panels on the right side of FIG. 7 tell an even more interesting
story. From the top right panel, it is clear that the mutant with
the serine at position 338 is not able to utilize N.sup.6
(cyclopentyl)ATP nearly as well as is the mutant with alanine at
that position. However, the bottom panel shows that the mutant with
glycine at position 338 is better able to use N.sup.6
(cyclopentyl)ATP as substrate than is the mutant with alanine at
that position.
[0301] These results are most promising. It appears that a single
mutation is enough to allow the use of this orthogonal substrate.
Notably, the mutant with glycine at position 338 appears to be the
best engineered v-Src mutant that produced to date. Moreover, it is
quite surprising that a glycine substitution would work here.
Generally, glycine substitution is usually not expected to work in
such situations, because it introduces too much flexibility into
the enzyme structure, and thus detrimentally affects the desired
outcome.
EXAMPLE 11
[0302] Identifying the Substrates of v-Src: A schematic
representation of an experimental approach to identifying v-Src
substrates is shown in FIG. 8. The engineered v-Src, such as
GST-XD(V323A, I338A), is added to cell extracts or permeablized
cells, along with a radiolabeled orthogonal substrate, such
as[.gamma.-.sup.32P] N.sup.6-(cyclopentyl)ATP. Typically, this
would be done in triplicate. After incubation, the cells would be
lysed (if not already lysed), and the resulting samples would be
separated by polyacrylamide gel electrophoresis. A western blot
taken from the gel and labeled with anti-phosphotyrosine would show
all phosphorylated proteins in the sample; and an autoradiogram of
the gel would reveal which of those were phosphorylated by
v-Src.
EXAMPLE 12
[0303] Synthesis of inhibitors: The pyiazolopyrimidine backbone for
the first six inhibitors is shown in FIG. 10A. Synthesis of
4-amino-1-tert-butyl-3-phenylpyrazolo [3,4-d] pyrimidine, having a
phenyl group in the "R" position, compound 1 (which is the same
structure as PP1, shown on FIG. 9, but without the para-methyl
group on the phenyl ring) was carried out according to the method
of Hanefeld et al. (76). Compounds 2-6, having cyclobutoyl,
cyclopentoyl, cyclohexoyl, benzoyl, and 2-furoyl substituents at
the "R" position (Figure 10B), respectively, were synthesized by
treatment of 1 with cyclobutoyl chloride, cyclopentoyl, cyclohexoyl
chloride, benzoyl chloride, or furoyl chloride, respectively in dry
pyridine for one hour at room temperature. The structures of each
of the substitutents are shown in Figure 10B. Purification by
silica gel chromatography afforded pure products in 16-84% yield.
Compounds 1-6 (FIG. 10B) were characterized by .sup.1H--NMR ad mass
spectral methods.
EXAMPLE 13
[0304] Screening of inhibitors which are orthogonal to wild-type
kinases: To identify compounds that would not inhibit any existing
cellular kinases, the panel of synthetic pyrazolo pyrimidine
analogs (1-6) (FIG. 10) were screened against two closely related
purified protein tyrosine kinases, v-Src and Fyn, in a peptide
phosphorylation assay using [.gamma.-.sup.32P] ATP as the
radiolabel tracer of kinase activity, as described in Shah et. al.
(79). The results showed that each of the compounds 2-6 had
IC.sub.50 values of over 400 .mu.M for inhibition of Src and
compounds 3 and 5 showed at over 400 .mu.M IC.sub.50 values for
inhibition of wild-type Fyn, indicating that these analogs (2 and
5) are orthogonal to (do not inhibit) these representative
wild-type kinases.
EXAMPLES 14-16
[0305] Deconvoluting protein kinase signaling pathways using
conventional genetic and biochemical approaches has been difficult
due to the overwhelming number of closely related kinases. If cell
permeable inhibitors of each individual kinase could be designed,
the role of each protein kinase could be systematically
assessed.
[0306] An approach of combining chemistry and genetics was
developed to obtain the first uniquely specific cell permeable
inhibitor of the oncogenic protein tyrosine kinase, v-Src. A
functionally silent active site mutation was made in v-Src in order
to distinguish it from all other cellular kinases. A tight binding
(IC.sub.50=430 nM) cell permeable inhibitor of this mutant kinase
was designed and synthesized which does not inhibit wild-type
kinases. In vitro and whole cell assays established the unique
specificity of the mutant v-Src/inhibitor pair. This inhibitor
reverses the transforming effects of cellular expression of the
engineered v-Src, but does not disrupt wild type v-Src mediated
cellular transformation. These cell lines differ only by a single
amino acid in a single protein kinase, establishing that dramatic
changes in cellular signaling can be directly attributed to
specific inhibition of the engineered kinase. The generality of
this method was tested by engineering another protein tyrosine
kinase. The generality of this method was tested by engineering
another protein tyrosine kinase, Fyn, to contain the corresponding
silent mutation. The same compound was found to be a potent
inhibitor (IC.sub.50=830 nM) of this mutant kinase as well,
confirming the generality of the strategy toward making allele
specific inhibitors of multiple protein tyrosine kinases.
[0307] Allele specific cell permeable inhibitors of individual Src
family kinases can be rapidly developed using a combined chemical
and genetic approach. Treatment of mutant v-Src transformed NIH 3T3
fibroblasts with a uniquely specific v-Src reverts the
morphological hallmarks of transformation. The inhibitor exhibits
no effect on cells transformed by the wild-type v-Src allele
strongly suggesting that the phenotype induced by inhibitor
treatment is a result of a single inhibitory event. The ability to
rapidly generate kinases specific inhibitors in a generalizable way
will be useful for deconvolution of kinase mediated cellular
pathways and for validating novel kinases as good targets for drug
discovery both in vitro and in vivo.
[0308] As stated earlier, a combined chemical and genetic strategy
has been devised which allows for the generation of "chemical
sensitive" mutant kinases which are uniquely inhibited by a
rationally designed small molecule inhibitor. The approach involves
engineering a unique pocket in the active site of the kinase of
interest with a functionally silent mutation. A specific inhibitor
of the engineered kinase is then synthesized by derivatizing a
known kinase inhibitor with a bulky group designed to fit the novel
active site pocket. The bulky group kills the potency of the
inhibitor for wild type kinases. Successful complementary design,
therefore, leads to favorable binding interactions that are only
possible in the engineered kinase/inhibitor complex. Transfection
of cells with the gene encoding the engineered kinase generates a
cell in which only one kinase can be blocked by the designed
inhibitor (see FIG. 13).
[0309] Importantly, since the mutant kinase serves the same
function as the wild-type kinase, an inhibitor of the mutant will
affect cell signaling in the same manner as a selective inhibitor
of the wild-type kinase in non-transfected cells. The ability to
observe the phenotype of cells after selective inhibition of any
protein kinase provides a rapid method for determining the unique
roles of individuals in signal transduction cascades.
[0310] The src family protein tyrosine kinases were targeted for
specific inhibitor design because of their ubiquitous importance in
mediating cell function. Despite intense investigation, the roles
of individual src family members have been difficult to assess
because of cellular co-localization and their high sequence
identities. Although some potent inhibitors of src family kinases
are known, no molecule which can effectively discriminate ((20 fold
selectively for one src family member) between these closely
related enzymes have been identified. Two functionally important
src kinases, v-Src and Fyn, were chosen as the primary targets of
the mutant kinase/inhibitor pair design. Src kinase has emerged as
a leading drug target because of its implication in the oncogenesis
of breast, lung, and colon cancers. Although v-Src is the prototype
for oncogenic protein tyrosine kinases, no small molecule
inhibitors which are highly selective for this kinase have been
discovered. Fyn is a src family protein tyrosine kinase which is
important in T cell receptor mediated lymphocyte activation. Src
and Fyn share a similar domain structure and have approximately 85%
amino acid identity in their catalytic domains. The close
structural relationship of the src family members provides the
ideal test of the ability to engineer enzyme/inhibitor specificity
between highly homologous kinases. If one can discriminate between
these closely related src members using a cell permeable inhibitor,
it is likely that specificity for members of other protein kinase
families can also be achieved using a similar approach.
MATERIALS AND METHODS
[0311] Chemical synthesis: All starting materials and synthetic
reagents were purchased from Aldrich unless otherwise noted. All
compounds were characterized by .sup.1H NMR and high resolution
mass spectrometry. 4-Amino-1-tert-butyl-3-phenylpyrazolo[3,4-d]
pyrimidine (2, FIG. 14) was synthesized according to Hanefeld, et
al.
[0312] General procedure for N-4 acylation of Compound 2 (3a-3g,
FIG. 14B). To a solution of 2 (100 mg) dissolved in 2 ml pyridine
was added 10 equivalents of the desired acyl chloride at 0(C. The
reaction mixture was allowed to warm to room temperature and
stirred for 12 hours. The reaction was quenched by the addition of
25 ml water. The resulting mixture was extracted with Et.sub.2O and
the combined Et.sub.2O extracts were washed with 1N HCl and 5%
NaHCO.sub.3. The Et.sub.2O layer was dried over MgSO.sub.4 and
evaporated. The residue was purified by flash chromatography on 25
g silica gel by elution with 1:1 Et.sub.2O/hexanes to yield pure
3a-3g.
[0313]
4-cyclobutylamido-tert-butyl-3-phenylpyrazolo[3,4-d]pyrimidine
(3a): yield 0.0116 g (16%), white powder; HRMS (EI) molecular ion
calcd. for C.sub.20H.sub.23N.sub.5O 349.19049, found 349.18762;
.sup.1HNMR (300 MHZ, CDCl.sub.3, ppm) d 1.86 (9H, s), 1.89-2.27
(6H, m), 3.58 (1H, m), 7.26-7.67 (5H, m), 8.69 (1H,s).
[0314]
4-cyclopentylamido-1-tert-butyl-3-phenylpyrazolo[3,4-d]pyrimidine
(3b): yield 0.0456 g (68%), white powder; HRMS (EI) molecular ion
calcd. for C.sub.21H.sub.25N.sub.5O 363.20615, found 363.20398;
.sup.1H NMR (270 MHZ, CDCl.sub.3, ppm) d 1.41-1.91 (8H, m), 1.87
(9H, s), 2.97 (1H, m), 7.51-7.67 (5H, m), 8.70 (1H,s).
[0315]
4-cyclohexylamido-1-tert-butyl-3-phenylpyrazolo[3,4-d]pyrimidine
(3c): yield 0.0575 g (84%), white powder; HRMS (EI) molecular ion
calcd. for C.sub.22H.sub.27N.sub.5O; .sup.1H NMR (270 MHZ,
CDCl.sub.3, ppm) d 1.21-1.93 (10H, m), 1.86 (9H, s), 2.43 (1H, m),
7.51-7.67 (5H, m), 8.70 (1H, s).
[0316]
4-2'-furylamido-1-tert-butyl-3-phenylpyrazolo[3,4-d]pyrimidine
(3d): yield 0.0342 g (60%), white powder; HRMS (EI) molecular ion
calcd. for C.sub.20H.sub.19N.sub.5O.sub.2 361.15407, found
361.15254; .sup.1H NMR (270 MHZ, CDCl.sub.3, ppm) d 1.87 (9H, s),
6.52 (1H, d), 7.23 (1H, d), 7.43-7.53 (5H, m), 7.95 (1H, s), 8.59
(1H, s).
[0317] 4-benzamido-1-tert-butyl-3-phenylpyrazolo[3,4-d]pyrimidine
(3e): yield 0.1309 g (56%), white powder; HRMS (EI) molecular ion
calcd. for C.sub.22H.sub.21N.sub.5O 371.17933, found 371.17324;
.sup.1H NMR (270 MHZ, CDCl.sub.3, ppm) d 1.41-1.91 (8H, m),
7.22-8.11 (10H, m), 8.48 (1H, s).
[0318]
4-(p-methyl)benzamido-1-tert-butyl-3-phenylpyrazolo[3,4-d]pyrimidin-
e (3f): yield 0.0751 g (33%), white powder; HRMS (EI) molecular ion
calcd. for C.sub.23H.sub.23N.sub.5O 385.19499, found 385.18751;
.sup.1H NMR (270 MHZ, CDCl.sub.3, ppm) d 1.88 (9H, s), 2.42 (3H,
s), 7.19 (2H, d), 7.41-8.11 (7H, m), 8.49 (1H, s).
