Fed. Cir. Affirms LexicographyAlnylam v. Moderna Claim Loss

In early June 2025, the U.S. Court of Appeals for the Federal Circuit dropped a very clear message for patent drafters everywhere: if you define a term in your specification, you’re going to have to live with that definition. No takebacks. That message came in
Alnylam Pharmaceuticals, Inc. v. Moderna, Inc., a high-profile patent battle over lipid nanoparticle (LNP) technology used in COVID-19 vaccines.

The key issue wasn’t validity, doctrine of equivalents, or even complicated infringement theories. It was a single claim term“branched alkyl”and whether the patentee’s own definition in the specification controlled over what it later wished the term to mean. The Federal Circuit said yes, Alnylam acted as its own lexicographer, and that definition doomed its infringement case against Moderna’s SPIKEVAX® vaccine.

For patent owners, in-house counsel, and anyone drafting biotech and chemical patents, this precedential decision is a cautionary tale. It shines a big spotlight on lexicography, claim construction, and the sometimes dangerous power of “Definitions” sections.

Background: mRNA Vaccines, Lipid Nanoparticles, and “Branched Alkyl”

The dispute centered on Alnylam’s U.S. Patent Nos. 11,246,933 and 11,382,979, which relate to cationic lipids used in LNPs for delivering nucleic acids, including mRNA. These lipids help form nanoparticles that protect fragile mRNA molecules and ferry them into cellsan essential part of modern mRNA vaccine technology.

Moderna’s COVID-19 vaccine, SPIKEVAX, uses a cationic lipid called SM-102 in its LNP formulation. Alnylam alleged that SM-102 fell within the scope of its claimed lipids, specifically because the hydrophobic tail allegedly included a “branched alkyl” group at a particular position in the molecule.

Moderna disagreed, arguing that when “branched alkyl” is given the meaning Alnylam itself provided in the patent specification, SM-102 simply doesn’t qualify. That disagreement set up the central claim construction battle.

The Patentee’s Own Definition: How Lexicography Entered the Scene

The patents’ specification included a section literally titled “Definitions.” There, Alnylam provided a description of the term “branched alkyl” that turned out to be the star of the show. In that section, the patent stated (paraphrased for clarity) that, unless otherwise specified, the term “branched alkyl” refers to an alkyl group where one carbon atom in the group is bound to at least three other carbon atoms and is not part of a ring.

Several features of this passage convinced both the district court and the Federal Circuit that Alnylam was speaking in definitional, not merely illustrative, terms:

• The term appeared in a “Definitions” section.
• “Branched alkyl” was placed in quotation marks.
• The text used the phrase “refer to,” which reads like classic definitional language.
• The sentence began with “Unless otherwise specified,” signaling a generally applicable rule that would govern unless explicitly overridden for a particular embodiment.

Taken together, those cues satisfied the high bar for lexicography: a clear and unmistakable intent to define the term for purposes of the patent.

The District Court: Clear Lexicography, No Infringement

In the district court (the District of Delaware), the parties presented competing constructions of “branched alkyl.” Alnylam wanted a broader meaning closer to the general organic chemistry understanding of a branched chainessentially any alkyl chain with a side branch, even if the branching carbon only attaches to two other carbons.

Moderna, by contrast, argued that the term must be construed in line with the specification’s express definition: a saturated hydrocarbon group where at least one carbon atom is bonded to at least three other carbons and is not a ring atom. That effectively requires tertiary or quaternary carbons at the relevant position, not merely secondary carbons.

The district court agreed with Moderna. It held that Alnylam had engaged in “clear and unequivocal lexicography,” adopted the narrow definition, and then asked the parties what that meant for infringement. Under that construction, the parties stipulated that Moderna’s SM-102 lipid does not meet the “branched alkyl” limitation because SM-102’s branching occurs at an alpha carbon that is not bound to three other carbons.

With that stipulation, the court entered final judgment of noninfringement across all asserted claims. Alnylam appealed.

The Federal Circuit’s Opinion: Lexicography Rules the Day

On appeal, the Federal Circuit reviewed the claim construction de novo because the analysis relied solely on intrinsic evidenceclaims, specification, and prosecution historywithout any factual disputes over extrinsic evidence.

Affirming Lexicography

The panel (in an opinion by Judge Taranto) affirmed the district court’s construction. It held that Alnylam had clearly defined “branched alkyl” in the specification and that this definition controlled over any ordinary meaning or isolated examples that might suggest something broader.

The court highlighted the same key signals the district court relied on:

• Placement in a “Definitions” section.
• Quotation marks around the term.
• Use of “refer to,” which reads like a dictionary entry.
• The phrase “unless otherwise specified,” implying a default rule.

In other words, this was not loose descriptive languagethis was the patentee acting as its own lexicographer. And once that definitional language is recognized as lexicography, it becomes the controlling meaning for claim construction.

