Ex Parte Xu et al

Patent Trial and Appeal Board

Mar 14, 2016

12439626 (P.T.A.B. Mar. 14, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
12/439,626 0612412009 Yan Xu
68705 7590 03/16/2016
TAROLLI, SUNDHEIM, COVELL & TUMMINO, LLP
1300 EAST NINTH STREET
SUITE 1700
CLEVELAND, OH 44114
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.
CWR-8669US PCT 5734
EXAMINER
PANDE, SUCHIRA
ART UNIT PAPER NUMBER
1637
NOTIFICATION DATE DELIVERY MODE
03/16/2016 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):
rkline@tarolli.com
dkinder@tarolli.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte YAN XU, STANTON GERSON, and LILI LIU
Appeal2013-010098
Application 12/439,6261
Technology Center 1600
Before RICHARD M. LEBOVITZ, MELANIE L. McCOLLUM, and
ULRIKE W. JENKS, Administrative Patent Judges.
LEBOVITZ, Administrative Patent Judge.
DECISION ON APPEAL
This appeal involves claims directed to methods of screening
therapeutic agents for inhibiting base excision repair. The Examiner has
finally rejected the claims as obvious under 35 U.S.C. § 103(a). We have
jurisdiction under 35 U.S.C. § 134. The Examiner's rejections are affirmed.
STATEMENT OF CASE
The claimed invention relates to an assay for measurement of genomic
DNA apurinic/apyrimidinic (AP) sites. '626 App. 2. The '626 Application
teaches that AP sites are generated through loss of damaged bases (purine or
1 The '626 Application" or "the '626 App."
Appeal2013-010098
Application 12/439,626
pyrimidine) in the DNA strands. Id. at 3. "Unrepaired AP sites are
mutagenic and lethal to cells." Id. "Therefore, quantitative measurement of
AP sites in cellular DNA is crucial for the assessment of DNA damage and
repair, as well as for the development of anti-cancer drugs that target the
[base excision repair] pathway" (id.) which can result in the loss of the
unrepaired AP sites (Liu and Gerson (2004)2).
The final rejection of claims 15 and 18-20 is appealed by Appellants.
Claims 15 and 18-20 stand rejected under 35 U.S.C. § 103(a) as obvious in
view of Liu and Gerson (2004), Liu (2001), 3 Makrigiorgos,4 Liu (2002),5
and Bauman.6 Answer 2.
Claim 15 is the only independent claim on appeal as is reproduced
below:
15. A method of screening therapeutic agents for inhibiting base
excision repair (BER), the method comprising:
contacting a sample of AP-DNA with an FARP reagent and at least
one therapeutic agent, wherein the FARP reagent comprises fluorescein-5-
2 Lili Liu & Stanton L. Gerson "Therapeutic impact of methoxyamine:
Blocking repair of abasic sites in the base excision repair pathway", Current
Opinion in Investigational Drugs, 2004, 5(6):623-627.
3 Liu et al., "Nanostructured Materials Designed for Cell Binding and
Transduction", Biomacromolecules, 2001, 2, 362-368.
4 Makrigiorgos et al., "Fluorescent labelling of abasic sites: a novel
methodology to detect closely-spaced damage sites in DNA", Int. J. Radiat.
Biol., 1998, vol. 74, no 1: 99-109.
5 Liu et al., "Base Excision Repair as a Therapeutic Target in Colon Cancer"
Clin Cancer Res., 2002, 8:2985-2991.
6 Bauman et al., "Cytochemical hybridization with fluorochrome-labeled
RNA, I. Development of a method using nucleic acids bound to agarose
beads as a model." The J oumal of Histochemistry and Cytochemistry, 19 81,
vol. 29: no 2. Pp 227-237.
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Application 12/439,626
thiosemicarbazide and the therapeutic agent comprises a compound capable
of forming a covalent linkage with an aldehyde group on AP-DNA;
removing unbound F ARP reagent and the at least one therapeutic
agent from the sample of AP-DNA; and
detecting FARP labeled AP sites in the sample of AP-DNA; and
correlating a level of F ARP labeled AP sites in the sample of AP-
DNA to the level ofFARP labeled sites in a control sample of AP-DNA that
is contacted with F ARP but is not contacted with the therapeutic agent,
wherein a reduced level ofFARP labeled AP sites in the sample of AP-DNA
compared to the level of F ARP labeled AP sites in the control sample is
indicative of an effective therapeutic agent or an effective combination of
therapeutic agents.
