Alnylam Pharmaceuticals, Inc. v. Moderna, Inc., Modernatx, Inc., Moderna Us, Inc.

United States Court of Appeals
for the Federal Circuit
______________________
ALNYLAM PHARMACEUTICALS, INC.,
Plaintiff-Appellant
v.
MODERNA, INC., MODERNATX, INC., MODERNA
US, INC.,
Defendants-Appellees
______________________
2023-2357
______________________
Appeal from the United States District Court for the
District of Delaware in Nos. 1:22-cv-00335-CFC, 1:22-cv-
00925-CFC, Chief Judge Colm F. Connolly.
______________________
Decided: June 4, 2025
______________________
P AUL WHITFIELD HUGHES , III, McDermott Will & Em-
ery LLP, Washington, DC, argued for plaintiff-appellant.
Also represented by IAN BARNETT BROOKS ; SARAH CHAPIN
COLUMBIA, SARAH J. F ISCHER , Boston, MA; WILLIAM G.
G AEDE , III, San Francisco, CA; BHANU SADASIVAN, Menlo
Park, CA.
J EFFREY A. L AMKEN, MoloLamken LLP, Washington,
DC, argued for defendants-appellees. Also represented by
SARA MARGOLIS , SARA T OFIGHBAKHSH , New York, NY.
G EOFFREY D ONOVAN BIEGLER , W. CHAD SHEAR, Cooley
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 2
LLP, San Diego, CA; ELIZABETH M. F LANAGAN, Minneap-
olis, MN.
______________________
Before T ARANTO, CHEN, and HUGHES , Circuit Judges.
T ARANTO, Circuit Judge.
Alnylam Pharmaceuticals, Inc., brought two suits
against Moderna, Inc., ModernaTX, Inc., and Moderna US,
Inc. (collectively Moderna) in district court, alleging that
Moderna’s activities involving its mRNA-based COVID-19
vaccine SPIKEVAX® infringed U.S. Patent
Nos. 11,246,933 (parent) and 11,382,979 (child), issued to
Alnylam as both applicant and assignee. Specifically, Al-
nylam alleged that Moderna’s vaccine contains a cationic
lipid, SM-102, that is claimed by the asserted patents. The
appeal here turns on a single issue of claim construction.
The district court concluded that Alnylam had acted as
lexicographer regarding the claim term “branched alkyl” in
the following portion of the specification:
Unless otherwise specified, the term[] “branched
alkyl” . . . refer[s] to an alkyl . . . group in which one
carbon atom in the group (1) is bound to at least
three other carbon atoms and (2) is not a ring atom
of a cyclic group.
’933 patent, col. 412, lines 13–17; ’979 patent, col. 380, lines
31–35; Transcript at 144:7–147:8, Alnylam Pharmaceuti-
cals, Inc. v. Moderna, Inc., No. 22-cv-335-CFC (D. Del. Aug.
9, 2023), ECF No. 115 (Aug. 10, 2023) (Transcript). The
district court treated that passage as a definition furnish-
ing the governing construction of a “branched alkyl” and
two related claim terms. Claim Construction Order at 1–
2, Alnylam Pharmaceuticals, Inc. v. Moderna, Inc., No. 22-
cv-335-CFC (D. Del. Aug. 21, 2023), ECF No. 125 (Order);
see Transcript, at 144:7–147:8. The parties stipulated that
Moderna did not infringe the asserted patent claims under
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 3
that claim construction, because Moderna’s product does
not meet the “branched alkyl” requirement of a carbon
atom bound to at least three other carbons, and the district
court entered final judgment accordingly. J.A. 5665–71;
J.A. 1–2.
Alnylam appeals. We conclude that Alnylam acted as
lexicographer in its requirement of a carbon bound to at
least three other carbons “[u]nless otherwise specified” and
that Alnylam did not otherwise specify for purposes of the
asserted claims. We therefore affirm.
