Archive for the ‘3rd Party IP: Drug DIscovery’ Category

How the ACLU Won the Fight Against Patenting Genes: Article and video on  the History of the Issue of Gene Patents

Curator: Stephen J. Williams, PhD


please see the TED talk below on how ACLU took on the Gene Patenting Industry:

Tania Simoncelli – How I took on the gene patent industry — and won – Ted Talks 2016

This fight started with the patenting of the BRCA1/2 gene mutants, which increase the risk of breast/ovarian cancer in women who harbor these mutation as well as their offspring, which would be the basis for genetic testing services offered by Myriad Genetics.

However, as seen below, these patent fights and the patenting of DNA has been around since the mid 1970’s, with the advent of cloning and other molecular biology techniques.


Robert Cook-Deegan and Christopher Heaney in Annu Rev Genomics Hum Genet. 2010 Sep 22; 11: 383–425.

In April 2009, the U.S. Patent and Trademark Office (USPTO) granted the 50,000th U.S. patent that entered the DNA Patent Database at Georgetown University. That database includes patents that make claims mentioning terms specific to nucleic acids (e.g., DNA, RNA, nucleotide, plasmid, etc.) (64). The specificity of many terms unique to nucleic acid structures makes it possible to monitor patents that correspond to and arise largely from research in genetics and genomics. Patents have been a part of the story of the rise of genetics and genomics since the 1970s, and not just because they can be counted but also because science and commerce have been deeply intertwined, one chapter in the story of modern biotechnology in medicine, agriculture, energy, environment, and other economic sectors. The first DNA patents were granted in the 1970s, but numbers surged in the mid-1990s as molecular genetic techniques began to produce patentable inventions.

This database (Delphion Patent Database) can be reached at (

From Cook-Deegan, R. and C. Heany. Annu Rev Genomics Hum Genet. 2010 Sep 22; 11: 383–425.

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U.S. Patents: DNA Patents and Patent Applications by Year, 1984–2008. The DNA Patent Database contains patents obtained by searching the Delphion Patent Database ( with an algorithm posted on the DNA Patent Database website that searches for granted U.S. patents (since 1971) and published applications (since 2001) in U.S. patent classes related to genetics and genomics as well as claims that include words specific to nucleic acids, genetics, and genomics. The year 1984 is the first for which more than 100 granted patents are in the DNA Patent Database. Data from Reference 64.

The authors make several points concerning obtaining patents in the genomics field including:

  • Differences in patent practice can be important to scientists working in genetics and genomics. In the United States, a patent goes to the first inventor. If patents or patent applications overlap and the first person to invent is in dispute, then the patent office initiates what’s called an interference proceeding, with intricate rules about deciding priority of invention.
  • Interferences are more than twice as common in biotechnology patents than in any other patent class, six times higher than patents on average (140).
  • The United States also allows a year’s grace period from publication of information pertinent to a patent claim, whereas any public disclosure becomes “prior art” that can defeat patent claims in other jurisdictions.


International harmonization of DNA patents exist including:

  1. 1973 European Patent Convention created the European Patent Office (EPO). EPO can issue a patent valid in signatory countries
  2. 1995 Trade-Related Aspects of Intellectual Property Rights (TRIPS) agreement committed signatory countries to adopt patent standards mainly modeled on the developed-country model of strong patent protection
  3. 1998 Biotechnology Directive: the Directive became an important element of European patent law that binds national governments to comply with it
  4. Both the United States House and Senate of the 111th Congress are considering bills similar to one passed by the House of Representatives (but not the Senate) in the 110th Congress (2007–2008). Two provisions particularly relevant to genetic and genomic inventions are (a) shifting from the current “first to invent” U.S. standard to “first inventor to file,” as in the rest of the world; and (b) establishing a mechanism to challenge patent claims closer to the European opposition process.

top 30 institutions holding patents in the DNA Patent Database. Among them are

  1. Agribusiness and chemical companies (Monsanto and DuPont)
  2. U.S. Government (largely attributable to the large intramural research program at the National Institutes of Health)
  3. Public and private universities (Universities of California and Texas, Johns Hopkins, Harvard, Stanford, MIT, etc.)
  4. Pharmaceutical firms (Novartis, Glaxo SmithKline, Pfizer, Merck, SanofiAventis, Takeda, Bayer, Novo Nordisk, Lilly, etc.)
  5. Established biotechnology firms (Genentech, Amgen, Genzyme, ISIS, etc.)
  6. Firms created to exploit genomic technologies (Incyte, Human Genome Sciences, etc.)
  7. Instrumentation and DNA chip firms (LifeTechnologies, Affymetrix, Becton, Dickinson, etc.)
  8. Academic research institutes (Institut Pasteur, Salk, Scripps, and Ludwig Institutes, Cold Spring Harbor Laboratories, etc.)
  9. Hospitals with research units (e.g., Massachusetts General Hospital)







Top U.S. DNA patent holders. The authors compiled a list of assignees with at least 100 patents, combined different names for the same assignee, and updated names to reflect corporate mergers and acquisitions. Patent counts are from the Delphion Patent Database for U.S. patents granted as of October 26, 2009, using the DNA Patent Database algorithm (64). Data from Reference 64. From Cook-Deegan, R. and C. Heany. Annu Rev Genomics Hum Genet. 2010 Sep 22; 11: 383–425.

