Ex Parte Leake et al

Patent Trial and Appeal Board

Jun 17, 2016

12626011 (P.T.A.B. Jun. 17, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
12/626,011 11125/2009
105841 7590 06/17/2016
Dorf & Nelson LLP
The International Coporate Center
555 Theodore Fremd A venue
Rye, NY 10580
FIRST NAMED INVENTOR
Devin Leake
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.
DHARMA 0064-US 1342
EXAMINER
BOWMAN, AMY HUDSON
ART UNIT PAPER NUMBER
1674
MAILDATE DELIVERY MODE
06/17/2016 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 DEVIN LEAKE, ANGELA REYNOLDS,
ANASTASIA KHVOROV A, WILLIAM MARSHALL,
YURIY FEDOROV, and KIMBERLY NICHOLS
Appeal2013-000821
Application 12/626,011 1
Technology Center 1600
Before ERIC B. GRIMES, RICHARD M. LEBOVITZ, and
CHRISTOPHER G. P AULRAJ, Administrative Patent Judges.
LEBOVITZ, Administrative Patent Judge.
DECISION ON APPEAL
This appeal involves claims directed to a double-stranded
polynucleotide with modified nucleotides for use as a silencing RNA.
Appellants appeal from the Examiner's final rejection of claims 1-5, 7, 11-
16, and 18-26 under 35 U.S.C. § 103 as obvious. We have jurisdiction
under 35 U.S.C. § 134. The obviousness rejection is affirmed.
1 The Specification of Application No. 12/626,011 is referred to herein as
"the '011 Specification" or "the '011 Spec."
Appeal2013-000821
Application 12/626,011
STATEMENT OF CASE
The claimed double-stranded modified polynucleotide is described in
the '011 Specification as useful in RNA-induced gene silencing. '011 Spec.
3, 9. Gene silencing with small interfering RNA ("siRNA")-the
polynucleotides covered by the claims -is also known as RNA interference
because the siRNA interferes with the expression of a target gene and
"silences" the gene so that it doesn't express its product. Id. at 3, 9. The
nucleotide modifications recited in claims 1 and 20 are said by the '011
Specification to address the specificity and stability of the siRNA. Id. at 8.
Claims 1-5, 7, 11-16, and 18-26 are pending and stand rejected by
the Examiner under 35 U.S.C. § 103(a) (pre-AIA) as obvious in view of
Tuschl et al. (US 2004/0229266 Al, publ. Nov. 18, 2004) ("Tuschl"), Giese
et al. (US 2004/0180351 Al, publ. Sept. 16, 2004) ("Giese"), Vargeese et al.
(US 2004/0110296 Al, publ. June 10, 2004), Parrish et al. (Functional
Anatomy of a dsRNA Trigger: Differential Requirement for the Two Trigger
Strands in RNA Interference, 6 Molecular Cell 1077-1087 (2000))
("Parrish"), Bartelmez et al. (US 6,841,542 B2, issued Jan. 11, 2005)
("Bartelmez"), and McSwiggen et al. (US 2004/0192626 Al, publ. Sept. 30,
2003) ("McSwiggen").
The only independent claims on appeal are claims 1 and 20. Claim 1
is representative and reads as follows:
1. A double stranded polyribonucleotide comprising:
(a) a duplex, comprising:
(i) a sense region comprising at least one pyrimidine
nucleotide;
a first nucleotide closest to the 5' end of the sense region,
said first nucleotide having a first 2'-0-alkyl modification; and
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a second nucleotide next closest to the 5' end of the sense
region, said second nucleotide having a second 2'-0-alkyl
modification,
wherein within said sense region, each pyrimidine
nucleotide has a 2'-0-alkyl modification and each nucleotide
other than the first nucleotide and the second nucleotide that is
not a pyrimidine nucleotide comprises a ribosyl moiety that is
unmodified at said ribosyl moiety's 2' position; and
(ii) an antisense region comprising a phosphate group on
the 5' end of said antisense region, and at least one pyrimidine
nucleotide, wherein each pyrimidine nucleotide in said
antisense region comprises a 2' fluoro modification and each
nucleotide within the antisense region that is not a pyrimidine
nucleotide comprises a ribosyl moiety that is unmodified at said
ribosyl moiety's 2' position; and
(b) either no overhang regions or at least one overhang
reg10n,
wherein the sense region and the antisense region are capable of
forming a duplex of between 18 and 30 base pairs; wherein said
antisense region is at least 80% complementary to said sense
region and \~\rherein said antisense region is at least 80%
complementary to a target nucleic acid.
