In Re: Qapsule Technologies, Inc. ( 2019 )

NOTE: This disposition is nonprecedential.
United States Court of Appeals
for the Federal Circuit
______________________
IN RE: QAPSULE TECHNOLOGIES, INC.,
Appellant
______________________
2018-1772
______________________
Appeal from the United States Patent and Trademark
Office, Patent Trial and Appeal Board in No. 13/882,773.
______________________
Decided: March 11, 2019
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DONALD GEORGE LEWIS, Lewis Kohn & Walker LLP,
San Diego, CA, for appellant.
THOMAS W. KRAUSE, Office of the Solicitor, United
States Patent and Trademark Office, Alexandria, VA, for
appellee Andrei Iancu. Also represented by SARAH E.
CRAVEN, FRANCES LYNCH.
______________________
Before NEWMAN, CHEN, and STOLL, Circuit Judges.
NEWMAN, Circuit Judge.
Qapsule Technologies, Inc. (“Qapsule”) appeals from
the Patent Trial and Appeal Board (“Board”) determination
that claims 1, 2, 5, 7, 13–15, 31, 33–35, and 38 of U.S. Pa-
tent Application No. 13/882,773 (“the ’773 Application”) are
2 IN RE: QAPSULE TECHNOLOGIES, INC.
anticipated by Perez 1 as evidenced by Mair, 2 Ye, 3 and Gon-
zales. 4 Because substantial evidence supports the Board’s
determination, and we discern no legal error in its analysis,
we affirm. 5
THE ’773 APPLICATION
The ’773 Application relates to “encapsulating recom-
binant enzymes and other cargo proteins within the inte-
rior space of protein nanoparticles.” ’773 Appl. at p. 2, ll.
32–34. The nanoparticles are assembled using shell pro-
teins, such as viral coat proteins, in the presence of bifunc-
tional polynucleotides and the desired cargo protein. Id. at
p. 3, ll. 7–26. Claim 1 is representative:
1. A synthetic capsule construct for providing a pro-
tected chemical milieu, the construct comprising:
a shell having a plurality of shell proteins, said plu-
rality of shell proteins being assembled with one
another for forming said shell and defining an en-
closure therein, each of said shell proteins, when
1 Perez et al., Functional Analysis of PA Binding by
Influenza A Virus PBJ: Effects on Polymerase Activity and
Viral Infectivity, 75 J. VIROLOGY 8127–36 (2001).
2 Mair et al., Receptor binding and pH stability- How
influenza A virus hemagglutinin affects host-specific virus
infection, 1838 BIOCHIMICA ET BIOPHYSICA ACTA 1153–68
(2014).
3 Ye et al., Association of Influenza Virus Matrix Pro-
tein with Ribonucleoproteins, 73 J. VIROLOGY 7467–73
(1999).
4 Gonzalez et al., Characterization of Influenza Virus
PBJ Protein Binding to Viral RNA: Two Separate Regions
of the Protein Contribute to the Interaction Domain, 73 J.
VIROLOGY 631–37 (1999).
5 Ex Parte Finn et al., No. 2017-001118, 2017 WL
6055117 (P.T.A.B. Nov. 27, 2017) (“Bd. Op.”).
IN RE: QAPSULE TECHNOLOGIES, INC. 3
assembled for forming said shell, having an inte-
rior surface facing inwardly toward said enclosure
and an exterior surface facing outwardly away
from said enclosure, said shell serving to restrict
permeability to and from said enclosure for provid-
ing the protected chemical milieu therein, said
shell proteins being recombinant;
a cargo protein, said cargo protein being recombi-
nant and optionally including a peptide tag; and
a bifunctional polynucleotide having both a first
aptameric activity for binding said cargo protein
and a second aptameric activity for retaining said
bifunctional polynucleotide within said enclosure
by assembly with the interior surface of said shell
protein,
said bifunctional polynucleotide being non-natu-
rally occurring; said bifunctional polynucleotide
serving to link said cargo protein within said enclo-
sure for providing the said cargo protein with the
protected chemical milieu therein.