The High Bar for Departing from Lexicography

Alnylam argued that other portions of the specification and examples showed that it did not intend to restrict “branched alkyl” to carbon atoms bound to three or more carbons, and that the phrase “unless otherwise specified” left room for a broader understanding in the claims. The Federal Circuit disagreed.

The court emphasized that once lexicography is established, departing from that definition requires strong, clear evidence. Boilerplate phrases like “unless otherwise specified” do not automatically create ambiguity or open the door to broader meanings unless the patent actually “otherwise specifies” a different meaning for a given context.

The intrinsic record, including examples and prosecution history, did not meet that high threshold. At most, those materials might create tension with the narrow definition, but tension is not enough. The court effectively warned that patentees cannot use examples or ambiguous language to claw back scope from a definition they chose to write.

The Bottom Line: Moderna Wins, Claims Narrowed

With the lexicographic definition locked in, the rest of the outcome followed easily. SM-102 did not have a “branched alkyl” group as defined by the patents, so the limitation was not met and there was no infringement. The Federal Circuit affirmed the judgment of noninfringement in full, ending Alnylam’s case against Moderna’s SPIKEVAX in this particular action.

Context: A Web of COVID-19 Vaccine Patent Disputes

The Alnylam v. Moderna decision is one piece of a larger puzzle of COVID-19 vaccine IP litigation. Alnylam has pursued similar claims against Pfizer and BioNTech over alleged use of its LNP technology, with mixed results. In a related case, Alnylam dropped its suit against Pfizer and BioNTech after a Delaware court construed its patents in a way that did not cover the accused vaccines.

Later in 2025, Moderna and Alnylam reached a settlement resolving broader patent disputes over SPIKEVAX technology, but that private resolution doesn’t undermine the precedential force of the Federal Circuit’s lexicography holding. The claim construction ruling stands as a clear, citable example of how express definitions can narrow patent scopeand how those definitions can decide billion-dollar disputes.

Key Takeaways on Lexicography and Patent Drafting

The decision is already being treated as a teaching case for patent prosecutors and litigators. Here are some of the most important lessons.

1. “Definitions” Sections Are Powerfuland Dangerous

Many patents, particularly in chemical and life sciences fields, include a “Definitions” section or boilerplate language defining common terms. Alnylam v. Moderna shows that courts will treat this section as a dictionary, not as gentle background color. If you define a term in that section, expect it to govern your claims.

That means drafters must:

• Resist the urge to copy-paste over-narrow definitions from earlier applications.
• Think about how the definition plays out against foreseeable competitor designs.
• Use “includes” or “comprises” when possible, instead of “refers to” plus rigid structural requirements, if the goal is flexibility.

2. “Unless Otherwise Specified” Is Not a Magic Escape Hatch

The phrase “unless otherwise specified” sounds like a safety valve, but it only works if the patent actually specifies something otherwise in a clear way. The Federal Circuit made it plain that generic boilerplate cannot silently expand scope beyond a definitional sentence.

If you want alternative meanings in specific contexts, you have to:

• Explicitly say that a term is used differently in a particular embodiment or claim set.
• Provide a clear, alternative definition for that context.
• Ensure that the claims or dependent claims reflect the intended flexibility.

3. Examples and Prosecution History Won’t Save You from a Bad Definition

Alnylam pointed to numerous examples in the specification and prosecution history that suggested a broader understanding of “branched alkyl,” including structures where the branching carbon was not bound to three other carbons. But the Federal Circuit was unmoved. Once lexicography is established, examples that don’t fit are more likely to be treated as outliers than as evidence that the definition doesn’t mean what it says.

Practically, this means that when you draft examples:

• Ensure they actually fall within your express definitions.
• Update definitions if your examples evolve during drafting or prosecution.
• Recognize that mismatches can later be used against you, not in your favor.

4. The Case Strengthens the “No Takebacks” Approach to Lexicography

Commentators have already described the decision as reinforcing a “no takebacks” rule: once a patentee clearly defines a term, courts will enforce that definition even if it dramatically narrows scope and undercuts infringement theories that arise years later.

For litigators, this offers a potent tool when facing broad, litigation-driven claim constructions. For patent owners, it’s a sobering reminder that the most important part of your future infringement case might be a single sentence you wrote in your “Definitions” section a decade earlier.

Broader Policy Reflections: Clarity vs. Flexibility

At a policy level, Alnylam v. Moderna highlights the constant tension in patent law between clarity and flexibility. Lexicography promotes clarity: competitors can read a patent, see the definition, and adjust their designs accordingly. But that clarity comes at a cost when the patentee later wishes the claims were just a bit broader.

The Federal Circuit has long encouraged patentees to use the specification as a guide for claim interpretation, but cases like this one show that when patentees go a step further and provide explicit definitions, courts treat those definitions as binding, not merely suggestive. That approach may feel harsh to patentees caught on the wrong side of their own language, but it also promotes predictable, stable claim constructionsomething heavily regulated industries like pharmaceuticals and vaccines depend on.