Rejection
The Examiner found the Tuschl describes double-stranded siRNA that
can be modified with 2 '-0-methyl groups at the 5' ends and at internal
locations as claimed, but teaches that modification of the entire double-
stranded RNA with 2'-0-methyl and 2'-deoxy substituents is not well
tolerated. Final Rej. 3--4. The Examiner further relied on teachings of Giese
of modifying the 5' end of the sense strand as recited in claim 1 "to reduce
off-target effects." Id. at 4. The Examiner also found that Giese teaches the
5' end of the antisense strand should preferably not comprise modifications
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and that internal 2'-0-alkyl groups, such as 2'-0-methyl groups, can reduce
RNAi activity. Id. McSwiggen was cited by the Examiner for its teaching
of siRNA with 2'-0-methyl pyrimidine nucleotides and pyrimidines in the
antisense region comprising 2'-fluoro modifications as in claim 1. Id. at 6.
The Examiner concluded that it would have been obvious to one of ordinary
skill in the art at the time of the invention to use the general conditions
described in Tuschl for making 2'-modified siRNA to discover the optimal
number and placement of 2'-sugar modifications in an siRNA molecule,
such that the resulting siRNA molecule retained its ability to silence gene
expression and possessed increased stability. Id.
Based on the teachings in the cited publications, the Examiner found
that it would have been routine optimization to determine the optimal
number and placement of the 2 '-0 modified groups to have arrived at the
claimed double-stranded polyribonucleotide. Id. at 7, 8-9. The Examiner
further buttressed the conclusion of obviousness by noting that McSwiggen
teaches differential modification of purines and pyrimidines in siRNA of the
same type which is claimed. Id. at 9.
Appellants contend that Tuschl "teaches away" from the claimed
subject matter since Tuschl is said by Appellants to teach minimal 2'
modifications, and limiting such modifications to the overhang region at the
siRNA ends. Appeal Br. 13-14. To support this argument, Appellants cited
a declaration by Dr. Devin Leake, dated September 6, 2011 ("Leake Deel.").
Id. at 14. Dr. Leake is a co-inventor of the claimed subject matter.
Appellants also contend that Giese teaches away from the claimed
requirement of "a second nucleotide next closest to the 5' end of the sense
region ... having a second 2'-0-alkyl modification" by its disclosure that
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Application 12/626,011
such nucleotide should be unmodified. Id. at 15. Appellants also contend
that the claimed features, i.e., "the presence of certain modifications should
be determined based on the location within the duplex (the first and second
sense nucleotides), while the presence of other modifications should be
based on the identity of the nitrogenous base (pyrimidine vs. purine)," were
not recognized as result-effective variables and therefore the doctrine of
routine optimization is not applicable. Id. at 15.
Before addressing these arguments, we are making the following
findings of fact:
Tuschl publication
FFl
Findings of Fact
[0015] In an especially preferred embodiment of the present
invention the RNA molecule may contain at least one modified
nucleotide analogue. The nucleotide analogues may be located
at positions where the target-specific activity, e.g. the RNAi
mediating activity is not substantially effected, e.g. in a region
at the 5'-end and/or the 3'-end of the double-stranded RNA
molecule.
FF2
Preferred modifications include 2 '-0-alkyl modifications. Tuschl
iT 16.
FF3
[O 140] To assess the importance of the siRNA ribose residues
for RNAi, duplexes with 21-nt siRNAs and 2-nt 3' overhangs
with 2'-deoxy- or 2'-0-methyl-modified strands were examined
(FIG. 14). Substitution of the 2-nt 3' overhangs by 2'-deoxy
nucleotides had no effect, and even the replacement of two
additional riboncleotides [sic] adjacent to the overhangs in the
paired region, produced significantly active siRNAs. Thus, 8
out of 42 nt of a siRNA duplex were replaced by DNA residues
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without loss of activity. Complete substitution of one or both
siRNA strands by 2'-deoxy residues, however, abolished RNAi,
as did substitution by 2'-0-methyl residues.
FF4
[0148] ... 2'-deoxy substitutions of the 2-nt 3' overhanging
ribonucleotides do not affect RNAi, but help to reduce the costs
of RNA synthesis and may enhance RNAse resistance of
siRNA duplexes. More extensive 2'-deoxy or 2'-0-methyl
modifications, however, reduce the ability of siRNAs to
mediate RNAi, probably by interfering with protein association
for siRNAP assembly.
Giese publication
FF5
[O 102] The various end modifications as disclosed herein are
preferably located at the ribose moiety of a nucleotide of the
ribonucleic acid. More particularly, the end modification may
be attached to or replace any of the OH-groups of the ribose
moiety, including but not limited to the 2'0H, 3'0H and 5'0H
position, provided that the nucleotide thus modified is a
terminal nucleotide.