As relevant herein, the limitations of claim 1 include
an enclosure made of recombinant “shell proteins,” a re-
combinant “cargo protein,” and a “bifunctional polynucleo-
tide” having the function of linking the cargo protein within
the enclosure. The ’773 Application defines “shell protein”
as “any protein or set of proteins capable of self-assembly
or directed-assembly to form a ‘shell,’” including viral and
non-viral proteins. ’773 Appl. at p. 40, ll. 26–30. The Ap-
plication defines “cargo protein” as “any recombinant pro-
tein capable of being incorporated into a synthetic capsule
construct.” Id. at p. 42, ll. 1–3. And “bifunctional polynu-
cleotide” is defined as a “polynucleotide having two or more
aptameric activities,” id. at p. 41, ll. 20–22, or “binding af-
finit[ies] . . . for a protein tag or protein binding site,” id. at
p. 39, ll. 23–25.
4 IN RE: QAPSULE TECHNOLOGIES, INC.
PROCEDURAL HISTORY
The ’773 Application’s claims were initially rejected as
anticipated and/or obvious in view of a set of references not
relevant to the present appeal. In view of the initial
grounds of rejection, Qapsule appealed to the Board and
obtained reversal of the examiner’s rejections for want of
reference disclosure of the claimed “aptameric activity for
binding.”
The Board, however, entered a new ground of rejection
for claims 1, 2, 5, 7, 13–15, 31, 33–35, and 38 as anticipated
by Perez as evidenced by Mair, Ye, and Gonzalez. Bd. Op.
at *4.
The Board found that Perez discloses a recombinant in-
fluenza A virus and relied upon Mair as evidence of the in-
herent structural features of such a virus:
Bd. Op. at *5 (citing Mair at 1155, Figure 1). The Board
found that the “M1” protein met the claim 1 limitation of
“shell protein,” that the mutated “PB1” protein of Perez
met the limitation of a recombinant “cargo protein,” and
the mutated viral RNA of the “RNPs” constituted the “bi-
functional polynucleotide” of claim 1, for it was non-natu-
rally occurring and was capable of binding both the M1
shell protein and the PB1 protein. See Bd. Op. at *6–7.
IN RE: QAPSULE TECHNOLOGIES, INC. 5
The Board relied on Ye for teaching that the M1 protein
binds to viral RNA. See Bd. Op. at *5 (citing Ye at p. 7467,
col. 2 (“Two domains in M1 have been shown to affect the
disposition of RNA. One domain residing in a palindromic
stretch of basic amino acids (101RKLKR105) has been
shown to bind vRNA . . . .”)). And the Board relied on Gon-
zalez as teaching that the PB1 protein binds to the viral
RNA. See Bd. Op. at *5 (citing Gonzalez at p. 636, col. 2
(“Since we show that PB1 protein on its own binds prefer-
entially the 5′-terminal sequence of vRNA . . . .”)). Accord-
ingly, the Board concluded that “the influenza virus
particles of Perez with mutated PB1 protein and vRNA in-
herently anticipate the requirements of claim 1.” Bd. Op.
at *7.
Faced with the new ground of rejection, Qapsule had
the option of reopening prosecution before the examiner, or
requesting rehearing. See 37 C.F.R. § 41.50(B)(2). Qapsule
chose the rehearing route. Treating claim 1 as representa-
tive, Qapsule argued that “Claim 1 includes a limitation
that the shell proteins are recombinant” whereas the shell
proteins identified by the Board in Perez “are not recombi-
nant.” ’773 Application, Request for Rehearing, filed Jan.
22, 2018, at 3 (J.A.64). Qapsule stated in its request for
rehearing that Ye disclosed recombinant shell proteins, but
not in combination with recombinant proteins as claimed.
See id. But Qapsule acknowledged that the Board’s new
ground of rejection was for anticipation by Perez and not
Ye. See id. Accordingly, Qapsule argued that Perez did not
anticipate the rejected claims.
The Board determined that Qapsule’s reliance on the
term “recombinant” was an attempt to impose a method
step into a claim for a product, that pursuant to In re
Dilnot, 300 F.2d 945, 950 (CCPA 1962), “addition of a
method step in a product claim, which product is not pa-
tentably distinguishable from the prior art, cannot impart
6 IN RE: QAPSULE TECHNOLOGIES, INC.
patentability to the old product.” 6 The Board concluded
that “whether the shell proteins were produced in a ‘recom-
binant’ eukaryotic expression system in MDCK cells or pro-
duced as taught by Perez by virus infection in the MDCK
cells, the final constructs including the shell proteins would
be expected to be structurally identical because they would
share the same amino acid sequence, same glycosylation
patterns (if any), as they were produced by the same cell.”