[0319]
4-(p-tert-butyl)benzamido-1-tert-butyl-3-phenylpyrazolo[3,4-d]pyrim-
idine (3g): yield 0.1050 g (42%), white powder; HRMS (EI) molecular
ion calcd. for C.sub.26H.sub.29N.sub.5O 427.23747, found 427.23474;
.sup.1H NMR (270 MHZ, CDCl.sub.3, ppm) d 1.35 (9H, s), 1.88 (9H,
s), 7.38-7.99 (9H, m), 8.50 (1H, s).
[0320] General procedure for the reduction of N-4 acyl compounds to
N-4 methylene compounds (4b, 4d, 4e, FIG. 14). A round bottom flask
was charged with (30 mg LiAlH.sub.4. The flask was equipped with a
pressure equalizing dropping funnel and flushed with dry argon. The
LiAlH.sub.4 was suspended in 3 mL THF over an ice bath.
Approximately 100 mg of the corresponding N-4 acyl 2 analogue was
dissolved in 5 mL THF and added dropwise to the suspension of
LiAlH.sub.4. The reaction mixture was stirred for 30 min. on the
ice bath and subsequently heated to reflux for 30 min. The reaction
was quenched by the sequential, dropwise additions of 1 mL EtOAc, 1
mL water, and 1 mL 6N NaOH. After stirring for five minutes, the
reaction mixture was filtered through a celite pad, diluted with
water and extracted with Et.sub.2O. The Et.sub.2O extracts were
combined, dried over MgSO.sub.4, and evaporated. The residue was
purified by flash chromatography on 10 g silica gel by elution with
4:1 hexanes/EtOAc.
[0321]
4-cyclopentylmethylamino-1-tert-butyl-3-phenylpyrazolo[3,4-d]pyrimi-
dine (4b): yield 0/0649 g (75%), clear oil; HRMS (EI) molecular ion
calcd. for C.sub.21H.sub.27N.sub.5 349.22691, found 349.22420;
.sup.1H NMR (270 MHZ, CDCl.sub.3, ppm) d 1.16-2.14 (9H, m), 1.84
(9H, s), 3.54 (2H, d), 5.51 (1H, s), 7.46-7.67 (5H, m), 8.43 (1H,
s).
[0322]
4-2'-furylmethylamino-1-tert-butyl-3-phenylpyrazolo[3,4-d]pyrimidin-
e (4d): yield 0.0620 g (66%), beige powder; HRMS (EI) molecular ion
calcd. for C.sub.2OH.sub.21N.sub.5O 347.17483, found 371.17330;
.sup.1H NMR (270 MHZ, CDCl.sub.3, ppm) d 1.83 (9H, s), 4.75 (2H,
d), 5.64 (1H, s), 6.25 (2H, d), 7.34-7.63 (6H, m), 8.45 (1H,
s).
[0323]
4-benzylamino-1-tert-butyl-3-phenylpyrazolo[3,4-d]pyrimidine(4e):
yield 0.0520g (54%), white powder; HRMS (EI) molecular ion calcd.
for C.sub.22H.sub.23N.sub.5 357.19559, found 357.19303; .sup.1H NMR
(270 MHZ, CDCl.sub.3, ppm) d 1.82 (9H, s), 4.76 (2H, d), 5.63 (1H,
s), 7.28-7.63 (10H, m), 8.44 (1H, s).
[0324] Protein Expression and Purification: Site directed
mutagenesis and cloning of the genes for the
glutathione-S-transferase fusion proteins of WT v-Src SH1 domain.
I338G v-Src SH1, WT Fyn, T339G Fyn, and WT Abl into the pGEX-KT
plasmid was carried out as described previously. These kinases were
expressed in DH5a E. Coli and purified on immobilized glutathione
beads (Sigma). PKA was purchased (Pierce) and used without further
purification. PKCd was expressed as the 6-His construct using the
Bac-to-Bac(expression system (pFastBac B vector). PKCd was purified
using a QIAexpress(Ni-NTA agarose column.
[0325] In Vitro Kinase Inhibition Assay: IC.sub.50's for putative
kinase inhibitors were determined by measuring the counts per
minute (cpm) of .sup.32P transferred to an optimized peptide
substrate for src family kinases (IYGEFKKK (SEQ ID NO: 12)).
Various concentrations of inhibitor were incubated with 50 mM Tris
(pH 8.0), 10 mM MgCl.sub.2, 1.6 mM glutathione, 1mg/mL BSA, 133 mM
IYGEFKKK (SEQ ID NO: 12), 3.5% DMSO, 0.05 mM Kinase and 11 nM (2
mCi) [g-.sup.32P]ATP (6000 Ci/mmol, NEN) in a total volume of 30 mL
for 30 minutes. Reaction mixtures (25 ml) were spotted onto a
phosphocellulose disk, immersed in 10% HOAc, and washed with 0.5%
H.sub.3PO.sub.4. The transfer of .sup.32P was measured by standard
scintillation counting. IC.sub.50 was defined to be the
concentration of inhibitor at which the cpm was 50% of the control
disk. When the IC.sub.50 fell between two measured concentrations
it was calculated based on the assumption of an inversely
proportional relationship between inhibitor concentration and cpm
between the two data points. Because the solubility limit of the
inhibitor analogues in aqueous solutions is (300 .mu.M, IC.sub.50
values to (250 .mu.M are approximately as full titrations to the
upper limit of inhibition could not be tested. IC.sub.50's for
non-scr family kinases were measured equivalently with the
following exceptions. Kemptide (Pierce, 133 mg/mL) was used as the
substrate for PKA. An optimized Abl; (EAIYAAPFAKKK (SEQ ID NO: 13),
133 mg/ml) was used for Alb assays. PKCd assays were performed in
the presence of 17 ng/ml diacyl glycerol (Sigma) and 17 ng/ml
phosphatidyl serine (Sigma) with 170 ng/ml histone (Sigma) as the
kinase substrate.
[0326] Murine B Cell Assay: Splenic lymphocytes were isolated from
6-20 week old Balb/c or C57/B6 mice. The cells were washed out of
the spleen into RPMI media containing 1 mg/mL DNase in and the red
blood cells were lysed in 17 mM tris-ammonium chloride, pH 7.2,
Approximately 4.times.10.sup.6 cells were incubated at 37.degree.
C. for 30 minutes with 100 mM of 3 g or 2 in 1.1% DMSO. B cell
stimulation was initiated by the addition of 2 mg of goat
anti-mouse IgM (Jackson Immuno Research, cat# 115-005-075) and
subsequent incubation for 5 minutes at 37(C. The cells were
isolated by centrifugation (13,000 rpm, 2 min) and lysed (lysis
buffer: 1% Triton X-100, 50 mM tris pH 7.4, 2 mM EDTA, 150 mM NaCl,
100 mM PMSF, 2 mM sodium orthovanadate, 10 mg/mL leupeptin, 10
mg/mL apoprotin). The cellular debris was then pelleted at 13,000
rpm for 15 min. Cellular proteins were separated by 10%
polyacrylamide gel electrophoresis and transferred to a
nitrocellulose membrane by Western blotting. Phosphotyrosine
containing proteins were visualized by immunoblotting with
anti-phosphotyrosine antibody (Upstate Biotechnology, Inc.).
[0327] Retroviral Infection of NIH 3T3 Fibroblasts: Genes encoding
WT and I338G v-Src were transfected into a packaging cell line and
NIH 3T3 fibroblasts were retrovirally infected using the pBabe
retroviral vector and a puromycin (2.5 mg/mL) selectable marker as
described (Shah, K., Liu, Y., Shokat, K. M., in preparation). WT
and I338G v-Src transformed cells were cultured in DMEM/10% BCS
containing 2.5 mg/mL puromycin).
[0328] Inhibition of v-Src in NIH3T3 Fibroblasts: Non-transformed
NIH3T3 cells, WT v-Src transformed NIH3T3 cells, and I338G v-Src
transformed NIH3T3 cells were incubated at 37.degree. C. with 1.1%
DMSO or 100 mM 3g in 1.1% DMSO. After 12 hours, the cells were
washed with PBS and lysed (lysis buffer: 1% Triton X-100, 50 mM
tris pH 7.4, 2 mM EDTA, 150 mM NaCl, 100 mM phenylmethylsulphonyl
fluoride, 2 mM sodium orthovanadate, 10 mg/mL leupeptin, 10 mg/mL
apoprotin). The lysate was clarified by centrifugation at 13,000
rpm for 15 min. Lysate protein concentrations were normalized and
equal volumes of the lysate were resolved electrophoretically and
analyzed for phosphotyrosine content as described above.
[0329] Microscopy: Non-transformed, WT v-Src transformed, and 1338G
v-Src transformed NIH3T3 fibroblasts were grown in DMEM/10% BCS on
tissue culture treated slides. V-Src expressing cells were treated
with either 1.1% DMSO or 100 mM 3g in 1.1% DMSO. After 48 hours
cells were photographed at 400(magnification on an Nikon TMS light
microscope. Immediately following light microscopy, the cells were
fixed for 20 min in 3.7% formaldehyde/PBS and permeabilized for 60
sec in 0.2% Triton X-100(/PBS. Permeabilized cells were incubated
with 200 ng/mL phalloidin-FITC/PBS for 20 min. Slides were rinsed
with PBS and polymerized actin was visualized by fluorescence
microscopy at 600( magnification on a Zeiss fluorescence
microscope.
RESULTS
[0330] Enzyme engineering: A functionally conserved residue in the
ATP binding pocket of v-Src (Ile 338) was developed which could be
mutated to glycine without altering the phosphoacceptor specificity
or biological function of the kinase. The space creating mutation
causes only a modest drop in k.sub.cat, a modest increase in the
K.sub.m for ATP and no quantitative changes in the level of
fibroblast transformation (Shah K, unpublished results). The
biological substrates of the mutant v-Src are unchanged and I338G
v-Src carries out the same biological functions as wild type v-Src.
All crystal structures of ATP bound protein kinases have revealed a
close contact interaction between the residue corresponding to 338
(Src numbering) and ATP. Analysis of protein kinase sequence
alignments confirmed that residue 338 contains a bulky side chain
(usually Thr, Ile, Leu, Met, or Phe) in all known eukaryotic
protein kinases. Thus, a glycine mutation at the 338 position
should create a novel pocket that is not present in any wild type
kinase. Due to the expanded ATP binding site, the glycine mutant
kinases should accept bulky inhibitors that could not bind wild
type kinases. Using standard methods the glutathione-S-transferase
(GST) fusion protein of the WT and I338G v-Src catalytic domains
was cloned, expressed and purified as described previously. WT Fyn,
T339G Fyn (Src numbering), and WT Abl were also expressed and
purified as GST fusion proteins.
[0331] Inhibitor design and synthesis: To test the basic design
strategy the WT and I338G v-Src SH1 domains against a previously
synthesized panel of N-6 substituted adenosine molecules for
selective inhibition of I338G v-Src over WR v-Src. Because
adenosine is only a moderate inhibitor or src family protein
tyrosine kinases, to discover a potent inhibitor of the engineered
kinase was not expected. As expected, all of the N-6 adenosine
analogues inhibited I338G v-Src more potently than WT v-Src. The
most potent inhibitor found in this screen was N-6
cyclopentyloxyadenosine (1, FIG. 14A) with a 50% inhibitory
concentration (IC.sub.50) of 1 mM for I338G v-Src. Subsequent
experiments to test for selectivity demonstrated that N-6
cyclopentyloxyadenosine showed no detectable in vitro inhibition of
WT v-Src or Fyn at concentrations up to 400 mM. This first screen
encouraged us to pursue the strategy of developing novel inhibitors
of I338G v-Src since the design had allowed us to readily over come
selectivity barriers which are major problems in conventional
inhibitor discovery.
[0332] As inhibitors, adenosine analogues are not ideal because of
the many cellular functions performed by adenosine as well as the
large number of cellular proteins which bind adenosine. N-6
adenosine analogues have been shown to act as adenosine receptor
agonists and antagonists, and one can imagine N-6 adenosine
analogues acting as substrates for nucleoside kinases. For these
reasons a class of known protein tyrosine kinase inhibitors that
are not direct analogues of biologically known molecules were used.