FF6
[0103] ... It is particularly advantageous to inactivate the sense
strand of any of the RNAi forms or embodiments disclosed
herein, preferably via an end modification, and more preferably
a 5' end modification. The advantage of this strategy arises from
the inactivation of the sense strand which corresponds to the
second strand of the ribonucleic acids described herein, which
might otherwise interfere with an unrelated single-stranded
RNA in the cell.
FF7
End modifications can include 0-alkyl modifications. Giese i-f 96.
FF8
[ 0123] In a preferred embodiment the second (penultimate)
nucleotide at the terminus of the strand and stretch,
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Application 12/626,011
respectively, is an unmodified nucleotide or the beginning of
group of unmodified nucleotides.
FF9
[0191] To test the nuclease resistance the different siRNA
versions were incubated in serum followed by PAA gel
electrophoresis. The result is shown in FIG. 15B (right panel
with the various sequences indicated on the left panel of FIG.
15B) . ... Molecules which contained modifications beginning
with the second nucleotide at the 5' end of the antisense strand
were more stable but had a strongly reduced activity in gene
silencing (molecules V13, V14) [Fig, 15C]. This result points
towards highly specific interactions between the involved
enzymes and precise nucleotides in the siRNA duplex. Taken
together the data shown herein demonstrate that 2'-0-methyl
modifications at particularly selected positions in the siRNA
duplex can increase nuclease resistance and do not necessarily
abolish RNAi completely.
FFlO
[0076] FIG. 12 shows that alternating 2'-0-methyl modification
result in activity of the modified RNAi molecules compared to
unmodified forms .... As may be taken therefrom RNAi
molecules with alternating modifications are stabilized against
endonuclease degradation and active in mediating a PTEN
protein knock down.
FFll
[0176] It is illustrated by the dose response curves shown for
various RNAi molecules in FIG. lOA that internal 2'-0-alkyl
groups reduce RNAi activity. Preferably such 2'-0-alkyl groups
are 2'-0-methyl or 2'-0-ethyl groups. However, molecules with
unmodified nucleotides in combination with 2'-0-alkyl
modification show significant activity. As is also depicted in
FIG. lOA no activity was obtained when the antisense strand is
all modified with 2'-0-methyl groups and the sense strand is not
modified (cf., e.g., RNAi molecule 79A28B). Taken the results
of a stability test such as incubation of the various RNAi
molecules in serum, as depicted in FIG. lOB, shows that 2'-0-
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Application 12/626,011
alkyl modifications stabilize RNAi molecules against
degradation. This clearly beneficial effect, however, is at least
to a certain degree counterbalanced by the effect that 2'-0-alkyl
modifications generally result in a reduced knockdown activity.
Accordingly, the design of RNAi molecules has to balance
stability against activity which makes it important to be aware
of the various design principles as disclosed in the present
application.
McSwiggen publication
FF12
[0025] In one embodiment, a siNA [short interfering nucleic
acid] molecule of the invention comprises a sense region and
antisense region, wherein pyrimidine nucleotides in the sense
region compri[s]es 2'-0-methyl pyrimidine nucleotides and
purine nucleotides in the sense region comprise 2'-deoxy purine
nucleotides.
FF13
[0080] ... In another embodiment, one or more, for example
about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more pyrimidine nucleotides
of the sense and/or antisense siNA strand are chemically-
modified with 2'-deoxy, 2'-0-methyl and/or 2'-deoxy-2'-fluoro
nucleotides, with or without one or more, for example, about 1,
2, 3, 4, 5, 6, 7, 8, 9, 10 or more phosphorothioate
intemucleotide linkages and/or a terminal cap molecule at the
3'-end, the 5'-end, or both of the 3' and 5'-ends, being present in
the same or different strand. [Emphasis added.]
FF14
[0026] In one embodiment, a siNA molecule of the invention
comprises a sense region and antisense region, wherein the
pyrimidine nucleotides when present in said antisense region
are 2'-deoxy-2'-fluoro pyrimidine nucleotides and the purine
nucleotides when present in said antisense region are 2'-0-
methyl purine nucleotides.
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FF15
[0691] ... To develop nuclease-resistant siNA for in vivo
applications, siNAs can be modified to contain stabilizing
chemical modifications. Such modifications include
phosphorothioate linkages (P=S), 2'-0-methyl nucleotides, 2'-
fluoro (F) nucleotides, 2'-deoxy nucleotides, universal base
nucleotides, 5' and/or 3' end modifications and a variety of other
nucleotide and non-nucleotide modifications, in one or both
siNA strands. Several of these constructs were tested in the
HCV /poliovirus chimera system, demonstrating significant
reduction in viral replication (FIGS. 34-37).