I
A
The asserted patents address “biodegradable lipids and
. . . their use for the delivery of active agents such as nu-
cleic acids.” ’933 patent, col. 1, lines 17–19.1 The specifi-
cation states that certain types of nucleic acids can be used
to reduce intracellular levels of specific proteins through
RNA interference and that such reductions may have broad
therapeutic applications. Id., col. 1, lines 23–33. But nu-
cleic acids themselves are “susceptib[le] to nuclease diges-
tion in plasma” and have “limited ability to gain access to
the intracellular compartment.” Id., col. 1, lines 37–42. Ac-
cordingly, the specification states, there is a need for lipid
nanoparticles that can protect the nucleic acid from degra-
dation while in transit, deliver the nucleic acid into the cell,
and then degrade for clearance from the body with minimal
toxic effects. Id., col. 1, lines 47–57; id., col. 2, lines 2–6.
The specification explains that lipid nanoparticles used
to deliver nucleic acids can be formed from cationic lipids,
1 Neither party has identified any difference in the
two patents’ specifications that is material to the issue on
appeal. Accordingly, though we discuss both patents, we
cite only to the ’933 specification.
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 4
along with other lipid components not relevant here. Id.,
col. 1, lines 42–46; see also J.A. 4433. Cationic lipids gen-
erally include three distinct domains: a “head group,” a
linker (referred to as a “central moiety” in the asserted pa-
tents), and hydrophobic tails. J.A. 4433. One example2 of
a cationic lipid from the specification is shown below, with
annotations that illustrate how the claim terms map onto
the molecule:
Alnylam Opening Br. at 12; ’933 patent, col. 34, lines 32–
42. In this example, each of the two hydrophobic tails is
made up of an alkyl group R12, a biodegradable group M1,
and an alkenyl group R13. The carbon atoms immediately
next to a M1 biodegradable group are located at the “alpha
position” relative to that biodegradable group. The claim-
construction dispute on appeal centers around the alpha-
position carbon within R13. Specifically, the dispute con-
cerns the degree of “branching” at that position that is
2 The parties agree that the depicted compound falls
outside the asserted claims for an unrelated reason—the
carbon-carbon double bond in the R13 group that makes it
an alkenyl group rather than an alkyl group. See Alnylam
Opening Br. at 12 n.6; Moderna Response Br. at 61; Al-
nylam Reply Br. at 29, 39. We use the figure simply for
explanatory purposes.
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 5
required by the claims: whether the alpha-position carbon
must be bound to at least three other carbon atoms (in
which case it must be a “tertiary” or “quaternary” carbon)
or whether it need only be bound to at least two other car-
bon atoms (in which case it can also be a “secondary” car-
bon).
J.A. 5012.
Representative claim 18 of the ’933 patent states as fol-
lows, with emphases on the claim terms at issue:
A cationic lipid comprising a primary group and
two biodegradable hydrophobic tails, wherein
the primary group comprises (i) a head group that
optionally comprises a primary, secondary, or ter-
tiary amine, and (ii) a central moiety to which the
head group and the two biodegradable hydrophobic
tails are directly bonded;
the central moiety is a central carbon or nitrogen
atom;
each biodegradable hydrophobic tail independently
has the formula -(hydrophobic chain)-(biodegrada-
ble group)-(hydrophobic chain), wherein the biode-
gradable group is —OC(O)— or —C(O)O—;
for at least one biodegradable hydrophobic tail, the
terminal hydrophobic chain in the biodegradable
hydrophobic tail is a branched alkyl, where the
branching occurs at the α-position relative to the
biodegradable group and the biodegradable hydro-
phobic tail has the formula —R12-M1-R13, where R12
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 6
is a C4-C14 alkylene or C4-C14 alkenylene, M1 is the
biodegradable group, R13 is a branched C 10 -C 20
alkyl, and the total carbon atom content of the tail
—R12-M1-R13 is 21 to 26;
in at least one hydrophobic tail, the biodegradable
group is separated from a terminus of the hydro-
phobic tail by from 6 to 12 carbon atoms; and
the lipid has a pKa in the range of about 4 to about
11 and a logP of at least 10.1.
’933 patent, col. 538, lines 13–38 (emphases added); see also
’979 patent, col. 493, line 42, through col. 494, line 43
(where representative claim 1 recites a lipid particle that
includes a materially similar cationic lipid); id., col. 495,
line 41, through col. 496, line 20 (where representative
claim 18 recites a method of preparing a lipid particle mix-
ture including a materially similar cationic lipid).