REJECTION
Claim 15 is directed to a method of screening therapeutic agents for
inhibiting base excision repair ("BER"). The claim has four steps.
The first step comprises contacting a sample of AP-DNA with:
(a) a fluorescent aldehyde reactive probe (FARP), where the FARP
probe comprises fluorescein-5-thiosemicarbazide, and
(b) a therapeutic agent which comprises a compound capable of
forming a covalent linkage with an aldehyde group on AP-DNA.
The FARP is able to detectably label apurinic/apyrimidinic ("AP")
sites in the AP-DNA.
In the second step, unbound F ARP and therapeutic agent are removed.
In the third step, FARP labeled sites in the AP-DNA are detected.
The fourth step of the claim is a correlation step, where F ARP labeled
sites are compared in the presence and absence (the "control") of the
therapeutic agent. The step recites that "a reduced level of F ARP labeled
AP sites in the sample of AP-DNA compared to the level ofFARP labeled
AP sites in the control sample is indicative of an effective therapeutic agent
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Application 12/439,626
or an effective combination of therapeutic agents." In other words, if the
therapeutic agent inhibits base excision repair, the F ARP labeled AP sites
are not excised from the DNA and the number of F ARP labeled AP sites is
greater than in a control which lacks the therapeutic agent.
The Examiner found that Liu (2002) and Liu and Gerson (2004)
describe all four steps of the claimed method, but not an F ARP which is
fluorescein-5-thiosemicarbazide. Answer 3--4. Rather, the Examiner found
that Liu (2002) and Liu and Gerson (2004) describe a non-fluorescent
aldehyde reactive probe ("ARP"). Id. at 4. To make up for this deficiency,
the Examiner cited Makrigiorgos for its teaching of a F ARP reagent to
detect the presence of abasic sites on nucleic acid. Id. While Makrigiorgos
does not teach the claimed fluorescein-5-thiosemicarbazide as an F ARP
probe, the Examiner found that fluorescein-5-thiosemicarbazide is described
in Liu (2001), albeit to label nanoparticles. Id.; Liu (2001), 364, Fig. 1.
Based on chemical principles, the Examiner determined that it would have
been reasonably expected that the fluorescein-5-thiosemicarbazide described
in Liu (2001) would react with AP sites of DNA in the same manner as the
F ARP of Makrigiorgos. Answer 7-8.
The Examiner found it obvious to utilize fluorescein-5-
thiosemicarbazide in the method of Liu (2002) and Liu and Gerson (2004)
because of the advantages of fluorescent detection using a F ARP as
described by Makrigiorgos. Answer 5. The Examiner further found it
obvious to have used Liu (2001 )' s fluorescein-5-thiosemicarbazide as the
F ARP because it was commercially available and would have been
recognized as a suitable F ARP for the method described in Liu (2002) and
Liu and Gerson (2004). Id. at 7.
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Application 12/439,626
Appellants contend that "one of ordinary skill in the art would not
have known that the aldehyde groups present on the AP sites of DNA can be
labeled by reacting a thiosemicarbazide derived from FITC, let alone
fluorescein-5-thiosemicarbazide." Appeal Br. 9. Furthermore, Appellants
contend that it was not known prior to their invention that fluorescein-5-
thiosemicarbazide would irreversibly attach to AP-DNA sites in the presence
of a competing therapeutic agent. Id. at 11. Citing paragraph 100 of the
Specification, Appellants state that it is "the irreversible binding of these
aminooxy and hydrazone nucleophiles, as discovered by the Appellants and
disclosed in the present specification, which allows for the successful
screening of therapeutic agents in accordance with the method of claim 15."
Id. at 12.
Discussion
Despite Appellants contention that it was "not know[ n] that the
aldehyde groups present on the AP sites of DNA can be labeled by reacting
a thiosemicarbazide derived from FITC, let alone fluorescein-5-
thiosemicarbazide" (App Br. 9), it is admitted in the Specification that "[i]t
was known that the aldehyde group of an AP site could easily condense with
aminooxy or hydrazone nucleophiles." '626 Spec. i-f 99. See also id. at
i-f 101 ("Since aminooxy and hydrazone nucleophiles can react with aldehyde
group of AP site and form condensation product.") See Appeal Br. 13.