And an opinion article by Harvard Law School arguing against the patent-ability of natural products such as DNA:

DNA Sequences as Unpatentable Subject Matter

by  Victor Song & Prof. Peter Hutt

How Merck’s attempt to patent Vitamin B12 may have started a precedent:

In addition to Kuehmsted, the case most frequently cited to support the patentability of “purified and isolated” substances is Merck & Company v. Olin Mathieson Chemical Corporation [44] . In 1958, the United States Court of Appeals for the Fourth Circuit addressed the metes and bounds of the product of nature exception in Merck . The invention at the center of Merck was entitled, “Vitamin B(12)-Active Composition and Process of Preparing Same”.

Prior to the discovery claimed by the patent, vitamin B(12) was unknown to man. What had been known was that patients who had pernicious anemia could mitigate the effects of their condition by consuming cow liver. For years the scientific community analyzed cow liver to determine what in cow liver was the therapeutically active compound. For lack of a better term, scientists named this unknown therapeutic agent the “anti-pernicious anemia” compound.

After a considerable amount of chemical analysis, scientists at Merck isolated the “anti-pernicious anemia” compound in cow liver. They also discovered an alternate source of the “anti-pernicious anemia” compound. Merck scientists were able to harvest the “anti-pernicious anemia” compound from the fermenting eluent of certain microorganisms. After isolating and characterizing the structure of the newly found “anti-pernicious anemia” compound, the scientist renamed it vitamin B(12) for its chemical similarities to the vitamin B family.

Having discovered vitamin B(12), Merck filed for and obtained U.S. patent 2,703,302 (‘the ‘302 patent”) covering both the process of making vitamin B(12) and the actual chemical compound for vitamin B(12). Only the product claims were at issue in Merck [45] . A representative product claim reads:

A vitamin B(12)-active composition comprising recovered elaboration products of the fermentation of a vitamin B(12)-activity producing strain of Fungi selected from the class consisting of Schizomycetes, Torula, and Eremothecium, the L.L.D. activity of said composition being at least 440 L.L.D. units per milligram and less than 11 million L.L.D. units per milligram.[46]

Prior to the appeal, the district court had determined that the product claims were invalid as products of nature. The Court of Appeals for the Fourth Circuit reversed. In reversing the District Court, the Fourth Circuit followed a line of reasoning similar to Kuehmsted.The Court of Appeals reasoned that the product of nature was the unpurified fermenting eluent which had no therapeutic value. However, Merck’s purified fermenting eluent had therapeutic value. Thus, the court believed Merck’s purified product, which was essentially vitamin B(12), was a different from unpurified fermenting eluent. Since Merck’s purified product was different from the product of nature, the court reasoned that it could not be a product of nature.

The main weakness in the Merck decision is similar to weakness of the Kuehmsted decision. Can vitamin B(12) be considered “new” if it always existed in cow liver? In addition, is it necessary to grant Merck both product and process claims? Even without the product claims, Merck will still be able to profit handsomely from the process claims alone. In addition, Merck could have applied for a vitamin B(12) use patent. Merck could have patented the therapeutic use of their vitamin B(12) for treating pernicious anemia.

There are two interesting aspects of the courts decision in Merck . First, in coming to its conclusion that the purified fermentate was not a product of nature the court turned to the phrase “new and useful” contained in section 101. This was an appropriate focus of analysis for the court because it is from this phrase that the product of nature exception is derived. However, in interpreting the phrase “new and useful” the court substituted the patent terms “novelty and utility”.[47]

The threshold for meeting the utility requirement for patentability is very low. Nearly all inventions meet the utility requirement. It is the Fourth Circuit’s reliance on the patent requirement of novelty for the term “new” which is more interesting. The court’s reliance of the novelty standard presents an interesting interpretation because the product of nature exception is not premised solely on the novelty requirement.[48] The product of nature doctrine simply states that products of nature are not patentable because they are made by nature, not by man. Furthermore, since products of nature existed in nature prior to man’s discovery of them, they are not new and thus excluded from patentability.

The novelty standard requires a different analysis. Although the issue of novelty also addresses the question as to whether or not an invention is new, the question of novelty is answered by looking at the prior art. Roughly speaking, the prior art exemplifies man’s entire body of scientific knowledge at the time of invention. In order to be novel, an invention must not be recited in one piece of prior art. For example, to demonstrate a lack of novelty, a single scientific journal article must describe how to extract vitamin B(12) from a fungal fermenting eluent.

