Patenting Complex Chemical Compounds Made Easy

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A person without a chemistry background is often found to wonder how a patent is granted for a chemical compound. As per popular belief, every compound is a mix and match of elements. This makes the world of chemistry a place with little left to research and obtain a worthy patent. But if patents are still being filed in this space, there is something more to this popular belief.

Most patents in this space claim only one compound, but that’s rare; most of the time there’s a structure with a bunch of R and X and Y groups hanging off of it. That’s a Markush structure, named after Eugene Markush, who filed a patent in 1924. The prosecution of this patent ended up establishing this as a legitimate way to make claims in the chemical space.

Markush structures are generic chemical structures, i.e., a combination of a core structure and its potential variants which the user wants to protect. They have placeholders for certain variants (substituents), e.g., R for organic moieties or X for halogens (fluorine, chlorine, bromine, iodine).pragya-1

Thus, a large variety of individual structures can be represented by one Markush structure. The placeholders R and X in the Markush structure below have two different substituents each, i.e., four potential structures can be represented by one formula.


To claim any new molecule developed, a researcher will need to scout for these structures. This is where Markush searches become cumbersome. The existing computational methods for doing it invariably open doors to a large set of patent filings that require a bulk of manual sorting thanks to the vague claim language. Here are a few tips on easing out the sorting process for complex chemical compound patents:

  • First look for patents that are in a similar domain of activity/ target/ disease that you are in. These are the ones that should be of highest concern when drafting a patent to ensure there is no infringement.
  • Understand the depth of claims in these patents to prevent overlaps with your research. Remember that Markush lists are never fully exemplified. This means that specific compounds are not always described with their unique physical properties to show that they were really prepared. A patent is required to state the best “embodiment” of the invention, and its claims are generally written in an order that narrows down to that.

The chemical space is large, insanely large, and there are almost always variations that will allow researchers to prepare a compound that has never been described. Fluorinate it over here, add a heteroatom over there, tie a ring back – there’s usually something different and it all depends on how much you want that part of chemical space and how much time and money you’re prepared to spend to find the right piece. Such checks will definitely serve in a researcher’s best interests if some of these changes can also make a difference in the compound’s activity and usefulness. This will work in tandem with the doctrine of equivalents that states that a difference that makes no difference is no difference, but you can generally find enough of a ledge to stand on.

Every drug composition-of-matter patent is, in theory, vulnerable to this sort of uncertainty. But for the most part, given the odds of this happening, it’s a better use of time and money to try to find something that’s clearer, unless the patent in question leaves obvious gaps and the potential benefit stands out.

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Pragya Arya
Pragya Arya

Dr. Pragya is a pharmaceutical patent expert and has extensive experience as a research scientist and Intellectual Property Specialist in generic pharmaceutical manufacturing and the chemical industry.

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