Ex Parte Burkhard

Patent Trial and Appeal Board

Jun 13, 2013

10545676 (P.T.A.B. Jun. 13, 2013)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte PETER BURKHARD
__________

Appeal 2011-012370
Application 10/545,676
Technology Center 1600
__________

Before FRANCISCO C. PRATS, ULRIKE W. JENKS, and JOHN G. NEW,
Administrative Patent Judges.

PRATS, Administrative Patent Judge.

DECISION ON APPEAL
This appeal1 under 35 U.S.C. § 134 involves claims to a peptidic
nanoparticle useful as a drug or antigen carrier. The Examiner entered
rejections for lack of written description, lack of enablement, and
anticipation.
We have jurisdiction under 35 U.S.C. § 6(b).
We reverse.

1 The Real Party in Interest is the inventor, Dr. Peter Burkhard (App. Br. 2).
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STATEMENT OF THE CASE
Claims 25-28, 34-37, 40, and 56 stand rejected and appealed (App. Br.
2). Claim 25, the only independent claim, illustrates the appealed subject
matter and reads as follows:
25. A peptidic nanoparticle consisting of an assembly of 10
or more peptides, in which each peptide is consisting of a continuous
chain of a peptidic oligomerization domain D1, a linker segment L,
and a peptidic oligomerization domain D2 of formula (I):
D1 – L – D2 (I),
wherein
each D1 is a synthetic or natural peptide, and a plurality of D1
form at least one protein oligomer assembly (D1)m, wherein the
protein oligomer assembly consists of m subunits of D1,
each D2 is a synthetic or natural peptide, and a plurality of D2
form at least one protein oligomer assembly (D2)n, wherein the
protein oligomer assembly consists of n subunits of D2,
the peptidic nanoparticle contains:
(a) one of m or n is 2 forming a dimer protein oligomer
assembly, and the other of m or n is 5 forming a pentamer protein
oligomer assembly; or
(b) one of m or n is 3 forming a trimer protein oligomer
assembly, and the other of m or n is 4 or 5 forming a tetramer or
pentamer protein oligomer assembly, respectively; or
(c) one of m or n is 4 forming a tetramer protein oligomer
assembly, and the other of m or n is 5 forming a pentamer protein
oligomer assembly;
L is a short flexible linker segment,
at least one D1 or D2 is a coiled coil peptide sequence, and
D1, D2 or L is optionally further substituted by a substituent
selected from a targeting entity, drug and antigen.

The following rejections are before us for review:
(1) Claims 25-28, 34-37, 40, and 56, under 35 U.S.C. § 112, first
paragraph, as failing to comply with the written description requirement
(Ans. 5-13);
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(2) Claims 25-28, 34-37, 40, and 56, under 35 U.S.C. § 112, first
paragraph, as failing to be fully enabled by the Specification (Ans. 14-26);
(3) Claims 25-28, 34-37, 40, and 56, under 35 U.S.C. § 102(b) as
anticipated by Yeates2 (Ans. 27-29);
(4) Claims 25-28 and 56, under 35 U.S.C. § 102(b) as anticipated by
Oldberg3 (Ans. 29-30);
(5) Claim 25, under 35 U.S.C. § 112, first paragraph, as failing to
comply with the written description requirement (Ans. 30-32); and
(6) Claims 25-28 and 56, under 35 U.S.C. § 102(b) as anticipated by
Gill4 (Ans. 32-33).
WRITTEN DESCRIPTION (I)
The Examiner’s position in the first written description rejection is
essentially that Appellants’ claims encompass a genus of compositions
which is effectively “limitless to any class of peptidic nanoparticle
consisting of peptidic oligomerization domains D1 and D2 and any linker
segment that can form peptide or amide bonds” (Ans. 8; see also id. at 9-10,
12-13).
In contrast, the Examiner contends, the Specification fails to describe
“sufficient variety of species to reflect this variance in the genus since the
specification does not provide any examples of derivatives or variances” (id

