Author Archives: David Rucando

Patent Lexicography: When “Branched Alkyl” ≠ “Branched Alkyl” – A Cautionary Tale

Before fancying yourself as your own lexicographer, read the cautionary tale told by the U.S. Court of Appeals for the Federal Circuit’s decision in Alnylam Pharmaceuticals, Inc. v. Moderna, Inc., No. 2023-2357. In this case, the court held Alnylam to their narrow definition of “branched alkyl” instead of its ordinary meaning. The narrow definition allowed Moderna’s COVID-19 vaccine SPIKEVAX® to avoid infringement of Moderna’s patents (U.S. Patent Nos. 11,246,933 and 11,382,979).

Estimated reading time: 2 minutes

Introduction: Conflict between a term’s ordinary meaning and an applicant’s own definition

Generally, words or phrases are given their ordinary and customary meaning in a patent claim. However, an inventor may act as their own lexicographer and define terms inconsistently from the term’s ordinary meaning. While drafting definitions of terms more narrowly than their ordinary meaning may be advantageous at times, such definitions may be disadvantageous if the broader ordinary and customary meaning is needed in litigation.

High Level Summary

In Alnylam’s case, Moderna did not infringe Alnylam’s patents because Alnylam defined its term “Branched Alkyl” too narrowly. The court held Alnylam to its patent definition of “Branched Alkyl” to mean an “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,” instead of Alnylam’s later suggested ordinary meaning of “a saturated hydrocarbon moiety that is not a straight chain.” The patent’s definition limited Alnylam’s claims to covering only lipids that comprised tertiary or quaternary carbons. Therefore, Alnylam’s claims could not cover Moderna’s cationic lipid SM-102, which only comprised primary or secondary carbons, as used in SPIKEVAX®.

The court treated the term “Branched Alkyl” as having a binding lexicographic definition because:
(1)  the term was located in a “Definitions” section,
(2)  the term was in quotation marks,
(3)  the definition included the phrase “refers to,” which confers definition intent,
(4)  other definitions used non-liming phrases such as “for example” and “including, but not limited to,” and
(5)  the definition included the phrase “unless otherwise specified,” which suggests that the rest of the sentence establishes a generally applicable rule or definition.

For further reading, see these other links to blogs discussing Alnylam v. Moderna:

Home » Archives for David Rucando

Updated Reference for Protecting Groups

Greene’s Protective Groups in Organic Synthesis, P. G. M. Wuts, 6th edition, John Wiley & Sons, 2025.
ISBN: 978-1-394-23318-2

Sample description for adding to a patent application specification:
[0001] Nitrogen protecting groups, oxygen protecting groups and sulfur protecting groups are well known in the art and include, but are not limited to, those described in Greene’s Protective Groups in Organic Synthesis, P. G. M. Wuts, 6th edition, John Wiley & Sons, 2025, incorporated herein by reference.

Caution! Before fancying yourself as your own lexicographer, read the cautionary tale told by the U.S. Court of Appeals for the Federal Circuit’s decision in Alnylam Pharmaceuticals, Inc. v. Moderna, Inc., No. 2023-2357. In this case, the court held Alnylam to their narrow definition of “branched alkyl” instead of its ordinary meaning.
Look out for an more detailed post on the case shortly.

Reference for Pharmaceutical Formulations

It is time to update your draft patent applications with the latest version of Remington.

Remington: The Science and Practice of Pharmacy
23rd Edition – October 30, 2020
Imprint: Academic Press
Editor: Adeboye Adejare
Language: English
Hardback ISBN: 978-0-12-820007-0

“A thorough discussion of pharmaceutically acceptable excipients is available in Remington: The Science and Practice of Pharmacy, A. Adejare, 23rd edition, Academic Press, New York, NY, 2020, incorporated herein by reference.”

SCHRÖDINGER’S POLYMORPH: WHEN A CRYSTALLINE FORM CLAIM IS OBVIOUS AND INVALID

Salix Pharmaceuticals, Ltd. v. Norwich Pharmaceuticals Inc., No. 22-2153 (Fed. Cir. 2024)

“Schrödinger’s cat,” is a paradoxical thought experiment devised by physicist Erwin Schrödinger, while debating quantum superposition in 1935. Oversimplified, in the thought experiment, there is a cat in a box, and you have no way of knowing what physical state the cat is in, like a quantum wave function, until you open the box and observe it.

