Ex Parte Sharif et al

Patent Trial and Appeal Board

Oct 19, 2012

11090689 (P.T.A.B. Oct. 19, 2012)

UNITED STATES PATENT AND TRADEMARKOFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
11/090,689 03/25/2005 Najam A. Sharif 45263-P006US 5699
58380 7590 10/19/2012
WINSTEAD PC
P.O. BOX 50784
DALLAS, TX 75201
EXAMINER
MARTIN, PAUL C
ART UNIT PAPER NUMBER
1653
MAIL DATE DELIVERY MODE
10/19/2012 PAPER
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte NAJAM A. SHARIF, COLENE D. DRACE,
and GARY W. WILLIAMS
__________

Appeal 2011-001817
Application 11/090,689
Technology Center 1600
__________

Before TONI R. SCHEINER, FRANCISCO C. PRATS, and
JACQUELINE WRIGHT BONILLA, Administrative Patent Judges.

BONILLA, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims directed to a
high throughput method of assaying for a compound that modulates human
Rho kinase protein activity. The Examiner has rejected the claims as
obvious. We have jurisdiction under 35 U.S.C. § 6(b). We affirm.

Appeal 2011-001817
Application 11/090,689

2
STATEMENT OF THE CASE
The Specification describes a high throughput assay for assaying test
compounds for the ability to modulate the activity of human Rho kinase (a
serine/threonine kinase enzyme) (Spec. [0004], [0009]). The assay involves
using γ33P-ATP, as well as vacuum filtration and automatic washing of assay
reaction samples, such as those on a 96-well plate (id. at [0014], [0025]).
Claims 1, 2, 4, and 6-12 are on appeal.1 Independent claim 1 is
representative and reads as follows:
1. A high throughput method of assaying a test compound for human
Rho kinase modulating activity comprising:
contacting the test compound, an agent having human Rho
kinase activity, γ33P-ATP, and a Rho kinase substrate in a medium
with mixing, in a microtiter plate format having a plurality of wells,
and for a time to allow phosphorylation of the substrate, thereby
forming a test mixture;
rapidly and simultaneously separating the test mixture from
each of the plurality of wells into a first portion containing γ33P-
labeled substrate onto a filter mat and a second portion containing
γ33P-ATP using automated vacuum filtration and automated washing
of the filter mat;
drying the filter mat using microwave radiation;
detecting the presence of γ33P in the first portion; and
comparing the presence of γ33P in the first portion with
presence of γ33P-label in a first portion of a control mixture lacking
the test compound,
wherein a greater presence of γ33P in the first portion of the test
mixture as compared to the presence of γ33P in the first portion of the

1 Claims 3 and 13-19 are withdrawn, and not appealed (App. Br. 2). The
Examiner has withdrawn all rejections of claim 5 (Ans. 3-4).

Appeal 2011-001817
Application 11/090,689

3
control mixture indicates stimulatory activity of the test compound for
human Rho kinase activity; and
wherein a lesser presence of γ33P in the first portion of the test
mixture as compared to the presence of γ33P in the first portion of the
control mixture indicates inhibitory activity of the test compound for
human Rho kinase activity.
The claims stand rejected under 35 U.S.C. §103(a) as follows:
(I) claims 1, 4, 6-8, 10, and 12 as obvious over Imanishi et al., U.S.
Appl. Publ. No. 2002/0077296 A1 (published Jun. 20, 2002);
(II) claims 1, 4, 6-8, 10, and 12 as obvious over Imanishi in view of
Armstrong et al., WO 03/087400 A1 (published Oct. 23, 2003);
(III) claims 1, 4, 6-8, and 10-12 as obvious over Imanishi in view of
Kaibuchi et al., U.S. Pat. No. 5,906,819 (issued May 25, 1999);
(IV) claims 1, 4, 6-10, and 12 as obvious over Imanishi in view of Poon
et al., “Reversible Immunoprecipitation Using Histidine- or
Glutathione S-Transferase-Tagged Staphylococcal Protein A,”
Analytical Biochemistry, Vol. 218: 26-33 (1994).
I.
Findings of Fact
1. In a publication entitled “High-Throughput Screening Method,”
Imanishi discloses “a high-performance, efficient screening system for
discovering inhibitors or activators” of proteins, such as Rho kinase.
(Imanishi, Title, [0001], [0010], [0120] and [0198]-[0205]).
2. Imanishi teaches that “inhibitors of Rho-kinase” refers to “a substance
that bind to Rho-kinase to inhibit the phosphorylation of the substrates such
as MLC [myosin light chain], Myelin basic protein, histone HI, and HF2A”
(id. at [0146]).
Appeal 2011-001817
Application 11/090,689

