Filing intellectual property (IP) on novel targets and epitopes
Building a strong IP portfolio is complex, especially when securing patents for novel targets and epitopes.
That’s why we invited two experts from Vossius & Partner to share their insights on how biotech startups can successfully protect their intellectual property.
This article summarizes their key takeaways, from the fundamentals of biotech IP to filing strong patent claims for novel targets and epitopes, and the differences between European and U.S. patent law.
Meet BaseLaunch
We provide early stage startups with the funding, expertise, and infrastructure they need to transform their ideas into therapies. So far, we’ve supported companies that have collectively raised over $800 million in follow-on financing.
We also collaborate with industry leaders, domain experts, and organizations to create opportunities for knowledge exchange and partnerships. Events like this webinar powered by Innosuisse, are a key part of that vision, bringing together thought leaders to tackle the challenges and opportunities shaping the future of biotech.
Meet the experts
Dr. Philipp Marchand, European, Swiss, and German patent attorney, Vossius
Philipp specializes in strategic portfolio management, antibody patenting, and the impact of AI on patent law.
He provided insights into European patent law for novel targets and epitopes, structuring claims, and meeting patent requirements for biotech inventions.
Richard Enmon, PhD, JD, U.S. and European patent attorney, Vossius
Richard specializes in patent prosecution, biopharmaceuticals, and freedom-to-operate assessments for emerging therapies.
He offered a U.S. perspective, focusing on the differences to the EU and recent legal rulings affecting the patentability of biotech innovations.
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The basics: IP for biotech startups
Protecting intellectual property is important for almost every startup, but essential in biotech. Bringing a new therapeutic product or method to market takes years of research and millions in funding. Without proper protection, a competitor could use your discoveries, putting all your hard work at risk.
Securing IP early on also attracts investors and business partners. They often consider a secured patent as a must-have when putting together a funding deal.
Four ways of securing IP for your biotech startup
- Trademark. Protects everything that distinguishes your company’s identity from others, such as name, logo, and branding.
- Copyright. Automatically safeguards original creative works, including software code and written materials, without requiring registration.
- Patent. Grants exclusive rights to an invention for a fixed length of time.
- Trade secret. Protects confidential business information through, for example, a Non-Disclosure Agreement (NDA).
There are more ways to secure intellectual property, like design rights and material transfer agreements (MTAs), but in this event, we focused specifically on patents for protecting novel targets and epitopes.
Patentability requirements for any invention
There are more ways to secure intellectual property, like design rights and material transfer agreements (MTAs), but in this event, we focused specifically on patents for protecting novel targets and epitopes.
1. Patentable subject matter
The invention must fall within an eligible category of intellectual property. This is typically:
- Compounds / compositions
- Medical uses of compounds / compositions
- Methods for producing compounds / compositions
- Methods for sequencing / assessing / determining
- Non-medical uses
- Apparatus and devices
Certain things can’t be patented, including naturally occurring species, purely biological processes, methods for treatment of the human or animal body by surgery or therapy, and diagnostic methods practiced on the human or animal body.
2. Industrial applicability
The invention must have a real-world application and be useful in the industry. If an invention can’t be practically applied in a relevant field, it doesn’t qualify for a patent.
3. Novelty
The invention must be new. Novelty is judged based on what is publicly known the day before a patent is filed, called prior art. Prior art includes, for example, scientific publications, existing patents, and product releases. Even informal disclosures, like speaking about your research at a conference, can count as prior art.
4. Inventive Step
The invention must be a significant, non-obvious improvement over prior art. If an expert in the field could easily deduce the invention based on existing knowledge, it won’t qualify for a patent.
5. Enablement
A patent must be detailed enough for a skilled professional to reproduce the invention without excessive experimentation. If the description is too vague or incomplete, the patent may be rejected or difficult to enforce.
For a deeper dive into the fundamentals of biotech IP, including best practices, common pitfalls, and key strategies for startups, check out our guide:
Keep reading to learn about claims to novel targets and epitopes with real-world examples and the most common challenges biotech startups face when filing IP in this space.
Claims to novel targets and epitopes
A novel target is a newly identified biological molecule that plays a role in disease and can serve as the basis for therapeutic intervention.
An epitope is the part of an antigen that is recognized by a binding agent. A binding agent can be anything — antibody, small molecule, receptor, cell, or any other entity that binds to the epitope with specificity.
- Linear epitopes. Defined by a specific amino acid sequence within a protein.
- 3D (conformational) epitopes. Formed by amino acids that are not adjacent in the sequence but come together when the protein folds.
Because patent claims must define the invention clearly and precisely, the way an epitope is described in a patent (sequence, structure, or function) affects the strength and enforceability of the patent.
A simplified example of a claim
”“A binding agent specifically binding to an epitope (on target XY) comprising SEQ ID NO:1 (peptide sequence).”
This claim describes a binding agent (which could be an antibody, small molecule, receptor, or other entity) that specifically binds to a linear epitope defined by its amino acid sequence (SEQ ID NO:1).
The patent examiner would likely ask several questions to assess whether the claim meets the necessary patentability requirements.
Does the claim cover all types of binding agents? Since a binding agent could be an antibody, small molecule, receptor, or even a cell, the examiner may ask for clarification on whether the claim is intended to include all of these or just a subset. If the claim is too broad, it might need to be narrowed down to a particular type of binding agent to avoid rejection.
What’s the purpose of the binding? Simply stating that a binding agent binds to an epitope isn’t always enough for patentability. The examiner may ask whether the binding serves a therapeutic or functional purpose, such as neutralizing a virus, inhibiting a receptor, or triggering an immune response. Without demonstrating a clear technical effect, the claim could be considered too vague or obvious.