Appellants admit that "fluorescein-5-thiosemicarbazide recited in claim 15 is
a hydrazone nucleophile." Id. at 11. In view of these admissions,
Appellants' argument about unpredictability has little merit.
Appellants also argue that it was not known that fluorescein-5-
thiosemicarbazide would irreversibly attach to the aldehyde group of the AP
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Application 12/439,626
DNA. Appeal Br. 11. To support this argument, Appellants identify the
following disclosure from the Specification:
It was known that the aldehyde group of an AP site could
easily condense with aminooxy or hydrazone nucleophiles.
However, the reversibility of the reaction was not clear,
especially in the presence of another competing nucleophile.
'626 Spec. ,-r 99 .
. . . it was concluded that the condensation reaction between
aminooxy or hydrazone nucleophiles and aldehyde group of
AP-DNA is irreversible under the assay conditions. This unique
feature of the assay can be used to screen MX-like compounds
in chemotherapeutic development.
'626 Spec. ,-r 100.
While it may be true that it was unknown whether the condensation
reaction between fluorescein-5-thiosemicarbazide and AP-DNA was
irreversible in the presence of a competing therapeutic agent (Br. 11 ),
Appellants have not established that such irreversibility was required for the
assay to be effective or for it to be reasonably be expected to be work.
As argued by the Examiner, at equilibrium and in accordance with the
law of mass action, the two competing species - fluorescein-5-
thiosemicarbazide and the therapeutic agent - would compete with the same
target chemical group, with the amount of each bound to the target
depending, inter alia, on the equilibrium constants and amounts of each
compound present. Answer 8-9. The Examiner's findings, based on
scientific principles are reasonable.
Appellants argue that without knowledge of the equilibrium constants
"it ... could not be determined given the prior art whether or not
fluorescein-5- thiosemicarbazide would supplant or replace MX-like
compounds bound to AP-DNA thus rendering fluorescein-5-
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Application 12/439,626
thiosemicarbazide unsuitable for use in a method of claim 15." Reply Br.
10. However, Appellants have not presented any factual evidence to support
this statement. An argument made by counsel in a brief does not substitute
for evidence lacking in the record. Estee Lauder, Inc. v. L 'Orea!, S.A., 129
F.3d 588, 595 (Fed. Cir. 1997). Appellants have not introduced evidence
that the concept of performing a competition assay with two competing
species, one labeled and other not, is new and required irreversibility to
work.
Furthermore, Appellants argue that the equilibrium equation defined
by the Examiner would not describe the situation where one nucleophile was
irreversibly bound. Reply Br. 10. However, Appellants have not provided
objective evidence to support this opinion, and the attorney argument is
given little weight, particularly since it has not been established that the
attorney is an expert in the pertinent field.
In addition, even if the Examiner's equilibrium equation is not correct,
it still does not undermine the position that a difference in the fluorescent
binding of the F ARP in the presence or absence of the therapeutic agent
would be reasonably expected in view of chemical principles based on the
law of mass action, i.e., both reactions between target and F ARP, and target
and therapeutic agent, would be occurring at the same time. Appellants have
not presented sufficient evidence that the Examiner's determination, based
on scientific principles, is erroneous.
Appellants also contend that knowledge of the "binding affinities of
both fluorescein-5-thiosemicarbazide and MX to AP-DNA" is necessary to
determine "the amount of free AP-DNA sites" in the sample. Reply Br. 11.
Claim 15, however, is not limited to MX, but rather is open to a "therapeutic
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Application 12/439,626
agent comprises a compound capable of forming a covalent linkage with an
aldehyde group on AP-DNA." Thus, Appellants' argument is not
commensurate with the full scope of the claim.
In addition, the claim requires "correlating a level of F ARP labeled
AP sites in the sample of AP-DNA to the level of F ARP labeled sites in a
control sample of AP-DNA." The claims do not require, as argued "the
amount of free AP-DNA sites" to be calculated. Adequate evidence has not
been provided that it would be unpredictable that a difference in the levels of
F ARP labeling would be undetectable in the presence of absence of the
therapeutic agent.
For the foregoing reasons, we affirm the rejection of claim 15. Claims
18-20 were not separately argue and thus fall with claim 15. 37 C.F.R.
41.37(c)
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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