Ex Parte Woods et al

Patent Trial and Appeal Board

Sep 28, 2017

13148289 (P.T.A.B. Sep. 28, 2017)

United States Patent and Trademark Office
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
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APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
13/148,289 10/28/2011 Robert J. Woods 235.01890101 1082
26813 7590 10/02/2017
MUETING, RAASCH & GEBHARDT, P.A.
P.O. BOX 581336
MINNEAPOLIS, MN 55458-1336
EXAMINER
PROUTY, REBECCA E
ART UNIT PAPER NUMBER
1652
NOTIFICATION DATE DELIVERY MODE
10/02/2017 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):
ptodocketing @ mrgs .com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte ROBERT J. WOODS, LORETTA YANG, and
KAUSARN. SAMLI1
Appeal 2017-001673
Application 13/148,289
Technology Center 1600
Before JOHN G. NEW, TAWEN CHANG, and
DEVON ZASTROW NEWMAN, Administrative Patent Judges.
NEW, Administrative Patent Judge.
1 Appellants state that the real party-in-interest is the University of Georgia
Research Foundation, Inc. App. Br. 3.
Appeal 2017-001673
Application 13/148,289
DECISION ON APPEAL
Appellants file this appeal under 35 U.S.C. § 134(a) from the
Examiner’s Final Rejection of Appellants’ claims 51—53, 55—62, 65—69, 72,
and 73 as unpatentable under 35 U.S.C. § 103(a) as being obvious over the
combination of A. Jokilammi et al., Construction of Antibody Mimics from a
Noncatalytic Enzyme-detection of Polysialic Acid, 295 J. Immunol. Meth.
149-60 (2004) (“Jokilammi”)), K. Karaveg and K.W. Moremen, Energetics
of Substrate Binding and Catalysis by Class 1 (Glycosylhydrolase Family
47) a-Mannosidases Involved in N-Glycan Processing and Endoplasmic
Reticulum Quality Control, 280(33) J. Biol. Chem. 29837-48 (2005)
(“Karaveg”), W.M. Patrick and A.E. Firth, Strategies and Computational
Tools for Improving Randomized Protein Libraries, 22 Biolmol. Eng. 105—
12 (2005) (“Patrick”), N.H. Barakat and J.J. Love, Molecular Diversity in
Engineered Protein Libraries, 11 Curr. Opin. Chem. Biol. 335—41 (2007)
(“Barakat”), and M.L. DeMarco et al. R.J. Woods, Structural Glycobiology:
A Game of Snakes and Ladders, 18(6) Glycobiol. 426-40 (2008)
(“DeMarco”).
Claim 69 also stands rejected as unpatentable under 35 U.S.C.
§ 103(a) as being obvious over Jokilammi, Karaveg, Patrick, Barakat,
DeMarco, and P. Kuhn et al. Active Site and Oligosaccharide Recognition
Residues of Peptide-N4-(N-acetyl-f-D-glucosaminyl)asparagine Amidase F,
270(49) J. Biol. Chem. 29493-97 (1995) (“Kuhn”).
We have jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.
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Application 13/148,289
NATURE OF THE CLAIMED INVENTION
Appellants’ invention is directed to “lectenz” molecules, which are
mutated carbohydrate processing enzymes that are catalytically inactive and
that have had their substrate affinity increased by at least 1.2 fold. Abstract.
