Ex Parte Choo et al

Board of Patent Appeals and Interferences

Oct 16, 2009

10309578 (B.P.A.I. Oct. 16, 2009)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

Ex parte YEN CHOO,
AARON KLUG, and ISIDRO SANCHEZ-GARCIA
____________

Appeal 2009-001813
Application 10/309,578
Technology Center 1600
____________

Decided: October 16, 2009
____________

Before DEMETRA J. MILLS, LORA M. GREEN, and
RICHARD M. LEBOVITZ, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

DECISION ON APPEAL
This is a decision on the patent applicants’ appeal from the patent
examiner’s rejection of claims 88, 89, 91, and 92 under 35 U.S.C. § 103(a).
The Board’s jurisdiction for this appeal is under 35 U.S.C. § 6(b). The
rejection is affirmed.

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STATEMENT OF THE CASE
The claims are directed to zinc finger binding proteins. A zinc finger
is a polypeptide which is capable of sequence-specific recognition of DNA
(‘988 patent,1 col. 1, ll. 15-23). Zinc fingers are often present in
transcription factors which regulate the transcription of DNA (id.) The
invention is said to provide a method of designing a zinger finger protein for
binding to a DNA of a desired sequence and to a method of producing zinc
finger proteins (id. at col. 1, ll. 9-12; col. 4, ll. 60-67).
Claims 88, 89, 91, and 92 are pending and stand rejected by the
Examiner under 35 U.S.C. § 103(a) as obvious in view of Jamieson
(Biochemistry, Vol. 33, pages 5689-5695, May 1994), Rebar (Science, Vol
.263, No. 5147, pages 671-673, February 1994), Gashler (Molecular and
Cellular Biology, Vol. 13, No. 8, pages 4556-4571, August 1993), and
Sadowski (Nature, Vol. 335, No. 6190, pages 563-564, October 1988) (Ans.
3). Claim 88 is representative and reads as follows:
88. A nucleic acid binding protein that binds to a target nucleotide sequence,
wherein the protein comprises

(i) at least two zinc finger binding motifs, each of which binds to a
nucleotide triplet within the target sequence, and

(ii) a heterologous functional domain selected from the group
consisting of an activation domain, a repression domain, a nuclear
localization signal, and a catalytic domain of a restriction enzyme

wherein the amino acid sequence of each of the at least two zinc finger
binding motifs which binds to a triplet is designed as follows:

1 This application is a continuation of a reissue application of U.S. Patent
No. 6,007,988 (“the ‘988 patent”) (App. Br. 2).
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a) if the 5' nucleotide of the triplet is G, position +6 of the binding
motif is Arg, or position +6 of the binding motif is Ser or Thr and position
++2 is Asp;

b) if the 5' nucleotide of the triplet is T, position +6 of the binding
motif is Ser or Thr and position ++2 is Asp;

c) if the middle nucleotide of the triplet is G, position +3 of the
binding motif is His;

d) if the middle nucleotide of the triplet is A, position +3 of the
binding motif is Asn;

e) if the middle nucleotide of the triplet is T, position +3 of the
binding motif is Ala, Ser or Val;

f) if the middle nucleotide of the triplet is C, position +3 of the
binding motif is Asp, Leu, Thr or Val;

g) if the 3' nucleotide of the triplet is G, position -1 of the binding
motif is Arg and position +2 is Asp;

h) if the 3' nucleotide of the triplet is A, position -1 of the binding
motif is Gln and position +2 is Ala

i) if the 3' nucleotide of the triplet is T, position -1 of the binding
motif is Asn, or position -1 of the binding motif is Gln and position +2 is
Ser; and

j) if the 3' nucleotide of the triplet is C, position -1 of the binding
motif is Asp.

STATEMENT OF THE ISSUES
Appellants contend that the Examiner erred in the following ways:
• the rejection was based on hindsight and an impermissible obvious
to try standard;
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• the prior art teaches away from rational design as required by claim
88; and
• there would have been no reason to use the prior art transactivator
domains with the zinc finger protein, Zif268.