2 WO 00/68248 A2 (published Nov. 16, 2000).
3 Åke Oldberg et al., COMP (Cartilage Oligomeric Matrix Protein) Is
Structurally Related to the Thrombospondins, 267 J. BIOL. CHEM. 22346-
22350 (1992).
4 Steven R. Gill et al., Dynactin, a Conserved, Ubiquitously Expressed
Component of an Activator of Vesicle Motility Mediated by Cytoplasmic
Dynein, 115 J. CELL BIOL. 1639-1650 (1991).
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at 8), and only “describes the fragment of cartilage oligomerization matrix
protein (COMP) and fragment of foldon protein from bacteriophage T4
protein fibritin for D1 and D2, and GG [glycine-glycine] or GGSG [glycine-
glycine-serine-glycine] as the linker segments” (id. at 11).
Thus, the Examiner finds, the Specification “fails to provide adequate
written description for the genus of the claims and does not reasonably
convey to one skilled in the relevant art that the inventor(s), at the time the
application was filed, had possession of the entire scope of the claimed
invention” (id. at 13).
As stated in In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992):
[T]he examiner bears the initial burden . . . of presenting a
prima facie case of unpatentability. . . .
After evidence or argument is submitted by the applicant
in response, patentability is determined on the totality of the
record, by a preponderance of evidence with due consideration
to persuasiveness of argument.

To meet the initial burden of establishing a prima facie case of
unpatentability based on a lack of written description, the Examiner must
“present[] evidence or reasons why persons skilled in the art would not
recognize in the disclosure a description of the invention defined by the
claims.” In re Alton, 76 F.3d 1168, 1175 (Fed. Cir. 1996).
We agree with Appellant that a preponderance of the evidence does
not support the Examiner’s finding that the claims lack adequate descriptive
support.
Our reviewing court has stated that, “[f]or generic claims, we have set
forth a number of factors for evaluating the adequacy of the disclosure,
including ‘the existing knowledge in the particular field, the extent and
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content of the prior art, the maturity of the science or technology, [and] the
predictability of the aspect at issue.’” Ariad Pharmaceuticals, Inc. v. Eli
Lilly and Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010) (quoting Capon v.
Eshhar, 418 F.3d 1349, 1359 (Fed. Cir. 2005).
Accordingly:
A claim will not be invalidated on section 112 grounds
simply because the embodiments of the specification do not
contain examples explicitly covering the full scope of the claim
language. That is because the patent specification is written for
a person of skill in the art, and such a person comes to the
patent with the knowledge of what has come before. Placed in
that context, it is unnecessary to spell out every detail of the
invention in the specification; only enough must be included to
convince a person of skill in the art that the inventor possessed
the invention and to enable such a person to make and use the
invention without undue experimentation.

Falkner v. Inglis, 448 F.3d 1357, 1366 (Fed. Cir. 2006) (quoting LizardTech,
Inc. v. Earth Resource Mapping, PTY, Inc., 424 F.3d 1336, 1345 (Fed. Cir.
2005)); see also Capon v. Eshhar, 418 F.3d at 1359 (“It is not necessary that
every permutation within a generally operable invention be effective in order
for an inventor to obtain a generic claim, provided that the effect is
sufficiently demonstrated to characterize a generic invention.”).
In this instance, we acknowledge that claim 25 recites a nanoparticle
composed of ten or more peptides, each of which has the structure D1-L-D2,
and that D1 and D2 can be any peptidic oligomerization domain capable of
forming a dimeric, trimeric, tetrameric, or pentameric structure, with the
requirement that either D1 or D2 must be a coiled coil. We also
acknowledge that the linker can be essentially any moiety capable of linking
the two oligomerization domains, with certain linkers being preferred (see
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Spec. 6).

We also acknowledge that claim 25 recites that either of the
oligomerization domains or the linker can optionally be substituted by a
targeting entity, drug, or antigen. We further acknowledge that the
Specification only exemplifies the COMP and foldon oligomerization
domains, as well as an apparently novel oligomerization domain prepared by
Appellant, designated as “de novo” (Spec. 25).
As Appellant points out, however, “[p]eptidic oligomerization
domains are well-known” (Spec. 6). This premise is supported not only by
Appellant’s citation to the Biochemistry5 textbook reproduced in Appendix
B of the Appeal Brief (“Many proteins exist in nature as oligomers,
complexes composed of (often symmetric) noncovalent assemblies of two or
more monomer subunits.”), but also by the fact that the Yeates reference
cited by the Examiner produces polyhedral peptidic particles similar to those
in Appellant’s claims, from the same oligomerization domain building
blocks used by Appellant (see Yeates generally). Moreover, the Examiner
does not dispute Appellant’s assertion (see, e.g. App. Br. 9) that the identity
of suitable oligomerization domains, including those with coiled coils, can
be retrieved through database searches.
Thus, we acknowledge that Appellant’s invention is recited in generic
terms. However, because a preponderance of the evidence supports
Appellant’s position that the claimed nanoparticle is composed of building
blocks whose identities and properties would have been recognized by a