Id. And the Board remarked that Qapsule had failed to
provide any evidence rebutting the inherency ruling. See
id.
Qapsule appeals, arguing that the Board erred in its
factual findings and application of the law of inherent an-
ticipation.
DISCUSSION
As to the Board’s factual findings, Qapsule argues that
Perez does not inherently disclose the “bifunctional polynu-
cleotide” claim limitation because Ye concluded that bind-
ing of the ribonucleoprotein to the viral shell proteins in
influenza A requires the presence of nucleoproteins in ad-
dition to the viral RNA and the ribonucleoprotein. Qapsule
asserts that the claimed synthetic capsule does not require
ribonucleoprotein in order for binding to occur between M1
and the viral RNA. And without the presence of ribonucle-
oproteins, Qapsule argues that “the Board’s proposed sub-
set of elements drawn from Perez, viz. M1, vRNA, and PD1,
would fail to assemble to form a virus particle.” Appellant
Reply Br. at 6. Accordingly, Qapsule contends that there
are structural differences between the shell proteins and
bifunctional polynucleotide as claimed, and those disclosed
by Perez.
6 Ex Parte Finn et al., No. 2017-001118, 2018 WL
799026, at *1 (P.T.A.B. Feb. 1, 2018).
IN RE: QAPSULE TECHNOLOGIES, INC. 7
A reference anticipates a patent claim under 35 U.S.C.
§ 102(b) if every claim limitation is present in the reference.
See Verizon Servs. Corp. v. Cox Fibernet Va., Inc., 602 F.3d
1325, 1336–37 (Fed. Cir. 2010). A reference may anticipate
inherently if a claim limitation that is not expressly de-
scribed “is necessarily present, or inherent, in the single
anticipating reference.” Id. at 1337 (quoting Schering
Corp. v. Geneva Pharm., Inc., 339 F.3d 1373, 1377 (Fed.
Cir. 2003)).
“[A]nticipation is a question of fact, including whether
an element is inherent in the prior art.” In re Gleave, 560
F.3d 1331, 1334–35 (Fed. Cir. 2009). Thus we review the
Board’s factual finding of inherent anticipation for support
by substantial evidence. 5 U.S.C. § 706(2)(E); Dickinson v.
Zurko, 527 U.S. 150, 152 (1999); In re Gartside, 203 F.3d
1305, 1316 (Fed. Cir. 2000). “Substantial evidence is some-
thing less than the weight of the evidence but more than a
mere scintilla of evidence,” In re Kotzab, 217 F.3d 1365,
1369 (Fed. Cir. 2000), and “means such relevant evidence
as a reasonable mind might accept as adequate to support
a conclusion,” Consol. Edison Co. of New York v. NLRB, 305
U.S. 197, 229 (1938).
A. Waiver
The PTO solicitor argues that Qapsule waived its pre-
sent arguments by failing to present them at the Board
hearing and rehearing. By electing rehearing under 37
C.F.R. § 41.50(b)(2), Qapsule was required to “address any
new ground of rejection and state with particularity the
points believed to have been misapprehended or overlooked
in entering the new ground of rejection and also state all
other grounds upon which rehearing is sought.” The PTO
states that Qapsule in its rehearing request only argued
that Perez failed to disclose a recombinant “shell protein,”
and that Qapsule’s new arguments about the binding of the
“bifunctional polynucleotide” and the application of inher-
ent anticipation are waived.
8 IN RE: QAPSULE TECHNOLOGIES, INC.
The court “retains case-by-case discretion over whether
to apply waiver.” Harris Corp. v. Ericsson Inc., 417 F.3d
1241, 1251 (Fed. Cir. 2005) (citing Singleton v. Wulff, 428
U.S. 106, 120 (1976)). Here the issues of Perez’s disclosure
of a shell protein binding to a bifunctional polynucleotide
and the Board’s application of inherent anticipation are ar-
guments about claim scope that are sufficiently developed
in the record before us. Because no party will be prejudiced
by our resolution of these issues, we proceed to the merits
without applying waiver.