Does the epitope maintain the same fold when isolated? If the binding site is structurally unstable or context-dependent, this could create enablement challenges, requiring further data to prove that the epitope is well-defined and consistently recognizable by binding agents.
The patent office will scrutinize your claim, often requiring you to provide experimental data to support its binding specificity and functional significance.
A real-world example of a claim
Philipp shared an example from a startup he worked with to illustrate how epitope and binding agent claims are structured in real-world biotech patents. This claim demonstrates how a patent application can be granted even when it relies on a functional outcome rather than just a structural definition.
”“An antibody, or an antigen-binding fragment thereof, that specifically binds to human GP73, wherein the antibody, or the antigen-binding fragment thereof, binds to an epitope within the amino acid sequence."
The claim involves a membrane protein with an external domain (GP73). Under natural conditions, part of this external domain is cleaved off, but the inventors discovered that one specific epitope, located right next to the membrane, remains intact.
This unexpected finding led to a patent claim for an antibody that binds to this membrane-adjacent epitope. The significance of this was that when the antibody binds to this epitope, the entire complex gets internalized into the cell, along with the membrane portion of the protein. This internalization creates a downstream effect, making it possible to deliver a cytotoxic agent into the cell by linking it to the antibody.
- The epitope was precisely defined and had a clear, demonstrable function.
- The claim was not just for an antibody but for the binding effect itself, meaning any binding agent targeting this epitope would achieve the same internalization effect.
- It showed that epitope-based claims can be successful, provided they are well-supported by experimental data and demonstrate a specific technical effect.
If you’re looking for expert guidance, Philipp Marchand is here to help you assess prior art, refine claim language, or prepare a strong patent application.
It’s different in the US
European and U.S. patent law share the same fundamental requirements, but the U.S. Patent and Trademark Office (USPTO) interprets and applies them differently. Richard Enmon provided insights into these differences.
Patentable subject matter before the USPTO
In the U.S., functional claims for antibodies and epitopes were historically easier to obtain, but recent legal rulings have made them harder to defend. Unlike the EPO, which allows second medical use claims, the USPTO is more restrictive, requiring applicants to show a clearly defined therapeutic application. Additionally, broad functional claims now face stricter review, making clear structural definitions more important in U.S. patents.
The standard for enablement has been made stricter
U.S. patent law mandates that an applicant prove that they had possession of the invention at the time of filing across its entire claimed scope and that the entire scope can be obtained by routine measures. This means that if a patent claims any binding agent to an epitope, you must identify the common features characterizing all such binding agents as well as demonstrate that all such obtained agents exhibit the same technical effect.
Diagnosis claims must be carefully drafted and contain active steps
A claim that merely states “detecting biomarker X for diagnosing disease Y” is unlikely to be granted. To be patentable, the claim must include an active step, such as a specific treatment or intervention based on the diagnosis. In contrast, Europe is generally more lenient with diagnostic claims as long as they are sufficiently detailed and applied to a medical context.
This is only an excerpt of Richard’s talk. For a deeper dive into the differences between EU and U.S. patent law, join our next free online event: Navigating US & EP Patent Law for Startups.
If you’re looking for expert guidance to navigate U.S. patent law, Richard Enmon is here to help.
The experts answer the audience’s questions
After the main discussion, the audience had plenty of time to ask their own questions, some of which are listed here with (abbreviated) expert insights from our speakers.
Superficial changes can be made to protein sequences that do not alter their function. How does the patent office perceive these modifications, and are there changes that are too insignificant to qualify for novelty?
If a change is too superficial (doesn’t significantly alter the structure or function of the protein), it may be considered obvious or anticipated by prior art. To strengthen novelty, applicants should demonstrate that the sequence change leads to a functional or structural advantage.
If a patent application includes two inventions in one claim, it can face a unity objection. How does the patent office determine whether a claim covers more than one invention?
Patent offices assess unity of invention by determining whether the claims share a single general inventive concept. If they don’t, the examiner may require you to split the application into separate filings.
New computational tools are revolutionizing protein structure predictions. If a tool can generate different conformational folds of a protein, how can we patent proteins in the future?
If a tool generates multiple possible conformations of a protein, simply claiming one of those conformations may not be novel. If AI-generated protein structures become widely accepted in the field, examiners may start treating them as prior art, making it even harder to claim novelty. Patents will likely need to focus on functional improvements, specific applications, or unexpected structural features rather than just the predicted conformation itself.
Is defining an invention by its amino acid sequence alone enough for patent protection?
Not always, especially for antibodies, epitopes, and protein-based inventions. While a specific sequence can establish novelty, patent offices also consider function, binding properties, and technical effect when assessing inventive step and enablement.
How does the patent office handle claims with two antibodies or molecules targeting different sites within the same application?
If a single patent application includes two antibodies or molecules targeting different sites, the patent office may issue a unity objection if the inventions are considered independent rather than part of a single inventive concept. If the molecules function independently, the examiner may require you to divide the application into separate filings (divisional applications).
How does the patent office handle claims with two antibodies or molecules targeting different sites within the same application?
If a single patent application includes two antibodies or molecules targeting different sites, the patent office may issue a unity objection if the inventions are considered independent rather than part of a single inventive concept. If the molecules function independently, the examiner may require you to divide the application into separate filings (divisional applications).
When filing medical use claims, is in vitro data sufficient to support these claims, or is in vivo validation required?
It depends on the jurisdiction and the specific invention. In Europe, in vitro data can be enough if it provides clear and credible evidence that the claimed medical use is plausible. If the effect is highly speculative or unprecedented, the examiner may request in vivo validation or additional supporting data. The U.S. tends to be stricter, and patent examiners often look for preclinical in vivo studies or strong mechanistic data to support the claimed therapeutic effect.
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