Ex Parte Hadwiger et al

Patent Trial and Appeal Board

Dec 17, 2012

10543048 (P.T.A.B. Dec. 17, 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.
10/543,048 01/26/2006 Philipp Hadwiger 29520-0920 3878
84717 7590 12/17/2012
LeClairRyan (Alnylam - ALX)
2318 Mill Road
Suite 1100
Alexandria, VA 22314
EXAMINER
CHONG, KIMBERLY
ART UNIT PAPER NUMBER
1635
MAIL DATE DELIVERY MODE
12/17/2012 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 PHILIPP HADWIGER, MATTHIAS JOHN,
CHRISTINA LORENZ, HANS-PETER VORNLOCHER, and
STEFAN LIMMER
__________

Appeal 2012-001846
Application 10/543,048
Technology Center 1600
__________

Before LORA M. GREEN, ERICA A. FRANKLIN, and
SHERIDAN K. SNEDDEN, Administrative Patent Judges.

SNEDDEN, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to double-
stranded ribonucleic acid. The Examiner has rejected the claims as obvious.
We have jurisdiction under 35 U.S.C. § 6(b). We affirm.

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STATEMENT OF THE CASE
Appellants‟ invention relates to double-stranded ribonucleic acid
(dsRNA) with “a complementary RNA strand having a nucleotide sequence
that is complementary to at least a part of a target gene and at least one
covalently linked lipophilic group.” (Spec. 4.) “The term „complementary
RNA strand‟ (also referred to herein as the „antisense strand‟) refers to the
strand of a dsRNA which is complementary to an mRNA transcript that is
formed during expression of the target gene, or its processing products, or a
region (such as the 3' -UTR) of a (+) strand RNA virus.” (Spec. 10.) “The
lipophilic group may be a steroid, such as a sterol (e.g., cholesterol).” (Spec.
4; see also, claim 96.) “[T]he lipophilic group is covalently attached to the
5' -end of the complementary strand, and the linkage comprises a
phosphodiester group.” (Spec. 17.) The Specification describes the instant
invention as follows:
It is currently believed by the skilled person that dsRNA
with 5'-modifications in the antisense strand is unable to cause
RNA interference (Nykänen et al., Cell (2001) 107:309-321,
Schwarz, D.S., et al., Mol. Cell (2002) 10:537-548, Chiu, Y.L.,
and Rana, T.M., Mol. Cell (2002) 10:549-561, Czauderna, F., et
al., Nucleic Acids Research (2003) 31:2705-2716). It is the
merit of the instant inventors to prove that 5'-modifications
where the modifying group is linked to the 5'-end of the
antisense strand via a phosphodiester group may very well
function as RNA interference agents.

(Spec. 17, ll. 24-30.)
Claims 86, 94-98, 100-102, 110, 111, and 114-119 are on appeal. The
claims have not been argued separately and therefore stand or fall together.
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37 C.F.R. § 41.37(c)(1)(vii). Claim 86, the only independent claim on
appeal, is representative and reads as follows:
86. A double-stranded ribonucleic acid (dsRNA) comprising a
complementary RNA strand, a sense RNA strand and only one
lipophilic group having a logKow exceeding 1,
wherein the complementary RNA strand has a nucleotide
sequence which is complementary to a target RNA, and
wherein the target RNA is an mRNA transcript of a
target gene or of a (+) strand RNA virus,
wherein the lipophilic group is covalently attached to a 5'
-end of the complementary RNA strand and a linkage between
the lipophilic group and the 5'-end of the complementary RNA
strand comprises a phosphodiester group.

The claims stand rejected as follows:
Claims 86, 94-98, 100-102, 110-111, and 114-119 under 35 U.S.C.
§ 103(a) as being unpatentable over the combination of Kay et al.,
1