5 REGINALD H. GARRETT AND CHARLES H. GRISHAM, BIOCHEMISTRY (3d. ed.,
Thomson Brooks/Cole, 2005).
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skilled artisan, we are not persuaded that the generically claimed invention
lacks adequate descriptive support when the Specification is viewed through
the eyes of that skilled practitioner.
We also acknowledge, as the Examiner appears to argue (see Ans. 12-
13), that an artisan would recognize that the claims encompass numerous
oligomerization domains and linkers not explicitly described in the
Specification, including oligomerization domains substituted with peptidic
targeting moieties, drugs, or antigens. In our view, however, the breadth of
the claims does not undercut the evidence of record supporting Appellant’s
position that the peptidic oligomerization domains which ultimately make up
the claimed nanoparticles belong to a class of peptides that a skilled artisan
would readily recognize, based on the peptides’ capacity to oligomerize into
the dimers, trimers, tetramers, and pentamers required by Appellant’s
claims.
Thus, as we are not persuaded, for the reasons discussed, that a
preponderance of the evidence supports the Examiner’s prima facie case of
lack of written description, we reverse the Examiner’s first rejection of claim
25, and its dependents, on that ground.
WRITTEN DESCRIPTION (II)
The Examiner also separately rejected claim 25 under 35 U.S.C.
§ 112, first paragraph, contending that the Specification failed to provide
adequate descriptive support for the language requiring the claimed particles
to consist of “an ‘assembly of 10 or more peptides’” (Ans. 30). In particular,
the Examiner contends that no word-for-word support exists, even in the
context of discussing the “even units” concept explained in Table 2 of the
Specification (id. at 31).
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Moreover, the Examiner contends, because of the “or more” language
in the claim, “any number, i.e., 100, 1,000, 10,000, 100,000 and so on is
implied. However, there is no support for such numbers of peptides” (Ans.
32; see also id. at 49-50).
We are not persuaded. Rather, we agree with Appellant that the
Specification provides adequate support for the limitation requiring
claim 25’s peptidic nanoparticle to consist of an assembly of 10 or more
peptides.
In particular, as Appellant points out, the Specification discloses that
the “[p]eptidic nanoparticles are formed from a multitude of monomeric
building blocks of formula (I)” (Spec. 5). Thus, the only upper limit on the
number of peptide subunits present in the disclosed nanoparticles is the
ultimate physical constraint of forming the nanoparticle from those peptide
subunits.
As Appellant also points out, the Specification states:
Peptidic nanoparticles are formed from monomeric
building blocks of formula (I). If such building blocks
assemble, they will form so-called “even units”. The number of
monomeric building blocks, which will assemble into such an
even unit will be defined by the least common multiple (LCM).
Hence, if for example the oligomerization domains of the
monomeric building block form a trimer (D1)3 (m=3) and a
pentamer (D2)5 (n=5), 15 monomers will form an even unit
(Figure 1 A, Example 5). If the linker segment L has the
appropriate length, this even unit may assemble in the form of a
spherical peptidic nanoparticle. Similarly, if the
oligomerization domains D1 and D2 of the monomeric building
block form a trimer (D1)3 (m=3) and a tetramer (D2)4 (n=4), the
number of monomers needed to form an even unit will be 12
(Figure 1 B).

