1 August 2025
Introducing Porta Sophia’s Chemical Structure Search Tool
By: Jeremy Rolquin
MAPS Bulletin: Volume XXXIV
At Porta Sophia, our mission is to support a future for psychedelic medicine grounded in ethical and evidence-based innovation. As interest in psychedelics continues to grow, so does the number of patent applications covering psychedelic compounds. But many of these filings make sweeping or overly broad claims, sometimes attempting to patent substances that have already been studied, synthesized, or even used in Indigenous, traditional, or cultural contexts.
That’s where Porta Sophia comes in. As a non-profit dedicated to protecting the public domain and supporting responsible innovation, Porta Sophia curates an extensive library of prior art — everything from published scientific research to historical and cultural knowledge related to psychedelics. Our goal is to make this knowledge accessible to the public, including the researchers and professionals shaping the future of psychedelic intellectual property.
Why Patent Quality Matters
Patents are meant to protect genuine innovation. But when a patent is granted for something that isn’t truly new, it can block researchers and clinicians from building on established knowledge. In the world of psychedelics, this can delay therapeutic development, limit access, and even lead to legal battles over rights that never should have been granted.
We’ve seen time and again how hard it is to assess novelty in psychedelic patents, especially when much of the prior art isn’t published in traditional scientific formats. That’s why we’ve built a tool to help.
The Rise of Chemical Structure Claims
In recent years, we’ve seen a dramatic rise in psychedelic patent applications that use chemical structure claims, particularly Markush structures, to describe broad families of compounds.
Markush claims allow applicants to define a class or “genus” of compounds by substituting variables on a core chemical scaffold with a wide range of functional groups. In theory, this helps inventors claim a useful range of potential innovations. In practice, it’s increasingly used to cover potentially millions of theoretical compounds, many of which are already known or obvious variants.
Our research tracking psychedelic patents shows the alarming trend that between 2016 and 2022, there was a 1,433% increase in applications focusing on chemical structures.
To make it relatable: imagine someone trying to patent clothing by claiming, “a wearable item composed of any fabric, in any shape, with any number of sleeves, zippers, or buttons, designed to cover any part of the body.” Instead of patenting one specific garment, they’re trying to claim every possible piece of clothing, from t-shirts to trench coats, just by listing all the interchangeable parts.
That’s essentially what’s happening with many psychedelic patents using chemical structure claims. By swapping in different chemical “accessories”, like functional groups or ring substitutions, applicants can construct a claim that appears specific, but actually tries to cover an enormous class of compounds, including ones that are already known
This is known in patent law as the genus-species problem, where a patent tries to protect a genus (like all clothing) without specifically enabling each species (individual garment types). When applied to psychedelics, these claims often try to capture core compounds like psilocybin, mescaline, or 5-MeO-DMT under the guise of obscure or overly technical language.
The result? Some patents may effectively claim large swaths of known psychedelics, cloaked in chemistry language that’s difficult for examiners, or even experts, to untangle. These overly broad or vague claims can block access, hinder research, and reduce the quality of the innovation ecosystem.
This growing pattern is one of the key reasons we built a new tool, to bring clarity, accuracy, and integrity to the psychedelic patent landscape.
How Broad Can These Claims Get?
Here is an example, in a patent application (US20250025483) published on January 23, 2025, a single claim describes a chemical compound (or salt thereof) featuring a substituted tryptamine scaffold (Structure I). The compound allows for extensive variation across both the indole ring and the amine side chain, significantly broadening the scope of coverage.
Even using a conservative count, treating each broad functional group class as one option, almost 5 million unique compounds are potentially covered. That number stems from the 99,954 possible substitution patterns across the ring, multiplied by 50 variations on the side chain.
To put that in perspective:
If each compound represented just one minute, reviewing them all would take nearly 9.5 years, nonstop, without sleeping.
This kind of structure-based claim highlights how applicants can use Markush language to cover vast chemical territory with a single compound definition, potentially encompassing natural products, known psychedelics, and a wide range of theoretical analogs under one umbrella. When a claim attempts to cover millions of compounds without sufficient examples or guidance, it also raises serious concerns about whether the invention is truly enabled under patent law. In response, Porta Sophia filed a Third-Party Submission against this application on March 20, 2025, to challenge the patentability of its claims.