PRINCIPLES OF LAW
The question of obviousness is resolved on the basis of underlying
factual determinations including: (1) the scope and content of the prior art;
(2) the level of ordinary skill in the art; (3) the differences between the
claimed invention and the prior art; and (4) secondary considerations of
nonobviousness, if any. Graham v. John Deere Co., 383 U.S. 1, 17-18
(1966).
“Often, it will be necessary . . . to look to interrelated teachings of
multiple [references] . . . and the background knowledge possessed by a
person having ordinary skill in the art, all in order to determine whether
there was an apparent reason to combine the known elements in the fashion
claimed.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 418 (2007). “[T]his
analysis should be made explicit,” and it “can be important to identify a
reason that would have prompted a person of ordinary skill in the relevant
field to combine the elements in the way the claimed new invention does.”
Id.
First, an invention would not have been obvious to try
when the inventor would have had to try all possibilities in a
field unreduced by direction of the prior art. When “what would
have been ‘obvious to try’ would have been to vary all
parameters or try each of numerous possible choices until one
possibly arrived at a successful result, where the prior art gave
either no indication of which parameters were critical or no
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direction as to which of many possible choices is likely to be
successful” an invention would not have been obvious.
O’Farrell, 853 F.2d at 903. This is another way to express the
KSR prong requiring the field of search to be among a “finite
number of identified” solutions. 550 U.S. at 421, 127 S.Ct.
1727; see also Procter & Gamble, 566 F.3d at 996; Kubin, 561
F.3d at 1359. It is also consistent with our interpretation that
KSR requires the number of options to be “small or easily
traversed.” Ortho-McNeil Pharm., Inc. v. Mylan Labs., Inc.,
520 F.3d 1358, 1364 [86 USPQ2d 1196] (Fed. Cir. 2008).
Second, an invention is not obvious to try where vague
prior art does not guide an inventor toward a particular solution.
A finding of obviousness would not obtain where “what was
‘obvious to try’ was to explore a new technology or general
approach that seemed to be a promising field of
experimentation, where the prior art gave only general guidance
as to the particular form of the claimed invention or how to
achieve it.” O'Farrell, 853 F.2d at 903. This expresses the same
idea as the KSR requirement that the identified solutions be
“predictable.” 550 U.S. at 421, 127 S. Ct. 1727; see also
Procter & Gamble, 566 F.3d at 996-97; Kubin, 561 F.3d at
1359-60.
Bayer Schering Pharma AG v. Barr Laboratories Inc., 575 F3d 1341, 1347
(Fed. Cir. 2009).
An obviousness “analysis need not seek out precise teachings directed
to the specific subject matter of the challenged claim, for a court can take
account of the inferences and creative steps that a person of ordinary skill in
the art would employ.” KSR, 550 U.S. at 418.
In assessing a claim’s obviousness, “[a] court must ask whether the
improvement is more than the predictable use of prior-art elements
according to their established functions.” Id. at 550 U.S. at 417. “The
combination of familiar elements according to known methods is likely to be
obvious when it does no more than yield predictable results.” Id.
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FACTS (“F”)
Scope and Content of the Prior Art
Jamieson “Biochemistry” publication
1. Jamieson described a random mutagenesis and phage display system to
alter the binding specificity of Zif268, a zinc finger protein with three zinc
finger motifs. Zif268 binds to a target nucleic acid having the nucleotide
sequence GCG-TGG-GCG (Jamieson, Abstract).
2. Utilizing phage display, the amino terminal finger (finger 1), which binds
to the third triplet (GCG) in the target sequence, was randomly mutagenized
at positions -1, 2, 3, and 6, and mutant fingers which retained the GCG
binding ability were selected (Jamieson, p. 5691, col. 2 in section titled
“Results”; Abstract). Jamieson teaches selecting different variants that
bound to the GCG triplet “to test the substitution tolerance at these four
positions and to look for other variants capable of binding the operator.”
(Id.)
3. Jamieson described a mutagenized zinc finger 1 “capable of binding to
the GCG triplet, where the zinc fingers have Arg at -1, Asp at +2, Asp at +3
and Arg at +6 (e.g. page 5692, paragraph bridging columns).” (Ans. 4-5.)
4. Mutagenized fingers were also selected which bound to different triplets
at the third triplet position of the target nucleotide sequence (Jamieson, p.
5692, col. 2 to p. 5693, col. 2).
5. “The ability to design these [zinc finger] molecules has many potential
applications including the directed control of gene expressions or the
development of biochemical reagents, such as tools for gene mapping.”
(Jamieson, p. 5689, col. 1.)
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6. Jamieson acknowledged that Rebar [described below] also utilized a
phage display system to alter the binding specificity of finger 1 of Zif268
(Jamieson, p. 5695, col. 1-col. 2). “These studies should further stimulate
the use of this technology to alter zinc finger binding specificity.” (Id.)
7. Jamieson states:
There are limitations of the phage display method that need to
be emphasized . . .. Although many of the finger 1 variants
isolated in sorting with the wild-type operator sequence were
native-like, the wild-type finger 1 . . . was not recovered in our
selection. We think the wild-type sequence should have been
present because wild-type residues were isolated at each of the
four positions among the selectants. It is possible that there are
a number of variants whose affinity for the operator is
comparable to or greater than the wild type and that not enough
clones were sequenced to isolate it. In addition, the selected
variants could bind with comparable affinity but generally
express better or be more stable than the wild type and so be
overrepresented in the phage pool. … Moreover, very small
differences in affinity can lead to a large selective advantage,
and the affinity measurements may not be precise enough to
determine the true difference between these clones. Any of
these could explain why the Asp3 variant competed out the
Glu3 wild type . . ..”
(Jamieson, p. 5694, col. 2, 3rd paragraph.)