The design strategy called for a core structure which exhibits
potent inhibition of multiple wild type kinases and is easily
synthesized. Also, the binding orientation of the molecule in the
enzyme active site must be known or readily predictable. In
addition, the molecule must bind in a manner in which the site
pointing toward Ile338 can be easily modified. As the core
inhibitor structure
4-amino-1-tert-butyl-3-phenylpyrazolo[3,4-d]pyrimidine (2, FIG.
14B) was used. This molecule is a derivative of
4-amino-1-tert-butyl-3-(p-methylph- enyl)pyrazolo[3,4-d]pyrimidine
(PP1) which was reported by Hanke and co-workers as a potent src
family kinase inhibitor. Based on the co-crystal structure of the
src family kinase, Hck, bound to the general kinase inhibitor,
quercetin (5, FIG. 15A), it was postulated that 2 binds to src
family kinases in a conformation similar to that of ATP. The
predicted binding orientation of 2 in Hck is shown in an overlay
with the known Hck co-crystal structures of AMP PNP (6) and
quercetin (FIG. 15B). In this conformation the easily derivatizable
N-4 position of 2 corresponds to the N-6 of ATP (close contact with
residue 338, FIG. 15C.) And the tert-butyl moiety roughly
corresponds to the ribose ring of ATP. It was hypothesized that in
this orientation, the C-3 phenyl ring of 2 could bind in a pocket
that surrounds the N-7 of ATP as seen in the Hck/quercetin
co-crystal structure. This analysis lead us to synthesize a small
panel of N-4 derivatized analogues of 2 (FIG. 14).
[0333] Identification of a uniquely selective inhibitor: The panel
of pyrazolo[3,4-d]pyrimidines was screened against WT and I338G
v-Src kinases. All of the analogues are better inhibitors of the
engineered v-Src as compared to wild type, confirming the
prediction of the binding orientation of 2 in the kinase active
site. Any derivatization of 2 at the N-4 position destroys the
inhibitory activity against WT v-Src (no detectable inhibition at
the limit of solubility, 300 mM). All 10 analogues demonstrated
measurable inhibition of I338G v-Src and several of the compounds
have IC.sub.50's in the low mM range. The
N-4-(p-tert-butyl)benzamido-1-tert-butyl-3-phenyl analogue (3g of
FIG. 15) is the most potent inhibitor of I338G v-Src in the panel
(IC.sub.50=430 nm). This molecule shows no inhibition of WT v-Src
at 300 mM suggesting that 3g is at least a 1000 fold better
inhibitor of the mutant v-Src as compared to wild type. The large
size of the derivatization needed to achieve sub-micromolar potency
for the I338G v-Src active site was rather unexpected. Only four
carbon atoms were removed from the ATP binding site and derivatized
the parent molecule with eleven carbon atoms. This discrepancy may
be due to an imperfection in the binding prediction. Also the Ile
to Gly mutation may confer greater flexibility to the enzyme active
site allowing the mutant kinase to accept a larger inhibitor
analogue than predicted. To confirm that 3 g does inhibit I338G
v-src at the ATP binding site it was investigated its kinetics of
inhibition at various ATP concentrations. Lineweaver-Burk analysis
confirmed that 3 g does inhibit I338G v-Src competitively with
respect to ATP with an inhibitory constant (K.sub.i) of
approximately 400 nM.
[0334] The panel of inhibitor analogues was next screened against
WT Fyn to investigate their potential to cross react with this
kinase. WT Fyn was chosen as the "worst case" control of wild type
kinases because the published parent molecule, PP1, and 2 (FIG. 14)
are highly potent (low nM) Fyn inhibitors. Many of the 10 synthetic
analogues did not display high selectivity for the target kinase.
The N-acyl analogues with saturated ring systems (3a-3c, FIG. 14)
effectively inhibit wild type Fyn. The N-methylene compounds (4b,
4d, 4e, FIG. 14) are sufficiently orthogonal to WT Fyn but show
only poor to moderate inhibition of the engineered v-Src.
Importantly, 3 g (FIG. 14), the most potent inhibitor of the mutant
v-Src inhibited WT Fyn very weakly (IC.sub.50=300 mM). Thus, 3 g
inhibits the engineered v-Src over 700 times more effectively than
WT Fyn, which is likely to be the wild type cellular kinase which
is most capable of binding the molecule. Other non-src family
kinases tested were fortuitously inhibited by 3 g in vitro. The
serine/threonine kinases, PKCd and PKA, were not detectably
inhibited at concentrations up to 300 mM. Likewise, 3 g exhibited
only weak inhibition (IC.sub.50>300 mM) of the Abl protein
tyrosine kinase. Therefore 3 g satisfied all of the initial design
requirements for potent selective inhibition of one engineered
kinase.
[0335] Selectivity in whole cells: To further demonstrate that 3 g
(FIG. 14) does not inhibit wild type protein tyrosine kinases it
was investigated the effects of 3 g treatment on the B cell
receptor (BCR) mediated phosphorylation cascade. Src family (Fyn,
Lyn, Lck, Blk) and non-src family protein tyrosine kinases (Btk,
Syk) are known to be activated upon BCR cross-linking. Due to the
amplifying nature of the BCR mediated cascade, inhibition of any of
these kinases would dramatically alter the distribution and
intensity of post-activation cellular phosphotyrosine. Because 3 g
was designed to be sterically incompatible with the active sites of
wild type kinases, it should not disrupt tyrosine phosphorylation
dependent signaling in wild type B cells. Treatment of 100 mM 3 g
with antigen receptor cross linked murine B cells has no effect on
the phosphotyrosine pattern of B cell stimulation. The signal
intensities of all the major bands are unchanged and only slight
depletion of some minor bands is detectable, confirming that 3 g
does not appreciably inhibit the panel of protein tyrosine kinases
that are activated by BCR cross linking. Treatment of B cells with
100 mM2, however, causes a significant reduction in tyrosine
phosphorylation (FIG. 4, lane 4) that is consistent with its potent
inhibition of wild types src family kinases.
[0336] Selective inhibition of I338G v-Src in NIH3T3 cells: In
order to use the selective inhibitor to study a Src mediated
pathway it was retrovirally introduced both WT and I338G v-Src into
NIH3T3 fibroblasts. These cells acquire a transformed phenotype
which is dependent on v-Src expression. It was shown that 3 g (FIG.
14) could selectively disturb the Src dependent signal transduction
pathway of I338G v-Src transformed cells while not affecting WT
transformed cells. Treatment of WT v-Src infected cells (100 mM 3g)
causes no loss of tyrosine phosphorylation compared to control DMSO
treated lanes (FIG. 16), demonstrating that the designed inhibitor
does not inhibit WT v-Src or any of the other protein tyrosine
kinases that are activated by v-Src mediated cellular
transformation. Equivalent treatment of I338G v-Src transformed
cells gives rise to a dramatic diminution in the tyrosine
phosphorylation of the putative v-Src substrate, p36, as well as a
moderate overall decrease in the cellular level of phosphotyrosine.
Previously, it has been shown that treatment of v-Src transformed
cells with general protein tyrosine kinase inhibitors causes a
reduction in the tyrosine phosphorylation of a 36 kD protein. It is
thought that p36 is associated with a specific phosphotyrosine
phosphatase, possibly explaining its rapid dephosphorylation in
inhibitor treated cells. The 3g IC.sub.50 for p36 phosphotyrosine
signal in I338G v-Src expressing cells ((50 mM) is roughly 100
times the in vitro value. This is presumably due to the fact that
the inhibitor must compete with millimolar concentrations of ATP
for the kinase active site in the cellular experiments.
[0337] Selective inhibition of I338G mutant v-Src reverses
transformed cell morphology: V-Src activity is required for Rous
sarcoma virus transformation of mammalian cells. Treatment of the
I338G v-Src expressing NIH 3T3 cells with 100 mM 3g (FIG. 14)
caused dramatic changes in cell morphology which are consistent
with the reversal of transformation (FIG. 17). The mutant cells
that were treated with inhibitor 3 g appeared flat and did not
exhibit growth characteristics of transformed cells (i.e. the
ability to grow on top of one another). Under identical conditions,
WT v-Src infected cells demonstrated the prototypical rounded
morphology and overlapping growth patterns of transformed
cells.
[0338] To further demonstrate the selective reversal of cell
morphology fluorescence microscopy was used to view 3 g treated
cells after staining the cellular polymerized actin with
phalloidin-FITC (FIG. 17). Non-transformed NIH3T3 cells show long
actin spindles that form across the cells. V-Src transformed cells
(both WT and I338G) appear rounded with no discernible pattern of
actin formation. In agreement with the light microscopy data,
inhibitor treated WT v-Src expressing cells appear
indistinguishable from untreated WT cells. However, 3 g treated
I388G v-Src expressing cells have defined polymerized actin
strings, strongly resembling the actin formations of
non-transformed NIH3T3 fibroblasts. These inhibitor treated cells
have an exaggerated flattened morphology and show peripheral actin
staining that is not present in the non-transformed NIH3T3 cells.
This data shows that 3 g can uniquely induce morphological changes
in cells which are engineered to contain a single amino acid change
in the kinase of interest. This is the first demonstration that a
small molecule inhibitor selective for a protein tyrosine kinase
oncogene product can revert the morphological changes associated
with cellular transformation. Previous examples of morphological
reversion of transformation by herbimycin A (and other benzoquinone
ansamycins) have recently been shown to operate via a mechanism
unrelated to kinase inhibition consisting of heat shock protein
(hsp90) mediated targeting of the oncogenic protein tyrosine kinase
to the proteasome.
[0339] Generalization to other kinases: The advantage of using
mutagenesis to provide a unique molecular difference between the
enzyme of interest and all others is that, due to the conserved
kinase fold, the approach should be extendible across the kinase
superfamily. Almost all known protein kinases contain a bulky side
chain at the position corresponding to residue 338 of v-Src.
Therefore a space creating mutation at this position should render
multiple kinases susceptible to selective inhibition. To test this
the inhibition of the analogues against T339G Fyn was measured.
There exists a striking similarity in the structure activity
relationships of the analogues for I338G v-Src and T339G Fyn. In
agreement with the data for I338G v-Src, 3 g was the most potent
inhibitor analogue against T339G Fyn, exhibiting an IC.sub.50 of
830 nM. This corresponds to greater than 300 fold selectivity for
T339G Fyn over WT Fyn. The implication of this data is that
multiple protein tyrosine kinases can be systematically engineered
to preferentially accept one inhibitor analogue without the need to
screen large libraries of putative inhibitors.
[0340] The above, describes a novel approach to selective protein
kinase inhibition through the complementary engineering of chemical
sensitive kinases and rationally designed inhibitors. It was
demonstrated that high selectivity for the target kinase can be
achieved in whole cells, and that active site inhibition of an
oncogenic protein tyrosine kinase can be sufficient for the
disruption of a transformed cell morphology. Because the approach
is easily generalized, it should have far reaching applications in
deconvoluting signal transduction pathways as well as validation of
kinases as targets for drug design. The pace of effective drug
discovery is limited by the identification and validation of
important drug targets. This is not a trivial problem in a milieu
of 2000 homologous proteins. The use of chemical sensitive mutants
of protein kinases expands the capability to probe the cellular and
physiological effects of pharmacological kinase inhibition. Since
transfected cell lines and even "knock-in" mice can now be
generated rapidly, the approach should greatly expedite the process
of testing the effects of selective inhibition of a given kinase in
a whole cell or animal model. As more inhibitor-bound protein
kinase crystal structures become available, this strategy will
allow for the systematic investigation of the effects of time and
dose dependent inhibition of any given kinase in the scope of an
entire signal transduction cascade.
