Ex Parte Smith

Board of Patent Appeals and Interferences

Feb 16, 2005

10203081 (B.P.A.I. Feb. 16, 2005)

1
The opinion in support of the decision being entered today was not written
for publication and is not binding precedent of the Board.
UNITED STATES PATENT AND TRADEMARK OFFICE
____________
BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________
Ex parte GARY KEITH SMITH
____________
Appeal No. 2005-0147
Application No. 10/203,081
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ON BRIEF
____________
WILLIAM F. SMITH, ELLIS and GREEN, Administrative Patent Judges.
ELLIS, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal pursuant to 35 U.S.C. § 134 from the examiner’s final rejection
of claims 1, 4-6, 9-14 and 17-20. Claims 2, 3, 7, 8, 15, 16 and 21 have been indicated
as being allowable. Paper No. 12, p. 1.
Appeal No. 2005-0147
Application No. 10/203,081
2
Claim 1 is representative of the subject matter on appeal and reads as follows:
1. A method of screening a compound to determine whether the compound
affects caspase activation induced by a viral reaper protein, said method
comprising:
a) obtaining a vertebrate cell extract in which the addition of isolated
viral reaper protein induces detectable caspase activation;
b) adding isolated viral reaper protein having at least 50% sequence
similarity to SEQ ID NO:2 and capable of inducing caspase activation in a
vertebrate cell, and a test compound to said vertebrate cell extract;
c) measuring caspase activation; and
d) comparing caspase activation that occurs in the presence of the
test compound to that which would be expected in the absence of the test
compound;
where a decrease in caspase activation compared to that which would be
expected in the absence of the test compound indicates that said compound
inhibits viral reaper-induced caspase activation, and an increase in caspase
activation compared to that which would be expected in the absence of the test
compound indicates that said test compound enhances viral reaper-induced
caspase activation.
The examiner relies on a single reference:
Murphy, “Virus Taxonomy,” in Fields Virology, 3rd edition, B. N. Fields et al., eds.,
Lippincott-Raven Publishers, Philadelphia, pp. 15-53, (1996).
The claims stand rejected as follows:
I. Claims 1, 4-6, 9-14 and 17-20 stand rejected under 35 U.S.C. § 112, first
paragraph, written description, as containing subject matter which was not described in
the specification in such a way as to reasonably to one skilled in the relevant art that
the inventor had possession of the claimed invention at the time the application was
Appeal No. 2005-0147
Application No. 10/203,081
1 We find that the appellant has submitted two briefs; one on August 4, 2003 and
one on December 15, 2003, each of which has been considered by the examiner. We
refer to the earlier-filed brief as Brief I, and the later-filed brief as Brief II.
3
filed.
II. Claims 1, 4-6, 9-14 and 17-20 stand rejected under 35 U.S.C. § 112, first
paragraph, as being based on a non-enabling disclosure.
We have carefully considered the respective positions of both the appellant and
the examiner and find ourselves in substantial agreement with that of the appellant.1
Accordingly, we reverse.
Background
Apoptosis is said to be “a form of programmed cell death, by which an organism
eliminates extraneous or harmful cells.” Specification, p. 1. It is said to occur “via the
activation of intrinsic cell-suicide programs” which are regulated by both intra- and extra-
cellular signals. Id. Several apoptosis inducer genes, as well as inhibitors of apoptosis
proteins (IAP), have been identified. Id. For example, in Drosophila melanogaster,
three apoptotic activator proteins known as reaper (rpr), head involution defective (hid)
and grim have been characterized. Id.
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The specification (page 2) discloses that
Viral infection of host cells, and replication therein, is often associated with
inhibition of apoptosis to enable viral replication and the subsequent stimulation
[of] apoptosis of the host cells for viral particle release. Certain viral gene
products have been shown to specifically inhibit or induce apoptosis. However,
many viruses additionally encode proteins that inhibit apoptosis, prolonging the
survival of infected cells and thereby aiding viral replication or viral persistence in
the host.