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(Id. at 10-11 (emphasis added).) The Specification then explains, in Table 2,
that when an oligomerization domain that forms a pentamer is combined
with an oligomerization domain that forms a dimer, the LCM is 10, and the
10 monomers will form a particle that is a dodecahedron or icosahedron (see
id. at 11 (Table 2)).
Given this disclosure that a peptidic nanoparticle can be formed from
10 peptidic subunits, and further given the disclosure that particles can also
form from many monomeric peptidic building blocks, and even units, we are
not persuaded that the language in claim 25 requiring the nanoparticle to
consist of an assembly of 10 or more peptides lacks adequate descriptive
support. We therefore reverse the Examiner’s rejection of claim 25 on this
ground.
ENABLEMENT
In rejecting claims 25-28, 34-37, 40, and 56 for lack of enablement,
the Examiner concludes, essentially, that the Specification enables the use of
the exemplified oligomerization domains and linkers to prepare peptidic
nanoparticles, but contends, nonetheless, that the Specification “does not
enable any person skilled in the art to which it pertains, or with which it is
most nearly connected, to make and/or use the invention commensurate in
scope with these claims” (Ans. 14).
Applying the oft-cited factors set forth in In re Wands, 858 F.2d 731,
737 (Fed. Cir. 1988), the Examiner notes the scope of the claims (see Ans.
15, 25-26), as well as the art-recognized unpredictability in determining a
peptide’s three-dimensional structure from its amino acid sequence, and also
notes the unpredictable effect of even small changes in a protein’s amino
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acid sequence (see id. at 15-21).6 The Examiner further notes the disclosure
of the COMP and foldon oligomerization domains in Appellant’s examples,
but finds that the Specification does not “describe any other peptidic
oligomerization domains of other proteins and peptides that are linked by
other flexible linkers. The specification does not disclose any other
targeting entity, since the targeting entity can be anything according to the
instant specification” (id. at 24).
The Examiner further contends that, although the “disclosure gives
examples of the targeting entities . . . these entities are not fully defined in
the specification. Description of COMP and foldon for proteins are not
sufficient to encompass numerous other proteins that belong to the same
genus” (id.).
Ultimately, the Examiner finds:
Given that one could not determine the structure of a protein
computationally, and that the effect of amino acid substitution
is unpredictable, it flows logically that one would be unduly
burdened with experimentation to determine the effect of amino
acid substitution(s) in a peptide or protein, with regards to
structure, function, or physical/chemical properties. Therefore,
making any peptidic nanoparticle consisting of an assembly of
10 or more peptides, having the formula D1-L-D2 that has the
same activity as the claimed peptide, one would be unduly
burdened with experimentation to determine the effect of amino

6 In support of the argument regarding unpredictability as to peptide
structure and function, the Examiner cites a number of references, including
“Rudinger” (Ans. 15), “SIGMA” (id.), “Schinzel” (id. at 16), “Berendsen”
(id.), “Voet” (id. at 17), and “Ngo” (id. at 18). While Appellant does not
dispute the Examiner’s characterization of these references, none of these
references is cited in the Evidence Relied Upon section of the Answer (see
Ans. 4), and our review of the record does not indicate that these references
have been made of record by the Examiner.
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acid content, substitution(s), addition and deletions in a peptide
or protein, with regards to structure, function, or
physical/chemical properties.

(Id. at 26.)

We are not persuaded.
It may be true, as the Examiner argues, that peptides’ three-
dimensional structures cannot be predicted from their amino acid sequences,
and that even minor changes in amino acid sequences can elicit significant
change in the function of the resulting protein. In the instant case, however,
rather than requiring extensive peptide manipulations, the oligomerization
domains suitable for forming the claimed nanoparticles include prior art
structures that a skilled artisan would readily recognize, as discussed above.
It might be true that a skilled artisan would not know, before actually
testing, precisely which oligomerization domains and linkers, and
substituted forms thereof, could be combined to produce peptidic
nanoparticles. However, the Specification’s examples explain the
procedures by which one can test potential combinations for particle
formation (see Spec. 25-32), and the Examiner has not pointed to any clear
or specific evidence suggesting that performing such tests would amount to
anything beyond routine experimentation. As Wands explains:
Enablement is not precluded by the necessity for some
experimentation such as routine screening. However,
experimentation needed to practice the invention must not be
undue experimentation. . . . The test is not merely quantitative,
since a considerable amount of experimentation is permissible,
if it is merely routine, or if the specification in question
provides a reasonable amount of guidance with respect to the
direction in which the experimentation should proceed.