Rebar “Science” publication
8. Rebar used a phage display system to select zinger finger proteins with
altered DNA binding specificity (Rebar, Abstract).
9. The three zinc fingers of the Zif268 protein were expressed on the surface
of filamentous phage, and a library of variants was prepared by randomizing
amino acid positions -1, 2, 3, and 6 of the first zinc finger. (Rebar, Abstract;
p. 672, Table 1.)
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10. “Affinity selections, using DNA [binding] sites with base changes in
the region recognized by the first [zinc] finger, yielded Zif268 variants that
bound tightly and specifically to the new sites.” (Rebar, Abstract.)
11. Rebar demonstrated that a new randomized zinc finger with the two
naturally occurring zinc fingers produced a protein with new DNA binding
specificity (p. 673, col. 1; Fig. 1; Ans. 5).
12. “Zinc finger proteins . . . exhibit a modular organization which suggests
that it may be possible to ‘mix and match’ fingers to obtain proteins with
novel DNA-binding specificities.” (Rebar, p. 671, col. 2).

Gashler “Molecular and Cellular Biology” publication
13. Gashler taught that Zif268 (referred to by its alternative name, “Egr-1”)
contains modular domains including a serine/threonine rich domain that
encodes its transactivation function and a zinc finger domain that encodes its
DNA-binding activity (Gashler, p. 4556, col. 1).
14. Gashler showed that the transactivation function of Zif268 can be
conferred on a heterologous DNA-binding domain by fusing the Zif268
serine/threonine rich domain (residues 3-281) to the GAL4 DNA-binding
domain (Gashler, p. 4559, col. 1; p. 4561, col. 2; p. 4565, col. 1; Ans. 6).
Therefore, the transactivation domain can be separated from the native zinc
finger domain and utilized with other heterologous DNA binding domains.

Sadowski “Nature” publication
15. Sadowski showed that the transactivation domain of the herpes simplex
virus protein VP16, when fused to the GAL4 DNA-binding fragment,
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potently activated transcription in mammalian cells of reporter genes
containing GAL4 binding sites (Sadowski, p. 563).
16. Sadowski states that its GAL4-VP16 protein is a “powerful activator”
which could be used “profitably” when expressed transiently in cells
(Sadowski, p. 564)

Differences between the claimed invention and the prior art
17. Claim 88 is directed to a nucleic acid binding protein that binds to a
target nucleotide sequence. The protein comprises:
18. “(i) at least two zinc finger binding motifs, each which binds to a
nucleotide triplet within the target sequence,” and
19. “(ii) a heterologous functional domain” selected from a list of five
functional domains.
20. The amino acid sequence of the zinc finger is “designed” by rules a)
through j) which specify the type and position of an amino acid in the zinc
finger binding motif as a function of the nucleotide base type and position in
the target nucleotide sequence.
21. The amino acids which altered in the zinc finger are at positions 2, 3, 6,
and -1.
22. Appellants did not dispute the Examiner’s findings that Jamieson
described a genetically modified zinc finger protein with one zinc finger
which is a species of the genus defined by rules listed in claim 88 (rules a),
f), and g); F3).
23. Jamieson did not describe a zinc finger protein with two zinc fingers
meeting the design rules of claim 88 (Ans. 5).
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24. Jamieson did not describe a zinc finger protein comprising a
heterologous functional domain as recited in claim 88 (ii) (F16; Ans. 5).
25. Gashler and Sadowski describe linking heterologous transactivation
domains to zinc finger DNA-binding domains (F12-13; Ans. 5).

Reasons to combine
26. The Examiner found that it would have been obvious to the skilled
worker to have added a second genetically modified finger to Jamieson’s
zinc finger protein meeting the design rules of claim 88 in view of Jamieson
and Rebar’s suggestion of using phage display to tailor DNA-binding
specificity and Rebar’s express teaching that zinc fingers can be mixed and
matched (F10; Ans. 6).
27. The Examiner also found that reason to “mix and match” zinc fingers
with altered binding specificity would have been to “design” modified zinc
fingers to direct gene expression and for other biochemical uses as taught by
Jamieson (F5; Ans. 6). Jamieson expressly pointed the skilled worker in this
direction by observing that its own work and that of Rebar “should further
stimulate the use of this [phage display and mutagenesis] technology to alter
zinc finger binding specificity.” (F6.)
28. The Examiner found that persons of ordinary skill in the art would have
had reason to utilize Sadowski’s heterologous VP16 transactivation domain
to achieve potent transcription of the gene bound by the genetically modified
zinc finger protein (Ans. 7; F13).