The appellant is said to have identified certain non-structural proteins (NSs) of
viruses of the family Bunyaviridae which have sequence similarity with the D.
melanogaster reaper protein and which are capable of activating cellular apoptotic
pathways. Specification, pp. 4-5 and 7; Brief II, p. 3. Specifically, the aforementioned
proteins are said to be capable of activating caspases in a vertebrate cell-based assay.
Id. Cellular death by apoptosis is said to be generally executed by a family of proteases
known as caspases. Specification, p. 4.
The present invention is directed to a method of screening a compound to
determine its affect on caspase activation induced by a viral reaper protein which
involves the use of an isolated viral reaper protein (i) comprising an amino acid
sequence selected from the group consisting of SEQ ID NOS:2-17; (ii) which has at
least 50% sequence similarity with SEQ ID NO:2, and which is capable of inducing
caspase activation in a vertebrate cell; or (iii) which has at least 75% sequence
similarity with SEQ ID NO:2, and which is capable of inducing caspase activation in a
vertebrate cell.
Discussion
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I. Written description
The examiner argues that the claimed method involves the use of a genus of
proteins which (i) originate from viruses; (ii) have at least 50% sequence similarity with
SEQ ID NO:2; and (iii) are capable of inducing caspase activation in a vertebrate cell.
Answer, p. 3. The examiner points out that the specification discloses fifteen (15)
proteins which have from 62%-87% sequence similarity with SEQ ID NO:2. Id. The
examiner further argues that two searches of the NCBI database which she conducted
at year two and year three after the filing of the present application did not uncover any
viral reaper proteins having at least 50% sequence similarity with SEQ ID NO:2, other
than proteins from the family Bunyaviridae. Id., p. 4. The examiner still further argues
that if proteins meeting the claim limitations exist in other viral families, the specification
does not “reasonably convey that Appellants [sic, appellant] know of them or possessed
them.” Id. The examiner still further argues that
. . . considering then [sic, the] limited range of examples, contrasted with the
broad scope of “viral reaper proteins” and the unpredictability of discovery of
similar proteins in other families of virus, it is maintained that the specification
does not reasonably convey possession of the full scope of “viral reaper proteins”
recited in the claims [emphases added]. Id.
In order to satisfy the written description requirement of 35 U.S.C. § 112, the
application must reasonably convey to one skilled in the art that the applicant was in
possession of the claimed subject matter at the time the application was filed.
Vas-Cath Inc. v. Mahurkar, 935 F.2d 1555, 1563, 19 USPQ2d 1111, 1117 (Fed. Cir.
1991)(“The invention is, for purposes of the ‘written description’ inquiry, whatever is now
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claimed”).
First, we note that the examiner has only rejected those claims which are
directed to the use of viral reaper proteins having at least 50%, and at least 75%,
sequence similarity with SEQ ID NO:2, and which are capable of inducing caspase
activation in a vertebrate cell. The examiner’s approach to determining whether or not
the specification provides an adequate written description of the claimed invention has
been to search protein databases and look for other proteins within the scope of the
claim. Having found none, other than those described in the specification, she then
argues that if there were some, then the appellants did not possess them at the time the
application was filed. This approach is not legally sound. The written description inquiry
focuses on whether the specification reasonably conveys to one skilled in the art
whether the applicant invented the claimed subject matter. Thus, the relevant inquiries
are: what is the appellant’s claimed invention? What is now claimed? Vas-Cath Inc. v.
Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1117. As stated above, the claimed
invention is directed to the use of proteins having specific structural and biological
properties. To that end, we point out that our appellate, reviewing court has held that in
some cases, the written description requirement might be satisfied if there is a
correlation between the structure of a compound and its function. University of
Rochester v. G.D. Searle & Co., 358 F.3d 916, 925, 69 USPQ2d 1886, 1893 (Fed. Cir.
2004); Enzo Biochem Inc. v. Gen-Probe Inc., 296 F.3d 1316, 1324, 63 USPQ2d 1609
(Fed. Cir. 2002). Given the claims in the present case (methods involving the use of
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compounds having differing levels of structural similarity to a disclosed compound, but
the same function), the examiner should have addressed this correlation in her analysis
of whether the specification provides an adequate written description of the invention.