EXAMPLE 17
Generation of Mutant Specific Nanomolar Protein Tyrosine Kinase
Inhibitors Via a Chemical Genetic Approach
[0341] Based on the experiments herein, directed structure-based
design of kinase/inhibitor pairs has yielded mutant specific,
cell-permeable inhibitors of engineered Src family kinases with
potencies that have not been attainable with conventional inhibitor
screening methods. By mutating the active site of v-Src it was not
only differentiated one protein kinase from all others but
simultaneously created a newly accessible binding site to use in
designing more potent inhibitors. Thus, one can increase both
potency and selectivity compared to traditional inhibitor design
strategies. The design is highly generalizable, owing to the
conservation of kinases at the site corresponding to Ile338 in
v-Src. In fact, recent work has shown that the sensitivity of
mitogen-activated protein kinases (MAPKs) to pyridinylimidazole
inhibitors is in large part controlled by the side chain of residue
106 which corresponds to 338 of Src. The primary advantage of the
approach to the design of selective kinase inhibitors for the study
of protein kinase function is the ability to genetically "program"
the kinase of interest for unique inhibition by a small molecule.
This allows for the unambiguous assignment of the activity of a
specific kinase to the induced phenotype. The combination of
genetic manipulation and small molecule control of enzyme activity
should have far reaching applications in the pharmacological
validation of protein kinases as viable drug targets in cells as
well as whole organisms.
MATERIALS AND METHODS
[0342] Protein Expression and Purification: Site directed
mutagenesis and cloning of the genes for the
glutathione-S-transferase fusion proteins of wild type v-Src
catalytic domain, I338G v-Src SH1, and WT Fyn into the pGEX-KT
plasmid was carried out as described previously. These kinases were
expressed in DH5a E. Coli and purified on immobilized glutathione
beads (Sigma).
[0343] In Vitro Kinase Inhibition Assay: IC.sub.50's for putative
kinase inhibitors were determined by measuring the counts per
minute (cpm) of .sup.32P transferred to an optimized peptide
substrate for src family kinases (IYGEFKKK, SEQ ID NO: 12). Various
concentrations of inhibitor were incubated with 50 mM Tris (pH
8.0), 10 mM MgCl.sub.2, 1.6 mM glutathione, 1 mg/mL BSA, 100 mM
IYGEFKKK (SEQ ID NO: 12), 3.3% DMSO, the appropriate kinase and 11
nM (2 mCi) [g-.sup.32P]ATP (6000 Ci/mmol, NEN) in a total volume of
30 mL for 30 minutes. Reaction mixtures (25 mL) were spotted onto a
phosphocellulose disk, immersed in 10% HOAc, and washed with 0.5%
H.sub.3PO.sub.4. The transfer of .sup.32P was measured by standard
scintillation counting. IC.sub.50 was defined to be the
concentration of inhibitor at which the cpm was 50% of the control
disk. When the IC.sub.50 fell between two measured concentrations
it was calculated based on the assumption of an inversely
proportional relationship between inhibitor concentration and cpm
between the two data points.
[0344] Chemical synthesis: All starting materials and synthetic
reagents were purchased from commercial suppliers unless otherwise
noted. Acid chlorides that were not readily commercially available
(3c, 3d, 3e, 3h, 3i) were synthesized by treating the corresponding
carboxylic acids with excess oxalyl chloride and catalytic DMF in
diethyl ether. All PP1 analogues were synthesized according to
Hanefeld, et al.
[0345]
4-amino-1-(tert-butyl)-3-(1-naphthyl)pyrazolo[3,4-d]pyrimidine (6a,
FIG. 18). White powder; .sup.1H NMR (270 MHZ CDCl.sub.3) d 1.92 (s,
9H), 5.04 (m, 2H), 7.43-7.73 (m, 4H), 7-92-8.02 (m, 3H), 8.34 (s,
1H); HRMS (EI) molecular ion calcd. for C.sub.19H.sub.19N.sub.5
317.16427, found 317.16247.
[0346]
4-amino-1-(tert-butyl)-3-(2'-naphthyl)pyrazolo[3,4-d]pyrimidine
(6b, FIG. 18). White powder; .sup.1H NMR (270 MHZ CDCl.sub.3) d
1.88 (s, 9H), 5.55 (m, 2H), 7.56-8.00 (m. 6H), 8.16 (s, 1H), 8.39
(s, 1H); HRMS (EI) molecular ion calcd. for C.sub.19H.sub.19N.sub.5
317.16427, found 317.16359.
[0347]
4-amino-1-(tert-butyl)-3-(m-phenoxyphenyl)pyrazolo[3,4-d]pyrimdine
(6c, FIG. 18). White powder; .sup.1H NMR (270 MHZ CDCl.sub.3) d
1.83 (s, 9H), 5.61 (m, 2H), 7.08-7.49 (m. 9H), 8.35 (s, 1H), HRMS
(EI) molecular ion calcd. for C.sub.21H.sub.21N.sub.5 359.17483,
found 359.17325.
[0348]
4-amino-1-(tert-butyl)-3-(m-benzyloxyphenyl)pyrazolo[3,4-d]pyrimdin-
e (6d, FIG. 18). White powder; .sup.1H NMR (270 MHZ CDCl.sub.3) d
1.85 (s, 9H), 5.17 (s, 2H), 5.55 (m, 2H), 5.74 (s, 2H), 7.10 (d,
J=8 Hz, 1H), 7.27-7.48 (m, 8H), 8.34 (s, 1H), HRMS (EI) molecular
ion calcd. for C.sub.22H.sub.23N.sub.5O 373.19049, found
373.18833.
[0349] 4-amino-1-(tert-butyl)-3-(m-(2',
6'-dichloro)benzyloxyphenyl)pyrazo- lo[3,4-d]pyrimdine (6e, FIG.
18). White powder; .sup.1H NMR (270 MHZ CDCl.sub.3) d 1.85 (s, 9H),
5.36 (m, 2H), 5.74 (s, 2H), 7.11-7.51 (m. 7H), 8.36 (s, 1H), HRMS
(EI) molecular ion calcd. for C.sub.22H.sub.21Cl.sub.2N.sub.5O
441.11263, found 441.11050.
[0350] 4-amino-1-(tert-butyl)-3-piperonylpyrazolo[3,4-d]pyrimdine
(6f, FIG. 18). White powder; 1H NMR (270 MHZ CDCl.sub.3) d 1.83 (s,
9H), 5.70 (m, 2H), 6.05 (s, 2H), 6.96 (d, J=8 Hz, 1H), 7.13-7.27
(m, 2H), 8.34 (s, 1H), HRMS (EI) molecular ion calcd. for
C.sub.16H.sub.17N.sub.5O.sub.2 311.13841, found 3111.13777.
[0351]
4-amino-1-(tert-butyl)-3-(p-tert-butylphenyl)pyrazolo[3,4-d]pyrimdi-
ne (6g, FIG. 18). White powder; 1H NMR (300 MHZ CDCl.sub.3) d 1.38
(s, 9H), 1.84 (m, 9H), 5.83 (s, 2H), 7.58 (dd, J=8 Hz, 12 Hz, 4H),
8.33 (s, 1H), HRMS (EI) molecular ion calcd. for
C.sub.19H.sub.25N.sub.5 323.21125, found 323.21024.
[0352]
4-amino-1-(tert-butyl)-3-(1'-naphthylmethyl)pyrazolo[3,4-d]pyrimidi-
ne (6h, FIG. 18). White powder .sup.1H NMR (270 MHZ CDCl.sub.3) d
1.85 (s, 9H), 4.76 (s, 2H), 5.04 (s, 2H), 7.19 (d, J=6 Hz, 1H) 7.39
(t, J=8 Hz, 1H) 7.55 (t, J=4 Hz, 2H), 7.79-7.92 (m, 2H), 8.20 (d,
J=8 Hz, 1H), 8.24 (s, 1H); HRMS (EI) molecular ion calcd. for
C.sub.20H.sub.21N.sub.5 331.17993, found 331.17951.
[0353]
4-amino-1-(tert-butyl)-3-(1'-naphthoxymethyl)pyrazolo[3,4-d]pyrimid-
ine (6i, FIG. 18). Beige powder .sup.1H NMR (270MHZ CDCl.sub.3) d
1.83 (s, 9H), 5.57 (m, 2H), 6.12 (s, 2H), 7.07 (d, J=6 Hz, 1H)
7.39-7.54 (m, 4H), 7.84 (d, J=8 Hz, 1H), 8.25 (d, J=8 Hz, 1H), 8.35
(s, 1H); HRMS (EI) molecular ion calcd. for
C.sub.20H.sub.21N.sub.5O found 347.17483 found 347.17408.
RESULTS
[0354] Inhibitor Design and Modeling: Initially the N.sup.4
exocyclic amine of the Src family kinase inhibitor
4-amino-1(tert-butyl)-3-phenylpy- razolo[3,4-d]pyrimidine (1, FIG.
19) was utilized as a chemical hook to which could be tethered to
bulky groups to destroy the molecule's affinity for wild type
kinases (1 is a des-methyl modified analogue of PP1, reported by
Hanke et al.). While this approach did yield a very selective
inhibitor (2, FIG. 19) of the engineered v-Src kinase (I338G
v-Src), it was not totally satisfactory because more than an order
to magnitude in binding energy from the starting affinity of the
parent molecule for wild type Src family kinases was lost (see FIG.
19).
[0355] To increase the potency of the inhibitors, the binding of 1
was modeled in the active site of the Src family kinase, Hck. Using
the molecular graphics program, GRASP, the protein was compared to
the surface map of the ATP binding pocket of Hck with the
corresponding predicted map of the expanded pocket in the
engineered protein kinase, T338G Hck. From this model, it was
deduced that derivatization of N.sup.4 was not the only means of
generating complementary van der Waal's interactions with the
unique binding pocket of I338G v-Src. It could be seen from the
surface map that derivatization of the C.sup.3 phenyl ring of 1
(ex: phenyl ring replaced with naphthyl ring system, compound 6a)
with a bulky group leads to steric clash between the derivatized
inhibitor and the molecular surface created by Thr338. Mutation of
residue 338 to glycine generates a unique binding pocket which is
predicted to be large enough to accept the naphthyl analogue of 1.
Derivatization of this phenyl group with hydrophobic substituents
affords compounds that complement the corresponding I338G v-Src
active site, without disrupting any potential hydrogen bonding
interactions at N.sup.4. In addition, this added bulk at the
C.sup.3 moiety causes these molecules to be sterically incompatible
with the active sites of wild type protein tyrosine kinases,
affording high specificity for the suitably engineered v-Src.
[0356] Inhibitor Synthesis and Screening: A small panel of C.sup.3
derivatized PP1 analogues (6a-6i) was synthesized as shown in FIG.
18. The group of modified inhibitors was screened against the
catalytic domain of the target kinase, I338G v-Src, which was
expressed in bacteria and purified as a glutathione-S-transferase
(GST) fusion protein. All of the C.sup.3 derivatized analogues are
more potent inhibitors of I338G v-Src than the most potent molecule
(2, IC.sub.50=430 nM) identified from the first generation panel of
N.sup.4 derivatized compounds (see Table 3). Four of the molecules
(6a, 6b, 6d, 6h) inhibit the target kinase at low nM concentrations
with the two naphthyl isomers (6a, 6b) exhibiting the greatest
potency (IC.sub.50=1.5 nM). Under the conditions of the assay the
parent molecule, PP1, inhibited its optimal target, Fyn, at only
IC.sub.50=30 nM). This date shows that an inhibitor design strategy
combining enzyme engineering with directed small molecule synthesis
can not only match the potency of molecules identified through
screening of large libraries, but can lead to a significant
increase (20 fold in the case of 6a, 6b) in affinity over
previously optimized inhibitors of wild type kinases. Compounds
having the formula of 6a and 6b are the most potent inhibitors of
any Src family protein tyrosine kinase that have been reported to
date.
7TABLE 3 50% inhibitory concentrations (IC.sub.50's) of C.sup.3
derivatized PP1 analogues for engineered and wild type Src family
protein tyrosine kinases. 1338G Compound v-Src (.mu.M) vSrc(.mu.M)
Fyn(.mu.M) 6a 0.0015 1.0 0.60 6b 0.0015 1.0 0.13 6c 0.14 40 0.80 6d
0.0070 26 6.0 6e 0.13 300 84 6f 0.025 3.1 0.040 6g 0.099 65 9.2 6h
0.0042 28 1.1 6i 0.045 >300 >300 6j 0.020 >300 >300
[0357] Importantly, all nine molecules show striking selectivity
for I338G v-Src with respect to the wild type enzyme. The in vitro
selectivities range from (120 for the piperonyl compound (6f) to as
high as >6500 for the naphthoxy methyl derivative (6i). This
range is similar to the selectivities generated by derivatization
of N.sup.4, further validating both the prediction of binding
orientation for the parent inhibitor as well as the modeling of the
expanded binding site of I338G v-Src. These selectivities compare
favorably to those from other strategies which combine protein
engineering with small molecule recognition, as well as strategies
that utilize selection techniques to identify tight binding
proteins from large pools of mutants.