REPRESENTATIVE CLAIM
Claim 51 is representative of the claims on appeal and recites:
51. A method for generating a lectenz comprising an
inactivated mutated carbohydrate-processing enzyme having
enhanced affinity for its substrate compared to a corresponding
wild-type carbohydrate-processing enzyme, the method
comprising:
(a) providing a 3D structure of an enzyme-substrate
complex comprising a substrate bound to a catalytically inactive
mutant carbohydrate-processing enzyme or a corresponding
wild-type carbohydrate-processing enzyme, wherein the
catalytically inactive carbohydrate-processing enzyme
comprises an amino acid sequence comprising at least one
inactivating mutation that eliminates catalytic activity of the
enzyme;
(b) performing a computational simulation on the enzyme-
substrate complex to predict the per-residue contributions to total
interaction energy (AEMm) and/or total binding free energy
(AGBinding) for amino acid residues of the enzyme;
(c) analyzing the per-residue energetic contributions to
identify at least one amino acid residue as a potential mutation
site for enhancing binding affinity of the inactivated enzyme for
its substrate as compared to a wild-type enzyme, wherein an
amino acid residue is identified as a potential mutation site for
enhancing binding activity when
o
(i) for an amino acid residue located within 5 A of
the substrate in the enzyme-substrate complex, the per-
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Application 13/148,289
residue contribution of the amino acid residue to at least
one of AEmmot AGBinding is > -0.7 kcal/mol; and
o
(ii) for an amino acid residue located more than 5 A
from the substrate in the enzyme-substrate complex, the
per-residue contribution of the amino acid residue to at
least one of is AEMm or AGBinding > 0.0 kcal/mol;
(d) expressing a library of inactivated mutated
carbohydrate-processing enzymes, each inactivated mutated
enzyme comprising a plurality of amino acid mutations, wherein
each inactivated mutated enzyme comprises at least
one inactivating mutation that eliminates catalytic activity
of the enzyme; and
each inactivated mutated enzyme further
independently comprises at least one potential affinity-
enhancing mutation at a site identified in step (c);
(e) assaying the inactivated mutated enzymes of step (d)
for their ability to form the enzyme-substrate complex; and
(f) identifying inactivated mutated enzymes from step (e)
that exhibit binding affinities to the substrate that are at least 1.2-
fold greater than those of the wild-type carbohydrate-processing
enzyme.
Claims App’x Br. 1—2.2
Issue
Appellants argue that the Examiner erred by failing to identify any
teaching or suggestion in the cited prior art of an inactivated, affmity-
2 The pages of Appellants’ Claims Appendix are not numbered. We
therefore provisionally number them seriatim, beginning with “1” as the first
page of the Appendix.
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Application 13/148,289
enhancing enzyme that has separate affinity-enhancing and inactivating
mutations. App. Br. 14.
Analysis
The Examiner finds Jokilammi teaches, in relevant part, a
catalytically-inactive enzyme that retains the substrate binding affinity of the
wild type enzyme can be used as an antibody mimic. Non-Final Act. 5
(February 19, 2015). The Examiner finds Jokilammi also teaches that the
advantages of such antibody mimics include ease of preparation, the “lack of
animal use,” and the lack of cross-reactions with antibody binding proteins,
as well as the ability to provide probes to any molecule that is poorly
immunogenic. Id. at 5—6. Furthermore, the Examiner finds that, because the
use of mutagenesis for the engineering of antibodies to increase their binding
affinities to the antigen is well known in the art, it would therefore have been
obvious to one of ordinary skill to use mutagenesis for the engineering
of antibody mimics to increase their binding affinities to the substrate. Id. at
6.
The Examiner finds Karaveg teaches methods of generating a mutant
mannosidase that is catalytically inactive and has higher binding affinity for
its substrate. Non-Final Act. 6. The Examiner finds Karaveg teaches: (1)
using the 3-D X-ray structure of a co-complex of the mannosidase and an
inhibitor to identify one or more amino acid residues that are
hypothesized to be involved in catalysis and/or substrate binding; (2)
mutating these residues; (3) screening the mutants produced for the
catalytic activity and the binding affinity to the substrate; and (4) selecting a
mutant that lacks substantial catalytic activity but has increased binding
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affinity. Id. The Examiner acknowledges that the methods of Karavag
differ from those claimed in that they do not specifically start with a
catalytically-inactive enzyme and screen for mutations that further increase
binding affinity and do not include a step of performing an in silico
computational screening of the residues hypothesized to be involved in
binding and/or catalysis prior to screening for a mutant with increased
binding affinity. Id.
