Ex Parte Smith et al

Patent Trial and Appeal Board

Nov 4, 2016

12999185 (P.T.A.B. Nov. 4, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
12/999, 185 09/29/2011
24239 7590 11/08/2016
MOORE & VAN ALLEN PLLC
P.O. BOX 13706
3015 Carrington Mill Boulevard, Suite 400
Research Triangle Park, NC 27709
FIRST NAMED INVENTOR
Harold E. Smith
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
035413.304.08-006US 3147
EXAMINER
STEADMAN, DAVID J
ART UNIT PAPER NUMBER
1656
NOTIFICATION DATE DELIVERY MODE
11/08/2016 ELECTRONIC
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.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address( es):
iplaw@mvalaw.com
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PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte HAROLD E. SMITH and FRANK T. ROBB 1
Appeal2015-004934
Application 12/999, 185
Technology Center 1600
Before ULRIKE W. JENKS, TIMOTHY G. MAJORS, and
RACHEL H. TOWNSEND, Administrative Patent Judges.
TOWNSEND, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a method
of enhancing protein folding in a bacteria host, which have been rejected as
obvious. We have jurisdiction under 35 U.S.C. § 6(b).
We affirm.
STATEMENT OF THE CASE
"Protein production in bacteria, typically Escherichia coli, offers a
number of advantages over other systems: ease of transformation and culture
growth, a wide range of inducible expression vectors that produce large
1 Appellants identify the Real Parties in Interest as the University of
Maryland, Baltimore and University of Maryland, College Park. (Appeal
Br. 3.)
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Application 12/999, 185
amounts of protein, and a variety of epitope tags that permit one-step affinity
purification." (Spec. i-f 3.) However, "protein insolubility remains a major
stumbling block for recombinant protein production." (Spec. i-f 4.) In
particular, "[t]he failure to fold properly leads to protein aggregation."
(Spec. i-f 6.) According to Appellants' Specification "[i]nsolubility of
recombinant proteins is likely a consequence of limited folding capacity in
the bacterial host." (Spec. i-f 7 .)
It is known that protein chaperones promote "[p ]rotein folding in vivo
... in all organisms." (Spec. i-f 6.) Appellants' invention is directed at the
use of such chaperones to enhance protein folding of a non-native protein in
a bacterial host. (Spec. i-f 9.)
Claims 1, 2, 7, and 8 are on appeal. Claim 1 is representative and
reads as follows:
1. A method of enhancing protein folding in a bacteria host, the
method comprising:
providing at least one expression vector comprising:
nucleic acid sequences encoding a single chaperone from
a hyperthermophilic or psychrophilic archaeon, wherein
the single chaperone is selected from the group
consisting of Pyrococcus furiosus Heat Shock Protein 60
(HSP60) having the amino acid sequence of SEQ ID NO:
14, and Pyrococcus furiosus NAC having the amino acid
sequence of SEQ ID NO: 16 and Methanococcoides
burtonii HSP60 having the amino acid sequence of SEQ
ID NO: 4; and nucleic acid sequences encoding a non-
native protein for expression in the host bacteria, wherein
the non-native protein is non-native to both the bacterial
host and archaeon;
transforming the bacteria host with the at least one expression
vector; and culturing the bacteria host at a temperature of 3 7 °C
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Application 12/999, 185
and conditions sufficient for expression of the non-native
protein and the single chaperone.
(Appeal Br. 16.)
The following ground of rejection by the Examiner is before us on
review:
Claims 1, 2, 7, and 8 under 35 U.S.C. § 103(a) as unpatentable over
Robb2 and lmanaka. 3
DISCUSSION
The Examiner finds that Imanaka teaches co-transforming a bacterial
cell with a gene encoding a single chaperone protein that aids in protein
folding and solubility and a gene encoding a desired protein. (Final Action
5; Ans. 5.) The Examiner further finds that Imanaka teaches culturing such
bacterial transformants at 37 °C. (Final Action 5; Ans. 4, 7 .) The Examiner
also notes that Imanaka teaches that Hsp60 is a known heat shock chaperone
protein. (Final Action 5; Ans. 4.)
The Examiner finds that Robb teaches Hsp60 is a chaperone protein
that catalyzes protein folding and can be used in that manner, as well as
teaching an Hsp60 chaperone protein that has "an amino acid sequence that
is 100% identical to SEQ ID NO: 14" recited in the claims. (Final Action 5;
Ans. 5.) The Examiner further notes that Robb teaches that sHsp is a
chaperone protein that is "known to be used to protect proteins ... from high
heat stress" but is "unable to refold proteins in a catalytic fashion." (Ans. 7.)
2 WO 2007 /028069 A2, published March 8, 2007.
3 EP 0774512 A2, published May 21, 1997.
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The Examiner notes that Robb teaches combining sHsp to provide
thermostability with Hsp60 to provide a composition that promotes refolding
at "high temperatures of 100 °C." (Id. (emphasis in original).)