[0358] To further confirm the selectivity for the target kinase,
the panel was screened against wild type Fyn (Table 3). This is
presumably a more stringent control inhibition of wild type v-Src
because Fyn is more potently inhibited by PP1. Three of the four
most potent inhibitors (6a, 6d, 6h, FIG. 18) showed sufficient
selectivity for the target kinase ((100 fold) with respect to wild
type Fyn. The most potent inhibitor of I338G v-Src, 6a, binds wild
type Fyn at 600nM representing 400 fold selectivity for the
designed target.
[0359] Cellular Inhibition of the Target Kinase: Two cell culture
systems were employed to investigate the utility of compound 6a as
a specific kinase inhibitor in the context of a whole cell. First
NIH3T3 fibroblast cell lines that express either wild type or I338G
v-Src were generated by retroviral infection. Because v-Src is a
highly activated, oncogenic protein tyrosine kinase the majority of
the tyrosine phosphorylation in these cells is a result of v-Src
expression. To investigate the selective inhibition of the
engineered v-Src, both wild type and I338G v-Src expressing cells
were incubated with varying concentrations of 6a.
Anti-phosphotyrosine blots of lysates derived from these cells
demonstrate that 6a strongly diminishes tyrosine phosphorylation in
a concentration dependent manner within minutes (FIG. 20, lanes
3-8). In agreement with the in vitro potencies, the ablation of
phosphotyrosine signal from 6a is much more rapid and complete than
that caused by the most potent N.sup.4 derivatized analogue in the
same cell line. Wild type v-Src expressing, cells in the presence
of 500 nM 6a show no loss of phosphotyrosine signal (lanes 1 and 2)
and can be grown in the presence of the compound for days with no
loss of tyrosine phosphorylation or apparent cytotoxicity.
[0360] To further confirm the selectivity of 6a, Jurkat cells (a
human derived T cell line with no engineered kinases) were treated
with the general protein tyrosine phosphatase inhibitor,
pervanadate, which covalently binds to a catalytically essential
cysteine in the active site of phosphotyrosine phosphatases. The
presence of pervanadate effectively shifts the cellular equilibrium
of phosphotyrosine giving rise to a large increase in tyrosine
phosphorylation (see FIG. 20, compare lane 10 to lane 9). When
these cells are treated with 500 nM 6a (lane 11) there is no
detectable decrease in phosphorylation, indicating that none of the
wild type protein tyrosine kinases in Jurkat cells are appreciably
inhibited by the designed inhibitor. PP1 was used as a positive
control for inhibition of wild type kinases at 10 .mu.M (lane 12)
the concentration at which it has previously been shown to strongly
suppress T cell receptor mediated tyrosine phosphorylation.
[0361] Selective Disruption of Cellular Transformation: The rapid
generation of highly selective kinase inhibitors should have far
reaching applications in the pharmacological validation of protein
kinases as viable drug targets. To test this idea it was
investigated whether or not compound 6a (FIG. 18) could selectively
disrupt oncogenic transformation in cells that expressed the target
kinase. Normal NIH3T3 fibroblasts have long fibers of polymerized
actin across the cells that can be visualized by staining the cells
with phalloidin conjugated to rhodamine (FIG. 21A.). Cells that
express an oncogenic protein (either wild type or I338G v-Src) are
rounded and therefore have a diffuse pattern of actin (FIG. 21B.).
Wild type v-Src expressing cells that are treated with 6a appear
indistinguishable from untreated wild type cells, suggesting that
6a has no effect on this non-mutant cell line. However, cells
expressing the target kinase have clear actin fibers and appear
indistinguishable from normal NIH3T3 fibroblasts when incubated
with 250 nM 6a for 16 hours. From this data it is clear that small
molecule inhibition of v-Src's catalytic activity is sufficient to
block its role in oncogenesis.
Example 18
Development of General Chemical Switch for Targeting Any Protein
Kinase of Choice for Specific Inhibition.
[0362] In the examples above Src family protein tyrosine kinases
were engineered to contain a unique binding pocket which is not
present in any wild-type protein kinase. These mutants are uniquely
sensitive to derivative of the Src family selective inhibitor PP1
(10, FIG. 28) (85-87) which have been modified to complement the
enlargement of the mutant's active site. All protein kinases
identified to date possess the conserved active site feature
exploited by this approach (88). However, since the PP1 scaffold is
selective for Src family kinases, it would presumably not provide a
widely generalizable strategy for inhibiting kinases across the
superfamily (not be the ideal parent compound for broad
applications across divergent kinase families) (85). Therefore it
is desirable to develop a general chemical switch, based on a more
promiscuous kinase inhibitor, which could be used to rapidly target
any protein kinase of choice for specific inhibition.
[0363] Indolocarbazole Natural Product(+)K252a and Mutant Kinases:
To re-engineer the kinase/inhibitor interface, indolocarbazole
natural product (+)-K252a (1, FIG. 22A) was selected. The product
satisfies three important design criteria: 1) 1 inhibits many
different families of protein kinases; 2) the binding orientation
of 1 is readily predictable; 3) rationally derivatized analogs of 1
are synthetically accessible. K252a is a very general protein
kinase inhibitor which was predicted to bind kinase active sites in
an orientation identical to that of the closely related compound,
staurosporine (2, FIG. 22A). K252a has been reported to be a potent
(IC.sub.50.ltoreq.30 nM) inhibitor of protein kinase C, protein
kinase A, cGMP dependent protein kinase, myosin light chain kinase,
and Trk family tyrosin kinases (89, 90). This example shows that
the same molecule can efficiently inhibit Src family kinases,
cyclin dependent kinases, and calmodulin dependent kinases (FIG.
27). The structures of 2 (FIG. 22A) bound to protein kinase A (91),
cyclin dependent kinase 2 (CDK2) (92), and Lck (93) have recently
been solved, allowing for structure based design to engineer unique
sensitivity to the indolocarbazole class of kinase inhibitors (FIG.
22B).
[0364] As shown in the examples above, mutation of I338 to glycine
was sufficient to confer unique inhibitor sensitivity to a PP1
derivative. The corresponding residue in CDK2 is F80, which is
close (3.7 .ANG.) to C(7) (K252a numbering ) of 2 (FIG. 22A) in the
crystal structure of CDK2 bound to staurosporine (FIG. 22B) (92).
Thus, it was anticipated that developing unique
indolocarbazole-based inhibitors of our sensitized kinases would
require selective manipulation of C(7) in either 1 or 2 (FIG. 22A).
To explore this hypothesis, total synthesis and the recently
developed approach that allows for the modular assembly of 1 (FIG.
22A), as well as derivatives of 1 which are stereospecifically
modified at C(7) (94, 95)
[0365] A small panel of C(7) substitute K252a derviatives were
synthesized. Given that F80 of CDK2 is not coplanar with the
indolocarbazole ring (FIG. 22B), it was anticipated that syntheses
utilizing S--(L)-amino acids would yield K252a derivatives that
would best complement the space creating mutation of F80 to glycine
or alanine. In addition to the S--C(7) analogs, R--C(7)-benzyl
(+)-K252a (6, FIG. 27) was prepared which, based on the binding
mode prediction, was presumed to inhibit engineered protein kinases
less potently than the corresponding S diastereomer (FIG. 27).
[0366] The K252a analogs described immediately above were screened
for inhibition against a panel of protein kinases comprised of both
tyrosine and serine/threonine kinases. The in vitro inhibition of
at least one protein kinase from four distinct and physiologically
important subfamilies (FIG. 26A; Src family (v-src, Fyn) (96, 97),
Abl family (c-Able)(98), Ca.sup.2+/Calmodulin dependent family
(CAMK II.alpha.) (99), and cyclin dependent family (CDK2) (100).
The amino acid corresponding to 338 of v-Src was mutated to a small
residue (glycine or alanine) for all of the above protein kinases
(FIG. 24B, for c-Abl the T315G mutant was unstable (101)) to
generate the following inhibitor sensitive kinases; I338G v-Src,
T339G Fyn, T315A Abl, F89G CAMK II.alpha. and F80G CDK2. Kinases
which are sensitive to K252a and one which is not (c-Abl) were
selected to represent both classes of target kinases (FIG. 27).
[0367] The K252a analogs were screened against the wild-type and
engineered protein kinases for in vitro inhibition of
phosphorylation of an exogenous substrate. As predicted all of the
C(7) substituted K252a derivatives were much less efficient than 1
(FIG. 22A) at inhibiting the panel of wild-type protein kinases
(FIG. 27). Of the five wild-type kinases, CAMK II.alpha. is the
most susceptible to inhibition by the K252a derivatives which is
not surprising because it is also the most sensitive to K252a
itself. For each of the kinases, the IC.sub.50 values of the K252a
analogs decreased in the presence of the mutation, confirming our
prediction of the binding orientation of 1. A derivatized partner
for each of the mutant kinases was found such that the binding
either approached or exceeded the affinity of the wild-type
kinase/1 pair. Strikingly, the 2-methyl-propyl analog (4, FIG. 27)
bound to the engineered Src family kinases (v-src and c-Fyn) with
sub-nanomolar IC.sub.50 values (230 pM and 550 pM, respectively),
roughly two orders of magnitude lower than the values for 1 against
the same wild-type kinases. These values represent the most potent
inhibition of any Src family kinase reported to date. Potent
(IC.sub.50<50 nM) and selective (.gtoreq.15 fold compared to all
wild-type kinases in the panel) matches were found for all of the
mutant kinases except for c-Abl. Abl is the only wild-type protein
kinase in the panel which is not effectively inhibited by K252a,
suggesting that sensitivity to 1 is a predictive determinant for
whether or not other kinases (not in FIG. 26) would be well suited
for inhibition by K252a analogs.
[0368] Initially, it was unclear whether the weak inhibition of
T315A c-Abl was due to the .beta.-methyl group of the alanine side
chain or due to the intrinsic insensitivity of c-Abl to inhibition
by 1 (FIG. 22A). To probe the effect of the .beta.-methyl group
more directly we checked another kinase with an Ala substitution.
We measured the inhibition of the two most potent I338G v-Src
inhibitors, 4 and 7 (FIG. 27), against I338A v-Src. The alanine
mutant of v-Src has IC50 values of 0.024 and 0.43 .mu.M,
respectively, for these compounds, roughly 100 times greater than
the values for I338G. However, the inhibition values differ between
I338G v-Src and T315A c-Abl by more than 10,000 fold, implying that
c-Abl is intrinsically less inhibitable by analogs of 1.
[0369] Generalized Inhibitor Capable of Inhibiting any Suitably
Mutated Kinase: In an effort to develop a more generalizable
inhibitor which could inhibit any suitably mutated kinase, a panel
of wild-type and mutant kinases were tested against a group of
C(3)-phenyl modified PP1 analogs. Although PP1 is Src family
selective, it was reasoned that the mutation of the 338 position
(v-Src) to a small amino acid may confer unique PP1 analog
sensitivity to other kinases, since this amino acid was shown to be
largely responsible for the selectivity of PP1 itself. From this
panel of inhibitors either C(3)- 1'-naphthyl PP1 (9, FIG. 28) or
C(3)-1'-naphthylmethyl PP1 (11, FIG. 28) was the most potent
inhibitor of every engineered kinase tested. Analysis of the PP 1
analog inhibition data in FIG. 28 reveals some striking trends.
PP1yielded analogs with wider utility in the context of the
engineered kinase/inhibitor pairs. Each of the five target kinases
were inhibited by PP1 analogs at low nanomolar concentrations with
target specificities ranging from 85 to 400 fold (measured against
the most inhibitable wild-type kinase). There is little or no
correlation between the wild-type PP1 IC.sub.50 and the PP1 analog
sensitivity of the same (engineered) kinase. This is most apparent
in the Ser/Thr kinases CDK2 and CMK II.alpha.. These wild-type
enzymes both possess weak PP1 IC.sub.50's of greater than 15 .mu.M.