Appellants argue that the Examiner failed to identify any teaching or
suggestion of an enzyme that includes an inactivating mutation and a
separate affinity-enhancing mutation. App. Br. 14. Appellants take issue
with the Examiner’s assertions that “there is no requirement that the
motivation or reason to modify the prior art be explicitly taught in the art
itself’ and that, because Jokilammi analogizes catalytically-inactive
enzymes to antibodies, “a skilled artisan would have found it obvious to use
known antibody engineering techniques on the catalytically inactive enzyme
which retains [the] substrate binding affinity of Jokilammi.” App. Br. 14
(quoting Final Act. 5—6).
In response, Appellants argue, first, that the Examiner failed to
specifically identify the “known antibody engineering techniques” that a
skilled artisan would have found it obvious to use. App. Br. 14. Second,
Appellants argue that, because the Examiner failed to clearly articulate a
specific technique or types of techniques, or the effects of those techniques,
the Examiner failed to provide the “explicit” analysis and “articulated
reasoning” required by KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 418
(2007) to show that the claimed combination was obvious. Id. at 14—15.
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Appellants argue further that, even if an artisan was motivated to use a
known antibody engineering technique on an enzyme, the Examiner does not
articulate why it would have been obvious to select an enzyme having an
inactivating mutation and a separate affinity enhancing mutation, as required
by the claims. App. Br. 15. Additionally, Appellants contend, even if a
skilled artisan would have found it obvious to use known antibody
engineering techniques on the catalytically inactive enzyme, the results of
such techniques would not have been predictable. Id.
The Examiner acknowledges that the rejection does not provide an
express teaching by any of the references to modify an enzyme having an
inactivating mutation to also and independently have a separate affinity
enhancing mutation. Ans. 10. However, the Examiner finds that the
teachings of Jokilammi, which explicitly analogizes a catalytically-inactive
enzyme that retains substrate binding affinity to an antibody, combined with
the knowledge of an ordinary artisan that engineering antibodies by
mutagenesis to increase their binding affinities to the antigen is common in
the art, provide a suggestion to modify an enzyme having an inactivating
mutation to also have a separate affinity enhancing mutation. Ans. 10. The
Examiner finds that a skilled artisan would therefore have found it obvious
to use known antibody engineering techniques on the catalytically-inactive
enzyme that retains substrate binding affinity, as taught by Jokilammi on
similar catalytically-inactive enzymes, which retain substrate binding
affinity, as taught by Karaveg. Id.
With respect to Appellants’ argument that the Examiner failed to
specifically identify the “known antibody engineering techniques” that a
skilled artisan would have found it obvious to use, the Examiner concludes
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that it would have been obvious to one of ordinary skill to use mutagenesis
for the engineering of antibody mimics to increase their binding affinities to
a substrate. App. Br. 14—15. The Examiner further concludes that it would
have been obvious to one of ordinary skill in the art to use a directed
evolution strategy (on the catalytically-inactive mutant of Karaveg) to
produce mutants having further increased binding affinity. Id. at 11.
Appellants reply that Jokilammi teaches that a catalytically inactive
enzyme is functionally similar to an antibody, but not structurally similar,
and the Examiner did not articulate how known antibody engineering
techniques — which depend on the structure of the antibody — could be
successfully applied to a catalytically inactive enzyme. Reply Br. 3.
Appellants argue that, because of the structural differences between
antibodies and enzymes, a skilled artisan would not have been motivated to
use the antibody engineering techniques identified by the Examiner. Id.
Appellants contend further that Karaveg teaches making several
single-site mannosidase mutants, and characterizing their roles in catalysis
and substrate binding. Reply Br. 6 (citing Karaveg Table I). Appellants
contend that Karaveg teaches that per-residue contributions to total binding
energy were evaluated for sugar residues within the oligosaccharide
substrate bound to mutant enzyme E330Q, but there are no data shown for
the substrate binding contributions of individual amino acid residues. Id.
(citing Karaveg 29844; Fig. 3; 29845; Tables IV and V).