While studying polymorphic forms, like Schrödinger’s hypothetical [albeit a long stretch], you do not know what form a solid compound is until you measure it with x-ray crystallography. However, unlike Schrödinger’s hypothetical, you may have a reasonable expectation of succeeding to figure out what form your compound is depending on the prior art and knowledge of a person of ordinary skill.

Shifting from quantum to organic chemistry patent law, if there is a reasonable expectation of success in characterizing a known crystalline product for potential polymorphism using routine, conventional methods and skill, then a claim to that crystalline product would be invalid for obviousness. Such was the decision in Salix Pharmaceuticals, Ltd. v. Norwich Pharmaceuticals Inc., No. 22-2153 (Fed. Cir. 2024).

Salix claimed a specific crystalline form (form β) of rifaximin. The United States patent and Trademark Office (USPTO) granted Salix a patent on it.  However, when litigated, the United States Court of Appeals for the Federal Circuit (CAFC) affirmed the District Court of Delaware’s finding that Salix’s claims to rifaximin form β were invalid for obviousness.*

“The difference between the prior art and the claims is thus effectively nothing more than the performance of routine characterization to identify the polymorphic forms that result from the known Cannata processes.”

Salix Pharmaceuticals, Ltd. v. Norwich Pharmaceuticals Inc., No. 22-2153 (Fed. Cir. 2024), at 15.

In other words, you cannot claim ownership of a compound just by making the expected crystalline form using someone else’s process and taking an x-ray crystal structure of it and giving a Greek letter name.

Background

  • Salix markets Xifaxan® (rifaximin), and Norwich wanted to sell a generic version.
  • Xifaxan® is a formulation of rifaximin crystalline form β.
    • Polymorph β is a commonly produced polymorph.
    • Polymorph β the most stable form of rifaximin.
  • Disputed patent claims: Claim 4 of U.S. Patent No. 7,612,199 and Claim 36 of U.S. Patent No. 7,902,206.
    • Claim 4. Rifaximin in polymorphic form β, wherein the rifaximin has x-ray powder diffraction pattern peaks at about 5.4°; 9.0°; and 20.9°2θ and wherein the rifaximin has a water content of greater than 5%.
  • Prior art: Cannata et al. U.S. Patent No. 4,557,866.
    • Although Cannata does not discuss rifaximin’s crystal structure in detail, it does disclose several preparation protocols for rifaximin that include solvents used for crystallization.
    • Experts testified that Cannata’s preparation of crystalline Rifaximin would have yielded its β form. But they could not say it would every time.
  • Rifaximin was a known compound with a known, useful activity (antibiotic).
    • While rifaximin was a known antibiotic, Salix owns rights to patents covering new method of use (hepatic encephalopathy). Salix won on appeal for such method-of-use claims.
  • Experts testified that Cannata’s preparation of crystalline rifaximin would have easily made and taken an X-Ray diffraction pattern to determine that rifaximin was in its β form.
    • The experts could not convince the judge that the prior art process would produce rifaximin form β “every time.” If they could, then Salix’s claims would have been anticipated (not novel) as inherently present in the prior art.‡
    • Although the experts could not convince the judge of the certainty of form β (novelty), they at least convinced the judge that form β was reasonably expected (obviousness).

    CAFC Opinion Discussion

    The CAFC decided that “the district court found a reasonable expectation of success in characterizing the crystalline product of Cannata for potential polymorphism using routine, conventional methods and skill [Salix Pharm., Ltd. v. Norwich Pharm., Inc., Civil Action No. 20-cv-430-RGA, (D. Del. Apr. 29, 2021), at *6–7].†  We see no clear error in that conclusion. Indeed, Salix has done no more than combine known elements of the prior art to verify readily accessible information concerning a compound already in the hands of those of ordinary skill in the art, and such routine efforts do not justify removing this polymorph from the public domain. See KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 427 (2007); see also Pfizer, 480 F.3d at 1367−68.”