B
In March 2022, Alnylam sued Moderna in the district
court for the District of Delaware, alleging that Moderna
infringed claim 18 and other claims of the ’933 patent (is-
sued the month before) through activities involving the
SM-102 lipid in its mRNA-based COVID-19 vaccine,
SPIKEVAX®. J.A. 33–46. In July 2022, after the ’979 pa-
tent issued, Alnylam filed a second, similar suit against
Moderna in the same forum, alleging infringement of claim
1 and other claims of the ’979 patent, and the two actions
were consolidated. J.A. 22; J.A. 5666.
In June 2023, the parties submitted a joint claim-con-
struction brief, J.A. 4418–4508, in preparation for a claim-
construction hearing set for August 2023, J.A. 23. Regard-
ing the “branched alkyl” and “branched C10-C20 alkyl”
terms, Alnylam asked the court to apply what it asserted
was the ordinary meaning: “a saturated hydrocarbon moi-
ety that is not a straight chain,” with the additional re-
quirement that a “branched C10-C 20 alkyl” contains 10 to 20
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 7
carbon atoms. J.A. 4477. Moderna requested a construc-
tion that tracked what Moderna viewed as a definitional
sentence in the specification: “Alkyl in which one carbon
atom in the group (1) is bound to at least three other carbon
atoms, and (2) is not a ring atom of a cyclic group.” J.A.
4477.
On August 9, 2023, the district court heard from coun-
sel and issued claim constructions from the bench. Tran-
script, at 90:3–162:24.3 The district court agreed with
Moderna that the passage in column 412 of the ’933 patent
“is clear and unequivocal lexicography.” Id. at 145:20–25.
Accordingly, it construed “branched alkyl” as follows:
A saturated hydrocarbon moiety group in which
one carbon atom in the group (1) is bound to at least
3 In the claim-construction session, the district court
addressed both the Moderna matter and also another mat-
ter that Alnylam initiated against BioNTech SE, BioNTech
Manufacturing GmbH, Pfizer Inc., and Pharmacia &
Upjohn Co. LLC. J.A. 7; J.A. 5519. The non-Moderna mat-
ter includes an additional dispute over whether the phrase
“R13 is a branched C10-C20 alkyl” requires that one carbon
atom is bound to at least three other carbon atoms within
the R13 group. Transcript, at 95:10–20, 150:19–25. The
district court answered that question in the negative. J.A.
5519–22. In the present case, the only dispute between the
parties is whether the alpha carbon in the claims at issue
needs to be connected to at least three carbon atoms; nei-
ther party further restricts the source of the connecting
carbons (e.g., to exclude carbons from the biodegradable
group). See Alnylam Opening Br. at 15–16, 33 n.11;
Moderna Response Br. at 19–20. We proceed on the as-
sumption, without deciding, that there is no such source
restriction.
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 8
three other carbon atoms, and (2) is not a ring atom
of a cyclic group.
Id. at 145:12–16. The district court explained that there
would need to be “some specification otherwise to depart
from that lexicography” “in every instance in which you
want to depart from the lexicography.” Id. at 146:1–5. It
reasoned that departure from lexicography had to be “clear
and unmistakable”—and Alnylam had not pointed to any
part of the claims or written description that showed such
a departure. Id. at 146:6–147:8.
On August 21, 2023, the district court entered a claim-
construction order consistent with its rulings from the
bench. Order, at 1–2 (also construing “a branched C10-C20
alkyl” and “R13 is a branched C10-C20 alkyl” in the same
way, with additional requirements not at issue here). A
few days later, the parties stipulated to noninfringement of
all asserted claims under the district court’s claim con-
structions and jointly moved for entry of final judgment.
J.A. 5665–71. The district court entered the requested fi-
nal judgment of noninfringement on August 30, 2023, dis-
missing Moderna’s counterclaims without prejudice. J.A.
1–2.
Alnylam timely appealed. We have jurisdiction under
28 U.S.C. § 1295(a)(1).
II
We review a district court’s claim construction without
deference “[w]here, as here, the intrinsic evidence alone de-
termines the proper claim construction.” Baxalta Inc. v.