With respect to the claims directed to a viral reaper protein having at least 75%
sequence similarity to SEQ ID NO:2, the examiner appears to have answered this
question in the affirmative. See summary of the examiner’s Answer on page 5 above,
and the Answer, p. 3. Thus, we find that the examiner acknowledges that the
specification provides an adequate written description of the subject matter set forth in
claims 5, 6, 11-14 and 17-20. What about the written description in the specification of
viral reaper protein having at least 50% sequence similarity to SEQ ID NO:2? We are
not so sure, but the examiner’s rejection in the regard has been misdirected. To that
end, attention is directed to our comments which immediately follow and in the section
entitled “Other Issues,” below.
Second, in making the rejection based on the failure of the specification to
provide an adequate written description of the claimed invention, the examiner appears
to be considering the factors that are normally applied when making an enablement
determination. (See our discussion of enablement and the factors set forth by the court
in In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988), below). In
fact, it is difficult to discern a difference between the examiner’s written description and
enablement rejections. We point out that “‘the written description’ requirement is
separate and distinct from the enablement requirement,” thus, the criteria for satisfying
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each requirement are different. See, e.g., University of Rochester v. G.D. Searle & Co.,
358 F.3d at 920-21, 69 USPQ2d at 1893; Enzo Biochem Inc. v. Gen-Probe Inc., 296
F.3d at 1324, 63 USPQ2d at 1612; Vas-Cath Inc. v. Mahurkar, 935 F.2d at 1563, 19
USPQ2d at 1116. Since the “Wands” factors discussed by the examiner are not
relevant to the issue of written description, the rejection, in its entirety, is not
sustainable.
II. Enablement
The examiner argues that the claims are directed to any “viral reaper protein”
having specific structural and functional characteristics. Answer, p. 5. The examiner
further argues that the specification only discloses fifteen (15) examples of such
proteins and that all were isolated from one viral family, Bunyaviridae. Id. The
examiner still further argues that the specification fails to provide any guidance as to the
isolation of the claimed proteins from other viral families. Id. The examiner contends
that because no similar proteins have been discovered outside the Bunyaviridae family
in two database searches several years after the filing of the application,
it is reasonably inferred that a large quantity of additional experimentation would
be required to discover “viral reaper proteins” among viruses and viral proteins
that were uncharacterized and unknown at the time the invention was made.
Considering the scope of the claims, the limited scope of the disclosure, and the
quantity of experimentation required, it is concluded that undue experimentation
would be required to make and use the full scope of the claimed invention
[emphasis added]. Id.
It is well established that the specification must teach those skilled in the art to
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make and use the full scope of the claimed invention without undue experimentation.
Enzo Biochem Inc. v. Calgene Inc., 188 F.3d 1362, 1371, 52 USPQ2d 1129, 1135 (Fed.
Cir. 1999); Genentech, Inc. v. Novo Nordisk, A/S, 108 F.3d 1361, 1365, 42 USPQ2d
1001, 1004 (Fed. Cir. 1997); PPG Ind., Inc. v. Guardian Ind. Corp., 75 F.3d 1558, 1564,
37 USPQ2d 1618, 1623 (Fed. Cir. 1996); In re Wright, 999 F.2d 1557, 1561-62, 27
USPQ2d 1510, 1513 (Fed. Cir. 1993); In re Vaeck, 947 F.2d 488, 495-96, 20 USPQ2d
1438, 1444-45 (Fed. Cir. 1991). “That some experimentation may be required is not
fatal, the issue is whether the amount of experimentation required is ‘undue.’” In re
Vaeck, 947 F.2d at 495, 20 USPQ2d at 1444. In determining whether a disclosure
would require undue experimentation, the court set forth several factors to be
considered. These factors include:
(1) the quantity of experimentation necessary, (2) the amount of direction or
guidance presented, (3) the presence or absence of working examples, (4) the
nature of the invention, (5) the state of the prior art, (6) the relative skill of those
in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of
the claims. In re Wands, 858 F.2d at 737, 8 USPQ2d at 1404.