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In re Wands, 858 F.2d at 736-37 (citations omitted, emphasis added).
We acknowledge that a skilled practitioner might not expect every
conceivable combination of oligomerization domains and linkers to result in
a nanoparticle as described in the Specification. That fact does not,
however, demonstrate non-enablement, since the claims may encompass
inoperative embodiments and still be enabled. See Atlas Powder Co. v. E.I.
du Pont De Nemours & Co., 750 F.2d 1569, 1576 (Fed. Cir. 1984).
Moreover, “[working] examples are not required to satisfy section
112, first paragraph.” In re Strahilevitz, 668 F.2d 1229, 1232 (CCPA 1982).
For example, in Falkner v. Inglis, the court affirmed the conclusion of this
Board’s predecessor that claims to a modified pox virus vaccine were
enabled, despite the fact that the specification focused on viruses other than
pox virus, provided no examples directed to pox virus, and discussed pox
virus only in general terms relating to the inventive disclosure. Falkner v.
Inglis, 448 F.3d at 1365.
In sum, as we are not persuaded that the preponderance of the
evidence supports the Examiner’s conclusion that the Specification fails to
enable the full scope of the claimed subject matter, we reverse the
Examiner’s enablement rejection.
ANTICIPATION – YEATES
Appellant argues that the Examiner did not make out a prima facie
case that Yeates anticipates claims 25-28, 34-37, 40, and 56 because Yeates
discloses using a rigid linker between the oligomerization domains of its
fusion proteins, rather than the flexible linker required by claim 25 (see App.
Br. 19)
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The Examiner responds that Appellant’s Specification does not
“define what a flexible linker is,” and notes that the Specification discloses
that a linker can be a peptide chain of 1 to 20 amino acids (Ans. 46). The
Examiner points out that, like Appellant’s Specification, Yeates discloses
that its linker was “incremented from 2 to 30 residues” and that Yeates
exemplified a helical linker 9 residues in length (id. at 47).
We agree with Appellant that the preponderance of the evidence does
not support the Examiner’s position.
It is well settled that inherency “may not be established by
probabilities or possibilities. The mere fact that a certain thing may result
from a given set of circumstances is not sufficient.” In re Oelrich, 666 F.2d
578, 581 (CCPA 1981).
Thus, the “very essence of inherency is that one of ordinary skill in
the art would recognize that a reference unavoidably teaches the property in
question.” Agilent Technologies, Inc. v. Affymetrix, Inc., 567 F.3d 1366,
1383 (Fed. Cir. 2009) (emphasis added).
In this case, Appellant’s claim 25 requires the linker segment “L” to
be “a short flexible linker segment” (App. Br. 28 (claim 25)). We agree that
claim 25 thus encompasses any degree of flexibility in its linker.
In contrast, however, as Appellant points out, Yeates expressly
discloses the importance of its linker being rigid:
A critical feature of the subject fusion proteins is that the
two or more naturally occurring protein components are rigidly
joined to each other in a manner such that the orientation in
space of each component relative to the other(s) in the fusion
protein is relatively static and can be anticipated in advance
based on the known structures of the components.