Genentech, Inc., 972 F.3d 1341, 1345 (Fed. Cir. 2020) (al-
teration in original) (quoting Allergan Sales, LLC v.
Sandoz, Inc., 935 F.3d 1370, 1373 (Fed. Cir. 2019)); see
Teva Pharmaceuticals USA, Inc. v. Sandoz, Inc., 574 U.S.
318, 331 (2015).
On appeal, Alnylam argues that the district court erred
in holding that Alnylam acted as lexicographer in the
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 9
column 412 passage, contending that the intrinsic record
shows that it did not intend to so limit the “branched alkyl”
terms and that the district court’s construction excludes
disclosed embodiments. Alnylam Opening Br. at 37–67.
Alnylam argues in the alternative that, even if the column
412 passage is definitional, the definition covers a second-
ary carbon at the alpha position in the asserted claims un-
der the “[u]nless otherwise specified” portion of the
definition. Id. at 67–70.
A
A patentee “may choose to be his own lexicographer
and use terms in a manner other than their ordinary mean-
ing, as long as the special definition of the term is clearly
stated in the patent specification or file history.” Vitronics
Corp. v. Conceptronic, Inc., 90 F.3d 1576, 1582 (Fed. Cir.
1996) (citing Hoechst Celanese Corp. v. BP Chemicals Ltd.,
78 F.3d 1575, 1578 (Fed. Cir. 1996)); see Markman v.
Westview Instruments, Inc., 52 F.3d 967, 980 (Fed. Cir.
1995) (en banc) (“[A]ny special definition given to a word
must be clearly defined in the specification.”), aff’d, 517
U.S. 370 (1996); CCS Fitness, Inc. v. Brunswick Corp., 288
F.3d 1359, 1366 (Fed. Cir. 2002). “[T]he intrinsic evidence
must ‘clearly set forth’ or ‘clearly redefine’ a claim term so
as to put one reasonably skilled in the art on notice that
the patentee intended to so redefine the claim term.” Bell
Atlantic Network Services, Inc. v. Covad Communications
Group, Inc., 262 F.3d 1258, 1268 (Fed. Cir. 2001) (citation
omitted); see Merck & Co. v. Teva Pharmaceuticals USA,
Inc., 395 F.3d 1364, 1370 (Fed. Cir. 2005). We conclude
that the column 412 passage at issue here is definitional
under that standard.
First, the sentence in question appears under the title
“Definitions.” ’933 patent, col. 410, line 55; see Thorner v.
Sony Computer Entertainment America LLC, 669 F.3d
1362, 1366 (Fed. Cir. 2012) (noting that this court has
found lexicography where the specification used the phrase
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 10
“defined below” (emphasis omitted) (citing AstraZeneca
AB, Aktiebolaget Hassle, KBI-E, Inc. v. Mutual Pharmaceu-
tical Co., 384 F.3d 1333, 1339 (Fed. Cir. 2004))). Second,
the term to be defined, “branched alkyl,” is set off in quota-
tion marks. ’933 patent, col. 412, line 13; see Sinorgchem
Co., Shandong v. International Trade Commission, 511
F.3d 1132, 1136 (Fed. Cir. 2007) (“The term . . . is set off by
quotation marks—often a strong indication that what fol-
lows is a definition.”). Third, the sentence uses the term
“refer to,” ’933 patent, col. 412, line 14, which generally
“conveys an intent for [that sentence] to be definitional,”
ParkerVision, Inc. v. Vidal, 88 F.4th 969, 976 (Fed. Cir.
2023); see also Vasudevan Software, Inc. v. MicroStrategy,
Inc., 782 F.3d 671, 679 (Fed. Cir. 2015) (collecting cases).
Indeed, Alnylam seemingly accepts the definitional charac-
ter of other language in the Definitions section that sets off
the term to be defined in quotation marks and uses “refer
to.” Alnylam Opening Br. at 52, 59, 61. Fourth, elsewhere
in the Definitions section, Alnylam used non-limiting
terms that contrast with the “refer to” language at issue
here. See, e.g., ’933 patent, col. 411, lines 16, 21–22, 38, 41–
42 (“[F]or example”); id., col. 411, line 37 (“e.g.”); id., col.
