Jiye Shi et al.

Patent Trials and Appeals Board

Jan 21, 2020

14897459 - (D) (P.T.A.B. Jan. 21, 2020)

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.
14/897,459 12/10/2015 Jiye Shi 15-1973-WO-US 5744
20306 7590 01/21/2020
MCDONNELL BOEHNEN HULBERT & BERGHOFF LLP
300 S. WACKER DRIVE
32ND FLOOR
CHICAGO, IL 60606
EXAMINER
BORIN, MICHAEL L
ART UNIT PAPER NUMBER
1631
MAIL DATE DELIVERY MODE
01/21/2020 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 JIYE SHI, TERENCE SEWARD BAKER,
ALASTAIR DAVID GRIFFITHS LAWSON, and
XIAOFENG LIU1
________________

Appeal 2019-001324
Application 14/897,459
Technology Center 1600
________________

Before JEFFREY N. FREDMAN, JOHN G. NEW, and
JAMIE T. WISZ, Administrative Patent Judges.

NEW, Administrative Patent Judge.

DECISION ON APPEAL

1 We use the word “Appellant” to refer to the “applicant” as defined in
37 C.F.R. § 1.142. Appellant identifies UCB Biopharma SPRL as the real
party-in-interest. App. Br. 2.
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SUMMARY
Appellant files this appeal under 35 U.S.C. § 134(a) from the
Examiner’s Final Rejection of claims 1–33, 44, and 45 as unpatentable under
35 U.S.C. § 101 as being directed to nonstatutory subject matter.
We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.

NATURE OF THE CLAIMED INVENTION
Appellant’s claimed invention is directed to methods and associated
apparatus involving designing a ligand, ab initio, that will bind to a binding
site of a macromolecular target, or of identifying a modification to a ligand
for improving the affinity of the ligand to a binding site of a macromolecular
target. Abstr.

REPRESENTATIVE CLAIM
Claim 1 is representative of the claims on appeal and recites:
1. A method for identifying a ligand that binds to a binding
site of a macromolecular target, the method comprising:

a) identifying a target list of atoms forming the surface of the
target binding site, each atom in the target list being
referred to hereinafter as a target theta atom;

b) classifying the target theta atoms according to atom type,
the atom type of each target theta atom being referred to
hereinafter as the target theta atom type and being selected
from a predetermined list of possible theta atom types;

c) extracting from a structural database of biological
macromolecules, information about non-bonding, intra-
molecular or inter-molecular atom to atom contacts, where
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the atom type of a first atom in a contacting pair of atoms,
hereinafter referred to as a reference theta atom, is one of
the predetermined list of possible theta atom types and the
atom type of the opposing, second atom of the pair,
hereinafter referred to as a reference iota atom, is one of a
predetermined list of possible iota atom types, said
information comprising spatial and/or contextual data
about the reference iota atom relative to the reference theta
atom, and said data collected for a plurality of contacts
involving a reference theta atom of the same theta atom
type from the said database is hereinafter referred to as a
theta contact set;

d) for each target theta atom identified in the target list in b ),
superimposing in or around the target binding site data
relating to a given iota atom type, or a predetermined
group of related iota atom types, from the corresponding
theta contact set extracted in c);

e) combining and/or parsing the superimposed data in such a
way as to predict one or more favoured regions of the
binding site where the given iota atom type, or the
predetermined group of related iota atom types, has high
theoretical propensity to be located; and

f) with a candidate ligand notionally docked into the binding
site, comparing the type and position of one or more of the
atoms of the candidate ligand with the predicted favoured
regions for the respective iota atom types, to identify a
modification to the candidate ligand, in terms of alternate
and/or additional candidate ligand atoms, that will produce
a greater intersection between the alternate and/or
additional candidate ligand atoms and the respective iota
atom type favoured regions, leading to an improvement in
the affinity of the modified candidate ligand to the binding
site compared to the unmodified candidate ligand;

wherein each non-bonding intra-molecular or inter-
molecular contact in the database is defined as a contact between
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opposing residues of a protein fold or between opposing
monomer units of a macromolecular fold or between two
interacting macromolecular partners and is specifically between
a reference theta atom on one side of the fold or first interacting
partner and a reference iota atom on the opposing side or second
interacting partner; in an instance where the following condition
is satisfied:

s - Rw ≤ t, wherein s is the separation between the two atoms of
the contact, Rw is the sum of the van de Waals radii of the two
atoms of the contact, and t is a predetermined threshold distance;
and

wherein the classification by target theta atom type in b) is
unique such that there is no intersection between the data of a
theta contact set extracted in c) for a given theta atom type and
the data of any other theta contact set extracted in c) for any other
theta atom type, apart from data concerning contacts involving
the given theta atom as the iota atom.