FF16
[0069] The chemically-modified nucleotide or non-nucleotide
of Formula II can be present in one or both oligonucleotide
strands of the siNA duplex, for example in the sense strand, the
antisense strand, or both strands. The siNA molecules of the
invention can comprise one or more chemically-modified
nucleotide or non-nucleotide of Formula II at the 3'-end, the 5'-
end, or both of the 3' and 5'-ends of the sense strand, the
antisense strand, or both strands. For example, an exemplary
siNA molecule of the invention can comprise about 1 to about 5
or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified
nucleotides or non-nucleotides of Formula II at the 5'-end of the
sense strand.
Parrish publication
FF17
... modification of at least 1/4 of bases to a 2' fluoro group
(which preserves A form structure; e.g., Cummins et al., 1995;
Lesnik and Freier, 1995) were compatible with function as an
RNAi trigger.
Parrish 1084.
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"Teaching away" by Tuschl
Discussion
The claims require a sense strand where "each pyrimidine nucleotide
has a 2'-0-alkyl modification and each nucleotide other than the first
nucleotide and the second nucleotide that is not a pyrimidine nucleotide
comprises a ribosyl moiety that is unmodified at said ribosyl moiety's 2'
position."
The claims also require an antisense strand "wherein each pyrimidine
nucleotide in said antisense region comprises a 2' fluoro modification and
each nucleotide within the antisense region that is not a pyrimidine
nucleotide comprises a ribosyl moiety that is unmodified at said ribosyl
moiety's 2' position."
Appellants argue that a skilled worker would not have made the
recited modifications, such as the claimed 2' -0-alkyl modifications, in the
duplex region because "the presence of modifications in the duplex region
would reduce the ability of siRNAs to mediate RNAi due to their
interference with protein association for siRNA precursors." Appeal Br. 14.
Appellants' Declarant, Dr. Leake, cites paragraph 148 of Tuschl which states
that "[m]ore extensive 2'-deoxy or 2'0-methyl modifications ... reduce the
ability of siRNAs to mediate RNAi," to support the conclusion that Tuschl
"teaches a person of ordinary skill in the art to avoid more extensive
modifications, such as those in our claimed molecules." Leake Deel. i-fi-1 9,
10.
The argument that one of skill in the art at the time of the invention
would not have made internal modifications to siRNA is not supported by a
preponderance of the evidence. Neither Appellants nor Dr. Leake addressed
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Application 12/626,011
the additional disclosures by Giese and McSwiggen. Giese specifically
teaches that siRNAs containing alternating 2'-0-methyl modifications in the
internal region possess siRNA knockdown activity and are stabilized against
endonuclease degradation. FF 10. McSwiggen also describes siRNA with a
plurality of internal modifications, including 2'-deoxy, 2'-0-methyl and 2'-
deoxy-2'-fluoro nucleotides, and teaches they possess gene silencing activity
("knockdown activity"), e.g., as measured by a reduction in viral replication
of the targeted gene. FF14, FF15. Thus, while it is well-established that 2'-
0-methyl and other internal modifications could reduce siRNA activity
(FF3, FF4, FF9, FFl 1), one of ordinary skill in the art knew how to
determine how a modification affected siRNA (e.g., FF15; see generally
each of Tuschl, Giese, and McSwiggen, each which modify siRNA and then
assay for siRNA activity). Giese specifically teaches 2'-0-alkyl
modifications are desirable because they impart resistance to endonuclease
degradation, providing an explicit reason to have used them in siRNA.
FF 11. While such modifications "generally result in a reduced knockdown
activity" of the siRNA construct, Giese did not warn against using them, but
rather stated "the design of RNAi molecules has to balance stability against
activity which makes it important to be aware of the various design
principles as disclosed in the present application." Id. We give little weight
to Dr. Leake's testimony, which did not address the significant teachings in
Giese, McSwiggen, and Parrish describing siRNA with internal
modifications, including with 2 '-0-alkyl and 2 '-fluoro modifications to the
pyrimidines as claimed. FF 13, FF 15. See also Parrish's teaching of 2' fluoro
group modifications. FF 1 7.
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Teaching away from modifying second nucleotide
All of the claims on appeal require that the second sense nucleotide be
modified with a 2' -0-methyl group. Citing paragraph 123 of Giese,
Appellants contend the Giese "explicitly teaches that the second nucleotide
in both strands of a duplex should be unmodified." Appeal Br. 15. For this
reason, Appellants argue that Giese "teaches away from the claimed
invention, and if a person of ordinary skill in the art were to combine it with
the other cited references, he or she would omit a modification on the second
5' sense nucleotide." Id.