Fosnaugh et al.,
2
Manoharan,
3
MacKellar et al.,
4
and Virta et al.
5

1
US 2003/0139363 A1, published Jul. 24, 2003.
2
US 2003/0143732 A1, published Jul. 31, 2003.
3
Calem MacKellar et al., Oligonucleotide Conjugates as Potential Antisense
Drugs with Improved Uptake, Biodistribution, Targeted Delivery, and
Mechanism of Action, 12 ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT
103-128 (2002).
4
Muthiah Manoharan, Synthesis and physical properties of anti-HIV
antisense oligonucleotides bearing terminal lipophilic groups, 20 NUCLEIC
ACIDS RESEARCH 3411-3417 (1992).
5
Pasi Virta et al., Solid-supported synthesis of oligomeric bioconjugates, 59
TETRAHEDRON 5137-5174 (2003).
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I.
Issue
The Examiner finds that Kay teaches “dsRNA that efficiently inhibit
viral gene expression and targeting hepatocyte cells using a dsRNA
molecule is capable of inhibiting the expression of a Hepatitis C Virus,” but
fails to teach “dsRNA comprising conjugates at the 5' end of the antisense
strand” where the conjugate is a “lipophilic group … linked at the 5' end
with a phosphodiester group.” (Ans. 5-6.)
The Examiner finds that Fosnaugh discloses dsRNA comprising “a
conjugate covalently attached … at the 5' end of either strand” and “linked
with biodegradable linkers as well as phosphodiester.” (Id. at 6.)
The Examiner finds that “Manoharan teach conjugation of a
cholesterol moiety to the 5' or 3' end of an antisense oligonucleotide,” and
that, as compared to unconjugated oligonucleotides, 5' cholesterol
conjugated oligonucleotides have increased “plasma half-life” and are “more
effective at reducing target gene expression in vivo.” (Id. at 6-7.)
The Examiner concludes that a
skilled artisan would have had an implicit motivation to
conjugate a cholesterol moiety to the end of the antisense strand
of a dsRNA given it was well known in the art that this
lipophilic group provides serum stability to the strand as well as
aids in cellular permeation. Fosnaugh et al. teach dsRNA can
comprise conjugates to either the 5' end or 3' end of an
antisense strand and because Manoharan teach conjugation of
cholesterol to the 5' end of an antisense molecule demonstrated
better serum stability and more importantly was more efficient
at reducing target gene expression in vivo, the skilled artisan

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would have wanted to conjugate this group at the 5' end of the
antisense strand of a dsRNA.