App. Br. 23.

ISSUES AND ANALYSES
We agree with, and adopt, the Examiner’s findings, reasoning, and
conclusion that the claims on appeal are directed to nonstatutory subject
matter. We address the arguments raised by Appellant below.

Issue
Appellant argues that the Examiner erred in concluding that the claims
are directed to a judicial exception to Section 101, viz., an abstract idea.
App. Br. 4.

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Analysis
The Examiner finds that the claims recite a method including the steps
of extracting and categorizing information, combining theoretical
information, comparing it with docking information of a ligand, and making
conclusions about possible changes in ligand structure. Final Act. 3. The
Examiner finds that all of these concepts relate to organization, processing,
comparing and deducing information, which can be performed mentally and
is an idea of itself. Id. Therefore, concludes the Examiner, the claims are
directed to an abstract idea, which is a judicial exception to Section 101. Id.
Appellant argues that the claims are directed to a method of
identifying a ligand that binds to a macromolecular target by
computationally quantifying and comparing various interactions between a
candidate ligand molecule and its putative macromolecular target to identify
modifications in the candidate ligand that will produce a greater affinity of
the modified candidate ligand for the macromolecular binding site compared
to the unmodified candidate ligand. App. Br. 4. Appellant asserts that the
method thereby identifies a ligand with enhanced affinity for the
macromolecular target. Id. According to Appellant, the method is a new
and non-obvious alternative to time consuming wet chemistry techniques
involving mutating candidate therapeutic molecules and testing their binding
to the macromolecular target, particularly because many different mutations
are generally required. Id. (citing Spec. 2).
Appellant argues that, because the claims are directed to an
improvement to another technology, the claims are not an abstract idea that
is ineligible for patentability. App. Br. 4 (citing MPEP §§ 2106.04(a)(I),
2106.05(a)(II)). In support of this contention, Appellant points to McRO,
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Inc. v. Bandai Namco Games Am. Inc., 837 F.3d 1299 (Fed. Cir. 2016). Id.
at 5. Appellant argues that the claims on appeal are analogous to those at
issue in McRO, in which the court considered the patent eligibility of “[a]
method for automatically animating lip synchronization and facial
expression of three-dimensional characters.” Id. (quoting McRO, 837 F.3d
at 1307).
Appellant argues that in McRO, the claimed method comprised a
series of computational steps that generated a “final stream of output morph
weight sets” that was subsequently applied “to a sequence of animated
characters to produce lip synchronization and facial expression control of
said animated characters.” App. Br. 5 (quoting McRO, 837 F.3d at 1308).
Appellant asserts that, in upholding the patentability of the McRO claims,
our reviewing court held that: “The claimed process uses a combined order
of specific rules that renders information into a specific format that is then
used and applied to create desired results: a sequence of synchronized,
animated characters.” Id. (quoting McRO, 837 F.3d at 1315).
Appellant also points to the Board’s prior decision in Ex Parte
Hakkani-Tur, Appeal No. 2017-010766, 2018 WL 2335121 (PTAB May 10,
2018). Appellant argues that the claims in Hakkani-Tur were directed to a
system that trained a spoken language understanding (SLU) classifier that
made use of a corpus of user utterances, then semantically parsed the
utterances and produced a parse graph representing all user utterances. App.
Br. 5. According to Appellant, the user utterances graph was then clustered
into intent-wise homogeneous groups of user utterances that were then used
to train the SLU classifier. Id. Appellant quotes the Board’s conclusion
that: “The utterance intent clustering limitation, which produces intent-wise
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homogeneous groups that are then used to train the SLU classifier, is
improving a technological process, as it is improving a specific process by
which an SLU classifier is trained,” and that the claims were therefore
directed to patent-eligible subject matter. Id. (quoting Hakkani-Tur at 8).
Appellant contends that the claimed method analogously uses a
combined order of specific rules that renders information into a specific
format that is then used and applied to create desired results: a molecule with
improved target binding affinity having particular modified structural
elements. App. Br. 5. Furthermore, argues Appellant, the claims do not
merely organize information into a new form, but rather go beyond
rendering the information into a new format used to create the desired result.
Id. at 6. Appellant asserts that, as in Hakkani-Tur, the presently claimed
method generates new information. Id.
Furthermore, asserts Appellant, the claims are also patent-eligible
because they recite an inventive concept, improving upon the laborious wet-
chemistry process of generating and testing mutant binding molecules and
thereby amounting to significantly more than merely reciting abstract ideas.
App. Br. 6 (citing Mayo Collaborative Servc’s v. Prometheus Labs., Inc.,