However the engineered versions of these kinases are very potently
inhibited by the PP1 analog (11; 5.0 nM and 8.0 nM, respectively).
This dichotomy is most likely due to a combination of the
importance of residue 338 in determining the PP1 sensitivity of a
given protein kinase (86) and the affinity of the naphthyl ring for
the expanded kinase active site. The IC.sub.50's for 11 for all of
the glycine mutants were within a 3 fold range (all <10 nM) of
one another even though their wild-type PP1 sensitivities vary by
more than 400 fold. Importantly, none of the wild-type kinases
tested are inhibited at concentrations less than 1 .mu.M 11,
demonstrating the high target selectivity of this compound.
[0370] The PP1 analogs, 10 and 11 (FIG. 28), are selective for
different space-creating mutations based on their size and
flexibility. The more rigid C(3)-1'naphthyl PP1 (10) shows a
broader range of potency between different kinase glycine mutants
(FIG. 28). However, it potently inhibits T315A c-Abl (7.0 nM) with
high specificity, yielding the first mutant inhibitor of this
protein tyrosine kinase (102). To determine if 10 could be
generally used to inhibit protein kinases which are mutated to
alanine at the 338 position we tested its potency against I338A
v-src. 10 inhibits the alanine mutant v-Src (IC.sub.50=1.0 nM) even
more strongly than it inhibits the corresponding glycine mutant,
suggesting that this molecule will provide a general scheme for the
development of mutant inhibitors for protein kinases whose activity
or stability is significantly compromised by the glycine mutation
(101).
EXAMPLE 19
PP1 Analog Sensitive Kinase Alleles
[0371] Subsequently, the above strategy was investigated to
determine whether it could be used to generate "PP1 analog
sensitive" (as) kinase alleles with in vivo utility. We have chosen
this nomenclature because the same mutant kinases can be used to
identify the direct cellular substrates of each kinase by use of
orthogonal ATP analogs designed to complement the "as" mutation
(154, 155).
[0372] It has been shown that C(3) derivatized PP1 analogs can be
used for target specific inhibition of retrovirally expressed v-src
in murine fibroblasts. It is, however, more interesting to
demonstrate mutant inhibition of endogenous kinase gene products in
an organism that has broad utility in traditional genetic screens.
The budding yeast, Saccharomyces cerevisiae, is widely used as a
unicellular model organism in genetic studies due to its
susceptibility to genetic manipulation and rapid growth (103). The
S. Cerevisiae genome encodes roughly 120 protein kinases including
homologues of proteins from many mammalian kinase families (104).
The yeast cyclin-dependent kinase, Cdc28, was chosen as the initial
target for in vivo inhibition. This enzyme is the major CDK in
budding yeast and is essential for cell viability at START and
mitosis in the S. Cerevisiae cell cycle (105). Cdc28 is 62%
identical to human CDK2, suggesting that the engineered F88G Cdc28,
Cdc28-as1, should be susceptible to inhibition by C(3) derivatized
PP1 analogs. Wild-type Cdc28 and Cdc28-as1 were expressed and the
sensitivity of the two kinases to PP 1 derivatives in vitro were
investigated. As with CDK2, 11 (FIG. 28)is a very potent inhibitor
of the engineered Cdc28 ( IC.sub.50=3.9 nM), but it does not
inhibit the wild-type protein (IC.sub.50=>50 .mu.M). It was also
found that the growth of yeast which express Cdc28-as1 was
completely ablated at concentrations of 11 that had no effect on
the growth of wild-type strains. Due to the fact that these cell
lines differ by only one amino acid side chain in one protein, this
selective cell cycle disruption is unambigously target specific.
Moreover, the ability of 11 to easily cross the yeast cell wall is
unusual and avoids the need to add extremely high concentrations of
the inhibitor during assays.
[0373] To determine whether this strategy could be extended to
identify analog sensitive alleles of other families of protein
kinases without individually purifying and assaying every enzyme in
vitro, the Saccharomyces cerevisiae MAP kinase, Fus3, which is
required for induction of pheromone inducible genes, cell cycle
arrest and cell fusion during mating was selected (106). In the
presence of mating factor pheromones, Fus3 phosphorylates Far1 and
Ste12. These phosphorylation events are required for G1 cell cycle
arrest and transcription of genes required for mating (107, 108).
No temperature sensitive (ts) alleles of Fus3 have been isolated,
possibly due to the temperature sensitivity of the mating process
(109).
[0374] To generate an analog sensitive allele of fus3, glutamine 93
(corresponding to I338 in v-Src) was mutated to glycine (D93G Fus
3, Fus-as1) and this enzyme was expressed in budding yeast that
lacks wild-type Fus3. Thefus3-as1 mutant fully complemented the
gene deletion as shown by the mating of equal numbers of haploid
wild-type or fus3-as1 cells (URA3 his3) to a
fus1.DELTA.fus2.DELTA.ura3 HIS3 strain followed by selection for
diploid progeny on media lacking uracil and histidine (FIG. 23).
Fus3 and Fus3-as1 expressing strains both yielded approximately
7.5.times.10.sup.4 colony forming units (cfu)/ml while mating of a
fus3.DELTA.strain gave only 0-100 cfu/ml under the same selection
conditions. When the mating of a fus3-as1 strain was carried out in
the presence of 50 .mu.M 10 (FIG. 28), the amount of diploids
formed was indistinguishable from a fus3 .DELTA.strain (FIG.
23B-23C). Even at 500 nM 10, the fus3-as1 strain gave only
1.7.times.10.sup.3 cfu/ml, a 44 fold decrease from equivalent
control cells (FIG. 23C). Due to the competition with millimolar
quantities of ATP in the yeast cell, this strong inhibition at 500
nM 10 implies an in vitro IC.sub.50 for Fus3-as1 in the low
nanomolar range. 11 (FIG. 28) also disrupted Fus3-as1 mediated
mating, but with less potency (85 fold decrease at 50 .mu.M). By
contrast, no decrease in mating efficiency was observed when
wild-type Fus3 expressing cells were treated with 10 or 11
(0.6-1.1.times.10.sup.5) cfu/ml at all concentrations up to 50
.mu.M, FIG. 23C). Therefore fus3-as1 represents the first
conditional allele of the MAPK, fus3. Through the in vivo addition
of 10, the activity of the fus3 gene product can be controlled
selectively, rapidly, and in a dose dependent fashion.
[0375] The analog sensitive alleles described here hold a number of
advantages over traditional ts alleles. They are subject to
stoichiometric and temporal control. Addition of a uniquely
specific inhibitor should not disrupt the stability of the enzyme
target or its protein-protein interactions. Inhibitor sensitized
strains can be generated for genes that function in cellular
processes which are inherently temperature sensitive (actin
cytoskeleton rearrangement, mating, etc.) (109, 110). In addition
protein kinase activity can be controlled specifically without
causing the non-specific transcriptional effects that are induced
by heat shock (111).
EXAMPLE 20
Cdc28 Mutant Kinase Sensitive Cell-Permeable Inhibitors
METHODS
[0376] Purification of Cdc28-His.sub.6, Cdc28-as1-His.sub.6,
MBP-Clb2: Lysate was prepared from insect cells co-infected with
baculoviruses encoding Cdc28-His.sub.6 or Cdc28-as1-His.sub.6 and
Cak1-HA.sub.3 (151). Cdc28-His.sub.6 and Cdc28-as1-His.sub.6 were
purified by metal affinity chromatography as described (152),
followed by anion-exchange (Pharmacia SP Sepharose Fast Flow) and
cation-exchange (Pharmacia Q Sepharose Fast Flow). MBP-Clb2 was
purified from lysates of bacteria expressing MBP-Clb2 (a gift of R.
Deshaies) on an amylose column (NEBL), followed by anion-exchange
chromatography (Pharmacia Q Sepharose Fast Flow).
[0377] Purified Cdc28-His.sub.6 (1 nM final concentration) and
MBP-Clb2 (3 nM final concentration) were incubated for 10 min at
23.degree. C. in a 25 .mu.l reaction mixture containing 5.mu.g
Histone H1 , 1.mu.Ci of .gamma.-.sup.32P-ATP (1.mu.Ci/10 .mu.M and
1.mu.Ci/1 mM), and several concentrations of 1-NM-PP1 in kinase
buffer (41). Reaction products were analyzed by 15% SDS-PAGE
followed by autoradiography. Phosphate incorporation was determined
at each inhibitor concentration by scintillation counting.
Inhibitor concentration vs. phosphate incorporation was plotted and
the 1-NM-PP1 concentration at which phosphate incorporation was 50%
that of the no inhibitor control was reported as the IC.sub.50.
[0378] Yeast Plasmid and Strain Construction: Media and genetic and
microbial techniques were essentially as described (148, 153). All
strains were derivatives of W30-3 (ura3-a, leu2-3, 112, trpl-1,
his3-11,15, ade2-1, can1-100, GAL+). All strains were grown at
23.degree. C. unless otherwise noted. To create cdc28-as1, the
CDC28 coding sequence and 400 bp of 5'-and 386 bp of 3'-flanking
DNA was PCR-amplified from genomic DNA and ligated into pRS306 to
make pJAU1. The F88G mutation was engineered by
oligonucleotide-directed mutagenesis of pJAU1. The plasmid was
integrated into the wild-type CDC28 locus following AflII digestion
by a pop-in-pop-out strategy as described (148, 153).
[0379] Cdc28 and Cdc28-as1 ATP kinetics: Purified Cdc28-His.sub.6
(1 nM final concentration) and MBP-Clb2 (3 nM final concentration)
were incubated for 10 min at 23.degree. C. in a 25 .mu.l reaction
mixture containing 5 .mu.g Histone H1 and several concentrations of
.gamma.-.sup.32P-ATP in kinase buffer (25 mM Hepes-NaOH pH 7.4, 10
mM NaCl, 10 mM MgCl.sub.2, and 1 mM dithiothreitol (DTT)). Reaction
products were analyzed by 15% SDS-PAGE followed by autoradiography.
Phosphate incorporation was determined at each ATP concentration by
scintillation counting. Eadie-Hofstee plots were then used to
calculate K.sub.m and k.sub.cat.
[0380] 1-NM-PP1 IC.sub.50 Values: Purified Cdc28-His.sub.6 (1 nM
final concentration) and MBP-Clb2 (3 nM final concentration) were
incubated for 10 min at 23.degree. C. in a 25 .mu.l reaction
mixture containing 5,.mu.g Histone H1 , 1.mu.Ci of
.gamma.-.sup.32P-ATP (1.mu.Ci/10 .mu.M and 1.mu.Ci/1 mM), and
several concentrations of 1-NM-PP1 in kinase buffer.
[0381] Purified Cdc28-His.sub.6 (1 nM final concentration) and
MBP-Clb2 (3 nM final concentration) were incubated for 10 min at
23.degree. C. in a 25 .mu.l reaction mixture containing 5 .mu.g
Histone H1 and several concentrations of .gamma.-.sup.32P-ATP in
kinase buffer (25 mM Hepes-NaOH pH 7.4, 10 mM NaCl, 10 mM
MgCl.sub.2, and 1 mM dithiothreitol (DTT)). Reaction products were
analyzed by 15% SDS-PAGE followed by autoradiography. Phosphate
incorporation was determined at each ATP concentration by
scintillation counting. Eadie- Hofstee plots were then used to
calculate K.sub.m and k.sub.cat.
[0382] Reaction products were analyzed by 15% SDS-PAGE followed by
autoradiography. Phosphate incorporation was determined at each
inhibitor concentration by scintillation counting. Inhibitor
concentration vs. phosphate incorporation was plotted and the
1-NM-PP1 concentration at which phosphate incorporation was 50%
that of the no inhibitor control was reported as the IC.sub.50.
[0383] DNA flow cytometry: Approximately 1.times.10.sup.7 cells for
each sample were fixed in 70% ethanol, resuspended in 50 mM
Tris-HCl pH 8.0, briefly sonicated, digested with 2mg/ml RNase for
2 hours at 37.degree. C., and resuspended in 0.2 ml protease
solution (5 mg/ml pepsin. 0.5% concentrated HCl ) and digested for
45 minutes at 37.degree. C. DNA was stained with 1.mu.M Sytox Green
(Molecular Probes) in 50 mM Tris-HCl pH 7.5 and 20,000 cells from
each sample were scanned with a FACScan FACS machine
(Becton-Dickinson).
