Alnylam Pharmaceuticals, Inc. v. Moderna, Inc., ModernaTX, Inc., Moderna US, Inc., decided June 4, 2025

Court: United States Court of Appeals for the Federal Circuit Case Number: 2023-2357 Date Decided: June 4, 2025 Appealing From: United States District Court for the District of Delaware (Nos. 1:22-cv-00335-CFC, 1:22-cv-00925-CFC, Chief Judge Colm F. Connolly)

Summary:

This case involves an appeal by Alnylam Pharmaceuticals, Inc. (Alnylam) against Moderna, Inc., ModernaTX, Inc., and Moderna US, Inc. (collectively Moderna) regarding alleged infringement of U.S. Patent Nos. 11,246,933 and 11,382,979 related to lipid nanoparticles used for the delivery of active agents like nucleic acids. Alnylam alleged that Moderna's mRNA-based COVID-19 vaccine, SPIKEVAX®, infringed these patents due to the presence of the cationic lipid SM-102, which Alnylam claimed was covered by its patents. The core of the appeal hinges on the claim construction of the term "branched alkyl" as used in Alnylam's patents.

The District Court concluded that Alnylam acted as its own lexicographer in the patent specification, defining "branched alkyl" as an alkyl group where "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." This definition requires a tertiary or quaternary carbon for branching. Under this construction, the parties stipulated that Moderna did not infringe, leading to a final judgment of noninfringement. Alnylam appealed, arguing the District Court's construction was erroneous and that "branched alkyl" should encompass branching involving a secondary carbon at the alpha position, as this was the ordinary meaning and supported by the specification and prosecution history.

The Federal Circuit affirmed the District Court's decision, finding that Alnylam did indeed act as lexicographer for the term "branched alkyl" and that nothing in the claims, specification, or prosecution history "otherwise specified" a different definition for the asserted claims.

Key Themes and Important Ideas/Facts:

1. Patent Infringement Litigation over mRNA Vaccine Technology: The case arises from Alnylam's assertion that Moderna's COVID-19 vaccine, SPIKEVAX®, infringes Alnylam's patents related to lipid nanoparticle technology. This highlights the ongoing legal disputes surrounding the proprietary aspects of key components in successful mRNA vaccines.

2. Importance of Claim Construction in Patent Litigation: The outcome of the entire appeal rests on the interpretation of a single claim term: "branched alkyl." This underscores the critical role of claim construction in determining the scope of patent rights and ultimately, infringement. The court states, "The appeal here turns on a single issue of claim construction."

3. Patentee as Lexicographer: A patent applicant has the right to define terms in their patent specification, even if that definition deviates from the term's ordinary meaning. However, this "special definition" must be "clearly stated in the patent specification or file history." The court emphasizes that the intrinsic evidence must "clearly set forth" or "clearly redefine" the term.

4. Evidence of Lexicography: The court found several factors in the Alnylam patent specification indicated an intent to act as lexicographer:

5. The definition appeared under the heading "Definitions".

6. The term "branched alkyl" was set off in quotation marks.

7. The sentence defining the term used the phrase "refer[s] to".

8. Elsewhere in the "Definitions" section, Alnylam used non-limiting terms like "for example," "e.g.," and "include," contrasting with the "refer to" language for "branched alkyl."

9. The phrase "[u]nless otherwise specified" within the definition itself suggests a general rule being laid out.

10. The court concluded that these characteristics, "at least taken together, confirm that the column 412 language at issue is definitional."
    

Interpretation of "Unless Otherwise Specified": The definition of "branched alkyl" included the phrase "[u]nless otherwise specified." Alnylam argued this clause allowed for a broader interpretation in the asserted claims, potentially including secondary carbons at the alpha position. The court rejected this, stating that "clarity would be required to support a different conclusion."

• The court reasoned that given the "high threshold for lexicography," a similarly "high threshold would have to be met before finding a departure from that controlling definition."

• The court noted that the primary purpose of the definition's first prong ("bound to at least three other carbon atoms") was to specifically address the degree of branching at the alpha position, and a lenient interpretation of "otherwise specified" would "nullify the reason for being of that first prong of the definition."
  

Application of the Definition to the Asserted Claims: The court found no clear evidence that the asserted claims "otherwise specified" a different meaning for "branched alkyl."

• Asserted Claims: The claims themselves, such as representative claim 18 of the '933 patent, recite a "branched alkyl" in the R13 portion of the hydrophobic tail, where branching occurs at the alpha position. Alnylam argued the claims were compatible with a secondary carbon at this position, but the court found this compatibility did not establish an exception to the definition. The court noted the asserted claims could still be met with a tertiary carbon at the alpha position in various configurations.

• Dependent Claims: Alnylam cited dependent claim 14, which required "only one carbon atom which is bound to three other carbon atoms." Alnylam argued that for the independent claim to be broader, it must include branching at a secondary carbon. The court found this inference did not follow, as the independent claims are broader because they cover branched alkyl groups with one or more tertiary carbons, satisfying the dependent-claim-is-narrower principle.

• Specification Embodiments: Alnylam pointed to various embodiments in the Summary and Detailed Description sections of the specification that contained a secondary carbon at the relevant alpha position. The court dismissed most of these, stating that they "fall outside the scope of the asserted claims for at least one reason" (e.g., containing a carbon-carbon double bond, while the claims required a saturated alkyl). The court noted that the claim construction did not read out disclosed embodiments that would be covered but for that construction. Alnylam's attempt to argue during oral argument that some Formula II embodiments fell within the asserted claims was deemed too late.

• Examples in Definitions Section: Alnylam highlighted examples of "representative saturated branched alkyl groups" in the Definitions section (e.g., isopropyl, sec-butyl) that include secondary carbons at the alpha position. The court found these examples fell outside the scope of the asserted claims for other reasons (e.g., too few carbon atoms) and did not necessarily require a secondary carbon at the alpha position depending on the molecule's structure.
  

Prosecution History: Alnylam argued that the prosecution history supported its interpretation, pointing to a 2021 communication differentiating the claims from prior art based on the "degree of branching" at the alpha position and including a figure showing branching that could involve a secondary carbon.

• The court acknowledged this "intrinsic evidence offers some support for Alnylam’s assertion of what it understood," but concluded it was "not sufficiently decisive to override the definition set forth in column 412." The court stated that this prosecution history could be interpreted as merely showing an example of branching, not necessarily the particular branching being claimed. Given the express definition and the need for specificity for an exception, the prosecution history was insufficient.

• Alnylam also argued that if the patents required a tertiary carbon for branching at the alpha position, it would have used that to distinguish from prior art compounds with secondary carbons at that position, instead of or in addition to citing tail length. The court declined to infer Alnylam's asserted meaning based on this choice of differentiation strategy.
  

Conclusion:

The Federal Circuit agreed with the District Court that Alnylam clearly defined "branched alkyl" in its patent specification, requiring a carbon atom bound to at least three other carbons for branching. The court found no sufficiently clear indication elsewhere in the intrinsic evidence to deviate from this definition for the asserted claims. As a result, the court affirmed the finding of noninfringement, as Moderna's SM-102 lipid did not meet this specific structural requirement of a tertiary or quaternary carbon at the alpha position.