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Level of ordinary skill in the art
29. Persons of ordinary skill in the art were familiar with techniques to
change the binding specificity of zinc finger proteins (F1-12), to fuse zinc
fingers to heterologous transactivation domains (F13-14), and to mix and
match zinc fingers of different and the same specificities (F12).
30. Based on the success of Jamieson, Rebar, Gashler, and Sadowski,
persons of ordinary skill in the art would have reasonably expected such
methods to work.
ANALYSIS
As summarized above, the Examiner thoroughly described the scope
and content of the prior art and identified specific reasons as to why persons
of ordinary skill in the art would have had reason to combine the prior art in
order to have made the claimed invention. The reasoning is sound and fact-
based; we therefore adopt it as our own. Consequently, we turn to
Appellants’ arguments.

Hindsight and obvious to try
Appellants contend that the Examiner did not identify a proper reason
for combining two genetically modified zinc fingers in a single zinc finger
protein.
Jamieson’s “encouragement” and Rebar’s “possibility” and
“exploration” that the examiner finds to motivate the use of a
second zinc finger motif that binds a GCG triplet according to
the rules of claim 88 only provide suggestions to explore a new
technology or describe a general approach that seems to be
promising a field of experimentation. Thus, the rejection is
based upon an impermissible obvious to try standard.
(App. Br. 8-9.)
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An invention is not obvious to try when an inventor would have had
to attempt all the possibilities in a field when no guidance was given or
when the prior art is vague and does not guide the inventor to a solution.
Bayer Schering Pharma AG v. Barr Laboratories, 575 F.3d at 1347. In this
case, the prior art provided clear guideposts and explicit suggestions on what
to do next. Both Jamieson and Rebar taught methods for producing
genetically modified zinc finger (F1-12). Jamieson explicitly observed that
its own publication, coupled with Rebar’s, would stimulate persons of
ordinary skill in the art to use the technology to design zinc fingers with
altered specificity (F6). Rebar suggested mixing and matching zinc fingers
(F12) to obtain proteins with new binding specificities, explicitly guiding the
skilled worker to combine zinc fingers with different (mix) and the same
(match) binding properties. The ordinary skilled worker would not have had
to attempt all possibilities in an arcane field. To the contrary, the prior art
provided the tools to design zinc fingers (F1-12), the impetus to do so (F5, 6,
& 12), and a reasonable expectation of success that such methods would
work (F29-30).
The Examiner did not invoke hindsight, but rather articulated why
persons of ordinary skill in the art would have had reason to combine the
prior art (F26-28).
Appellants contend that there would have been no motivation to have
made a zinc finger protein with binding specificity for two GCG triplets
because Zif268 already possessed such specificity. (App. Br. 9.)
The fact that two of the zinc fingers would have had the same binding
specificity as the parent molecule does not undermine the Examiner’s
reasoning. The whole purpose of the Jamieson and Rebar publications was
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to advance the engineering of zinc finger proteins by providing new and
alternative technologies. The Jamieson/Rebar technology was equivalent to
the conventional way of producing native Zif268 by recombinant expression
(Jamieson, p. 5690, col. 2) because it could reproduce Zif268 activity, albeit
with a protein having a different amino acid sequence. Accordingly, it was
not inventive to use Jamieson’s and Rebar’s technology to produce a
molecule with the same binding specificity as Zif268, but merely the
application of the prior art in a way that a person of ordinary creativity in the
art would have done. As observed by the Examiner, Jamieson himself used
his system to reproduce Zif268 activity but with an altered amino acid
sequence (Ans. 10).
In assessing obviousness, “[a] court must ask whether the
improvement is more than the predictable use of prior-art elements
according to their established functions.” KSR, 550 U.S. at 417. “The
combination of familiar elements according to known methods is likely to be
obvious when it does no more than yield predictable results.” Id. In this
case, the claimed subject matter is a combination of two known zinc fingers
selected for their established function.2 Because this is a predictable use of
known elements, the Examiner did not err in concluding that the
combination was obvious.

