Ex Parte Crouch et al

Patent Trial and Appeal Board

Jun 26, 2013

10892285 (P.T.A.B. Jun. 26, 2013)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte SHARON PATRICIA MARY CROUCH and
KEVIN JOHN SLATER
__________

Appeal 2011-008725
Application 10/892,285
Technology Center 1600
__________

Before LORA M. GREEN, JACQUELINE WRIGHT BONILLA, and
ANNETTE R. REIMERS, Administrative Patent Judges.

BONILLA, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal1 under 35 U.S.C. § 134 involving claims directed to
a method for detecting protein kinase activity. The Examiner has rejected
the claims as obvious. We have jurisdiction under 35 U.S.C. § 6(b). We
affirm.

1 The Real Party in Interest is Lonza Nottingham, Ltd., previously known as
Cambrex Bio Science Nottingham, Ltd., and Lumitech (UK) Limited (App.
Br. 2).
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STATEMENT OF THE CASE
Protein kinases transfer phosphate groups from adenosine
triphosphate (ATP) to certain amino acids in a protein substrate, which can
affect that protein’s function in a cell (Spec. 1). The Specification describes
a protein kinase assay, i.e., an assay for detecting a kinase’s phosphorylating
activity. In particular, the Specification describes using an enzyme-based
bioluminescence detection system, such as one involving luciferins (light
emitting compounds) and luciferase enzymes, and not radioactive ATP with
32P or 33P gamma phosphates (id. at 1-2, 12; App. Br. 9).
Claims 43, 45-56, and 78 are on appeal. Independent claims 43 and
45 are representative (emphasis added):
43. A method for detecting protein kinase activity comprising
(a) establishing a reaction mixture comprising adenosine
triphosphate (ATP), a protein kinase and a substrate to be
phosphorylated by the protein kinase;
(b) using a bioluminescence reaction to detect whether any
change in ATP concentration occurs in the reaction mixture, and
(d) comparing any change in ATP concentration detected in the
reaction mixture to a reference result indicative of the reaction
mixture in the absence of the protein kinase, whereby a decrease in
ATP concentration relative to the reference result indicates protein
kinase activity.
45. A method for identifying a compound which modulates the
activity of a protein kinase, said method comprising:
(a) establishing a reaction mixture comprising adenosine
triphosphate (ATP), a protein kinase, a substrate to be phosphorylated
by the protein kinase and the compound;
(b) using a bioluminescence reaction to detect whether any
change in ATP concentration occurs in the reaction mixture, whereby
the detection provides information of protein kinase activity;
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(c) comparing the information of protein kinase activity
obtained using the bioluminescence reaction for detecting any change
in ATP concentration according to step (b) with activity information
about the protein kinase obtained in the absence of the compound for
identifying whether the compound modulates the activity of the
protein kinase.
Independent claim 78 is similar to claim 45, but is directed to a method for
identifying a compound which inhibits (rather than modulates) the activity
of an active protein kinase.
Claims 43, 45-56, and 78 stand rejected under 35 U.S.C. § 103(a) as
obvious over Handa2 in view of Heasley3 and further in view of Gustafsson.4
Issue
Does the Examiner establish by a preponderance of the evidence that
Handa, in view of Heasley and Gustafsson, renders method claims 43, 45-
56, and 78 obvious?

