Ex Parte Hubbell et al

Patent Trial and Appeal Board

Dec 19, 2012

12563201 (P.T.A.B. Dec. 19, 2012)

UNITED STATES PATENT AND TRADEMARK OFFICE
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.
12/563,201 09/21/2009 Jeffrey A. Hubbell 2968.03US02 5929
62274 7590 12/19/2012
DARDI & HERBERT, PLLC
Moore Lake Plaza, Suite 205
1250 East Moore Lake Drive
Fridley, MN 55432
EXAMINER
HADDAD, MAHER M
ART UNIT PAPER NUMBER
1644
MAIL DATE DELIVERY MODE
12/19/2012 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 JEFFREY A. HUBBELL and DOMINIQUE A. ROTHENFLUH
____________

Appeal 2011-010886
Application 12/563,201
Technology Center 1600
____________

Before DONALD E. ADAMS, JEFFREY N. FREDMAN, and
STEPHEN WALSH, Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL
This appeal under 35 U.S.C. § 134 involves claims 1-5, 10-16, and
19-26 (App. Br. 3; Ans. 3).
1
We have jurisdiction under 35 U.S.C. § 6(b).
STATEMENT OF THE CASE
The claims are directed to a medicament (claims 1-5 and 19) and a
delivery system for delivering a therapeutic agent (claims 10-16 and 20-26).
Claim 1 is representative and is reproduced below:

1
Pending claims 9, 17, and 18 stand withdrawn from consideration (App.
Br. 3; Ans. 3).
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Application 12/563,201

2
1. A medicament comprising a pharmaceutically acceptable carrier and a
substantially pure polypeptide not found in nature comprising an amino
acid sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, or a
conservative substitution thereof, wherein the polypeptide specifically
binds a cartilage tissue.

Claims 1-5, 10-16, and 19-26 stand rejected under the written
description provision of 35 U.S.C. § 112, first paragraph.
Claims 1-5, 10-16, and 19-26 stand rejected under the enablement
provision of 35 U.S.C. § 112, first paragraph.
Claims 1, 2, and 21 stand rejected under 35 U.S.C. § 102(b) as being
anticipated by Skeiky.
2

We affirm the written description and anticipation rejections. We
reverse the enablement rejection.

Written Description:
ISSUE
Does the preponderance of evidence on this record support
Examiner‟s conclusion that Appellants‟ Specification fails to provide written
descriptive support for the claimed invention?
FACTUAL FINDINGS (FF)
FF 1. Examiner finds that Appellants‟ Specification lacks written
descriptive support for modified peptides, which retain the ability of the
peptide to specifically bind cartilage tissue (Ans. 8).
FF 2. Examiner finds that Appellants‟ Specification lacks written
descriptive support for peptides longer than six amino acids, as represented
by SEQ ID NOs: 1-3, that bind cartilage tissue (id.).

