Navigating Emerging Legal Frontiers - Washington State Bar News

Patenting UW’s Nobel Prize-winning biochemist’s work with artificial proteins

BY VENU N. SAREEN AND ALICIA MCNAMARA

In 2024, Dr. David Baker,¹. a professor of biochemistry at the University of Washington (UW), was honored with the Nobel Prize in Chemistry for his groundbreaking contributions to computational protein design. His work out of the Institute of Protein Design at the UW School of Medicine² has helped scientists understand and predict protein structure, something that has eluded scientists for decades.³

Harnessing the power of artificial intelligence (AI) and years of research, Baker and his team have been able to develop new protein structures (artificial proteins). Proteins are fundamental to life, playing a crucial role in processes ranging from cell repair to immune defense. Proteins that do not develop correctly (known as misfolded proteins), may not work properly and can even become harmful to the body.⁴ The significance of the development of artificial proteins in the medical field cannot be understated and could lead to major advancements in the treatment of, among other things, viruses, cancer, Alzheimer’s, Parkinson’s disease, and cystic fibrosis.⁵ The applications of artificial proteins, however, also extend beyond medicine, reaching into fields like energy—where they can serve as catalysts for biofuels—and technology, where they can enable the development of novel materials and biosensors.⁶

As with any cutting-edge invention, artificial proteins require strong legal protections to secure their commercial viability and safeguard the intellectual efforts behind their creation. As innovation continues to outpace traditional legal frameworks, particularly in patent law, the need for adaptation becomes increasingly urgent. This article examines the complex process of patenting emerging technologies like artificial proteins and highlights how legal practitioners can prepare to navigate the evolving landscape of emerging innovation.

We will begin with an overview of the patenting process as it applies to artificial proteins.

The Patenting Framework

Inventions are subject to rigorous evaluation under U.S. patent law. Here’s how it works:

Subject Matter Eligibility

Section 35 U.S.C. § 101 specifies that an invention must meet two key criteria. It must: 1) constitute eligible subject matter; and 2) demonstrate utility.⁷

Eligible subject matter. This is a threshold question that asks if the invention is a process, machine, manufacture, or composition of matter. Laws of nature, natural phenomena, and abstract ideas are generally not patentable, unless the claim, as a whole, amounts to significantly more than the exception itself. For example, naturally occurring DNA isolated from the surrounding genetic material is not patentable, but DNA that is synthesized in a lab and lacks aspects found in natural DNA can be patentable because it is not naturally occurring. Association for Molecular Pathology v. Myriad Genetics, Inc. (2013).⁸

Utility (usefulness). The invention must be useful. In other words, it should have a specific, substantial, and credible utility.⁹

In practice:

The applicant must show that a medical innovation has a clear application in treating or diagnosing disease, improving health outcomes, or enhancing clinical techniques.
For drugs or biologics, experimental data (like in vitro or animal studies) are often included to support the claimed therapeutic effect.
Broad or speculative claims (e.g., “this compound might be useful for any disease”) are not sufficient.

Written Description and Enablement

Section 35 U.S.C. § 112 provides that the patent application includes a written description of the invention that enables a person skilled in the art to make and use it without undue experimentation.¹⁰ The claims of the invention must be adequately supported by the specification, which is the core written part of the patent application. The written description must describe the invention in clear, concise, and exact terms.¹¹ It serves as the primary disclosure of the invention to the public. This requirement reflects the fundamental “patent bargain”: in exchange for a full and enabling disclosure of the invention, the inventor receives a limited-term grant of exclusive rights—typically lasting 20 years from the filing date—conferred by the government on behalf of the public.

In practice:

The description should explain how the invention works and include sufficient detail; e.g., chemical structures, biological sequences, formulation processes, or diagrams.
For medical devices, this includes schematics and operating principles.
For methods of treatment, the patent must disclose the condition treated, the therapeutic agent, dosage, route of administration, and supporting evidence (e.g., experimental data or clinical trial protocols).
Think of it as an instruction manual for the invention—a document created to assist a user in using and understanding a particular product with step-by-step instructions.

Novelty and Non-Obviousness

Sections 35 U.S.C. § 102¹² and § 103¹³ specify that an invention must meet two additional criteria: 1) it must be novel; and 2) it must be non-obvious.

Novelty. Section 35 U.S.C. § 102 provides that, to be patentable, an invention must be truly new. If someone else has already patented the same thing—or something very similar—before the inventor’s filing date, the invention isn’t considered new and can’t be patented. This is called being “anticipated” by prior art. The goal of this rule is to make sure patents are only granted for ideas that haven’t already been shared with the public. It protects the public from losing access to existing knowledge and encourages inventors to keep pushing forward with new ideas.