    The District Court supported its factual determinations of obviousness with expert testimony that:

    (1)  a skilled artisan would have had good reason to characterize the crystalline rifaximin obtained by following the Cannata protocols,

    (2)  such characterization was routine and could have been performed “in one day,” and

    (3)  doing so would have led the skilled artisan to have “detected rifaximin β.” 

    Salix argued that a person of ordinary skill in the art would not have “expect[ed] to succeed” because, as of the critical date, the polymorphic nature of rifaximin had not yet been reported and the identity of the β form remained undisclosed. They further argue that a skilled artisan would not have been able to predict which polymorphic form Cannata made. This argument was flawed. The CAFC states that Salix’s is incorrect in framing of the issue, as it suggests that no unknown entity could ever be obvious, as one cannot reasonably expect what was hitherto unknown.

    * In the same appeal, The CAFC did affirm the District Court’s finding that Salix’s other claims to methods of treating hepatic encephalopathy were valid and nonobvious.

    † Whether or not there would have been a reasonable expectation of success is a question of fact. “Whether or not there would have been a reasonable expectation of success is a question of fact, (IXI IP, LLC v. Samsung Elecs. Co., 903 F.3d 1257, 1262 (Fed. Cir. 2018)), which we review for clear error, Hospira, 946 F.3d at 1328. We review the ultimate conclusion of obviousness de novo.” Did the Justices themselves believe that the claims were obvious? Unknown. The CAFC perhaps equivocated or sidestepped the question. The justices did not say that they themselves believe that the polymorph claims were obvious. Rather, they merely said that they found no clear error in the District Court’s finding of obviousness. 

    ‡ The CAFC did not opine on whether or not the polymorph claims were invalid for being inherently anticipated (§102). The court said that they did not need to go that far since they already determined that the claims were invalid for obviousness (§103). The district court said that the polymorph claims were not anticipated as being inherent because Norwich did not prove with clear and convincing evidence that the prior art method would produce rifaximin form β “every time.” The inherency issue may deserve its own post. Question for discussion: Does the “every time” requirement go too high for “clear and “convincing evidence?” Perhaps requiring a specific result Every time may go up to the realm of “beyond a reasonable doubt,” which is not the level of burden of proof for patent law. Recall last year’s discussion of the Amgen case where there were arguments about how many examples enable the “full scope” of a claim. Stay tuned.

    Additional Information

    OrganicPatents.com page on Obviousness of Stereoisomers &Purified Compounds

    Obviousness of Stereoisomers & Purified Compounds

    See also PatentDocs’s post: https://www.jdsupra.com/legalnews/salix-pharmaceuticals-ltd-v-norwich-3362384/.


    May 8, 2024

    Stereogenic Oxygen!

    I have been updating my page on patentability / non-obviousness of chiral compounds. While working on it, I read about a new molecule ─ a chiral triaryloxonium ion ─ in Chemical & Engineering News (C&EN). Astoundingly, the stereocenter is the oxygen, rather than a carbon, the atom most famous for its chiral capabilities. Chemists synthesized the first stable molecule whose chirality is solely attributed to a stereogenic oxygen. They published their work in Nature. See, O. Smith et al., Control of Stereogenic Oxygen in a Helically Chiral Oxonium Ion, Nature, 615, 430–435 (2023). 

    Link to C&EN article: This New Molecule Owes its Chirality to Oxygen Alone

    Can someone patent a chiral oxonium ion?

    We do not know if the chemists filed a patent application claiming the composition. But that didn’t stop me from speculating as to such a possibility. I think that a patent application claiming a chiral oxygen would be robust. Firstly, the inventors reduced the molecule to practice. They physically made it. It surely is not an abstract idea. Secondly, if the molecule is truly the first stable molecule, then novelty should be no problem. Thirdly, I think that such a compound is non-obvious and inventive.

    Might a chiral oxygen be obvious?

    Let’s focus on non-obviousness. Might a chiral oxonium ion be obvious? I think that, most likely, a chiral oxonium ion would not be obvious. As noted on Organic Patent’s page, Obviousness of Stereoisomers & Purified Compounds, critical support for arguing non-obviousness includes evidence of unexpected properties and difficulties associated with resolving compounds. Other secondary considerations / “Graham” factors are super helpful too, such as long felt but unsolved needs. The articles cited above have an abundance of such evidence.