2 Handa et al., Assay of Adenosine 3’, 5’ Cyclic Monophosphate by
Stimulation of Protein Kinase: A Method Not Involving Radioactivity, 102
ANALYTICAL BIOCHEMISTRY 332-339 (1980).
3 Heasley et al., Regulation of Protein Kinase C by Nerve Growth Factor,
Epidermal Growth Factor and Phorbol Ester in PC12 Pheochromocytoma
Cells, 264 J. BIOLOGICAL CHEMISTRY 8646-8652 (1989).
4 Gustafsson et al., Differential and Selective Inhibition of Protein Kinase A
and Protein Kinase C in Intact Cells by Balanol Congeners, 56 MOLECULAR
PHARMACOLOGY 377-382 (1999).
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Findings of Fact (FF)
1. Handa describes an assay for measuring cyclic AMP (cAMP) using
cAMP-dependent protein kinase, where the assay “does not require use of
[γ-32P]ATP” (Handa 332, abstract).
2. Handa teaches that:
Instead of measuring the cAMP-stimulated increase in the rate of
transfer of [γ-32P] phosphate from [γ-32P]ATP to protein, the rate of
loss of ATP from the reaction mixture is determined. The ATP
remaining after the protein kinase reaction is assayed by ATP-
dependent chemiluminescence of the firefly luciferin-luciferase
system.
(Id.)
3. Handa further teaches that “the determination of the amount of ATP
remaining at the end of the protein kinase reaction by the luciferase-luciferin
system provides a sensitive and specific method for the measurement of
cyclic AMP” (id. at 333, 2nd col.), referring to measurement of the activity of
a protein kinase that is activated by cAMP.
4. Handa describes how to perform such an assay in the Materials and
Methods section of the reference, in a subsection entitled “Protein kinase
assay using firefly luciferase-luciferin system (PLK)” (id. at 335, 2nd col. –
336, 1st col.)
5. Handa describes results obtained using the disclosed kinase assay,
including a determination of the “loss of ATP from the reaction mixtures”
(id. at 336-37).
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Analysis
Appellants argue that “Handa is concerned only with determining the
(unknown) amount of cAMP in a sample; Handa is not concerned with
measuring or detecting the activity of any protein kinase” (App. Br. 16).
Appellants state that in Handa, “the use of a known cAMP-dependent
protein kinase is essential; the assay is not described as having any relevance
beyond that context” (id.). Appellants further argue that “the Examiner
relies on his hindsight-gained understanding of the claimed invention to
speculate that a worker would extrapolate Handa’s technique to use other
protein kinases and substrates and to connect the ATP consumption to the
kinase activity” (id.).
In addition, Appellants state that “Handa does not teach or suggest
that a change ATP concentration can be used to determine the activity of a
protein kinase, which is a key concept underlying the claimed invention” (id.
at 25, see also id. at 29). Appellants also contend that “[n]owhere does
Handa suggest that a comparison of the measured bioluminescence detection
(i.e., the measurement of residual ATP) with a reference result indicative of
the reaction mixture in the ‘absence of the protein kinase,’ as required by the
assay method of claim 43, would have any significance” (id. at 17).
We disagree with Appellants characterization of Handa. Handa
expressly describes detecting protein kinase activity. In addition, as stated
by the Examiner, “Handa et al. clearly teach protein kinase assay by
measuring depletion of ATP from the reaction mixture with a
bioluminescence assay by applying firefly luciferase-luciferin system” (Ans.
8, 4-5; see also FF 1-5). In addition, Handa assessed ATP concentrations
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before and after a relevant kinase assay, i.e., in the absence of the kinase,
and after establishing the reaction mixture. For example, Handa taught
adding 1 nmol of ATP “to start the reaction” and thereafter “determin[ing]
the amount of ATP remaining in the reaction mixture by the firefly
luciferase-luciferin system” (Handa, 335, 2nd col.; FF 4).
Furthermore, Handa’s method involved “comparing any change in
ATP concentration detected in the reaction mixture to a reference result
indicative of the reaction mixture in the absence of the protein kinase” (as
recited in claim 43) as the mechanism of determining kinase activity. See,
e.g., Handa 336, 2nd col. – 337, 1st col.; see also Ans. 8. Based on (1) how
much ATP was added to the kinase reaction, and (2) “the amount of ATP
remaining in the reaction mixtures after the stimulation of protein kinase by
cAMP,” Handa determined the activity of the protein kinase by comparing
the two ATP amounts, i.e., determining the “loss of ATP from the reaction
mixture” (Handa, ¶ spanning 336-37; FF 5). An ordinary artisan would have
understood Handa to disclose such teachings, even if the reference also
taught that the loss in ATP during the kinase reaction directly correlated
with levels of cAMP, a compound that stimulated the kinase.
When discussing claim 43, Appellants state that their invention is the
“discovery of using the bioluminescence assay in connection with a protein
kinase catalyzed reaction to assess the activity of the protein kinase by
measuring the change in ATP that occurs as a consequence of the reaction”
(App. Br. 17-18). That is exactly what Handa discloses.
Regarding other cited references and declaration evidence, Appellants
assert that “Heasley and Gustafsson, along with the testimony provided by
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Mr. Pitt as to the continued reliance of the prior art on the radioactive assay