The Examiner finds that it would have been obvious to one having
ordinary skill in the art to use the Hsp60 chaperone protein taught in Robb in
the method of Imanaka with a reasonable expectation of achieving success,
i.e., recombinantly co-expressing Hsp60 with a non-native protein in a
bacterial host to aid in protein folding and solubility. (Final Action 5---6;
Advisory Action 3-5; Ans. 6-8.)
We agree with the Examiner's factual findings and conclusion that the
claimed method, which involves transforming a bacterial host cell with "at
least one expression vector" comprising a single chaperone "selected from
the group consisting of Pyrococcus furiosus Heat Shock Protein 60 (HSP60)
having the amino acid sequence of SEQ ID NO: 14 ... "would have been
obvious from the teachings of Imanaka and Robb.
Appellants seem to argue that Robb cannot be interpreted as teaching
that Hsp60 alone provides for protein folding because "it has always been
understood in the past that Hsp60 ( GroEL) must be combined with co-factor
chaperone HsplO (GroES) to provide for protein folding," which is a fact
implicit from Robb's citation to "Hartl (1996) and Hartl/Hayer-Hartl (2002)"
and comports with statements "in the present application" at paragraphs 8
and 64 (Reply Br. 3) as well as Imanaka's disclosure of using GroESL,
which is a combination of GroEL and GroES (Reply Br. 5-6). We do not
find this argument persuasive. It cannot be disputed that Robb discloses
"Hsp60s[, as compared to sHsps, which can prevent denatured proteins from
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Application 12/999, 185
aggregating but are unable to refold non-native proteins in a catalytic
fashion,] on the other hand catalyze ATP-dependent protein folding,"
regardless of what articles are cited after that statement. (Robb 1.)
Moreover, Imanaka also notes that GroEL, which is in the HSP60
chaperonin family, is "involved in the conformation and the conformational
change of a protein." (Imanaka 2.) Furthermore, we note that Robb
demonstrates that Hsp60 works by itself to promote protein folding of Taq
polymerase at 100 °C. (Robb 13 ("The level of protection by the Hsp60
alone, Figure 2, closed and open squares, was comparable to that of the sHsp
alone (Figure 2, crosses) .... ");Robb 14 ("The Hsp60 alone caused a slight
improvement of approximately 2 fold compared to controls (Figure 3 closed
and open squares, respectively).").)
In addition, we disagree with Appellants' argument that Robb
"teaches the necessity of using two chaperones in combination and in
light of this reference one would never consider the use of a single
chaperone, for example Hsp60, without a co-chaperone." (Appeal Br. 10
(emphasis in original).) As the Examiner noted "Robb teaches a method that
is conducted at high temperatures of 100 °C." (Ans. 7 (emphasis in
original); Robb 11.) As explained in Robb, Taq polymerase is a
thermophilic bacterium that can denature at exposure to 95 °C, but that sHsp
provides thermal stability by preventing precipitation of denatured Taq
polymerase. (Robb 11-12.) The experimentation in Robb proceeded to
examine "the cooperative effects of several P. furiosus molecular
chaperones," noting that Hsp60s are known to be "active proteins," whereas
sHsps are "passive." (Robb 13.) And as Appellants recognize, it was
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determined that at 100 °C, "using co-chaperones such as prefoldin or sHsp
in combination with Hsp60 was essential for optimal Hsp60 turnover ...
facilitat[ing] its performance by five-fold," whereas, by itself, Hsp60 "was
comparable to that of the sHsp alone." (Appeal Br. 9--10 (emphasis in
original); Robb 14 ). ) Thus, Robb does not teach that Hsp60, by itself, fails
to promote protein folding of Taq polymerase at 100 °C. Rather, Robb is
reasonably interpreted as teaching that performance is optimized with the
addition of sHsp or pre-foldin. (Robb 13-14 (referring to results depicted in
Figs. 2 and 3 and noting that "[t]he present results indicated that prefoldins
and sHsps have analogous roles as they both improve the efficiency of
Hsp60 catalysis.") Indeed, Appellants appear to concede as much. (Reply
Br. 4 ("Clearly, using a single chaperone did not provide effective results
when compared to the use of a combination of sHsp and Hsp60") (emphasis
added); see also Appeal Br. 10 ("The level of protection by the Hsp60 alone,
Robb Figure 2, closed and open squares, was comparable to that of the sHsp
alone (Robb Figure 2, crosses). . . . It is evident that when Hsp60 and sHsp
were used alone by Robb, the results were not much better than the
control.").) We note that Appellants' claims do not require "optimal"
protein folding or specify any particular degree of folding required. Thus,
with respect to Appellants' claimed invention, we disagree with Appellants
that Robb teaches the necessity of two chaperones.
Second, while Appellants argue that using Hsp60 alone was not much
better than the control (Reply Br. 5), we note that Robb indicates that
enzyme activity was 2 fold better when Hsp60 was added compared to the
control where no Hsp60 was added and no pre-foldin. (Robb 14 (referring
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to Fig. 3).) Appellants argue that a "between 2 to 2.5 fold" increase
demonstrated in the Specification is "impressive" (Appeal Br. 7 (referring to
Figure 2 and Spec. i-f 59 ("GFP fluorescence was increased between 2 to 2.5
fold compare[d] to cells expressing GFP alone.").) Thus, we disagree with
Appellants that Robb teaches away from using Hsp60 by itself (Appeal Br.