Experiences and Practical Lessons from the Alnylam–Moderna Aftermath

Since the decision came down, practitioners and in-house teams have been using Alnylam v. Moderna as a case study in what can go rightand very wrongwith lexicography. While every organization is different, several common “experience themes” have emerged in how companies and law firms are updating their patent strategies around definitions.

1. In-House Teams Rewriting Their Template “Definitions” Sections

One recurring story from the in-house side involves template cleanup. Many life sciences and chemical companies have been relying on specification templates that date back years, sometimes decades. Those templates often contain dense, highly technical definitions that were originally written for specific projects but then migrated into boilerplate used for everything.

After Alnylam, several companies have reportedly launched internal review projects where patent counsel sit down with R&D leads and systematically audit definition lists: What terms do we truly need to define? Which definitions are unnecessarily narrow? Where are we sneaking in structural requirements that might not be essential to our core invention?

These internal audits can be eye-opening. Teams frequently discover that a single sentence could exclude entire classes of competitor products or, more dangerously, their own next-generation designs. The case gives in-house counsel a concrete example to show business leaders why it’s worth investing time and budget in “boring” tasks like template maintenance.

2. Prosecutors Building “Lexicography Checkpoints” into Drafting

On the prosecution side, practitioners are increasingly treating definitions as a discrete risk-control checkpoint. Instead of allowing a “Definitions” section to sit untouched at the front of a spec, some firms now add a specific drafting step toward the end of the process: revisit every defined term and ask, “If this definition controlled in litigation, would we still be happy with it?”

That exercise often leads to small but important edits:

• Replacing “refers to” with “includes” or “encompasses” to reduce the impression of a closed definition.
• Dropping obscure limitations that made sense in an early embodiment but no longer match the broader invention.
• Addition of explicit language clarifying that certain examples are non-limiting, especially where chemical structures can be drawn in more than one way.

While no wording is litigation-proof, consciously treating definitions as high-impact languagerather than just front-matter boilerplatehelps align drafting choices with long-term enforcement goals.

3. Litigators Using Alnylam as a Playbook for Attacking Overbroad Constructions

On the litigation side, defense teams now have a fresh, fact-rich precedent to cite when they believe a patentee is running away from its own definitional language. The Alnylam opinion walks through the kinds of textual cuesheadings, quotation marks, “refer to,” “unless otherwise specified”that signal lexicography. In future disputes, litigators can map those cues onto new patents and argue that the patentee has already answered the “what does this term mean?” question in the spec.

Conversely, plaintiffs’ teams are taking a hard look at their portfolios for potential Alnylam-style vulnerabilities. If a core enforcement patent depends heavily on a term that was defined aggressively, counsel may adjust enforcement strategy, leaning more on patents with flexible language or developing continuation strategies that clean up problematic definitions before litigation even begins.

4. Deal and Diligence Teams Asking Sharper Questions

The case also has implications for licensing, acquisitions, and due diligence. When evaluating a patent portfolio tied to revenue-critical productslike vaccines or biologicsdeal teams are increasingly asking outside counsel not just “Are there validity and freedom-to-operate risks?” but also “Are there lexicography landmines?”

Experience from post-Alnylam diligence work suggests that reviewers are now:

• Scanning for “Definitions” sections and flagging any term that has structural, numeric, or positional requirements built into it.
• Comparing those definitions against currently marketed products and foreseeable design-around options.
• Factoring the rigidity of key definitions into deal value or royalty rate discussions.

In other words, lexicography has moved from a niche doctrinal twist to a line item in risk assessments and deal modeling.

5. A Cultural Shift: From “More Boilerplate” to “Smarter Boilerplate”

Perhaps the most subtle experience emerging from the Alnylam saga is a cultural shift in how organizations think about boilerplate. The instinct in patent drafting has long been to add more boilerplate to cover more eventualities. But this case shows that certain types of boilerplateespecially definition-heavy sectionscan actually shrink scope and weaken litigation options.

The new mindset is not “get rid of boilerplate,” but rather “use it intentionally.” Definitions that reinforce clarity and support broad, well-reasoned constructions still have value. What practitioners are learning from Alnylam is that every definition has the potential to be Exhibit A in a future Markman hearingso it needs to earn its place in the specification.

For patent professionals working in fast-moving, high-stakes fields like mRNA and LNP technology, the practical experiences drawn from Alnylam v. Moderna can be summarized in one sentence: treat every definition as if it will someday decide a billion-dollar case, because sometimes, it will.

Conclusion

Alnylam v. Moderna is a textbook example of how a single sentence in a patent’s “Definitions” section can determine the outcome of complex, high-value litigation. By affirming that Alnylam acted as its own lexicographer and enforcing the narrow definition of “branched alkyl,” the Federal Circuit underscored the controlling power of express definitions and the high bar for departing from them.

For drafters, the message is simple but demanding: write definitions with the same care you devote to claims. For litigators, the decision is a powerful precedent for holding patentees to the words they chose. And for companies operating in the mRNA vaccine and biotech landscape, it’s a reminder that claim construction is not an abstract academic exerciseit’s where real-world rights over transformative technologies are won and lost.