(Pitt Declaration ¶¶ 10-17), underscores the fact that the protein kinase prior
art had no appreciation of the universal applicability of a luciferase-luciferin
system in an assay for protein kinase activity” (Reply Br. 3). This assertion
disregards, however, what was taught in Handa, as discussed above.
In relation to claims 45 and 78, Appellants argue that “[n]othing in
Handa discloses or even remotely suggests there would be any benefit
associated with conducting the Handa assay in the presence of a compound
for assaying the impact of that compound on the progression of the protein
kinase-related reaction” (App. Br. 18). Appellants also argue that adding “a
compound that inhibits the activity of an active protein kinase” (as recited in
claim 78) “would obliterate the sole purpose of the Handa assay,” i.e., to
assess cAMP levels (id. at 18-19).
An ordinary artisan would not have read Handa solely with an eye of
learning how to determine cAMP levels, but would have understood that
Handa suggested, if not taught outright, the method recited in claim 43. In
re McDaniel, 293 F.3d 1379, 1385 (Fed. Cir. 2002) (stating that anticipation
is the epitome of obviousness).
Regarding claims 45 and 78, as noted above, the Examiner analyzes
Handa in view of Heasley and Gustafsson, three references that all discuss
protein kinase activity (Ans. 4-6). One would have had reason to read
references relevant to methods for assessing protein kinase activity, such as
those describing the use of radioactive ATP in a cell free environment (as
taught in Heasley), those identifying inhibitors of protein kinases (as taught
in Gustafsson), and those describing a non-radioactive method for detecting
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protein kinase activity (as taught by Handa) (Ans. 5-6). An obviousness
“analysis need not seek out precise teachings directed to the specific subject
matter of the challenged claim,” but “can take account of the inferences and
creative steps that a person of ordinary skill in the art would employ.” KSR
Int’l Co. v. Teleflex Inc., 550 U.S. 398, 418 (2007).
For example, Handa teaches that “[b]ecause the 32P decays rapidly, [γ-
32P]ATP is both expensive and short-lived” (Handa 333, 1st col.), and
Handa’s described assay is “free from the hazards, costs, and inconvenience
of the methods using 32P” (id. at 338, 1st col.). Thus, an ordinary artisan
would have had reason to “take account of the inferences” from Handa that
its kinase assay—involving bioluminescence, not radioactivity—would have
been useful in other assay involving other protein kinases, including those
used to identify modulators or inhibitors of protein kinases (as recited in
claims 45 and 78). KSR, 550 U.S. at 418.
In relation to Gustafsson, Appellants state that this reference “contains
no discussion of any connection between ATP concentration and protein
kinase activity” (App. Br. 22). Appellants further state that “Gustafsson
disparages to some extent the use of the induction of the construct of CRE-
luciferase as a measure of protein kinase A activity, for being an endpoint
distant in time and place from balanol’s putative target, protein kinase” (id.
at 22-23).
The statement in Gustafsson that “[l]uciferase induction as an
endpoint is distant in time and place from balanol’s putative target, PKA”
does not suggest, however, that the method disclosed in Handa would not
work to assess protein kinase A activity (Gustafsson 380, 1st col.). See In re
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Mouttet, 686 F.3d 1322, 1334 (Fed. Cir. 2012) (finding no teaching away
when no cited reference suggested that the claimed invention was unlikely to
work). In addition, Appellants disregard the Examiner’s point in citing
Gustafsson, i.e., the reference establishes that one would have had reason to
identify protein kinase inhibitors using a protein kinase assay as a general
matter. (Ans. 6, 9 (stating that “Gustafsson et al. was cited for teaching that
inhibition of protein kinase A (i.e., PKA) activity by balanol could be
measured in a protein kinase assay”).)
We agree with the Examiner that an ordinary artisan would have had
reason to use the luciferase-luciferin system described in Handa to assay
protein kinase activity, such as the activity of cAMP-dependent protein
kinase, where the method involved detecting a change in ATP concentration
in a reaction mixture and comparing that change to “a reference result” in
the absence of the protein kinase, where a decrease in ATP indicates protein
kinase activity, as recited in claim 43. Likewise, the Examiner establishes
by a preponderance of the evidence that it would have been obvious to an
ordinary artisan to use such a method to identify compounds that modulated
or inhibited the activity of a protein kinase, as recited in claim 45 and 78.
Appellants arguments and cited evidence, such as the Declaration by Mr. Pitt
(which does not discuss Handa), does not persuade us otherwise.
Thus, the Examiner establishes by a preponderance of the evidence
that Handa, in view of Heasley and Gustafsson, renders claims 43, 45, and
78 obvious. Because Appellant do not argue dependent claims separately,
claims 46-56 fall with independent claims 43 and 45 upon which they
depend. 37 C.F.R. § 41.37(c)(1)(vii).
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SUMMARY
We affirm the rejection of claims 43, 45-56, and 78 under 35 U.S.C.
§ 103(a) as obvious over Handa in view of Heasley and Gustafsson.

TIME PERIOD FOR RESPONSE
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).

AFFIRMED

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