566 U.S. 66, 72–73 (2012) (holding that claims are patent eligible when they
“contain other elements or a combination of elements, sometimes referred to
as an ‘inventive concept,’ sufficient to ensure that the patent in practice
amounts to significantly more than a patent upon the [ineligible concept]
itself”)).
Appellant disputes the Examiner’s finding that the claims recite:
“steps of extracting and categorizing information, combining theoretical
information, comparing it with docking information of a ligand, and making
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conclusions about possible changes in ligand structure” and the Examiner’s
conclusion that: “[a]ll of these concepts relate to organization, processing,
comparing and deducing information, which can be performed mentally and
is an idea of itself.” App. Br. 6 (quoting Final Act. 3). To the contrary,
asserts Appellant, the claims are not directed merely to the concepts of
organization, processing, comparing, and deducing information, but instead
recite a limited, very specific set of rules, something the Federal Circuit
considered such an important distinction in McRO. Id. (citing McRO, 837
F.3d at 1316; also citing MPEP § 2106.04(a)(I)). Similarly, argues
Appellant, the claims on appeal produce a technological improvement that
results in a concrete, tangible thing (a molecule with improved target
binding affinity) and are therefore not directed to merely an abstract idea.
Id. at 7.
We do not find Appellant’s arguments persuasive. In performing an
analysis of patentability under Section 101, we follow the framework set
forth by the Supreme Court in Mayo. We are also mindful of, and guided
by, the United States Patent and Trademark Office’s 2019 Revised Patent
Subject Matter Eligibility Guidance, 84(4) Fed. Reg. 50–57 (January 7,
2019) (the “2019 Guidance”).
Appellant’s claim 1 recites: “A method for identifying a ligand that
binds to a binding site of a macromolecular target….” Following the first
step of the Mayo analysis, we find that the claims are directed to a process,
or method, and therefore fall into one of the broad statutory categories of
patent-eligible subject matter under 35 U.S.C. § 101.
In the next step of the Mayo analysis, we determine whether the
claims at issue are directed to a nonstatutory, patent-ineligible concept, i.e., a
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law of nature, a phenomenon of nature, or an abstract idea. Mayo, 566 U.S.
at 70–71. If the claims are so directed, we next consider the elements of
each claim both individually and “as an ordered combination” to determine
whether additional elements “transform the nature of the claim” into a
patent-eligible application. Id. at 78–79; see also Ariosa Diagnostics, Inc. v.
Sequenom, Inc., 788 F.3d 1371, 1375 (Fed. Cir. 2015). Specifically, the
Supreme Court considered this second step as determining whether the
claims recite an element or combination of elements that is “sufficient to
ensure that the patent in practice amounts to significantly more than a patent
upon the [ineligible concept] itself.” Mayo, 566 U.S. at 72–73.
More specifically, in this second step of the Mayo analysis, we look to
whether the claim recites one of the judicially-created exceptions to Section
101, i.e., an abstract idea, a law of nature, or a natural phenomenon. See
2019 Guidance 54 (step 2A, prong 1).
If we determine that the claim recites a judicial exception, we then
determine whether the limitations of the claim reciting the judicial exception
are integrated into a practical application. Id. (Step 2A, Prong 2).
Finally, if we determine that the claim is directed to a judicially-
created exception to Section 101, we evaluate the claim under the next step
of the Mayo analysis, considering the elements of each claim both
individually and “as an ordered combination” to determine whether
additional elements “transform the nature of the claim” into a patent-eligible
application. Mayo, 566 U.S. at 78–79; 2019 Guidance at 56 (Step 2B).
Claim 1 is directed to: “A method for identifying a ligand that binds to
a binding site of a macromolecular target” and recites the following steps:
(1) identifying a target list of atoms forming the surface of the target binding
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site (i.e., target theta atoms) (step a); (2) classifying the target theta atoms
according to atom type (step b); (3) extracting from a database information
about non-bonding, intra-molecular or inter-molecular atom-to-atom
contacts between target theta atoms and other atoms (i.e., iota atoms) (step
c); (4) for each identified target theta atom, superimposing in or around the
target binding site data relating to a given iota atom type (step d); (5)
combining and/or parsing the superimposed data in such a way as to predict
one or more favored regions of the binding site where the given iota atom
type has a high theoretical propensity to be located (step e); (6) modeling
binding of the ligand to the binding site, and comparing the type and
position of one or more of the atoms of the candidate ligand with the
predicted favored regions for the respective iota atom types, to identify a
modification to the candidate ligand, leading to an improvement in the
affinity of the modified candidate ligand to the binding site compared to the
unmodified candidate ligand (step f); (7) and subject to certain conditions
(remaining limitations)).