411, line 43 (“Non-limiting examples”); id., col. 411, lines
58, 60 (“include”); id., col. 412, lines 2, 10, 60 (“include”);
id., col. 412, lines 17, 23 (“For example”); id., col. 412, line
38–39 (“Examples of . . . include, but are not limited to”).
Fifth, the inclusion of the phrase “[u]nless otherwise spec-
ified” within the potentially lexicographic sentence sug-
gests that the rest of the sentence lays out a generally
applicable rule or definition. Id., col. 412, line 13. We con-
clude that the foregoing characteristics, at least taken to-
gether, confirm that the column 412 language at issue is
definitional.
B
We also conclude that the “otherwise specified” clause
does not support Alnylam’s bottom-line position that the
claims at issue cover a secondary carbon at the alpha
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 11
position. Nothing in the claims, specification, or prosecu-
tion history “specifie[s]” a different definition of a branched
alkyl for purposes of the asserted claims.
1
We agree with the district court that clarity would be
required to support a different conclusion. Transcript, at
146:1–147:8.
The column 412 passage states that the definition ap-
plies “[u]nless otherwise specified.” ’933 patent, col. 412,
line 13. That language itself connotes (doubtless overlap-
ping) notions of specificity, definiteness, explicitness, par-
ticularity, precision, or detail. See, e.g., Specify, Webster’s
Unabridged Dictionary (2d ed. 2001) (“to mention or name
specifically or definitely; state in detail”); Specific, Black’s
Law Dictionary (9th ed. 2009) (“Of, relating to, or designat-
ing a particular or defined thing; explicit.”); Specify, Black’s
Law Dictionary (6th ed. 1990) (“To mention specifically; to
state in full and explicit terms; to point out; to tell or state
precisely or in detail; to particularize, or to distinguish by
words one thing from another.”); Kucana v. Holder, 558
U.S. 233, 243 n.10 (2010) (“‘specify’ means ‘to name or state
explicitly or in detail’” (quoting Webster’s New Collegiate
Dictionary 1116 (1974))); HRE, Inc. v. United States, 142
F.3d 1274, 1276 (Fed. Cir. 1998) (construing a contract
where “[t]he use of the word ‘specified,’ instead of a more
general word like ‘indicated,’ strongly suggests that any
such exception must be explicitly stated”).
Moreover, as a general matter, once the high threshold
for lexicography is met in a patent, it makes sense that a
high threshold would have to be met before finding a de-
parture from that controlling definition. In the statutory-
definition context, it is familiar law that “[s]tatutory defi-
nitions control the meaning of statutory words . . . in the
usual case.” Burgess v. United States, 553 U.S. 124, 129–
30 (2008) (omission in original) (quoting Lawson v. Suwan-
nee Fruit & Steamship Co., 336 U.S. 198, 201 (1949)).
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 12
There are familiar reasons that definitions in the patent
context deserve at least as much force: Public notice is a
central policy, public reliance is a known reality, precision
is at a premium, and the applicant has ample control over
provision of definitions, so when a definition is expressly
stated, the public is generally entitled to expect clear notice
of exceptions. See Bell Atlantic, 262 F.3d at 1268; Merck,
395 F.3d at 1370.
A requirement of clarity is particularly called for here.
The very point of the first prong of the definition—requir-
ing that one carbon atom in the alkyl group “(1) is bound to
at least three other carbon atoms”—is to address the de-
gree of branching at the alpha position. An “alkyl” group
is composed of only carbon and hydrogen atoms, with single
bonds between the carbon atoms. ’933 patent, col. 411,
lines 53–54; Alnylam Opening Br. at 52, 59, 61; Moderna
Response Br. at 11–12 (citing J.A. 5008); see also J.A. 5010–
12. Because a carbon that makes non-branching connec-
tions to other carbons inside a chain is already secondary,
branching at such locations necessarily involves a tertiary
or quaternary carbon; thus, Alnylam agreed that the “only
time” that branching without a carbon that is connected to
at least three other carbons “can exist is when you have it
in the alpha position.” Oral Arg. at 3:17–30, https://oralar
guments.cafc.uscourts.gov/default.aspx?fl=23-2357_04112
025.mp3. It would be odd to conclude that “otherwise spec-
ified” is a loose or lenient standard if the effect is to nullify
the reason for being of that first prong of the definition.