4
3. Imanishi discloses that a “solid support” bound to a protein, e.g., Rho
kinase, can be used in the disclosed screening method (id. at [0119], [0200]).
Imanishi further teaches that “the solid support may be 96-well microplate
…” (id. at [0160]).
4. One method disclosed in Imanishi:
comprises proceeding the reaction of the protein function in the wells
of the plate, transferring the solution into anther plate or filter after
completion of the reaction, and performing the necessary steps therein
to determine the activity, likely in Multiscreen method, or a filter-spot
method.
(Id. at [0119].)
5. When discussing a multiscreen method, Imanishi teaches that after
completing the reaction, the method comprises stopping the reaction, adding
the mixture to “Multiscreen HV (Millipore, MHVB N45),” and “[t]hen, the
material is filtered with suction, and washed three times … with suction” (id.
at [0129]). (See http://www.millipore.com/catalogue/item/mahvn4550)
(showing Multiscreen HV to be a 96-well plate filtering system) (Appendix
A).)
6. When discussing a filter-spot method, Imanishi also teaches drying
material on a filter in a microwave oven (id. at [0133]).
7. Example 7 in Imanishi describes “Examination of the Effect of the
Rho-kinase-immobilized Plate using Inhibitors of Rho-kinase” (id. at
[0198]). Example 7 describes dissolving a “test compound” in a reaction
solution comprising “Histone HF2A” (a Rho kinase substrate) and 33P-ATP,
and adding the solution to a Rho-kinase-immobilized plate (id. at [0200]).
Appeal 2011-001817
Application 11/090,689

5
8. Table 1 in Example 7 presents “IC50” values as measured using
“ROKa/ROK-II active Cat” as Rho kinase, and Fasudil (HA-1077) or Y-
27632 as a Rho kinase inhibitor, or chelerythirne, a protein kinase C
inhibitor acting as a control (id. at [0203]-[0205]; see also Herbert et al.,
“Chelerythrine is a potent and specific inhibitor of protein kinase C,”
Biochem. Biophys. Res. Commun., 172(3):993-9 (1990)
(http://www.ncbi.nlm.nih.gov/pubmed/2244923) (Appendix B).
9. The instant Specification discusses various prior art methods for
assaying Rho kinase activity, including “[γ-33P]-ATP-linked phosphorylation
of myelin basic protein followed by P30 membrane-based isolation of the
phosphorylated product and liquid scintillation counting (PCT Published
Patent Application No. WO 02/076977)” (Spec. [0007]).
10. In Example 1, the Specification describes that “enzyme assays are
performed using a Biomek 2000 Robotic Workstation (Beckman
Instruments, Palo Alto, CA) in a 96-well format using γ-33P-ATP (Perkin-
Elmer Life Sciences, Boston, MA)” (id. at [0028]).
11. The Specification discloses vacuum filtration and automatic washing
of a filter, and drying the filter with a microwave (Spec. [0021]). In
Example 1, the Specification also teaches that kinase assays:
are terminated by rapid simultaneous aspiration of the reaction
mixtures from each of the 96-wells onto a pre-wetted negatively-
charged P30 glass filter mat (Wallac Inc., Turku, Finland) by vacuum
filtration using a cell harvester (Mach II; TomTec, Hamden, CT),
followed by rapid automated washing of each sample area of the filter
mat ….”
(Id.)
Appeal 2011-001817
Application 11/090,689