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(Yeates 5 (emphasis added).)
Yeates explains that “[a]ny linking group capable of providing the
requisite static orientation of the disparate components of the fusion protein
may be employed. Of particular interest in many embodiments is the use of
a linking group that comprises an alpha helical structure” (id. at 6 (emphasis
added)). Yeates thus exemplifies a helical linker 9 residues in length (id. at
16).
We note, as the Examiner points out, that Appellant’s Specification
states that the linker may be “preferably, a peptide chain, e.g. a peptide chain
consisting of 1 to 20 amino acids, in particular 1 to 6 amino acids” (Spec. 6).
We also note Yeates’ disclosure that, given the suitable physical lengths of
its linker, “the number of residues in the linking group generally ranges from
about 1 to 35, usually from about 2 to 20 and more usually from about 4 to
15” (Yeates 6).
We thus agree with the Examiner that Yeates’ linkers can have the
same number of amino acid residues as the linkers described by Appellant.
The Examiner has not, however, advanced any clear or specific evidence
suggesting that, based solely on the number of amino acid residues in them,
the particular linkers described by Yeates would necessarily or unavoidably,
that is inherently, be flexible, particularly given Yeates’ express and
repeated emphasis on the requirement for a rigid, rather than flexible linker.
Thus, given Yeates’ express and repeated disclosure of the
requirement for a rigid linking group, and given the Examiner’s failure to
advance any clear or specific evidence suggesting that the particular linkers
employed by Yeates would have some degree of flexibility, we are not
persuaded that the Examiner has shown that Yeates’ linkers would
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inherently be flexible, as required by claim 25. We therefore reverse the
Examiner’s rejection of claim 25, and its dependents, as anticipated by
Yeates.
ANTICIPATION – OLDBERG
Appellant argues, among other things, that the Examiner did not make
out a prima facie case that Oldberg anticipates claim 25 because Oldberg
“fails to disclose any protein made up of an assembly of 10 or more peptides
in which peptides have a different oligomerization state, such as the protein
oligomer assemblies (a), (b), or (c), as required by the present invention”
(App. Br. 23).
The Examiner responds that claim 25 can be interpreted such that the
“only requirement is that the peptide nanoparticle consists of an assembly of
10 or more peptides. Again, any two amino acids having an amide bond is a
peptide. Thus, this implies that the nanoparticle have at least 21 amino
acids, wherein, 1 amino acid acts as a linker” (Ans. 48). Therefore, the
Examiner argues, because the COMP sequence described in Oldberg
includes a “GG” moiety which Appellant uses as a linker, the corresponding
“D1 is a pentamer, and D2 is a long peptide sequence that is either a trimer
or tetramer. Since the reference teaches a peptide having more than 21
amino acids, this meets the limitation of an assembly of 10 or more
peptides” (Ans. 49).
We again find that Appellant has the better position.
We note Oldberg’s disclosure that “COMP is a homopolymer
composed of five identical disulfide-linked subunits” (Oldberg 22346). The
Examiner does not, however, direct us to any clear or specific evidence
suggesting that the pentamer-forming oligomerization domain of COMP is
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linked to a dimer-, trimer-, or tetramer-forming oligomerization domain as
required by options (a), (b), or (c) of claim 25, or that Oldberg prepares an
assembly of at least 10 such linked assemblies, as claim 25 also requires.
Thus, as we are not persuaded that Oldberg describes a peptidic nanoparticle
having all of the features recited in claim 25, we reverse the Examiner’s
rejection of that claim, and its dependents, as anticipated by Oldberg.
ANTICIPATION – GILL
Appellant argues that the Examiner did not make out a prima facie
case that Gill anticipates claim 25 because the dynactin protein described in
Gill “does not meet the requirements of the presently claimed invention (i.e.,
2 domains with different oligomerization states as required by sections (a),
(b) and (c) of claim 25). Furthermore, the reference clearly fails to disclose
an assembly of 10 or more peptides each having the required structure of
D1-L-D2” (App. Br. 26).
The Examiner reiterates the argument that “a peptide sequence having
at least 21 amino acids, wherein 1 amino acid acting as a linker would meet
the limitation of the claim” (Ans. 51-52).
We again find that a preponderance of the evidence does not support
the Examiner’s position.
We note Gill’s disclosure that the protein described in the reference,
“dynactin,” is a dimeric protein (see Gill 1639, abstract (“We show here that
a ~20S polypeptide complex (referred to as Activator . . .) stimulates dynein-
mediated vesicle transport. A major component of the activator complex is a
doublet of 150-kD polypeptides for which we propose the name dynactin (for
dynein activator.” (Emphasis added)).
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The Examiner does not, however, direct us to any clear or specific
evidence suggesting that the dimer-forming oligomerization domain of
dynactin is linked to a pentamer-forming oligomerization domain as required
by option (a) of claim 25, or that Gill prepares an assembly of at least 10
such linked assemblies, as claim 25 also requires. Thus, as we are not
persuaded that Gill describes a peptidic nanoparticle having all of the
features recited in claim 25, we reverse the Examiner’s rejection of that
claim, and its dependents, as anticipated by Gill.

SUMMARY
We reverse each of the Examiner’s rejections.

REVERSED

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