We thus look for whether there is a clear reason to con-
clude that “branched alkyl” as it is used in the asserted
claims encompasses a secondary carbon at the alpha posi-
tion, in contradiction to the definition in the specification
and despite a definition whose very point in the respect at
issue is to address carbons in the alpha position. We do not
find such a reason.
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 13
2
The asserted claims do not on their face require the in-
clusion of a “branched alkyl” having a secondary carbon at
the alpha position. Alnylam contends that the asserted
claims “cover,” or are compatible with, a “branched alkyl”
containing a secondary carbon at the alpha position, as well
as one with a tertiary carbon. Alnylam Opening Br. at 42–
46. But an exception to the definition is not shown by not-
ing that the claims would be broader in the absence of the
definition. And Alnylam’s point about coverage or compat-
ibility does not show that the claims make no sense when
read in light of the definition, so as to require them to be
treated as an exception. As Moderna points out, the as-
serted claims could have a tertiary carbon at the alpha po-
sition for branching in several ways—in particular,
connecting to a carbon in the biodegradable group and to
two carbons on the tail side to create two hydrophobic tails,
or connecting to a non-carbon in the biodegradable group
and to three carbons on the tail side to create three hydro-
phobic tails. Moderna Response Br. at 19–20.
Alnylam looks for support to unasserted claim 14 of the
’933 patent, Alnylam Opening Br. at 45–46, which depends
on a claim that contains the branched-alkyl language at is-
sue (claim 1) and further requires that “the branched alkyl
group has only one carbon atom which is bound to three
other carbon atoms,” ’933 patent, col. 537, lines 56–58 (em-
phasis added). Relying on the principle that independent
claims are generally construed to have broader scope than
their dependent claims, Alnylam argues that the independ-
ent claims should be interpreted to cover a carbon atom at
the alpha position that is bound to as few as two other car-
bon atoms. Alnylam Opening Br. at 45–46. But the infer-
ence Alnylam would draw does not follow from the
underlying principle, because dependent claim 14 narrows
the scope of the independent claim on which it depends in
a way that does not require allowance of a secondary car-
bon—namely, “the branched alkyl group has only one
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 14
carbon atom which is bound to three other carbon atoms.”
’933 patent, col. 537, line 56–58 (emphasis added). That is
enough to satisfy the dependent-claim-is-narrower princi-
ple. And the prosecution history confirms that Alnylam
considered the number of tertiary carbons as a distinguish-
ing feature. Alnylam differentiated claim 14 from the prior
art by stating as follows:
[Claim 14] recites that the branched alkyl group
has only one carbon atom which is bound to three
other carbon atoms. The compounds on page 58 of
[the prior art reference] each have three carbon at-
oms which are bound to three other carbon atoms.
J.A. 4942 (emphases in original). Thus, even under the dis-
trict court’s construction, the independent claims still have
broader scope than dependent claim 14 because they cover
branched alkyl groups that contain one or more tertiary
carbons.
3
The specification also fails to specify that the asserted
claims cover a branched alkyl with a secondary carbon at
the alpha position where the claimed branching occurs. Af-
ter providing the relevant background information, the
specification includes a “Summary” section containing de-
scriptions of cationic-lipid chemical “formulas” I–VIII (col-
umns 1–29), which is followed by a “Detailed Description”
section containing nearly two hundred pages of disclosed
embodiments (columns 29–410) and then Definitions and
methods of preparation. We address Alnylam’s arguments,
which focus on the Summary and Detailed Description.
In the Summary section, each of the cationic-lipid for-
mulas includes a chemical structure with multiple posi-
tions where substitutions can occur, followed by a
description of the different groups or atom(s) that can be
substituted at each of those positions, resulting in a large
number of possible combinations. The parties agree that
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 15
only Formulas I, II, and VIII depict any level of branching
at the alpha position and that Formula VIII is a generic
description that does not differ from Formulas I and II for
our purposes. Alnylam Opening Br. at 17 n.8; Moderna Re-
sponse Br. at 23 n.9. Alnylam further concedes that For-
mula I “fall[s] outside the asserted claims.” Alnylam
Opening Br. at 18 n.9; Moderna Response Br. at 59.