6
12. Table 1 in the Specification presents IC50 values (concentration of a
test component that inhibits enzyme activity by 50% of a maximum), as
calculated using known computer programs (id. at [0030]-[0032]). Test
compounds include Fasudil and Y-27632 (id. at [0032]).
Principles of Law
The Examiner bears the initial burden, on review of the prior art or on
any other ground, of presenting a prima facie case of unpatentability. In re
Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992). If the Examiner meets that
initial burden, the burden of coming forward with evidence or argument
shifts to the applicant. In re Rijckaert, 9 F.3d 1531, 1532 (Fed. Cir. 1993).
After the applicant submits such evidence or argument, the PTO then
determines patentability “on the totality of the record, by a preponderance of
evidence with due consideration to persuasiveness of argument.” Oetiker,
977 F.2d at 1445.
Analysis
The Examiner rejects claims 1, 4, 6-8, 10, and 12 as obvious over
Imanishi (Ans. 5). Appellants argue that claims 1 and 12 recite a process
where a test mixture “is rapidly and simultaneously separated from each of
the plurality of wells in a microtiter plate format,” and that Imanishi “does
not disclose a process for high throughput screening” (App. Br. 9-10, 12;
Reply Br. 2-3). Appellants also assert that the cited prior art does not teach
comparing the presence of γ-33P in a first portion of a test mixture to the
presence of γ-33P in a first portion of a control mixture lacking the test
compound, as recited in the claims (id. at 10, 12; Reply Br. 3-4).
Appeal 2011-001817
Application 11/090,689

7
Appellants also argue that the Examiner cites no evidence indicating that
33P-labeled ATP disclosed in Imanishi is labeled in the γ position (id.). In
addition, Appellants argue that the prior art teaches a manual process and a
plate, and the Examiner’s assertions regarding the obviousness of
automating a manual process are incorrect and insufficient to establish a
prima facie case of obviousness (id. at 11-12; Reply Br. 4-5).
We disagree with Appellants. In a publication entitled “High-
Throughput Screening Method,” Imanishi discloses “a high-performance,
efficient screening system for discovering inhibitors or activators of protein
functions” (Imanishi [0001]; FF 1). In this capacity, Imanishi discloses a
method for assaying a test compound, such as an inhibitor, for Rho kinase
activity (FF 1, 2). As part of that method, in addition to describing a step of
contacting a test compound, Rho kinase, 33P-ATP, and a Rho kinase
substrate (Histone HF2A) in a microtiter plate (FF 7), Imanishi also
discloses rapidly and simultaneously separating samples from each of a
plurality of wells in a microtiter plate format. Specifically, Imanishi
describes conducting relevant assays on a 96-well microplate (FF 3), and
vacuuming 96-well filter plates (via “suction”) (FF 4, 5; Ans. 5). Such steps
would rapidly and simultaneously separate a test mixture in each well of the
96-well filter plate into a first portion containing the 33P-labelled substrate
onto a filter and a second portion containing 33P-ATP, i.e., the material that
filters through when suction/vacuum is applied (Ans. 5).
In addition, the Examiner notes, and Appellants do not dispute, that
33P in the γ-position is necessary for the transfer of 33P from the ATP to a
substrate during a kinase reaction (Ans. 6, 16). Thus, the Examiner’s
Appeal 2011-001817
Application 11/090,689