    Below are a few powerful quotes:

    • “Oxygen has been less cooperative.”
    • “Oxonium ions … have the potential to be chiral, but they are notoriously reactive”
    • “The few previous examples of chiral oxonium ions are too unstable to be isolated … so the search for chiral oxonium ions languished in the literature”

    Gilead Wins Another Sofosbuvir Challenge: U. Minnesota v. Gilead

    Regents of the U. of Minnesota v. Gilead Scis., Inc., 2021-2168, — F.4th — (Fed. Cir. Mar. 6, 2023)

    The Court of Appeals for the Federal Circuit (CAFC) analyzed whether the written description found in UMN’s priority applications supported the claims in the resulting patent # US 8,815,830. The CAFC said no.

    While the ‘830 patent claims covered sofosbuvir, The CAFC affirmed an IPR’s invalidation of U. Minnesota’s claims because they could not properly claim priority to its provisional application. The reasoning was that the provisional with its nebulous multiple dependent claims, that were themselves dependent on further multiple dependent claims, did not adequately describe the subgenus eventually claimed in the non-provisional application.

    See Patently-O’s posts for more:

    March 7, 2023 — Laundry Lists of Components are Insufficient Written Description for a Particular Combination | Patently-O (patentlyo.com)

    March 9, 2023 — Multiple dependent claims, blaze marks, and ipsis verbis support | Patently-O (patentlyo.com)

    SOVALDI® (soh-VAHL-dee) (sofosbuvir)



    Said Goodbye to Ribbons – Now Say Goodbye to Paper: USPTO Officially Transitions to Issuing Electronic Patent Grants in 2023

    Get ready for Electronic Patent Grants!*   

    * And be ready to file continuations or divisionals earlier.

    USPTO-Ribbon small

    Recently in 2018 [okay perhaps ancient history to some] the USPTO stopped attaching actual ribbons to issued patents. Now the USPTO will stop automatically printing paper copies. This is of course good news for trees. This is also good news for applicants who want applications issued more efficiently. However, applicants need to be ready to file any continuing applications earlier than they have been accustomed because the USPTO will issue patents more quickly after providing applicants with a Notice of Issuance. Meanwhile, applicants still need to file continuing applications before issuance.

    Electronic Patent Grants – When:

    Effective April 18, 2023, the USPTO Officially Transitions from issuing patent grants on paper to Issuing electronic patent grants (Federal Register).

    Transition Period – USPTO will still provide free ceremonial copies

    • The USPTO will provide patentees a ceremonial paper copy of the issued patent during the transition period as a courtesy, free of charge.
    • The ceremonial paper copy resembles the paper patent that the USPTO traditionally provided to patent applicants as the issued patent.
    • The ceremonial paper copy will be bound with a cover sheet with both an embossed seal and the signature of the USPTO Director.
    • Length of Transition Period? TBD – Do not know.

    $$ After Transition Period

    • The ceremonial paper copy will be available for purchase for a nominal fee after the transition period, in addition to the presentation copy and certified copy.
    • How much is the “nominal fee” for a “ceremonial” copy? TBD –  Do not know. Though a “presentation copy” is presently $25.

    BE READY TO FILE CONTINUING APPLICATIONS!

    Patent Prosecution Best-Practice Note:  File Continuing applications (CON/DIV) as early as possible. Applicants will not have as much time between receiving an Issue Notification and seeing the patent office issue the granted patent.

    Warning from the USPTO:

    “The USPTO will issue the patent shortly after the payment of the issue fee. As a result, applicants will have less time, after the payment of the issue fee, to file continuing applications, Quick Path Information Disclosure Statements, or petitions under 37 CFR 1.313(c) to withdraw an application from issue. Therefore, the best practice would be for applicants to file these submissions as early as possible. Preferably, continuing applications should be filed before the payment of the issue fee. See Manual of Patent Examining Procedure (9th ed. Rev. 10.2019) (MPEP) sec. 211.01(b)(I).” (Federal Register/Vol. 88, No. 39/Tuesday, February 28, 2023/Rules and Regulations; Page 12561)

    Updated USPTO Form PTOL-85B (Issue Fee Transmittal) includes a reminder to file any continuing application prior to issue-fee payment so as not to jeopardize co-pendency. The newly modified form can be found here. The form no longer allows for advance orders of patent copies, because patents may be printed directly from Patent Center when issued. Advance orders for copies of patents issuing on or after April 18 will not be processed.