Non-obviousness.Section 35 U.S.C. § 103 addresses the obviousness requirement for patents. Even if an invention is new, it still might not be patentable if it would have been obvious to someone with ordinary skill in the field at the time the invention was made. In other words, if the invention is just a small or predictable change to something that already exists, it may not qualify for a patent. This rule prevents patents from being granted for ideas that don’t represent a real leap forward and encourages meaningful innovation.

In practice:

The novelty rule essentially means that you can’t be awarded a patent if an earlier source—like a published document or product—already shows everything your invention does before you filed your application. If that one source came out before you filed your patent, it can be used to prove that your invention isn’t new or novel. In that case, the invention is said to be “anticipated,” and you can’t get a patent for it.
An invention is considered obvious and cannot be patented if someone with basic knowledge in the field could easily come up with it based on existing ideas.

All of these conditions must be satisfied for a patent to be granted, and a patent examiner can reject claims under any or a combination of these sections.

The Framework & Artificial Proteins

Now let’s apply the patent framework to Dr. Baker’s groundbreaking artificial protein research at UW. To get patented, artificial proteins must meet the patentability requirements detailed above, including subject matter eligibility/utility, written description/enablement, and novelty and non-obviousness. Artificial proteins have their own unique set of challenges during patent examination under these rules, so let’s take a closer look.

Subject Matter Eligibility and Utility

Artificial proteins are generally subject matter eligible because they fall under the “composition of matter” category. They are not merely discovered and isolated, they are invented and created. Applying the Myriad precedent, artificial proteins are “markedly different” from what exists in nature. Artificial proteins are designed and created by humans. If the claims encompass a naturally occurring protein—meaning there is a combination of an artificial protein and a protein already found in nature—they may be rejected under 35 U.S.C. § 101, which prohibits patenting naturally occurring substances.¹⁴ To overcome this, narrowing the claim scope to exclude the naturally occurring protein is advisable.

Moving on to the second part of § 101, for an artificial protein to be patentable, it must also demonstrate a specific and substantial utility.¹⁵ Generally, utility is considered a low bar to overcome, as it can be argued that most inventions have a useful function. However, for artificial proteins, there has been a recent trend among patent examiners to reject patent applications based on a lack of utility. This is often because many artificial proteins serve as starting points, as a foundational structure, or as a scaffold component that can be used as a part of a larger, developing protein structure—which is not always considered sufficient for the utility standard. Accordingly, it might be more effective to claim the entire scaffold or fusion protein instead of a particular protein component.

Written Description and Enablement

35 U.S.C. § 112 requires that an invention be fully described and enabled in the patent application.¹⁶ Due to their novel structures and complex functions, this can be a major hurdle in patenting artificial proteins. One type of rejection under this requirement is based on claim scope. In U.S. patent law, claim scope refers to the extent of protection granted by a patent.¹⁷ Broad protein claims are often rejected because they may cover more than what is described in the detailed description of the patent application. This issue is not unique to proteins but is especially common in biotechnology and chemical patent prosecution. Broad claims are also more susceptible to being anticipated by prior art. Inventors or the entity applying for the patent should assess whether the claim scope resulting from patent prosecution holds value for their business.

Further, protein claims require specificity, often necessitating the inclusion of amino acid sequences. Claiming a protein based solely on its function, without detailing the specific sequences, is typically insufficient.

Novelty and Non-Obviousness

Novelty is another key requirement in patenting inventions. During patent prosecution, inventors and their attorneys must show that the invention is new and has never been previously disclosed or used. Prior art, or publications out in the public, can destroy novelty if it describes part or all of the invention. In the field of artificial protein science, many proteins are considered de novo, meaning they are entirely new compositions that have never existed before. If the claims do not broadly cover naturally occurring proteins, the artificial proteins developed in Dr. Baker’s labs are generally novel and less likely to face § 102 rejections than other inventions. However, if too many distinct inventions are included in a single patent application, the USPTO may issue a restriction requirement—a procedural response that asks the applicant to choose one invention to pursue in the application.

The Road Ahead for Artificial Proteins

The future of artificial protein design is promising, with significant potential across a wide range of fields, including those that may extend far beyond medicine. The pace of innovation is expected to accelerate further as computational design algorithms become more advanced and widely adopted.

However, the future of patent law in the biological sciences is inherently uncertain. Subject matter eligibility under 35 U.S.C. § 101 continues to be ambiguous, though the USPTO is expected to continue to issue updated guidance to navigate court decisions.

Meanwhile, the expanding role of AI in drug discovery and biological data analysis presents new challenges for both inventorship and obviousness. Under current U.S. patent law, only human inventors are recognized, as reaffirmed in Thaler v. Vidal and the USPTO’s 2024 AI guidance. The debate over whether AI can qualify as an inventor is ongoing, and it could potentially reshape how we think about innovation as technology continues to advance.

In addition, the standard for obviousness could change as AI tools become increasingly effective at solving biological problems. As a result, the number of patent applications involving AI-driven algorithms is expected to increase.