A teaching that a result would be inferior or less desirable is not a
teaching away unless the use "would render the result inoperable." In re
ICON Health and Fitness, Inc., 496 F.3d 1374, 1381 (Fed. Cir. 2007).
Under the proper legal standard, a reference will teach away
when it suggests that the developments flowing from its
disclosures are unlikely to produce the objective of the
applicant's invention. A statement that a particular
combination is not a preferred embodiment does not teach away
absent clear discouragement of that combination.
Syntex (U.S.A.) LLC v. Apotex, Inc., 407 F.3d 1371, 1380 (Fed. Cir. 2005)
(citations omitted).
In this case, Giese teaches that "[i]n a preferred embodiment the
second (penultimate) nucleotide at the terminus of the strand and stretch,
respectively, is an unmodified nucleotide or the beginning of group of
unmodified nucleotides." FF8. Giese does not teach that modifying the
second nucleotide would make the siRNA lose activity completely and be
"inoperable," but rather it indicates that modification at this position is less
preferred because it has strongly reduced activity in the specific siRNA
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tested. FF9. On the other hand, McSwiggen describes "an exemplary siNA
molecule ... can comprise about 1 to about 5 or more ... chemically-
modified nucleotides or non-nucleotides of Formula II at the 5'-end of the
sense strand." FF16. Even if McSwiggen's disclosure is not an explicit
teaching to modify the second nucleotide at the 5 '-end of the sense strand, it
does indicate modifications in a region that could include a second
nucleotide from the terminus and that activity may differ, depending on the
specific siRNA modifications in a given siRNA molecule. Furthermore, as
already discussed, the skilled worker knew to balance stability, e.g., by
including a modified nucleotide at the second position, against activity.
FF 11. Thus, there is insufficient evidence of record that the skilled worker
would have been dissuaded from placing a 2' -0-alkyl at the penultimate 5'-
end of the sense strand because such worker would have recognized that it
would be beneficial in its added stability and would have been expected it to
possess sufficient activity to be useful as an siRNA.
Routine optimization
Appellants contend that the claimed siRNA would not have been
arrived at by routine optimization because it was not known that "the
presence of certain modifications should be determined based on the
location within the duplex (the first and second sense nucleotides), while the
presence of other modifications should be based on the identity of the
nitrogenous base (pyrimidine vs. purine)." Appeal Br. 16. Appellants
contend that these modifications are "not capable of being optimized"
because are not described by values or ranges of a parameter. Reply Br. 3.
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Appellants' arguments do not persuade us that the Examiner erred.
As to the presence of modified nucleotides at the first and second positions
of the sense strand, both Giese and McSwiggen recognized that
modifications at these positions affect siRNA knockdown activity and
specificity. FF5, FF6, FF8, FF9, FF16. With regard to the claimed (i) sense
strand comprising pyrimidines having a 2 '-0-alkyl modification and
unmodified at other positions, McSwiggen describes such configuration as a
desired one. FF13. McSwiggen also describes (ii) an antisense with
pyrimidines comprising 2 '-fluoro modifications and unmodified nucleotides.
FF13. Consequently, contrary to Appellants' contentions, the cited
publications teach that modifications in the same positions recited in the
claim 1 were known to influence activity and therefore were optimizable
features of an siRNA, such as the molecule which is claimed.
Dr. Leake states that "possible synergy" of the claimed configuration
had not been recognized, but did not provide evidence of synergy. Leake
Deel. i-f 11. Dr. Leake also states there was "nothing routine about trying to
optimize [the nucleotide modifications], given the infinite number of
modifications and modification patterns that are possible." Id. However, as
indicated above, the claimed modifications were known. McSwiggen's
disclosure in paragraph 80 explicitly covers siRNA with pyrimidine
modified with 2'-0-methyl or 2'-fluoro in either the sense, anti-sense, or both
strands, explicitly leading one of ordinary skill in the art to the claimed
pyrimidine modifications. FF 13. Dr. Leake has not addressed the disclosure
in McSwiggen cited by the Examiner which discloses the same pyrimidine
modifications which are claimed.
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Summary
For the foregoing reasons, we conclude that Appellants did not
demonstrate an error in the Examiner's determination that claim 1 is obvious
in view of Tuschl, Giese, McSwiggen, Parrish, Vargeese, and Bartelmez.
Claims 2-5, 7, 11-16, and 18-26 were not argued separately and therefore
fall with claim 1. 37 C.F.R. § 41.37(c)(iv).
TIME PERIOD
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(l )(iv).
AFFIRMED
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