2
Skeiky, et al., WO 01/81581 A2, published November 1, 2001.
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FF 3. Appellants disclose the sequences “WYRGRL (SEQ ID NO:1),
DPHFHL (SEQ ID NO: 2), or RVMLVR (SEQ ID NO:3)” (Spec 1: 28).
FF 4. Appellants define the term “conservative substitutions or mutations”
as “an amino acid belonging to a grouping of amino acids having a particular
size or characteristic” (id. at 18: 2-4).
ANALYSIS
While Appellants contend that claim 22 is “not part of the other claim
sets in the Application,” Appellants do not present separate arguments for
claim 22 or claim 23, but instead direct our attention to their arguments
regarding claim 1 (Reply Br. 5). Accordingly, we find that claims 22 and 23
are not separately argued and, therefore, fall together with claim 1.
Examiner finds that Appellants‟ Specification lacks written
descriptive support for polypeptides longer than those defined by SEQ ID
NOs: 1-3 or modified polypeptides of SEQ ID NOs:1-3, of any length, that
specifically bind a cartilage tissue (Ans. 8-9).
Appellants contend that the claimed sequences “are six (6) residues in
length, and … provide a specific definition, by structure and formula, for the
particular structural features of the polypeptides, which must include the
specific sequences and/or have conservative amino acid substitutions” (App.
Br. 16; Reply Br. 6). We are not persuaded. Notwithstanding Appellants‟
contention to the contrary, the medicament of claim 1 comprises a
polypeptide of undefined length that comprises the six amino acid sequence
of SEQ ID NO: 1, 2, or 3 (see Claim 1). Accordingly, the polypeptide of
claim 1 has an undefined structure. Therefore, we are not persuaded by
Appellants‟ contention that “what is claimed is predictable and has a
structure tied to the claimed property of binding cartilage” (App. Br. 17; see
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generally Reply Br. 6). In addition, Appellants do not identify which set of
amino acids within SEQ ID NO:s 1-3 are critical to the function of binding.
Indeed, based upon the teaching in the Specification, where “[s]ubstitutions
may include, e.g., 1, 2, 3, or more residues” (Spec 18, l. 19) “from other
members of the class to which the amino acid belongs” (Spec. 18, ll. 5-6; FF
4), the peptide of SEQ ID NO: 1, WYRGRL, may reasonably have four
“conservative changes” which will result in the entirely different peptide
sequence. There is no way, other than trial and error, to identify which
members of this very large class retain the function of binding cartilage. See
University of Rochester v. G.D. Searle & Co., 358 F.3d 916, 925 (Fed. Cir.
2004) (“Even with the three-dimensional structures of enzymes such as
COX-1 and COX-2 in hand, it may even now not be within the ordinary skill
in the art to predict what compounds might bind to and inhibit them.”)
Appellants fail to identify a disclosure in their Specification of
polypeptides representative of the full genus of the claimed invention that
are longer than six amino acids, comprise SEQ ID NO: 1, 2, or 3 or a
modified form thereof, and specifically bind a cartilage tissue.
For the foregoing reasons we are not persuaded by Appellants‟
contention that a skilled artisan would understand how to make polypeptides
within the scope of the claimed invention and screen these polypeptides for
the required binding activity (App. Br. 17; Cf. Ans. 14-15). Ariad
Pharmaceuticals, Inc. v. Eli Lilly and Co., 598 F.3d 1336, 1345-1346 (Fed.
Cir. 2010).

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CONCLUSION OF LAW
The preponderance of evidence on this record supports Examiner‟s
conclusion that Appellants‟ Specification fails to provide written descriptive
support for the claimed invention. The rejection of claim 1 under the written
description provision of 35 U.S.C. § 112, first paragraph is affirmed. Claims
2-5, 10-16, and 19-26 are not separately argued and fall together with claim
1. 37 C.F.R. § 41.37(c)(1)(iv).

Enablement:
ISSUE
Does the evidence of record support Examiner‟s conclusion that
undue experimentation would be required to practice the claimed invention?
FACTUAL FINDINGS (FF)
FF 5. Examiner finds that Appellants‟ Specification provides an enabling
disclosure of “a substantially pure polypeptide consisting of the amino acid
sequence of SEQ ID NOs: 1-3, wherein the polypeptide specifically binds a
cartilage tissue, and a delivery system thereof” (Ans. 5).
FF 6. Examiner finds that Appellants‟ Specification does not provide an
enabling disclosure of a polypeptide of undefined length that comprises an
amino acid sequence of SEQ ID NOs:1-3, wherein the polypeptide
specifically binds a cartilage tissue (id. at 5).
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FF 7. With reference to Yokoyama3 and Aina,4 Examiner finds “that minor
structural differences among structurally related compounds or compositions
can result in substantially different biological activities” (id. at 6).
ANALYSIS
Examiner finds
Given that SEQ ID NOs: 1-3 are a key determinant of the
activity of the claimed polypeptides, the skilled in the art would
conclude that all the amino acids of SEQ ID NOs: 1-3 are
essential for the activity of the claimed peptide. Because of the
lack of sufficient guidance and predictability in determining
which modifications would lead to a polypeptide that exhibits
specific binding to a cartilage tissue, and that the relationship
between a polypeptide and its activity was not well understood.
Residue substitutions that are conservative (e.g., Glu in
equilibrium Asp, Asn in equilibrium Asp, Ile in equilibrium
Leu, Lys in equilibrium Arg and Ala in equilibrium Gly) can
have severe phenotypic effects. There is no simple way to infer
the likely effect of an amino acid substitution on the basis of
sequence information alone. Therefore, one skill in the art
would not be able to predict what residue substitutions can be
replaced. Undue experimentation is needed to practice the
claimed invention.