Finally, the U.S. Supreme Court’s decision in Amgen v. Sanofi reinforced the requirement that a patent specification must enable a person skilled in the art to make and use the full scope of the claimed invention without undue experimentation.¹⁸ This is particularly challenging in the biotechnology sphere, where examiners often push back on broad claims covering entire classes of biological molecules. Moving forward, we may see a trend towards narrower, more clearly defined patent claims for biological inventions.

Takeaways for Legal Practitioners

As new technologies and scientific advancements continue to reshape industries, the role of legal practitioners becomes even more critical in helping clients navigate the complexities of securing intellectual property protections in these emerging fields. The following strategies can help attorneys support clients working in cutting-edge fields:

Include robust experimental data. Strong data supports arguments for patent eligibility, enablement, and non-obviousness. Experimental data can be demonstrated through crystallography, NMR, Cryo-EM, binding assays, enzyme kinetics, and cell-based assays.
Adopt a flexible claim strategy. Draft claims that cover a range of aspects, including, for example: (1) specific amino acid sequences; (2) structural motifs and functional characteristics; (3) methods of protein design, function, and use; and (4) compositions containing the protein.
Detail the design process. Disclose the algorithms, computational models, machine learning approaches, or experimental techniques used. Where applicable, include specific datasets and parameters.
Provide concrete structural information. For example, include and describe specific amino acid sequences and key structural features or motifs.
Articulate specific utility. For example, clearly state what the protein (or other patentable technology) does and why it is useful. This helps satisfy the utility requirement and strengthens arguments for non-obviousness.
Anticipate enablement. Ensure the specification includes sufficient examples and guidance to enable the full scope of the claims without requiring undue experimentation.
Collaborate closely with inventors. Open, ongoing communication with inventors is key to fully understanding the nuances of the design process and distinguishing features of the invention. Ask questions, repeatedly, for clarification.
Monitor legal developments. Patent law pertaining to biotechnology and software is constantly evolving. Monitor USPTO guidance and relevant court decisions.

Effectively navigating patent law in emerging areas like artificial protein design requires legal practitioners to be proactive, informed, and collaborative. By integrating scientific insight with a forward-thinking legal strategy, attorneys can help clients secure strong intellectual property rights and set up their inventions for long-term success and protection in a rapidly changing innovation landscape.

About the authorS

Venu N. Sareen is the Associate Director, Patents at CoMotion at the University of Washington, where she leads the patent team and oversees IP strategy and portfolio management for university innovations. A registered U.S. patent attorney, her practice has spanned life sciences, software, and mechanical arts. Her background includes developing patent portfolios in-house, advising startups through her solo firm, and roles as a consultant and staff scientist. Sareen also serves on the board of the Washington State Patent Law Association.

Alicia McNamara is a third-year law student at Seattle University School of Law from San Francisco, CA. She is a member of the Women’s Law Caucus and the Intellectual Property Law Society. She has experience in patent law, personal injury law, and corporate law. After graduating in May 2025, she will take the California Bar Exam in July and pursue a career in transactional corporate law in the Bay Area.

NOTES

The authors would like to thank Dr. David Harper for his guidance on IPD patents.

1. www.ipd.uw.edu/david-baker/.

2. www.ipd.uw.edu/.

3. www.bakerlab.org/2021/07/15/accurate-protein-structure-prediction-accessible/.

4. Forum on Neuroscience and Nervous System Disorders; Board on Health Sciences Policy; Institute of Medicine. Neurodegeneration: Exploring Commonalities Across Diseases: Workshop Summary. Washington (DC): National Academies Press (US); 2013 Dec 12. 3, Protein Aggregation. Available at www.ncbi.nlm.nih.gov/books/NBK208522/.

5. www.cancer.org/cancer/managing-cancer/treatment-types/targeted-therapy.html.

6. Patarasuda Chaisupa and R. Clay Wright, “State-of-the-art in engineering small molecule biosensors and their applications in metabolic engineering,” SLAS Technol. (April 2024) 29(2):100113, available at https://pubmed.ncbi.nlm.nih.gov/37918525/.

7. www.uspto.gov/web/offices/pac/mpep/s2104.html.

8. Assoc. for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576 (2013).

9. Supra, note 6.

10. www.uspto.gov/web/offices/pac/mpep/s2163.html.

11. Id.

12. www.uspto.gov/web/offices/pac/mpep/s2152.html.

13. www.uspto.gov/web/offices/pac/mpep/s2158.html.

14. Supra, note 6.

15. Id.

16. www.uspto.gov/web/offices/pac/mpep/mpep-9015-appx-l.html#d0e302824.

17. www.uspto.gov/web/offices/pac/mpep/s2111.html.

18. Amgen Inc. v. Sanofi, 598 U.S. 594 (2023).