RESULTS
[0384] Cdc28-His.sub.6 and Cdc28-as-1-His.sub.6 were expressed and
purified from Sf9 insect cells. They formed active complexes with
purified MBP-Clb2 from bacteria. Lysate was prepared from insect
cells co-infected with baculoviruses encoding Cdc28-His.sub.6 or
Cdc28-as1 -His.sub.6 and Cak1-HA.sub.3 (48). Cdc28-His.sub.6 and
Cdc28-as1 -His.sub.6 were purified by metal affinity chromatography
as described (49, followed by anion-exchange (Phamacia SP Sepharose
Fast Flow) and cation-exchange (Pharmacia Q Sepharose Fast Flow).
MBP-Clb2 was purified from lysates of bacteria expressing MBP-Clb2
(a gift of R. Deshaies) on an amylose column (NEBL), followed by
anion-exchange chromatography (Pharmacia Q Sepharose Fast
Flow).
[0385] Relative to wild-type Cdc28, Cdc28-as1 displayed a moderate
reduction in activity, including a 10-fold reduction in binding
affinity for ATP and a 6-fold reduction in maximum ATP turnover
rate (Table 4). More importantly, Cdc28-as1 was exquisitely
sensitive to the inhibitor 1 -NM-PP 1. In the presence of 1 MM ATP,
which roughly approximates intracellular ATP concentration,
Cdc28-as1 was about 15,000-fold more sensitive to 1-NM-PP1 than
wild-type Cdc28 (IC.sub.50 .apprxeq.3 nM for Cdc28-as1 and 44,000
nM for Cdc28). Thus, the single substitution of a glycine for a
phenylalanine results in a Cdc28 mutant that displays both high
affinity and specificity for 1-NM-PP1.
[0386] To examine the function of Cdc28 in vivo, a yeast strain in
which the wild-type copy of CDC28 was replaced by cdc28-as1 was
constructed. Media and genetic and microbial techniques were
essentially as described (148, 153). All strains were derivatives
of W303 (ura3-1, leu2-3, 112, trpl-1, his3-11,15, ade2-1, can1-100,
GAL+). All strains were grown at 23.degree. C. unless otherwise
noted. To create cdc28-as1 , the CDC28 coding sequence and 400 bp
of 5'- and 386 bp of 3'-flanking DNA was PCR-amplified from genomic
DNA and ligated into pRS306 to make pJAU1. The F88G mutation was
engineered by oligonucleotide-directed mutagenesis of pJAU1. The
plasmid was integrated into the wild-type CDC28 locus following
AfII digestion by a pop-in-pop-out strategy as described (148,
153).
[0387] In the absence of 1-NM-PP1, cdc28-as1 cells displayed normal
viability and growth on plates, although they were hyperpolarized
and larger than an isogeneic CDC28 strain, and had a 20% longer
doubling time in liquid culture. Flow cytometric analysis of
asynchronously dividing cells revealed that the cdc28-as1 and CDC28
strains displayed similar DNA content profiles. Finally, synthetic
oligonucleotide DNA arrays were used to measure genome-wide
transcriptional differences between asynchronous wild-type and
cdc28-as1 cells (127).
[0388] Changes were deemed significant if they were greater than or
equal to 2-fold or if the transcript changed present/absent status
(as indicated by Affymetrix software) in the following comparisons:
for non-specific drug effects: CDC28+1-NM-PP1 vs. CDC28; for
cdc28-as1 effects: cdc28-as1 vs. CDC28. For specific Cdc28
inhibition effects, changes were deemed significant if they were
greater than or equal to 2.5-fold for cdc28-as1 1-NM-PP1 vs.
Cdc28-as1 AND a greater than or equal to 2.0-fold change for
cdc28-as1 1-NM-PP1 vs. CDC28+1-NM-PP1.
[0389] In two separate experiments, greater than two-fold changes
were observed in only eleven transcripts (0.2% of the genome).
Greater than 2-fold differences were observed in expression of the
following genes in a comparison of wild-type and cdc28-as1 cells:
Experiment 1: LEU2, YDL241W, YFL057C, YHR071W, CBP1 YJR130C, CWP1,
YLL060c; ATR1 YML128C, YMR095C, YMR096W, YNL275W, YNR065C, ARG1,
YOL101C, SPS4, SSU1, SVS1, OYE3, RLF2, and YPR203W, TWT1, YHR209W,
YIL011W, YIL023C, DAL4, YKL218C, YLL060C, YLO108C, YLR237W,
YLR437C, YML071C, ATR1, YMR095C, YMR096W, YNR065C, ARG1, YOR302W,
SPS4, YPL088W, SVS1, YPR013C, CTR1.
[0390] The minor growth defect in cdc28-as1 cells was suspected to
be due to the 6-fold lower k.sub.cat of the mutant enzyme, which
would result in a 6-fold lower activity at the high ATP
concentrations in vivo (the lower ATP binding affinity of the
mutant should not be relevant in vivo, where ATP concentration is
much greater than K.sub.m). Thus, cdc28-as1 is a slightly weakened
allele of CDC28 that can nevertheless support cell cycle
progression.
[0391] Next, the effects of the inhibitor 1-NM-PP1 on cell growth
and morphology were analyzed. Proliferation of wild-type cells was
unaffected by the inhibitor except at very high concentrations
(50,000 nM), when doubling times increased about 2-fold. DNA
microarray analysis revealed that transcription of only 6 genes
(0.1%) was changed greater than two-fold after 30 minutes treatment
of wild-type cells with 500 nM 1-NM-PP1.
[0392] Of the six transcripts that changed in wild-type cells after
30 minutes of inhibitor treatment, three have no known function
(YGR035C, YLR346C, YPL222W) and the others have roles in heat shock
(SSA4), osmotic stress response (GRE2), and drug resistance (YOR1).
The transcription of only one of these genes (YGR035C) is cell
cycle regulated (150). Treatment of wild-type cells with inhibitor
for 120 minutes resulted in changes in only 3 genes (YGR035 C and
two genes encoding ribosomal proteins: RPS26A and RPL26B).
[0393] Treatment of cells for 120 minutes caused even fewer
transcriptional responses: greater than two-fold changes were seen
for only three transcripts. Interestingly, no significant
activation of stress-responsive transcripts was observed,
consistent with the proposal that many drug-sensing mechanisms
respond to the function rather than the presence of the drug (122).
Therefore, it was concluded that 500 nM 1-NM-PP1 treatment has no
significant effects on wild-type cell physiology, suggesting that
it does not inhibit or stimulate any wild type kinase or other
enzyme in yeast.
[0394] The single amino acid change in the Cdc28-as1 kinase makes
it exceedingly sensitive to the inhibitor 1-NM-PP1 in vivo. Growth
of the cdc28-as1 strain was inhibited 50% at 50 to 100 nM
inhibitor; complete growth arrest occurred above 500 nM. The close
correspondence between the IC.sub.50 in vivo and those measured in
kinase assays (Table 4) illustrates the efficacy with which 1
-NM-PP1 can penetrate a yeast cell, a feature not exhibited by
other small molecule CDK inhibitors (122).
8TABLE 4 Comparison of Activity of Cdc28 and Cdc28-as1 in the
Presence of an Inhibitor ATP Kinetics.sup.1/ 1-NM-PP1
IC.sub.50.sup.2/ K.sub.m k.sub.cat k.sub.cat/K.sub.m (.mu.M) Kinase
(.mu.M) (min.sup.-1) (.mu.M.sup.-1 .multidot. min.sup.-1) @ 10
.mu.M ATP @ 1 mM ATP Cdc28 .multidot. MBP-Clb2 35 132 3.730 22 44
Cdc28-as1 .multidot. MBP-Clb2 322 21.3 0.066 .0020 .0029
.sup.1/Purified Cdc28-His.sub.6 (1 nM final concentration) and
MBP-Clb2 (3 nM final concentration) were incubated for 10 min at
23.degree. C. in a 25 .mu.l reaction mixture containing 5 .mu.g
Histone H1 and several concentrations of .gamma.-.sup.32P-ATP in
kinase buffer (25 mM Hepes-NaOH pH 7.4, 10 mM NaCl, 10 mM
MgCl.sub.2, and 1 mM dithiothreitol (DTT)). Reaction products were
analyzed by 15% SDS-PAGE followed by autoradiography. #Phosphate
incorporation was determined at each ATP concentration by
scintillation counting. Eadie-Hofstee plots were then used to
calculate K.sub.m and k.sub.cat. .sup.2/Purified Cdc28-His.sub.6 (1
nM final concentration) and MBP-Clb2 (3 nM final concentration)
were incubated for 10 min at 23.degree. C. in a 25 .mu.l reaction
mixture containing 5 .mu.g Histone H1, 1 .mu.Ci of
.gamma.-.sup.32P-ATP (1 .mu.Ci/10 .mu.M and 1 .mu.Ci/1 mM), and
several concentrations of 1-NM-PP1 in kinase buffer (147). Reaction
products were analyzed by 15% SDS-PAGE followed by autoradiography.
Phosphate incorporation #was determined at each inhibitor
concentration by scintillation counting. Inhibitor concentration
vs. phosphate incorporation was plotted and the 1-NM-PP1
concentration at which phosphate incorporation was 50% that of the
no inhibitor control was reported as the IC.sub.50.
[0395] Cdc28-as1 is highly sensitive to 1-NM-PP1 in vitro and is a
slightly weakened kinase. Active cyclin-Cdk complexes were formed
by the addition of excess MPB-Clb2 to purified Cdc28-His.sub.6, or
Cdc28-as1 -HiS.sub.6, and their ability to phosphorylate Histone H1
at different ATP concentrations was measured to generate and
k.sub.m and k.sub.cat values. To determine IC.sub.50, the inhibitor
concentration at which the kinase is 50% inhibited, we measured the
kinase activity of Cdc28-MBP-Clb2 or Cdc28-as1MBP-Clb2 in the
presence of varying concentrations of 1-NM-PP 1, at two different
ATP concentrations.
[0396] Detailed analysis of DNA content and morphology of cdc28-as1
cells revealed that lower concentrations of 1-NM-PP 1 caused a
delay (50 nM) or arrest (500 nM) with a G2/M DNA content and large
hyperpolarized buds. Higher inhibitor concentrations (5,000 nM)
caused a non-uniform arrest that included unbudded GI cells as well
as large-budded G2/M cells; bud hyperpolarization was no longer
evident. Thus, it appears possible to titrate the level of
Cdc28-as1 activity in vivo, allowing the identification of cell
cycle events that are differentially sensitive to decreases in the
catalytic activity of Cdc28.
[0397] When cdc28-as1 cells were synchronized in G1 with the yeast
mating pheromone, .alpha.-factor factor, and then released into
fresh media containing 500 nM 1-NM-PP 1, initiation of budding and
DNA synthesis were delayed about 30 to 60 minutes, while
accumulation of the mitotic cyclin Clb2 was delayed 60 to 90
minutes. Cells went on to arrest with moderate Clb2 levels, highly
hyperpolarized buds, and a G2M DNA content, much like the arrest
observed in asynchronous cells. Microscopic analysis of
microtubules and DNA revealed that these cells lacked a mitotic
spindle and arrested with a single DNA mass correctly positioned at
the bud neck. Thus, cells treated with low concentrations of the
inhibitor are slightly delayed during progression through early
stages of the cell cycle, but eventually arrest due to a failure to
assemble a mitotic spindle and enter mitosis.
[0398] When GI-synchronized cdc28-as1 cells were released into
media containing 5,000 nM 1-NM-PP1, they arrested with a IC DNA
content and initially failed to bud, suggesting an arrest at START.
These cells eventually budded after 180 to 240 minutes and arrested
with a IC DNA content, large hyperpolarized buds, a single DNA mass
in the mother cell, and an interphase astral microtubule array.