8
finding that Imanishi’s 33P-labeled ATP is, in fact, γ-33P-ATP, rather than
ATP having the radioactive phosphate group in the α- or β-position, is
entirely reasonable, and Appellants have provided no evidence to the
contrary. Consistently, the instant Specification acknowledges that γ-33P-
ATP was commercially available, and well known in the prior art (FF 9, 10).
We also agree with the Examiner that “those of ordinary skill in the
art would recognize the obviousness of scaling up a single well Rho-
kinase/single compound screening assay in a microtiter plate to performing a
multiwell screen of Rho-kinase to multiple compounds in the same
microtiter plate” (Ans. 13). Furthermore, as noted by the Examiner,
“automating a manual process for the known advantages of increased speed,
smaller volumes, and improved efficiency, for example, are well known in
the art” (id. at 12). Consistently, the instant Specification acknowledges that
apparatuses, machines and materials used to conduct automated vacuum
filtration of samples on a 96-well filter system, as well as automated
washing of the filter system, were well known in the prior art (FF 3 (e.g.,
Mach II, commercially sold by TomTec)).
Thus, it would have been obvious to an ordinary artisan reading
Imanishi to conduct Rho kinase reactions in the presence of different test
compounds in wells of a 96-well plate (FF 3), thereby allowing many
samples to be tested at once, and then transferring the test mixtures to a 96-
well filter system after completion of reactions, and performing necessary
steps to determine Rho kinase activity (FF 4), such as those involving
vacuuming and washing of the filters (FF 5) (e.g., using commercially
available material and automated apparatuses) (FF 11), as well as drying
Appeal 2011-001817
Application 11/090,689

9
relevant material on the filter system in a microwave (FF 6), before
measuring relevant radioactive levels. Even if Imanishi does not expressly
spell out the use of a 96-well filter system and automated vacuum filtration
and washing in relation to Rho kinases assays in particular, one reading
Imanishi would have understood that use of such materials and techniques
were implied, and readily available for commercial purchase.
The Examiner does not simply cite a per se rule that automation of a
manual activity is obvious, as asserted by Appellants (App. Br. 8). As noted
by the Examiner (Ans. 18-19), an ordinary artisan would have understood
that Imanishi suggested automated vacuum filtration and washing when it
taught “a high-performance, efficient screening system for discovering
inhibitors or activators of protein functions” in relation to Rho kinase (FF 1),
especially in light of commercially available systems and equipment. One
would have been motivated to use such systems and equipment for the
reasons stated by the Examiner, e.g., increased speed and efficiency (Ans.
12), in an effort to achieve “a high-performance, efficient screening system”
(FF 1).
We also agree with the Examiner that it would have been obvious to
one of ordinary skill to involve a “comparing” step as recited in present
claims in the method described in Imanishi (Ans. 6-7, 14-15). As stated by
the Examiner, “the determination of a control portion for purposes of
comparison in experimental procedures is well known in the scientific arts as
a means of determining whether a result is in fact a real change due to the
effect of some variable over normal experimental (control) levels” (id. at
15).
Appeal 2011-001817
Application 11/090,689

10
Consistently, Imanishi discloses IC50 values as determined for
different inhibitors of Rho kinase, such as Fasudil (HA-1077) or Y-27632,
similarly to the instant Specification (FF 8, 12). Imanishi compares those
IC50 values with an IC50 value determined using a control sample, i.e., one
including chelerythirne, a specific protein kinase C inhibitor, not a Rho
kinase inhibitor (FF 8). As part of the process of assessing radioactive levels
to determine IC50 values, and comparing IC50 values of Rho kinase inhibitors
to that of an inhibitor having specificity for a different kinase, one would
have necessarily compared the presence of γ33P in a first portion of a test
sample with presence of γ33P-label in a first portion of a control mixture
lacking that test compound.
For the reasons discussed above, we conclude that a preponderance of
evidence supports the Examiner’s conclusion that claim 1 is obvious over
Imanishi. In relation to the rejection over Imanishi, Appellants do not assert
any arguments regarding independent claim 12 that are not equally
applicable to independent claim 1. Appellants likewise do not argue
dependent claims 4, 6-8, and 10 separately. Thus, claims 4, 6-8, 10, and 12
fall together with claim 1. 37 C.F.R. § 41.37(c)(1)(vii).
II.
The Examiner rejects claims 1, 4, 6-8, 10, and 12 as obvious over
Imanishi in view of Armstrong (Ans. 8-9). Appellants assert that “the
Examiner has not identified SEQ ID NO:1 as claimed,” but rather “identified
only SEQ ID NO:2” (App. Br. 13). Appellants also contend that Armstrong
(“the ‘400 publication”) does not disclose SEQ ID NO:1 (id.).
Appeal 2011-001817
Application 11/090,689