B. Inherent Anticipation
The Board found that Ye discloses that the M1 protein
(i.e., the recombinant “shell protein” as claimed) binds to
viral RNA (the recombinant “bifunctional polynucleotide”
as claimed). Bd. Op. at *5. The Board quoted Ye’s disclo-
sure that “[t]wo domains in M1 have been shown to affect
the disposition of RNA. One domain residing in a palin-
dromic stretch of basic amino acids (101RKLKR105) has
been shown to bind vRNA . . . .” Id. (quoting Ye at p. 7467,
col. 2). This is substantial evidence supporting the Board’s
conclusion that Perez inherently discloses “a bifunctional
polynucleotide having . . . a second aptameric activity for
retaining said bifunctional polynucleotide within said en-
closure by assembly with the interior surface of said shell
protein.”
Qapsule acknowledges that the Board’s understanding
of Ye is correct. Appellant Reply Br. at 5 (“Although Ye
teaches that vRNA binds to M1, Ye also teaches that ribo-
nucleoproteins (RNP) also binds to M1 and that binding by
both vRNA and ribonucleoproteins (RNP) are necessary for
virus assembly . . . .”). Qapsule, however, attempts to dif-
ferentiate the present claims by arguing that viral assem-
bly in Ye occurs in the presence of ribonucleoprotein.
However, the present claims use the open-ended term
“comprising,” and do not exclude capsule assembly in the
presence of ribonucleoprotein as long as the claimed
IN RE: QAPSULE TECHNOLOGIES, INC. 9
“bifunctional polynucleotide” (here, the viral RNA) assem-
bles with the interior surface of the “shell protein.” See
Crystal Semiconductor Corp. v. TriTech Microelectronics
Int’l, Inc., 246 F.3d 1336, 1348 (Fed. Cir. 2001):
When a patent claim uses the word “comprising” as
its transitional phrase, the use of “comprising” cre-
ates a presumption that the body of the claim is
open. In the parlance of patent law, the transition
“comprising” creates a presumption that the re-
cited elements are only a part of the device, that
the claim does not exclude additional, unrecited el-
ements.
Similarly, the word “having,” in the clause “a bifunctional
polynucleotide having . . . a second aptameric activity for
retaining said bifunctional polynucleotide within said en-
closure by assembly with the interior surface of said shell
protein” does not exclude additional, unrecited elements
from participating in capsule assembly. See id.:
The transition “having” can also make a claim
open. However, the term “having” does not convey
the open-ended meaning as strongly as “compris-
ing.” “Having,” for instance, does not create a pre-
sumption that the body of the claim is open.
Therefore, this court examines the claim in its full
context to determine whether [Applicant’s] use of
“having” limits claim 1 to its recited elements.
(internal citation omitted).
Claim 1 does not require that the claim excludes cap-
sule assembly in the presence of ribonucleoproteins, as
Qapsule has argued. First, the whole of the claimed “syn-
thetic capsule construct” is offset by the “comprising” tran-
sitional, signaling the intent to have an open-ended claim
that would allow for additional, unrecited elements beyond
the listed shell protein, cargo protein, and bifunctional pol-
ynucleotide. The specification defines “synthetic capsule
10 IN RE: QAPSULE TECHNOLOGIES, INC.
construct” broadly to mean “a non-naturally occurring cap-
sule,” ’773 Appl. at p. 39, ll. 19–20, and defines the term
“capsule” in equally broad language to mean “a nanoparti-
cle sized structure having a well organized outer layer that
defines an enclosure . . . ,” id. at p. 39, ll. 14–16. Qapsule
has not directed us to any language that would rebut the
presumption that has arisen from its choice to use the
“comprising” transitional.