[0399] Pho85, a Cdk that is closely related to Cdc28, has been
implicated in the initiation of budding in S. cerevisiae (128,
129). Therefore, the budding observed in cdc28-as1 cells released
into 5,000 nM 1-NM-PP1 due to residual Cdc28-as1 activity or due to
Pho85 activity was investigated. A cdc28-as1 strain lacking PCL1
and PCL2, which encode the two G1 activating cyclins of Pho85 were
constructed. When these cells were synchronized in G1 and released
into 5,000 nM 1-NM-PP1, they arrested with a 1C DNA content and
never budded, even after 6 hours. It was concluded that Pc11- and
Pc12-associated Pho85 activity, and not residual Cdc28 activity,
are responsible for the greatly delayed budding observed in
cdc28-as1 cells treated with high concentrations of inhibitor.
[0400] To further characterize the cell cycle arrest caused by
inhibitor treatment, genome-wide transcription after treatment of
asynchronous cdc28-as1 cells with 500 nM 1-NM-PP1 was analyzed
(FIGS. 25A-D). Two hours treatment caused 2.5-fold or greater
changes in the transcription of 104 genes (66 decreases, 38
increases) (FIGS. 25B and C). Of the down-regulated transcripts, 60
are cell cycle-regulated and 32 have peak expression at G2/M. This
downregulated G2/M subset contains a broad range of
well-established mitotic regulators, including CLB2, SW15, CDC20,
and CDC5. Decreased levels of the CLB2 transcript are consistent
with the delay in Clb2 accumulation following release from GI
arrest. The downregulated G21M subset also included 11 transcripts
of unknown function, these transcripts may encode G2M regulators
under transcriptional control by Cdc28. 30 minutes treatment with
I-NM-PPI produced a similar G2/M transcriptional block (37 of the
42 down-regulated genes are cell cycle regulated and 57% of these
peak at G2/M) (130).
[0401] Two-hour drug exposure also increased the expression of 38
transcripts over 2.5-fold (10 cell cycle regulated) (FIG. 25A-D).
All but one of these cell cycle regulated transcripts are expressed
at peak levels in G1. This group includes genes encoding G I
cyclins (Cln2 an PcI I). This result, combined with the observation
that the Cln-Cdc28 inhibitor Far 1 was down-regulated 20-fold,
suggests that prolonged Cdc28 inhibition and G2/M arrest leads to a
transcriptional program that boosts the activity of G I cyclin-Cdk
complexes.
[0402] To assess general trends in the transcriptional response to
Cdc28 inhibition, mean changes in the expression of all genes from
each of the major cell cycle gene clusters were calculated (FIG.
25D). This analysis confirmed that inhibitor treatment of cd28-as1
cells led primarily to decreased expression of genes that are
normally expressed in the G2/M and M/G1 stages of the'cell
cycle.
[0403] In addition to being required for mitotic entry, Cdk1is also
known to control the exit from mitosis (131, 132). Cdk1 activity
inhibits progression from anaphase to G1, and therefore Cdk1
inactivation (primarily by cyclin proteolysis) is required for
mitotic exit. In addition, Cdk 1 inhibits its own inactivation in
late mitosis by phosphorylating and inactivating components of the
anaphase-promoting complex (APC) that targets cyclins for
destruction (133, 134). If cells are arrested in mitosis with the
microtubule poison nocodazole, cyclin destruction and mitotic exit
can be triggered by overexpression of the Cdk inhibitory protein
Sic 1(135). Consistent with these results, treatment with 500 nM
I-NM-PPI was found to lead to rapid (<60 min) cyclin destruction
and rebudding of cdcM-as1 cells arrested in late mitosis with the
cdc15-2 mutation (136).
[0404] Although Cdks inhibit progression from anaphase to G1, they
also appear to promote APC activity and sister chromatid separation
at the metaphase-to-anaphase transition (131, 132, 137). For
example, genetic evidence suggests that certain weak alleles of
CDC28, including cdcM-as1 , display minor defects in progression
through anaphase (137); in addition, one ts mutant of CDC28
(cdc28-IN) exhibits a metaphase arrest at the restrictive
temperature (138). Experimental conditions where inhibitor
treatment causes a metaphase arrest in cdc28-as1 cells have not
been determined, presumably because low inhibitor concentrations
either prevent mitotic entry or trigger premature mitotic exit.
Furthermore, the metaphase arrest in cdc28-IN cells may not be due
to a general decrease in kinase activity, but instead could be due
to a limited defect in activity toward substrates involved in
metaphase-to-anaphase progression.
EXAMPLE 21
Generation of Mutant Specific Inhibitors of Lipid
Kinases-Phosphatidyl Inositol-3 Phosphate Kinase (PI-3K) Alpha
(.alpha.).
[0405] A family of protein kinases which phosphorylate inositol
triphosphates in cells is called phosphatidyl inositol-3 phosphate
kinases (PI-3K's). These proteins utilize ATP as the phosphodonor
substrate. They are key regulators of cell signalling which is
important in cancer.
[0406] Based on previous examples, residues in protein kinases
which can be altered to allow binding of inhibitor molecules that
do not inhibit any wild-type kinases have been identified. Using
the methods described previously, a protein sequence alignment
between protein kinases and PI-3K's is generated. This alignment is
also based on the crystal structure of PI-3K.gamma.. Based on the
structural similarity between PI-3K.gamma.and PI-3K.alpha.and on
the sequence alignment of protein kinases and PI-3K's, it is
proposed that residue I848 in PI-3K.alpha.corresponds to residue
I338 in v-Src. Therefore, mutating I848 to Ala or Gly generates
mutant I848A PI-3-K.alpha.or I848G PI-3-K.alpha.that is expected to
be sensitive to the inhibitors disclosed herein.
EXAMPLE 22
Generation of Mutant Specific Inhibitors of Aminoglycoside
Kinases.
[0407] Another family of enzymes which can be engineered by the
methods previously described is the bacterial kinases which
phosphorylate aminoglycoside antibiotics such as kanamycin. An
example of an aminoglycoside kinase is APH (III-a').
[0408] Following the methods described previously, a sequence
alignment between APH (III-a') and v-Src is generated. This
alignment is also based on the crystal structure of APH (III-a').
Based on the sequence alignment, it is proposed that methionine
residue 90 in APH (III-a') corresponds to I338 in v-Src. M90 in
APH(III-a') is mutated to alanine and glycine to generate mutant
M90A APH (III-a') or M90G APH (III-a') which is expected to be
sensitive to the inhibitors of the present invention.
[0409] The foregoing detailed description has been given for
clearness of understanding only and no unnecessary limitations
should be understood therefrom as modifications will be obvious to
those skilled in the art.
[0410] While the invention has been described in connection with
specific embodiments thereof, it will be understood that it is
capable of further modifications and this application is intended
to cover any variations, uses, or adaptations of the invention
following, in general, the principles of the invention and
including such departures from the present disclosure as come
within known or customary practice within the art to which the
invention pertains and as may be applied to the essential features
hereinbefore set forth and as follows in the scope of the appended
claims.
[0411] Thus, this invention may be embodied in other forms or
carried out in other ways without departing from the spirit or
essential characteristics thereof. The present disclosure is
therefore to be considered as in all respects illustrative and not
restrictive, the scope of the invention being indicated by the
appended claims, and all changes which come within the meaning and
range of equivalency are intended to be embraced therein.
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Sequence CWU 1
1
20 1 27 PRT Homo sapiens 1 Asn Phe Pro Phe Leu Val Lys Leu Glu Phe
Ser Phe Lys Asp Asn Ser 1 5 10 15 Asn Leu Tyr Met Val Met Glu Tyr
Val Pro Gly 20 25 2 27 PRT Rous sarcoma virus 2 Asn His Pro Asn Ile
Val Lys Leu Leu Asp Val Ile His Thr Glu Asn 1 5 10 15 Lys Leu Tyr
Leu Val Phe Glu Phe Leu His Gln 20 25 3 26 PRT Rous sarcoma virus 3
Arg His Glu Lys Leu Val Gln Leu Tyr Ala Val Val Ser Glu Glu Pro 1 5
10 15 Ile Tyr Ile Val Ile Glu Tyr Met Ser Lys 20 25 4 30 DNA Rous
sarcoma virus 4 tttggatcca tggggagtag caagagcaag 30 5 30 DNA Rous
sarcoma virus 5 tttgaattcc tactcagcga cctccaacac 30 6 26 DNA Rous
sarcoma virus 6 tgagaagctg gctcaactgt acgcag 26 7 26 DNA Rous
sarcoma virus 7 ctgcgtacag ttgagccagc ttctca 26 8 24 DNA Rous
sarcoma virus 8 ctacatcgtc gctgagtaca tgag 24 9 24 DNA Rous sarcoma
virus 9 ctcatgtact cagcgacgat gtag 24 10 7 PRT Artificial Sequence
Description of Artificial Sequence Imaginary sequence for enzyme
modelling 10 Asp Met Phe Arg Asp Lys Glu 1 5 11 7 PRT Artificial
Sequence Description of Artificial Sequence Imaginary sequence for
enzyme modelling 11 Asp Met Ile Arg Glu Lys Asp 1 5 12 8 PRT
Artificial Sequence Description of Artificial Sequence Optimized
substrate for src kinases 12 Ile Tyr Gly Glu Phe Lys Lys Lys 1 5 13
12 PRT Artificial Sequence Description of Artificial Sequence
Optimized substrate for Abl 13 Glu Ala Ile Tyr Ala Ala Pro Phe Ala
Lys Lys Lys 1 5 10 14 40 PRT Rous sarcoma virus v-Src kinase 14 Arg
His Glu Lys Leu Val Gln Leu Tyr Ala Met Val Ser Glu Glu Pro 1 5 10
15 Ile Tyr Ile Val Ile Glu Tyr Met Ser Lys Gly Ser Leu Leu Asp Phe
20 25 30 Leu Lys Gly Glu Met Gly Lys Tyr 35 40 15 40 PRT Homo
sapiens c-Fyn kinase 15 Lys His Asp Lys Leu Val Gln Leu Tyr Ala Val
Val Ser Glu Glu Pro 1 5 10 15 Ile Tyr Ile Val Thr Glu Tyr Met Asn
Lys Gly Ser Leu Leu Asp Phe 20 25 30 Leu Lys Asp Gly Glu Gly Arg
Ala 35 40 16 41 PRT Homo sapiens c-Abl kinase 16 Lys His Pro Asn
Leu Val Gln Leu Leu Gly Val Cys Thr Arg Glu Pro 1 5 10 15 Pro Phe
Tyr Ile Ile Thr Glu Phe Met Thr Tyr Gly Asn Leu Leu Asp 20 25 30
Tyr Leu Arg Glu Cys Asn Arg Gln Glu 35 40 17 39 PRT Homo sapiens
CamK II, calcium/calmodulin-dependent kinase 17 Lys His Pro Asn Ile
Val Arg Leu His Asp Ser Ile Ser Glu Glu Gly 1 5 10 15 His His Tyr
Leu Ile Phe Asp Leu Val Thr Gly Gly Glu Leu Phe Glu 20 25 30 Asp
Ile Val Ala Arg Glu Tyr 35 18 40 PRT Homo sapiens Cdk2,
cyclin-dependent kinase 18 Asn His Pro Asn Ile Val Lys Leu Leu Asp
Val Ile His Thr Glu Asn 1 5 10 15 Lys Leu Tyr Leu Val Phe Glu Phe
Leu His Gln Asp Leu Lys Lys Phe 20 25 30 Met Asp Ala Ser Ala Leu
Thr Gly 35 40 19 42 PRT Saccharomyces cerevisiae Cdc28,
cyclin-dependent kinase 19 Lys Asp Asp Asn Ile Val Arg Leu Tyr Asp
Ile Val His Ser Asp Ala 1 5 10 15 His Lys Leu Tyr Leu Val Phe Glu
Phe Leu Asp Leu Asp Leu Lys Arg 20 25 30 Tyr Met Glu Gly Ile Pro
Lys Asp Gln Pro 35 40 20 42 PRT Saccharomyces cerevisiae Fus3,
mitogen-activated kinase 20 Lys His Glu Asn Ile Ile Thr Ile Phe Asn
Ile Gln Arg Pro Asp Ser 1 5 10 15 Phe Glu Asn Phe Asn Glu Val Tyr
Ile Ile Gln Glu Leu Met Gln Thr 20 25 30 Asp Leu His Arg Val Ile
Ser Thr Gln Met 35 40
* * * * *