Here, we find that the examiner has not applied the facts of this case to the
Wands factors in a meaningful way, but simply states that it can be “inferred” that it
would require undue experimentation for one skilled in the art to discover new viral
reaper proteins from other viral families based on her own inability to find such proteins
in a database search. More than inferences are required to make a prima facie case of
non-enablement. Although enablement is a question of law, it must nevertheless be
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Application No. 10/203,081
10
based on underlying factual findings. In re Wands, 858 F.2d at 735, 8 USPQ2d at 1402;
In re Vaeck, 947 F.2d at 495, 20 USPQ2d at 1444.
In our view, one skilled in the art would understand whether a particular protein
has at least 50%, or at least 75%, sequence similarity with SEQ ID NO:2 as set forth in
the claims. In addition, we find that the functional assays disclosed in the specification
provide sufficient guidance for one skilled in the art to determine whether a particular
protein is within the scope of the claims. Accordingly, we agree with the appellant that it
would not require undue experimentation for one skilled in the art to “make and use” the
claimed methods.
As a final matter, with respect to the subject of taxonomy, we find the arguments
raised by both the examiner and the appellant to be misdirected. The relevant issue
here is whether the specification disclosure would have enabled one skilled in the art to
“make and use” a viral protein having the claimed characteristics, regardless of its name
or origin.
Other Issues
Upon return of this application to the corps, the examiner may wish to re-consider
whether claims 1 and 4 are unpatentable under § 112, first paragraph, written
description, as containing subject matter which was not described in the application in
such a way as to reasonably convey to one skilled in the relevant art that the inventors
had possession of the claimed invention at the time the application was filed.
The examiner states, and the appellant does not contest, that the fifteen viral
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proteins disclosed in the specification having from 62% to 87% sequence similarity with
SEQ ID NO:2. However, claims 1 and 4 are directed to viral reaper proteins having as
little as 50% sequence similarity with SEQ ID NO:2 and which are capable of inducing
caspase activation in a vertebrate cell. To satisfy the written description requirement,
the application “must describe an invention and do so in sufficient detail that one skilled
in the art can clearly conclude that ‘the inventor invented the claimed invention.’”
Lockwood v. American Airlines, Inc., 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966
(Fed. Cir. 1997); In re Gostelli, 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir.
1989). Thus, the examiner may wish to consider whether the specification describes a
viral reaper protein having the characteristics set forth in claim 1 in sufficient detail, and
with reasonable clarity, such that those skilled in the art can conclude that he was in
possession of the claimed invention, or whether the appellant had “just a mere wish or
plan for obtaining” said protein. Fiers v. Revel, 984 F.2d 1164, 1171, 25 USPQ2d 1601,
1606 (Fed. Cir. 1993). In this regard, attention is directed to the courts holding with
respect to the DNA sequences set forth in Fiers. The examiner may wish to consider
whether viral reaper proteins having less than 62% sequence similarity with SEQ ID
NO:2 require “more than a mere statement that they are part of the invention.” Cf.,
University of California v. Eli Lilly and Co., 119 F.3d 1559, 43 USPQ2d 1398 (Fed. Cir.
1997). That is, does the specification reasonably convey to those skilled in the art that
the inventor was in possession of a method of using a protein having the claimed
characteristics at the time the application was filed? Vas-Cath Inc. v. Mahurkar, 935
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F.2d at 1563, 19 USPQ2d at 1117.
Accordingly, in view of the foregoing, the examiner’s decision is reversed.
REVERSED
WILLIAM F. SMITH )
Administrative Patent Judge )
)
)
)
) BOARD OF PATENT
JOAN ELLIS ) APPEALS
Administrative Patent Judge ) AND
) INTERFERENCES
)
)
)
LORA GREEN )
Administrative Patent Judge )
Appeal No. 2005-0147
Application No. 10/203,081
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David J. Levy
Corporate Intellectual Property
Glaxo SmithKline
Five Moore Drive
P.O. Box 13398
Research Triangle Park, NC
27709-3398