12). We do not agree with Appellants that, in light of Robb, "one would
never consider the use of a single chaperone, for example Hsp60, without a
co-chaperone" (Appeal Br. 10). And, we disagree with Appellants that "the
Robb reference never recognized that the use of the Hsp60 chaperone
'alone' was a result-effective variable" (Appeal Br. 10).
Moreover, even if it were true that Hsp60 used alone "were not much
better than the control," we disagree that one of ordinary skill in the art
would not consider using the Hsp60 alone. Even ifbetter alternatives exist
in the prior art, that "does not mean that an inferior combination is inapt for
obviousness purposes." In re Mouttet, 686 F.3d 1322, 1334 (Fed. Cir.
2012).
Where "a patent claims a structure already known in the prior art that
is altered by the mere substitution of one element for another known in the
field, the combination must do more than yield a predictable result."
See KSR Int'! Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007). Robb teaches
that Hsp60 by itself promotes folding of protein, and that, even at 100 °C,
Hsp60 is two-fold better than in the absence of Hsp60. (Robb 14.) Thus, we
do not find Appellants' argument that a "2 to 2.5 fold" increase in
expression of and folding of proteins compared to cells that did not include
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Hsp60 was surprising or unexpected (Appeal Br. 13-14). Rather, the
evidence of record indicates that the result is predictable.
We also disagree with Appellants that Robb teaches away from the
effectiveness of using Hsp60 by itself in Imanaka's method. (Appeal Br.
12.) As just discussed, Robb demonstrates that Hsp60 functions by itself
even at 100°C. Appellants do not argue, nor do we find anything in Robb,
that teaches Hsp60 would not be expected to function at lower temperatures.
As the Examiner noted (Final Action 5), Imanaka teaches an in vivo method
where co-transformation takes place at 37 °C. (See, e.g., Imanaka at 9 (Ex. 6
(noting that transformed cells were cultured at 37 °C in NZCYM medium)),
10 (Ex. 9 (noting that cells co-transformed with a protein of interest and a
chaperone were "cultured in NZCYM medium in the same manner as in
Example 6")), (Ex. 10) (same)). Thus, we agree with the Examiner that
"since Robb teaches sHsp protects proteins from the effects of high heat
stress (100 °C) and sHsp does not catalyze protein folding, one would have
recognized that Robb's Hsp60 alone is sufficient to catalyze protein folding
in lmanaka's method, which is conducted at low temperature (37 °C)."
(Ans. 7.)
Appellants further argue that there is nothing in the prior art that
teaches the use of a single chaperone to increase protein folding of a non-
native protein by a bacterial host. (Appeal Br. 13.) According to
Appellants, Imanaka "did not use just a SINGLE [Hsp60] chaperone."
(Reply Br. 5 (emphasis in original).) While it may be the case that in
Example 7, Imanaka described the use of GroEL with GroES, as Appellants
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concede (Reply Br. 6), Imanaka's examples 9 and 10 employed Hsp from
KOD-1, as did example 11. (Imanaka 10-11.)4
Moreover, in light of example 11 of Imanaka (referred to by the
Examiner (Ans. 9)), which teaches expression of soluble sFV in a bacterial
host using a single Hsp, we disagree with Appellants that the prior art does
not teach using a single chaperone protein in a bacterial host to produce a
non-native protein.
In their Reply Brief, Appellants argue that the fact that Imanaka
teaches production of proteins as soluble proteins, it does not teach the
proteins produced by the bacterial host were properly folded. (Reply Br. 6.)
This argument is deemed waived. 37 C.F .R. § 41.41 (b )(2) ("Any argument
raised in the reply brief which was not raised in the appeal brief, or is not
responsive to an argument raised in the examiner's answer, including any
designated new ground of rejection, will not be considered by the Board for
purposes of the [present] appeal, unless good cause is shown.").
In light of the foregoing reasons, we conclude the Examiner
established by a preponderance of the evidence that claim 1 would have
been obvious over Robb and Imanaka.
4 We also agree with the Examiner, however, that the claims by the use of
the transitional phrase comprising and the phrase "at least one expression
vector" do not exclude provision of an additional expression vector that can
encode an additional chaperone. (Ans. 8.) Thus, to the extent that Imanaka
is deemed to require both GroEL and GroES, we agree with the Examiner
that Imanaka envisions providing them individually as well as by a
recombinant expression of both as GroESL. Thus, such a method would
also be deemed obvious.
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Claims 2, 7, and 8 have not been argued separately and, therefore, fall
with claim 1. 37 C.F.R. § 41.37(c)(l)(iv).
SUMMARY
We affirm the rejection of Claims 1, 2, 7, and 8 under 35 U.S.C.
§ 103(a) as unpatentable over Robb and lmanaka.
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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