(Ans. 7.) We are not persuaded.
As Appellants explain their Specification and the prior art establishes
that, at the time the instant invention was made, a skilled artisan would have
been able to make and screen for polypeptides within the scope of the

3
Y. Yokoyama and S. Ramakrishnan, Improved biological activity of a
mutant endostatin containing a single amino-acid substitution, 90 BRITISH
JOURNAL OF CANCER 1627-1635 (2004).
4
Olulanu H. Aina, et al., Therapeutic Cancer Targeting Peptides, 66 Wiley
Periodicals, Inc. Biopolymers (Pept Sci) 184-199 (2002).
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claimed invention without undue experimentation (App. Br. 10-12). We
agree.
CONCLUSION OF LAW
The evidence of record fails to support Examiner‟s conclusion that
undue experimentation would be required to practice the claimed invention.
The rejection of claims 1-5, 10-16, and 19-26 under the enablement
provision of 35 U.S.C. § 112, first paragraph is reversed.

Anticipation:
ISSUE
Does the preponderance of evidence on this record support
Examiner‟s finding that Skeiky teaches Appellants‟ claimed invention?
FACTUAL FINDINGS (FF)
FF 8. Skeiky‟s invention relates to polypeptides that “comprise at least a
portion of a Propionibacterium acnes protein that includes an amino acid
sequence selected from the group consisting of SEQ ID NOs: 300-29,212
and variants and derivatives thereof” (Skeiky 2: 23-26).
FF 9. Skeiky teaches an SEQ ID NO: 12465 is a Propionibacterium Acnes
Open Reading Frame (Skeiky 389: Table 3).
FF 10. Examiner finds that Skeiky‟s SEQ ID NO: 12465 “is a 95 amino
acid polypeptide comprising an amino acid sequence of … [Appellants‟]
SEQ ID NO: 1” (Ans. 9).
FF 11. Appellants disclose that “a pharmaceutically acceptable carrier is a
material that is combined with the substance for delivery to an animal”
(Spec. 32: 26-27).
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FF 12. Skeiky‟s “invention provides pharmaceutical compositions
comprising a polypeptide … and a physiologically acceptable carrier”
(Skeiky 39: 28-30 and 108: 19-32; see generally Ans. 9).
FF 13. Examiner finds that the phrase “„polypeptide not found in nature”
reads on an isolated polypeptide (Ans. 9).
FF 14. Appellants disclose that “[t]he term purified … refers to a
polypeptide that … has been chemically synthesized and is thus substantially
uncontaminated by other polypeptides, or has been separated or purified
from other most cellular components by which it is naturally accompanied”
(Spec. 19: 1-5).
FF 15. Skeiky teaches the purification of polypeptides (Skeiky 55: 17-25;
Ans. 9).
ANALYSIS
The claims were not argued separately and therefore stand or fall
together. 37 C.F.R. § 41.37(c)(1)(iv). Claim 1 is representative.
Examiner finds that Skeiky teaches a polypeptide (SEQ ID NO:
12465) that comprises Appellants‟ SEQ ID NO: 1, as well as, the
purification of polypeptides and pharmaceutical preparations comprising the
polypeptide (Ans. 9; FF 8-10, 12 and 15).
We are not persuaded by Appellants‟ contention that Skeiky fails to
teach “„substantially pure‟ compositions” (App. Br. 19-20; Cf. FF 13-15).
We are not persuaded by Appellants‟ contention that Skeiky fails to
teach a “[p]harmaceutically acceptable carrier” (App. Br. 19-20; Cf. FF 11-
12).
SEQ ID NO: 12465 is taught to be a polypeptide within the scope of
Skeiky‟s invention (FF 8-10; Ans. 16-17). Skeiky teaches that polypeptides
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within the scope of Skeiky‟s invention are purified and combined with a
pharmaceutically acceptable carrier (FF 12 and 15; Ans. 17). Accordingly,
we are not persuaded by Appellants‟ contention that Skeiky does not
exemplify the purification of SEQ ID NO: 12465 (App. Br. 20).
Appellants contend that Skeiky “states that „the present invention
provides pharmaceutical compositions comprising a polypeptide … as
described above and a physiologically acceptable carrier.‟ But the disputed
SEQ ID NO:12465 does not appear „above‟” (App. Br. 20; Reply Br. 3-5).
We are not persuaded (see FF 8).
CONCLUSION OF LAW
The preponderance of evidence on this record supports Examiner‟s
finding that Skeiky teaches Appellants‟ claimed invention. The rejection of
claim 1 under 35 U.S.C. § 102(b) as being anticipated by Skeiky is affirmed.
Claims 2 and 21 are not separately argued and fall together with claim 1. 37
C.F.R. § 41.37(c)(1)(iv).

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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