    More information from other insightful publications:

    Ready, Set, Go: Implications of USPTO’s Shift to Electronic Patent Grants (foxrothschild.com)

    eGrants and Quick Issuances | Patently-O (patentlyo.com)

    USPTO ushers in new era with introduction of electronic patent grants | USPTO

    USPTO Transitions to eGrants from Paper Patents | JDSupra

    USPTO To Transition To Electronically Granted Patents In April 2023 | Blogs | PharmaPatents | Foley & Lardner LLP

    Supreme Court Sizes Up the Genus – Enablement

    The Supreme Court of the United States (SCOTUS) is set to hear arguments on Monday, March 27, 2023 for Amgen v. Sanofi.

    ACS’s Chemistry and the Law (CHAL) Division weighs in

    The American Chemical Society’s Chemistry and the Law (CHAL) division filed an Amicus brief supporting Amgen’s petition and reversing the Federal Circuit’s decision. Indeed, the resolute CHAL even petitioned the court to get 5 minutes to participate in arguments.

    Stay Tuned!

    Amgen Inc. v. Sanofi – SCOTUSblog

    Amgen’s X-Ray crystallography studies of antibodies 21B12 & 31H4 bound to PCSK9

    Idenix v. Gilead: Split CAFC Panel at Least Agrees – Valid or Not, Either Way it’s Idenix Loss – Claims Too Broad

    Idenix Pharmaceuticals LLC v. Gilead Sciences Inc. (Fed. Cir. 2019); 941 F.3d 1149 (2018 WL 922125) CAFC Panel: Chief Judge Prost and Circuit Judges Newman and Wallach
    Opinion by Chief Judge Prost; dissenting opinion by Circuit Judge Newman

    Idenix claims invalid / not enabled

    Chemical structure of sofobuvir
    sofosbuvir

    Background: Idenix’s sued Gilead claiming Gilead’s sofosbuvir (Solvadi®) HCV treatment would infringe U.S. Patent No. 7,608,597, directed to methods for treating hepatitis C virus (HCV). Gilead argued that they should not be liable for infringement because the ‘597 patent was not valid since the patent’s specification did not enable the claims. At first, a jury at the district court level said that the claims of the ‘597 patent were enabled and therefore valid. However, the district court judge disagreed and granted Gilead’s Motion for a Judgment as of Matter of Law (JMOL), overruling the jury. When Idenix appealed, the United States Court of Appeals for the Federal Circuit (CAFC) affirmed the district court’s decision, agreeing that the ‘597 patent was invalid and therefore Gilead was not liable for infringement. In the end, the U.S. Supreme Court refused to hear the case [cert. denied, 141 S. Ct. 1234 (2021)].

    CAFC Panel Split: In the Opinion, Chief Judge Prost and Circuit Judges Wallach agreed that Idenix’s ‘597 patent claims were not enabled. Circuit Judge Newman dissented, arguing that the ‘597 patent, although having overly broad claims, was still valid. However, while still valid, the claims should be interpreted narrowly, allowing Gilead to avoid liability anyway.

    Common Ground: Let’s focus upon where all three judges agreed – Idenix should loose. While much attention has been given to how the panel was split as to whether the ‘597 patent was valid or not, we should remind ourselves that all three at least agreed that Gilead should not be liable for infringement. All three judges appeared to agree that Idenix’s claims were too broad. They diverged on how to get Gilead off the hook.

    Loss either way:

    (1) Majority – Rule that the claims are invalid by lack of enablement.

    (2) Dissent – Rule that the claims are valid but not enforceable.

    Forward to Amgen vs. Sanofi:

    Circuit Judge Lourie’s Opinion in AMGEN INC. v. SANOFI, No. 20-1074 (Fed. Cir. 2021) referenced Idenix in concluding that Amgen’s claims were invalid as non-enabled.

    The Supreme Court of the United States is set to hear arguments in Amgen on March 27, 2023. Stay tuned!