Put more succinctly, the claims are directed to a computer-based
method of modeling how the atomic structure of an existing or candidate
ligand can be modified to improve binding of the ligand at a binding site on
a target protein, using information derived from a database of information
about non-bonding, intra-molecular or inter-molecular atom-to-atom
contacts. See Spec. 1, 3–4.
All of the steps (1)–(6) recite procedures that are essentially
computational in nature in that they involve extracting information from a
database concerning atomic interactions in a ligand-binding site complex
and predicting the interactions that will yield advantageous ligand binding.
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See Spec. 1. Furthermore, all of the steps recited in the claims may be
performed on a general-purpose computer. See Spec. 21 (“In an
embodiment, the method of identifying a modification to a candidate ligand
is a computer-implemented method. In an embodiment, any one or more of
the steps S1-S7 [i.e., steps (1)-(7) supra] is/are performed on a computer”);
see also Spec. Fig. 7.
Because the steps recited in the claim require nothing more than the
identification, comparison, and manipulation of data (values) in a general
purpose computer, we agree with the Examiner that the claims are directed
to an abstract idea, of the sort that could be performed mentally. That is, a
person, armed with paper and pencil, could perform the steps of comparing
known target atoms to a database of atom-to-atom interactions and using that
information to design an advantageous design for a ligand binding site. Any
such abstract idea, when coupled to a generic computer performing functions
that are within the regular repertoire of computer functions, are not patent
eligible. See CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366,
1371 (Fed. Cir. 2011) (citing Parker v. Flook, 437 U.S. 584, 586 (1978));
see also CyberSource, 654 F.3d at 1372–73.
Appellant argues that the claims are not directed to an abstract idea,
because the claims are directed to an improvement to another technology
See App. Br. 5–6 (citing McRO, 837 F.3d at 1307). We disagree. The
analysis in McRO expressly looked to “whether the claims in these patents
focus on a specific means or method that improves the relevant technology
[in that case, vocal synchronization of animated characters] or are instead
directed to a result or effect that itself is the abstract idea and merely invoke
generic processes and machinery.” McRO, 837 F.3d at 1314. In the appeal
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before us, the abstract idea of optimizing ligand binding by designing a
binding site that advantageously selects atomic interactions from a stored
basis is “directed to a result or effect that itself is the abstract idea and
merely invoke generic processes and machinery.” Id.
Furthermore, “[i]n cases involving software innovations, th[e] inquiry
often turns on whether the claims focus on ‘the specific asserted
improvement in computer capabilities . . . or, instead, on a process that
qualifies as an ‘abstract idea’ for which computers are invoked merely as a
tool.” Finjan, Inc. v. Blue Coat Sys., Inc., 879 F.3d 1299, 1303 (Fed. Cir.
2018) (emphasis added) (quoting Enfish, LLC v. Microsoft Corp., 822 F.3d
1327, 1335–36 (Fed. Cir. 2016) (internal quotation marks omitted)).
Appellant’s claims are not directed to the improvement of a computer-based
technology, as in McRO, but rather use a general-purpose computer as a tool
for calculating the maximally advantageous atomic design for a ligand
binding site. As such, we conclude that the claims are directed to a judicial
exception to Section 101, i.e., an abstract idea. (Step 2A, prong 1).
Having determined that the claims are directed to an abstract idea, we
next look to see whether the claims are integrated into a practical
application. 2019 Guidance 54 (step 2A, prong 2). The Guidance provides
additional context for this analysis, stating that: “A claim that integrates a
judicial exception into a practical application will apply, rely on, or use the
judicial exception in a manner that imposes a meaningful limit on the
judicial exception, such that the claim is more than a drafting effort designed
to monopolize the judicial exception.” Id. at 53.
In the present case, we find that the claims recite no additional steps
other than the abstract idea, as implemented on a general-purpose computer,
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that would constitute integration into a practical application. As such, we
find that the claims do not impose meaningful limits upon the abstract idea
recited in the claims. For the same reason, we find that, considering the
elements of each claim both individually and “as an ordered combination”
the claims recite no additional elements or steps that would suffice to
“transform the nature of the claim” into a patent-eligible application. Mayo,
566 U.S. at 78–79; 2019 Guidance at 56 (Step 2B).
We therefore conclude that the claims are directed to nonstatutory
subject matter, and we affirm the Examiner’s rejection of the claims.

CONCLUSION
The Examiner’s rejection of claims 1–33, 44, and 45 under 35 U.S.C.
§ 101 is affirmed.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(1)(iv).

AFFIRMED

Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
1–33, 44,
45
101 Nonstatutory subject
matter
1–33, 44,
45

Overall
Outcome
1–33, 44,
45