11
As noted by the Examiner, Armstrong discloses SEQ ID NO:1 (Ans.
7-8). Armstrong discloses peptide substrates for protein kinases, including
KEAKEKRQEQIAKRRRLSSLRASTSKSGGSQK, as substrates for
ROCK-II, a Rho kinase (Armstrong, p. 30, l. 26). This peptide corresponds
to the same 32-amino acid sequence of SEQ ID NO:1 presented in the
Specification as commercially sold by Upstate USA, Inc. (Spec. [0028]).
Other arguments raised by Appellants in relation to this rejection
(App. Br. 13-14) mirror those already discussed and addressed in the section
above. We therefore conclude that a preponderance of evidence supports the
Examiner’s conclusion that claims 1, 4, 6-8, 10, and 12 are obvious over
Imanishi in view of Armstrong.
III.
The Examiner rejects claims 1, 4, 6-8, and 10-12 as obvious over
Imanishi in view of Kaibuchi. Claim 11, which depends on claim 1, recites
that “the agent having human Rho kinase activity comprises p160ROCK.”
Appellants acknowledge that p160ROCK (disclosed by Kaibuchi) is an
isozyme of human ROK, but assert that isozymes represent different genes,
and do not have the same structure (App. Br. 14).
Kaibuchi teaches that the “kinase domain of human Rho-kinase (the
amino acid sequence 90-359 in SEQ ID NO.4) was highly homologous to
the kinase domain of human p160ROCK (the amino acid sequence 74-343 in
Ishizaki, T. et al., EMBO J., 15,1885-1893 (1996)*) with 92% similarity”
(Kaibuchi, col. 32, ll. 5-14; see also Ans. 9-10). Based on this teaching, we
agree with the Examiner that it would have been obvious to an ordinary
artisan that p160ROCK exhibited human Rho kinase activity, and it likewise
Appeal 2011-001817
Application 11/090,689

12
would have been obvious to substitute an agent comprising p160ROCK for
the Rho kinase agent used in Imanishi.
Other arguments raised by Appellants in relation to this rejection
(App. Br. 14-15) mirror those already discussed and addressed above
regarding Imanishi. We therefore conclude that a preponderance of
evidence supports the Examiner’s conclusion that claims 1, 4, 6-8, and 10-12
are obvious over Imanishi in view of Kaibuchi.
IV.
The Examiner rejects claims 1, 4, 6-10, and 12 as obvious over
Imanishi in view of Poon. Claim 9, which depends on claims 1 and 8,
recites that “the agent having human Rho kinase activity comprises a fusion
with a hexahistidine tag.” Appellants assert that the Examiner concludes
that one of ordinary skill in the art would have recognized the functional
equivalency of Imanishi’s GST tag and that of Poon’s hexahistidine tag
(App. Br. 15). In response, Appellants argue that “the mere recitation of a
chemical purification process and an abstract statement [in Poon] that one of
ordinary skill in the art would find the swap obvious is not enough to
establish a prima facie case of obviousness” (id.).
We agree with the Examiner that an ordinary artisan would have
recognized that hexahistidine tagging was a well-known method for tagging
and purifying proteins, and that it “would have been an obvious alternative
to GST tagging as both methods were known in the art at the time of the
invention (Poon et al. (abstract)” (Ans. 11). In other words, it would have
been obvious to one reading Imanishi to use a hexahistidine tag as taught in
Poon (describing the purification of a protein kinase (Poon, 26, abstract and
Appeal 2011-001817
Application 11/090,689