Formula II is described as having “a branched alkyl at
the alpha position adjacent to the biodegradable group (be-
tween the biodegradable group [M1] and the terminus of
the tail, i.e., Z1 . . .)”4 and is accompanied by the following
figure:
’933 patent, col. 3, line 63, through col. 4, line 10. The spec-
ification states that each of R1, R', R2, Q, X, Y, M1, M2, Rz,
Z1, and Z2 can be substituted by multiple different groups
or atom(s). Id., col. 4, line 13, through col. 5, line 50. Of
the four bonds to the relevant alpha-position carbon (lo-
cated between M1 and Z1), H represents a hydrogen, and Rz
and Z1 are groups that each supply a carbon-carbon bond
to the alpha-position carbon. Id., col. 5, lines 18–19, 22–36.
4 There is also a relevant alpha-position carbon be-
tween M2 and Z2, but we discuss only the one hydrophobic
tail for simplicity (and because the asserted claims do not
require a branched alkyl in more than one tail). See ’933
patent, col. 538, line 25 (requiring a branched alkyl in “at
least one biodegradable hydrophobic tail”).
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 16
Alnylam points out that, where M1 does not supply a car-
bon-carbon bond to the alpha-position carbon, the alpha-
position carbon is bound to only two other carbon atoms.
Alnylam Opening Br. at 17–19, 47–48.
Alnylam’s arguments regarding Formula II fail for sev-
eral reasons. Crucially, there is a missing link between
Formula II and the asserted claims, which do not expressly
claim Formula II or otherwise direct a relevant artisan,
faced with all the embodiments covered in over two hun-
dred pages of the specification, towards Formula II. In-
deed, Alnylam acknowledges that not all embodiments
disclosed in the specification are covered by the asserted
claims, Alnylam Opening Br. at 12 n.6, 18 n.9; Alnylam Re-
ply Br. at 29, 39, so a “branched alkyl” that is redefined in
relation to Formula II is not necessarily redefined in the
asserted claims. Furthermore, once the relevant artisan is
focused on Formula II, only a subset of the compounds cov-
ered by that formula contain a secondary carbon at the al-
pha position, depending on the selection of particular
options in the list of examples provided for biodegradable
group M1. ’933 patent, col. 5, lines 1–17. This is not “spec-
ifying” an exception to the definition.
In addition, Alnylam argued both in the district court
and in its briefing in this court that Formula II falls outside
the asserted claims. Alnylam Opening Br. at 18 n.9; J.A.
4496 n.26. Alnylam reversed course during oral argument,
Oral Arg. at 5:10–6:48, but its new position that some ver-
sions of Formula II embody the asserted claims comes too
late, due to both its affirmative arguments to the contrary
and its failure to make this argument in its opening brief
here. Wisconsin Alumni Research Foundation v. Apple
Inc., 112 F.4th 1364, 1375–76 (Fed. Cir. 2024); SmithKline
Beecham Corp. v. Apotex Corp., 439 F.3d 1312, 1319 (Fed.
Cir. 2006). We discern no exceptional circumstances that
warrant allowing Alnylam to change positions so late.
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 17
Moving on to the Detailed Description section of the
specification, Alnylam points to various embodiments that
contain a secondary carbon at the relevant alpha position.
Alnylam Opening Br. at 20–26, 46–53. Nearly all the em-
bodiments, however, fall outside the scope of the asserted
claims for at least one reason5 and thus cannot redefine a
“branched alkyl” in relation to the asserted claims. See ’933
patent, col. 34, lines 32–43; id., col. 36, lines 4–15, 57–66;
id., col. 37, lines 3–20; id., col. 44, lines 25–30; id., col. 49,
lines 45–50; id., col. 60, lines 55–65; id., col. 61, lines 4–20.