(Ans. 8.)
Appellants contend the following:
1) “there is no direction given why one skilled in the art would pursue
the path identified by the examiner rather than the many other disclosed
alternatives” (App. Br. 6);
2) “none of the references provide one skilled in the art with the
requisite motivation to conjugate a lipophilic group to the 5' end of the
antisense strand of a dsRNA through a phosphodiester linkage” (id. at 8-9);
3) “one skilled in the art would have expected that a dsRNA with 5'
end modifications in the antisense strand, regardless the type of the
conjugates, is unable to cause RNA interference” (id. at 11); and
4) a finding of nonobviousness is supported by evidence of
“unexpected results” (id. at 11-14).
The issue presented is: Does the evidence of record support the
Examiner‟s conclusion that the cited combination of references renders
claim 86 obvious?
Findings of Fact
The following findings of fact (“FF”) are supported by a
preponderance of the evidence of record.
FF1. The Specification discloses as follows:
It has been observed that blocking the hydroxyl group
located at the 5'-terminus of the complementary strand in an
siRNA … abolishes the ability of the siRNA to interfere with the
expression of its target gene in Drosophila embryo lysates
(Nykänen et al., Cell (2001) 107:309-321). Schwarz, D.S., et al.
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(Mol. Cell (2002) 10:537-548) employed end-modified siRNA
to confirm the conservation of the RNAi mechanism between
flies and mammals. After blocking the 5'-OH of the
complementary strand by methylation, the endogenous kinase
which usually phosphorylates the 5'-OH of dsRNA, was not
able to add a 5'-phosphate to the siRNA and consequently
RNAi activity was largely abolished, both in Drosophila
extracts as well as in cultured human HeLa cells. However, a
5'-phosphodiester on the antisense strand, i.e. 6-aminohexyl
phosphodiester, rendered the resulting duplex active in target
mRNA silencing, although activity was reduced compared to a
5'-OH bearing duplex….
Modification of the 3'-ends was well tolerated, irrespectively
whether the sense or the antisense was altered. This picture
changed for the 5' -modification, where the modifying entity
was tolerated exclusively on the sense strand. In contradiction
to the results of Schwarz…, this 5'-phosphodiester-modification
of the antisense strand abolished RNAi activity. Czauderna …
similarly found reduced gene expression inhibitory activity in
dsRNA modified at the 5'-end of the complementary strand.
(Spec. p. 2, l. 29 to p. 3, l. 20.)
FF2. Fosnaugh discloses a siRNA that “has RNAi activity that
modulates expression of RNA encoded by an ADORAl gene.” (Fosnaugh, ¶
[0032].)
FF3. Fosnaugh discloses as follows:
In one embodiment, the invention features a chemically
modified short interfering RNA (siRNA) molecule capable of
mediating RNA interference (RNAi) against ADORAl inside a
cell or reconstituted in vitro system, wherein the chemical
modification comprises a conjugate covalently attached to the
siRNA molecule. In another embodiment, the conjugate is
covalently attached to the siRNA molecule via a biodegradable
linker. … In another embodiment, the conjugate molecule is
attached at the 5'-end of either the sense strand, antisense
strand, or both strands of the siRNA.
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…
In another embodiment, the invention features conjugates
and/or complexes of siRNA molecules of the invention. Such
conjugates and/or complexes can be used to facilitate delivery
of siRNA molecules into a biological system, such as a cell. …
The present invention encompasses the design and synthesis of
novel conjugates and complexes for the delivery of molecules,
including, but not limited to, small molecules, lipids,
phospholipids, nucleosides, nucleotides, nucleic acids,
antibodies, toxins, negatively charged polymers and other
polymers, for example proteins, peptides, hormones,
carbohydrates, polyethylene glycols, or polyamines, across
cellular membranes. … Conjugates of the molecules described
herein can be attached to biologically active molecules via
linkers that are biodegradable, such as biodegradable nucleic
acid linker molecules.
(Fosnaugh, ¶¶ [0068] and [0172]; emphasis added.)
FF4. Fosnaugh discloses that the “biodegradable nucleic acid linker
molecule … can comprise a single nucleotide with a phosphorus-based
linkage, for example, a phosphoramidate or phosphodiester linkage.”
(Fosnaugh, ¶ [0173]; emphasis added.)
FF5. Manoharan “summarizes the effect of conjugating small
molecules and large biomacromolecules to antisense oligonucleotides.”
(Manoharan, Abst.)
FF6. Manoharan discloses that “[c]onjugation of lipophilic
molecules is [a] . . . way to solve the cellular permeation problem,” that
“[v]arious lipophilic molecules have been conjugated to antisense
oligonucleotides,” where “cholesterol is perhaps the best characterized.”
(Manoharan, 106, right col.)
FF7. Manoharan reports on a study demonstrating that “conjugation
of cholesterol to oligonucleotide phosphorothioates increased the plasma
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half-life,” where “[s]ixty minutes after injection into female mice, the levels
of 3'-cholesterol conjugates were nearly 4-fold higher than those of
unconjugated oligonucleotides, and the levels of 5'-cholesterol and 5',3'-
cholesterol-conjugated oligonucleotides were nearly 7-fold higher.”
(Manoharan, 109, left col., last ¶.)
FF8. Schwarz6 discloses “[a]n siRNA in which the guide [or
complimentary] strand contained a 5' amino modifier group–6-amino-hexyl
phosphoester–was significantly more effective in suppressing target mRNA
expression than the siRNA with the 5' methoxy group.” (Schwarz, 544,
right col.)
Principles of Law
To establish a prima facie case of obviousness, the Examiner must
find “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.” KSR Int’l. Co. v. Teleflex Inc., 550 U.S. 398, 418 (2007).
O’Farrell states that “[o]bviousness does not require absolute
predictability of success.” In re O’Farrell, 853 F.2d 894, 903 (Fed. Cir.
1988). O’Farrell identifies
two kinds of error. In some cases, 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 direction as to which of

6
Dianne S. Schwarz et al., Evidence that siRNAs Function as Guides, Not
Primers, in the Drosophila and Human RNAi Pathways, 10 MOLECULAR
CELL 537-548 ( 2002).

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many possible choices is likely to be successful…. In others,
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.