We find that Appellants have the better position. Claim 51 expressly
requires, inter alia, that: “[E]ach inactivated mutated enzyme comprises at
least one inactivating mutation that eliminates catalytic activity of the
enzyme; and each inactivated-mutated enzyme further independently
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comprises at least one potential affinity-enhancing mutation at a site
identified in step (c)” (emphasis added). Jokilammi teaches “[a]n
engineered noncatalytic bacteriophage-encoded endosialidase [enzyme that]
binds specifically to polySia but does not degrade it and can thus be used as
the equivalent of an immunohistological stain,” and which is fused to green
fluorescent protein (“GFO”). Jokilammi, Abstr., 150. Jokilammi thus
teaches a polysialic-binding enzyme that is inactivated, in that it binds to its
substrate but does not catalyze the substrate, but is not binding affinity-
enhanced.
Karaveg teaches mutants of glycosylhadrase and, in particular,
mutants containing a single-site mutation at the -1 subsite (E330Q), that
“ha[ve] minimal catalysis under the conditions . . . routinely use[d] for SPR
binding studies (10°C, pH 7.0), yet. . . retain[] high affinity glycan binding
with reduced on- and off-rates.” Karaveg 29846. Furthermore, Karaveg
teaches that “[mjutations in the -1 subsite or conditions that significantly
reduce dMNJ binding affinity or catalysis either have a minimal effect on
Man9GlcNAc2 glycan binding (F659A mutant or Ca2 + depletion) or
actually increase glycan binding affinity (T688A and E330Q mutants).” Id.
(emphases added). Karaveg thus teaches a single-site mutation that
decreases catalysis and increases the binding affinity as the result of a single
site (-1) subsite mutation.
But neither Jokilammi nor Karaveg, upon which the Examiner relies,
teaches an enzyme with a mutation that eliminates catalytic activity of the
enzyme and further independently comprises at least one potential affinity-
enhancing mutation, as required by claim 51. In other words, claim 51
requires that the enzyme contain a mutation that eliminates the catalytic
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function of the enzyme and another, independent, mutation that enhances the
affinity of the enzyme for the substrate. Jokilammi does not teach an
affinity-enhancing mutation. Karaveg teaches a single-site mutation that
both enhances affinity and decreases catalysis. Neither references teaches
mutations that independently perform each required function.
Nor are we persuaded by the Examiner’s position that, because
Jokilammi functionally analogizes its fusion protein to an antibody, that a
person of ordinary skill in the art would understand that the mutagenesis
techniques employed in enhancing antibody binding affinity can be equally
applied to enzymatic binding affinity. As Appellants explain in detail in
their Reply Brief, the complex structural and functional differences between
antibodies and enzymes is such that the mutagenic mechanisms for altering
binding affinity in the former cannot be obviously employed to alter binding
affinity in the latter. See Reply Br. 3—5.
In the Answer, the Examiner adduces two additional pieces of prior
art, A. Rajpul et al., A General Method for Greatly Improving the Affinity of
Antibodies by Using Combinatorial Libraries, 102(24) Proc. Nat. Acad.
Sci. 8466—71 (2005) (“Rajpul”) and P.S. Chowdhury and I. Pastan,
Improving Antibody Affinity by Mimicking Somatic Hypermutation in vitro,
17 Nature Biotech. 568—72 (1999) (“Chowdury”). Both references are
directed to means of enhancing binding affinity in antibodies via
mutagenesis, and thus speak to the knowledge of a person of ordinary skill
in that particular field. However, neither reference speaks to the state of the
art of altering enzyme-substrate binding affinity, or to whether techniques
directed to altering antibody binding affinity can be successfully directed to
altering or increasing the binding affinity of enzymes.
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We therefore conclude that the Examiner has failed to establish a
prima facie case of obviousness because: (1) the references fail to teach or
suggest all of the limitations of the claims; and (2) the Examiner has not
adequately demonstrated that the knowledge of a person of ordinary skill in
the art of enzyme chemistry would be sufficient to cure the deficiencies of
the cited references. We consequently reverse the Examiner’s rejection of
the claims. Because we find this issue to be dispositive of the rejections, we
do not reach Appellants’ additional arguments.
DECISION
The Examiner’s rejection of claims 51—53, 55—62, 65—69, 72, and 73
as unpatentable under 35 U.S.C. § 103(a) is reversed.
REVERSED
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