For the same reason, the district court’s claim construction
does not read out disclosed embodiments that would be cov-
ered but for that construction, as Alnylam argues. Alnylam
Opening Br. at 53, 57. Of the remaining embodiments, one
alkyl group, shown as part of a table of alkyl groups, could
potentially be combined with other structures to create an
embodiment that falls within the asserted claims, but the
specification does not characterize this structure as a
“branched alkyl.” ’933 patent, col. 74, lines 50–58. In the
single instance where “a branched alkyl” is used to describe
an embodiment in this section, there is no description of
the degree of branching at the alpha position. Id., col. 55,
lines 13–14.
Finally, Alnylam points to a line within the Definitions
section that states that “[r]epresentative saturated
branched alkyl groups include isopropyl, sec-butyl, isobu-
tyl, tert-butyl, and isopentyl.” Alnylam Opening Br. at 25–
26, 52–53, 61–62 (quoting ’933 patent, col. 411, lines 60–
5 Each structure contains a carbon-carbon double
bond, whereas the claims require that R13 is a branched al-
kyl, defined in the specification as a “saturated hydrocar-
bon moiety,” which contains only carbon-carbon single
bonds. ’933 patent, col. 411, lines 53–54; Alnylam Opening
Br. at 12 n.6; Moderna Response Br. at 11–12 (citing J.A.
5008); see also J.A. 5010–12.
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 18
61). Alnylam points out that isopropyl and sec-butyl both
include a secondary carbon at the alpha position. Id. Those
two groups, however, fall outside the scope of the claims for
the unrelated reason that they do not contain the 10–20
carbon atoms required by the claims. ’933 patent, col. 538,
line 32. Furthermore, the two examples do not require a
secondary carbon at the alpha position: Where the biode-
gradable group supplies a carbon-carbon bond to the alpha-
position carbon, that carbon is tertiary.
4
Though the prosecution history comes closest to sug-
gesting that Alnylam understood a branched alkyl to in-
clude a secondary carbon, we conclude that it is not
sufficiently decisive to override the definition set forth in
column 412. See Boss Control, Inc. v. Bombardier Inc., 410
F.3d 1372, 1378 (Fed. Cir. 2005) (concluding similarly that
prosecution history failed to overcome a “clear definition”
found in the specification).
In 2021, while prosecuting the application for the ’933
patent (great-grandchild of the original 2012 application),
Alnylam differentiated the claims from the prior art based
on the degree of branching. J.A. 4940–41. Alnylam noted
that the prior-art compounds “do not have branching” at
the alpha position and stated that “[s]uch compounds with
branching at the α-position would have a moiety as shown
below”:
J.A. 4941 (second emphasis added). Alnylam argues that
this figure shows that it understood a branched alkyl to
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ALNYLAM PHARMACEUTICALS, INC. v. MODERNA, INC. 19
encompass an alkyl group with a secondary carbon at the
alpha position. Alnylam Opening Br. at 26–31, 53–56.
This intrinsic evidence offers some support for Alnylam’s
assertion of what it understood, but it might also be read
as merely stating an example of what branching at an al-
pha position could look like—in contrast to the prior art’s
complete lack of branching at that position, but not neces-
sarily the particular branching being claimed by Alnylam.
With the express definition in the specification, and the
need for specificity to establish an exception, we conclude
that this prosecution history is not sufficient.
In the same communication in the prosecution history,
Alnylam differentiated the proposed claims from other
compounds in the prior art based on the length of the hy-
drophobic tail. J.A. 4941. Alnylam noted that the proposed
claims required “that the total carbon atom content of the
tail . . . is 21 to 26,” whereas the hydrophobic tails of the
compounds in the prior art contained fewer than 21 carbon
atoms. J.A. 4941. Alnylam points out that the prior art
compounds contain secondary carbons at the alpha position
and asserts that, if it had intended for the claims to require
at least a tertiary carbon at the alpha position, it would
have differentiated the claims from the prior art on that
basis, in addition to or instead of citing tail length. Al-
nylam Opening Br. at 55. Where there were multiple ways
for Alnylam to distinguish the proposed claims from the
prior art, and no further illumination of the reason for Al-
nylam’s choice, we decline to read Alnylam’s asserted
meaning into the choice of one route as opposed to another.
III
We have considered Alnylam’s remaining arguments
and find them unpersuasive. We affirm the decision of the
district court.
AFFIRMED
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