13
2nd col., see also id. at 32, 1st col.)) in place of the GST tag used in Imanishi,
to achieve similar results. As noted by the Examiner, an ordinary artisan
would have had a reasonable expectation of success using either well-known
protein tagging method. Poon describes how both hexahistidine tagging (see
id. at 27, 1st col. (describing the “addition of six histidine codons”) and GST
tagging are useful for purifying proteins, such as a protein kinase (id. at 26,
abstract, see also id. 32, 2nd col.)
Other arguments raised by Appellants in relation to this rejection
(App. Br. 15) again mirror those already discussed and addressed above
regarding Imanishi. We therefore conclude that a preponderance of
evidence supports the Examiner’s conclusion that claims 1, 4, 6-10, and 12
are obvious over Imanishi in view of Poon.
SUMMARY
We affirm the four obviousness rejections of claims 1, 2, 4, and 6-12
over Imanishi alone, or in view of Armstrong, Kaibuchi, or Poon.

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

dm

Notice of References Cited

Application/Control No.

11/090,689
Applicant(s)/Patent Under
Reexamination
Appeal No.2011-001817
Examiner

BPAI
Art Unit

1600

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V

http://www.millipore.com/catalogue/item/mahvn4550) (showing Multiscreen HV to be a 96-well plate filtering system) (Appendix
A).)

W

Herbert et al., “Chelerythrine is a potent and specific inhibitor of protein kinase C,” Biochem. Biophys. Res. Commun.,
172(3):993-9 (1990) (http://www.ncbi.nlm.nih.gov/pubmed/2244923) (Appendix B).

X

*A copy of this reference is not being furnished with this Office action. (See MPEP § 707.05(a).)
Dates in MM-YYYY format are publication dates. Classifications may be US or foreign.

U.S. Patent and Trademark Office
PTO-892 (Rev. 01-2001) Notice of References Cited Part of Paper No.
Biochem Biophys Res Commun. 1990 Nov 15;172(3):993-9.
Chelerythrine is a potent and specific inhibitor of protein kinase
C.
Herbert JM, Augereau JM, Gleye J, Maffrand JP.
Sanofi Recherche, Toulouse, France.
Abstract
The benzophenanthridine alkaloid chelerythrine is a potent, selective antagonist of the
Ca++/phospholopid-dependent protein kinase (Protein kinase C: PKC) from the rat brain. Half-
maximal inhibition of the kinase occurs at 0.66 microM. Chelerythrine interacted with the catalytic
domain of PKC, was a competitive inhibitor with respect to the phosphate acceptor (histone IIIS)
(Ki = 0.7 microM) and a non-competitive inhibitor with respect to ATP. This effect was further
evidenced by the fact that chelerythrine inhibited native PKC and its catalytic fragment identically
and did not affect [3H]- phorbol 12,13 dibutyrate binding to PKC. Chelerythrine selectively
inhibited PKC compared to tyrosine protein kinase, cAMP-dependent protein kinase and
calcium/calmodulin-dependent protein kinase. The potent antitumoral activity of celerythrine
measured in vitro might be due at least in part to inhibition of PKC and thus suggests that PKC
may be a model for rational design of antitumor drugs.
PMID:2244923[PubMed - indexed for MEDLINE]
Display Settings: Abstract
Performing your original search, (http://www.ncbi.nlm.nih.gov/pubmed/2244923), in
PubMed will retrieve 21 records.
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Page 1 of 1Chelerythrine is a potent and spe... [Biochem Biophys Res Commun. 1990] - PubMed - N...
10/17/2012http://www.ncbi.nlm.nih.gov/pubmed/2244923
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