2 Additionally, Jamieson stated that certain sequences may express better or
have improved affinity as compared to the native wild-type sequences (F7).
Appellants disparaged these remarks as speculation (App. Br. 10).
Nevertheless, Jamieson’s statements indicated that the skilled worker
believed that certain advantages could come from zinc fingers having the
same binding target as the native protein, but having a different amino acid
sequence.

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Prior art does not teach rational design
Appellants state that Jamieson and Rebar taught randomization and
selection as the “only method for designing zinc finger proteins having new
binding specificities.” (App. Br. 11.) They contend that, by contrast, “claim
88 recites zinc finger proteins whose specificity is obtained by de novo
synthesis of a polypeptide or nucleic acid, utilizing rational design.” (Id.)
“Thus, rational design rules, such as those recited in claim 88, provide an
improved method of ZFP [zinc finger protein] design, compared to the more
laborious procedures of randomization and selection described by Jamieson
and Rebar.” (App. Br. 12.)
Claim 88 is to a nucleic acid binding protein. Rules a) through j) of
the claim specify the type and position of an amino acid in the zinc finger
binding motif as a function of the target nucleotide sequence (F20).
Appellants have interpreted the claim to be drawn to a design method, rather
than a protein. However, we discern no language in the claim that would
require specific design steps to have been carried out. Rather, as long as the
protein satisfies all the claim conditions – e.g., having a “His” if the middle
nucleotide of the target nucleotide sequence triplet is G as recited in rule
“c)” of claim 88 – all the limitations of the claim would be met. While the
protein may have been produced using “an improved method of ZFP design”
(App. Br. 12), it is the protein product which is currently claimed, not the
method, itself. Appellants are therefore attempting to distinguish the
claimed subject matter over limitations that do not appear in claim 88.
For this same reason, Wu’s statement about the lack of zinc finger
design rules is not a “teach[ing] away.” (App. Br. 13-14). The properly
interpreted claim 88 is to a zinc finger protein product, not a method of
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producing the protein using design rules. Appellants’ interpretation of the
claim is narrower than the words of the claim dictate.
Appellants contend that the Jamieson/Rebar methods would produce a
“myriad” of zinc fingers and that there is no teaching that would have led
persons of ordinary skill in the art to a single zinc finger meeting the claimed
limitations (App. Br. 12-13).
This argument is not persuasive. Appellants did not dispute the
Examiner’s finding that Jamieson describes a zinc finger which meets the
conditions specified in claim 88 (F22). Therefore, no selection is necessary.
The species is specifically named by Jamieson. See Perricone v. Medicis
Pharm. Corp., 432 F.3d 1368, 1376 (Fed. Cir. 2005).

No reason to use prior art transactivators with Zif268
Appellants contend that there would have been no reason to combine
the transactivation domains of Gashler and Sadowski with Jamieson’s zinc
finger protein because the latter already contained its own native activation
domain (App. Br. 15) and because the former were “silent with respect to
rational design of zinc finger proteins” (id. at 16).
Appellants’ arguments ignore the explicit and implicit goals of the
prior art. Jamieson recognized that the development of zinc fingers with
novel engineered binding specificities had “many potential applications.”
(F5). Sadowski also acknowledged the practical applications of its work
with the VP16 domain when it observed that VP16 is a “powerful activator”
which could be used “profitably” in certain expression systems (F16). In
other words, Sadowski contemplated the use of VP16 to direct expression of
other recombinant proteins. Thus, while the cited prior art references were
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directed to single experiments and to elucidating basic mechanisms, it is
undeniable that the underlying purpose was to optimize zinc fingers and
transactivators for practical applications. The statements in Jamieson and
Sadowski provide firm evidence of this goal. Using Sadowski’s VP16
transactivator with a zinc finger protein is merely using a known element for
its known activity in a predictable way as the skilled worker in this field
would have ordinarily done (F29-30).

Claims 91 and 92
Claims 91 and 92 depend on claim 88 and incorporate all its
limitations. Claim 91 further requires that the functional domain of claim 88
is an activation domain; claim 92 requires that the activation domain of
claim 91 is VP16. Appellants contend that Gashler and Sadowski were
improperly combined with Jamieson for the same reasons as for claim 88.
As we found these arguments unconvincing for claim 88, we also find them
deficient for claims 91 and 92.

CONCLUSION OF LAW & SUMMARY
The Examiner did not err in concluding that claims 88, 91, and 92
would have been obvious to a person of ordinary skill in the art in view of
the teachings of Jamieson, Rebar, Gashler, and Sadowski. The obviousness
rejection is affirmed.
Claim 89 was not argued separately (App. Br. 16) and therefore falls
with claim 88. See C.F.R. 41.37(c)(1)(vii).

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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

alw

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