Additionally, the use of the “having” transitional does
not alter the construction, for it is specific to the recited
“bifunctional polynucleotide” limitation and not the
claimed “synthetic capsule construct” as a whole. The
“having” transitional within this claim offsets two “ap-
tameric activit[ies],”which the specification defines as
“binding affinit[ies] . . . for a protein tag or protein binding
site,” ’773 Appl. at p. 39, ll. 23–25. Although this usage, in
conjunction with the “bifunctional” qualifier of nucleotide,
could imply that the number of “aptameric affinities” of the
polynucleotide should be limited, this does not restrict un-
recited elements from participating in capsule assembly as
long as the “bifunctional polynucleotide” possesses the two
recited aptameric affinities.
In sum, it does not affect the Board’s ground of rejec-
tion that Qapsule has purportedly created a capsule that
will assemble in the presence of only a shell protein, cargo
protein, and bifunctional polynucleotide, see Appellant Re-
ply Br. at 6, for representative claim 1 is not so limited.
Thus substantial evidence supports the Board’s conclusion
that the Perez recombinant viral RNA inherently meets
the “bifunctional polynucleotide” limitation in claim 1.
Qapsule further argues that the Board misapplied the
requirement of structural identity for inherent anticipation
under In re Best. 562 F.2d 1252, 1256 (CCPA 1977)
(“Where, as here, the claimed and prior art products are
identical or substantially identical, or are produced by
identical or substantially identical processes, the PTO can
IN RE: QAPSULE TECHNOLOGIES, INC. 11
require an applicant to prove that the prior art products do
not necessarily or inherently possess the characteristics of
his claimed product.”). We find that the Board properly ap-
plied the concept of inherency on an element-by-element
basis in order to establish that the M1 protein, viral RNA,
and PB1 protein would meet the claimed “shell protein,”
“bifunctional polynucleotide,” and “cargo protein” limita-
tions, respectively.
On appeal, Qapsule points to the presence of additional
elements in Perez, such as a lipid envelope and other pro-
teins, as evidencing a structural difference between Perez’s
influenza A disclosure and the recited limitations of repre-
sentative claim 1. See Appellant Br. at 9–12. Qapsule con-
tends that these structural differences negate anticipation.
That is incorrect, as applied herein, for as discussed supra,
Qapsule’s claims are not limited to the three recited com-
ponents. The Board correctly found that the Examiner met
his burden of establishing structural identity of the
claimed synthetic capsule construct in view of the scope of
representative claim 1, and that this prima facie case has
not been rebutted by the Applicant. See In re Jung, 637
F.3d 1356, 1362 (Fed. Cir. 2011) (explaining the burden-
shifting framework during prosecution); In re Mousa, 479
F. App’x 348, 352 (applying the same specifically to inher-
ency).
Qapsule also argues that unlike the influenza A of Pe-
rez, Qapsule’s synthetic capsule is functionally different
because it is non-infective and has utility in the chemical
industry. Appellant Reply Br. at 8 (“Appellant’s claimed
synthetic capsule construct is a simple system with three
components and is employable in industrial chemical pro-
cesses; in contrast, Perez’s virus particles are complex with
many components and lack industrial applicability, but
they might be employable for germ warfare.”). However,
unclaimed functional distinctions or uses are insufficient
to overcome anticipation. It is not before us to decide
12 IN RE: QAPSULE TECHNOLOGIES, INC.
whether further specificity in the claims might distinguish
these references.
“First, and most importantly, the language of the claim
defines the scope of the protected invention.” Bell
Commc’ns Research, Inc. v. Vitalink Commc’ns Corp., 55
F.3d 615, 619 (Fed. Cir. 1995); see Yale Lock Mfg. Co. v.
Greenleaf, 117 U.S. 554, 559 (1886) (“The scope of letters-
patent must be limited to the invention covered by the
claim, and while the claim may be illustrated it cannot be
enlarged by language used in other parts of the specifica-
tion.”). Unclaimed limitations cannot distinguish the
claims. Ventana Med. Sys., Inc. v. Biogenex Labs., Inc., 473
F.3d 1173, 1181 (Fed. Cir. 2006) (“[I]t is improper to limit
the claim to other, unclaimed features.”).
The structures of Perez anticipate representative claim
1. Unclaimed differences do not avoid anticipation, for
claim 1 as written, in its breadth, reads on Perez. The
Board correctly rejected claim 1 on this ground.
We have considered all of Qapsule’s arguments, and af-
firm the judgment of the Board.
AFFIRMED
No costs.