(Id.) See also, KSR, 550 U.S. at 418 (There must be “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.”).
Analysis
Appellants contend that “there are numerous possibilities disclosed
within [Fosnaugh] (or generally known by one of ordinary skill in the art)
for choosing different linkages, different conjugates, and different ways to
attach the conjugate to the dsRNA,” but that “there is no direction given why
one skilled in the art would pursue the path identified by the examiner rather
than the many other disclosed alternatives.” (App. Br. 6.) Appellants
further contend that “none of the references provide one skilled in the art
with the requisite motivation to conjugate a lipophilic group to the 5' end of
the antisense strand of a dsRNA through a phosphodiester linkage” (id. at 8-
9).
We are not persuaded. Here, the art teaches conjugated siRNA
molecules (dsRNA) where the “conjugate molecule is attached at the 5'-end
of either the sense strand, antisense strand, or both strands of the siRNA.”
(FF3; App. Br. 6.) The art teaches that “[v]arious lipophilic molecules have
been conjugated to antisense oligonucleotides,” where “cholesterol is
perhaps the best characterized.” (FF6; App. Br. 6-7.) The art teaches the
use of biodegradable linkages such as a phosphodiester linkage. (FF3 and
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FF4; App. Br. 6.) Furthermore, the prior art as combined does not only
provide general guidance, but in fact provides specific guidance by
disclosing a dsRNA conjugated on the 5‟-end of the antisense
(complimentary) strand (FF3; App. Br. 6) using a phosphodiester linkage
(FF3 and FF4; App. Br. 6.), where “[v]arious lipophilic molecules have been
conjugated to antisense oligonucleotides,” where “cholesterol is perhaps the
best characterized” (FF6; App. Br. 6-7). We therefore do not find error in
the Examiner‟s reliance on the cited combination of references to establish a
prima facie case of obviousness.
Appellants further argue that “just because Manoharan teaches a
conjugation method to an antisense oligonucleotide in an antisense
technology does not mean the same technology would be applicable for a
dsRNA to show stability and gene silencing activity” and that “the problems
associated with conjugating at the 5' end of the antisense strand--problems
that have been well documented by Appellants--need to be keenly observed
in making this analysis.” (App. Br. 10.) In this regard, Appellants contend
that, “[a]s shown in the specification as well as in various references in the
art at the time of the invention, the 5' end phosphodiester modification of an
antisense strand of a dsRNA of a lipophilic group completely abolished, or
at least reduced, its activity compared to an unmodified antisense strand,
because blocking the 5' -OH of the antisense strand inhibited the ability of a
siRNA to interfere with the expression of its target gene.” (App. Br. 14;
citing Spec. 2-3.) Appellants add that the Specification presents evidence of
unexpected results because “one skilled in the art would not have expected,
before this invention, that dsRNA with 5' end modifications in the antisense
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strand would cause RNA interference.” (App. Br. 13; citing Spec. 32-33 and
Fig 3.)
The Examiner refutes, however, such statements made in the
Specification with reliance on Schwarz as evidence that “it was known in the
prior art that the 5' end of the antisense strand of a dsRNA did not require a
free OH for RNAi and in fact was able to reduce gene expression wherein
the 5' end was linked with a phosphodiester group.” (Ans. 16.) Here,
Schwarz discloses a siRNA complimentary strand modified at the 5‟-end
with 6-amino-hexyl phosphoester that retained the ability to suppress target
mRNA expression. (FF8; Ans. 16.)
Appellants do not rebut the Examiner‟s specific findings with regard
to Schwarz, but instead argue that the Examiner improperly relies on the
teachings of, inter alia, Schwarz because “the examiner cannot rely on the
teachings of a reference … without making those references part of the
rejection.” (Reply Br. 3; see also, App. Br. 14-15.) We conclude that the
Examiner has set forth a prima facie case of obviousness without
considering the Schwarz reference. That is, after weighing the evidence of
record before us, we find that the Examiner has provided a rational basis for
combining the references relied upon in making the rejection. The Examiner
only relies on the Schwarz to rebut certain of Appellants‟ arguments. That
is, the Examiner relies on Schwarz to rebut Appellants‟ argument that “one
skilled in the art would not have expected, before this invention, that dsRNA
with 5' end modifications in the antisense strand would cause RNA
interference.” (App. Br. 13.)
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Appellants further argue that the teachings of Manoharan “cannot be
used as a motivation for one skilled in the art to attach conjugates to the 5'
end rather than the 3' end.” (Id. at 9.) This argument is unpersuasive, as
Manoharan supports that it would have been obvious to conjugate the
cholesterol moiety to either the 3‟ or the 5‟end. See KSR, 550 U.S. at 419
(“What matters is the objective reach of the claim. If the claim extends to
what is obvious, it is invalid under § 103.”).
Conclusion of Law
The evidence of record supports the Examiner‟s conclusion that the
cited combination of references renders claim 86 obvious.
SUMMARY
We affirm the rejection of claim 86 under 35 U.S.C. § 103(a) as being
unpatentable over the combination of Kay, Fosnaugh, Manoharan,
MacKellar, and Virta. Claims 100-102, 110-111, and 114-119 fall with
claim 86. 37 C.F.R. § 41.37(c)(1)(vii).

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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