Enablement and Undue Experimentation
Enablement refers to the legal requirement that a patent must clearly teach someone skilled in the art how to make and use the full scope of the claimed invention without undue experimentation. In practice, whether experimentation is “undue” depends on factors like how much trial and error is required, how much guidance the patent provides, whether working examples are included, and how predictable the technology is.
For example, consider a chemistry Markush claim that describes a tryptamine scaffold with five positions, each independently substitutable with one of ten broad functional group categories. If the claim covers millions of possible compounds, but the patent only discloses a handful of examples with limited instructions, a chemist would need to spend significant time and resources to figure out how to make or test the rest. That level of guesswork may render the claim not enabled under patent law.
In such cases, overly broad claims without adequate support can be invalidated or rejected for failing to meet the enablement requirement.
This growing pattern of broad, under-supported claiming is one of the key reasons we built a new tool, to bring clarity, accuracy, and integrity to the psychedelic patent landscape.
You can read more about the enablement requirement in the USPTO’s Manual of Patent Examining Procedure, § 2164.
Introducing the Chemical Structure Search Tool
Porta Sophia’s new Chemical Structure Search Tool is designed to make psychedelic patent research faster, easier, and more precise. Launched in March, it enables users to search chemical structures, including specific functional groups, substitutions, and related features, across a curated database of psychedelic-related patents and applications.
This is the only freely available tool that supports individualized substitution searching, allowing users to explore structural analogs and instantly identify whether similar compounds have already been disclosed. This capability is especially valuable for evaluating novelty, refining patent claims, and spotting potential overlap with existing filings.
The tool is powered by Porta Sophia’s rigorously curated prior art library, with each structure carefully mapped and indexed to deliver relevant, high-quality search results.
The tool is also designed to support the wider innovation ecosystem:
- Researchers can use it in early-stage discovery to steer clear of previously claimed compounds and focus on truly novel work.
- Patent professionals can draft stronger, more defensible claims and reduce the risk of invalidation.
- Examiners gain a clearer view of existing disclosures when assessing novelty and non-obviousness.
- Investors and due diligence teams can evaluate IP strength, uncover red flags, and better understand the competitive landscape.
By providing open access to this information, we aim to improve transparency, raise the standard for patent quality, and support more ethical innovation in the psychedelic field.
You can read more about our collaborations on our press release page.
Try the Tool and Share Your Feedback
The Chemical Structure Search Tool is available for free on our website, and we’re actively collecting feedback from users to improve it. The tool currently supports tryptamine derivatives, and we’re working to expand it to include additional core structures, such as those related to MDMA, phenethylamines, ibogaine, and ergoline analogs. If there are specific scaffolds you’d like to see prioritized, we’d love to hear from you.
Whether you’re involved in IP, research, investment, or policy, this is a resource built to help you navigate an increasingly complex landscape with confidence.
Try the tool now
Share your feedback
As the psychedelic field continues to evolve, we’re committed to ensuring that innovation is strong, ethical, and transparent. Thank you for being a part of that mission.
– The Porta Sophia Team
*Porta Sophia has no conflicts of interest to disclose. A full list of our current funders and contributors is available at portasophia.org/contributors*
Jeremy Rolquin
Jeremy Rolquin is the Chemistry Patent and Data Analyst at Porta Sophia, a nonprofit dedicated to protecting the psychedelic public domain. He leads chemical structure analysis efforts to identify overlapping or overly broad patent claims and supports the development of the Chemical Structure Search Tool, a free resource that enables structure-based prior art searches. Jeremy works at the intersection of chemistry, data, and IP strategy, helping researchers and legal professionals navigate complex psychedelic patent filings. His work focuses on improving transparency in psychedelic innovation by highlighting unclaimed knowledge and safeguarding access to shared scientific heritage. Prior to joining Porta Sophia, Jeremy worked in early-stage biotech and academic research, where he focused on molecular modeling and compound screening.
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