The problem with using the novelty requirement to interpret “new” with regard to product of nature purposes is that no product of nature would be found in the prior art before it was discovered. In effect, using the novelty standard eviscerates the product of nature exception. The novelty standard also circumvents the purpose of the product of nature doctrine which is to prevent man from claiming “manifestations of [the] laws of nature”.[49]

For illustrative purposes we can use vitamin B(12) as an example. According to the Fourth Circuit, in order for vitamin B(12) to be considered a product of nature it must lack novelty. To lack novelty, vitamin B(12) must be recited in a single prior art source. Before its discovery by Merck, vitamin B(12) was unknown and hence could not be found in any prior art source. However, vitamin B(12) has always existed as a naturally occurring substance in cow liver (i.e. a product of nature). Despite clear evidence that vitamin B(12) is a product of nature, the Fourth Circuit would permit a patent on vitamin B(12).

This approach nullifies the purpose of the product of nature doctrine. By using the novelty standard, the court never asks the question whether or not vitamin B(12) was made by man. The purpose of the product of nature doctrine is to prevent man from patenting what is made by nature and should thus be accessible to everyone. The Fourth Circuit’s novelty analysis does not consider this.

The second interesting point about Merck is the product claim itself. In claim 1 recited above, vitamin B(12) is claimed only as a product of fermentation. Merck did not claim the vitamin B(12)chemical formula. This is a significant distinction because competitors could design around Merck’s product claim if they could manufacture vitamin B(12) without utilizing the fermenting eluent of fungi. For example, a manufacturer who processed cow livers to obtain vitamin B(12) could sell its version of vitamin B(12) product without infringing Merck’s product claims[50] . With cases such as Kuehmsted and Merck on one side of the product of nature debate, there are several cases which fall on the other side of the debate[51] . In addition to Funk Brothers, General Electric Co. v. De Forest Radio Co. [52] is representative of a court decision upholding the product of nature exception. The invention at the center of General Electric was the chemical element tungsten (W). General Electric was assigned U.S. Patent 1,082,933 (the ‘933 patent) for tungsten.

Is DNA Patentable Subject Matter?

As the cases discussed indicate, it is not entirely clear whether or not DNA sequences are patentable subject matter. What is clear is that processes for isolating DNA sequences are permissible as are product claims that use DNA sequences (such as Chakrabarty’s genetically modified micro-organism). In addition, inventors could get patents for the therapeutic uses of their DNA sequence products.

The Supreme Court’s decision in Chakrabarty indicates an intention by the court to expand the scope of patentable subject matter, but the product of nature doctrine still remains. Whether or not the product of nature exception will apply to DNA sequences depends upon how the courts view DNA sequences. If the courts analogize isolated and purified DNA sequences to aspirin or vitamin B(12), then DNA sequences would be moved outside the product of nature exception and into the scope of patentable subject matter. On the other hand, if DNA sequences are comparable to tungsten or “manifestation of laws of nature” then the product of nature exception would apply.

As the law is currently interpreted by patent practitioners, the product of nature exception to patentable subject matter is considered a technical problem related to drafting DNA sequence product claims. For the patent attorney, all that is necessary to get around the product of nature exception is to not claim a DNA in its naturally occurring form. In order to resolve this technical problem, a patent attorney will claim DNA sequences in an “isolated and purified” form. For example, Amgen’s DNA sequence claim to EPO in United States Patent 4,703,008 reads, “A purified and isolated DNA sequence consisting essentially of a DNA sequence encoding human erythropoietin.”[57]

DNA sequences have been described as molecular strands of genetic information.[59] Information which is so fundamental that it is akin to the natural laws of science. This fundamental information, in the words of Funk Brothers , is “part of the storehouse of knowledge of all men. They are manifestations of laws of nature, free to all men and reserved exclusively to none.”[60] As manifestations of the laws of nature, DNA sequences should be free to all men. By unlocking the hidden secrets of the genetic code, scientists will be able to produce new medical therapies to treat a wide range of illnesses. It is these new therapeutic inventions, their uses, and the processes for making them which should be patented, not the DNA sequences used to implement these inventions.

Although DNA sequences have been analogized to long polymer chains[65] and as a result should be treated similarly to synthesized polymers, this is not entirely correct. The analogy fails because an inventor’s ingenuity plays a part in designing a polymer chain. A chemist will manipulate reaction conditions to produce a polymer with certain characteristics such as strength, durability, and flexibility. This is not the case with DNA. The inventor’s ingenuity, once again, plays no part in designing the DNA sequence as this was the work of nature over thousands of years of evolution.

So the Harvard Law School article concludes:

  1. Patentable subject matter is statutorily defined in 35 U.S.C. Section 101 to include new and useful products (machines, manufactures, and compositions of matter) and processes. However, subject matter which fall outside the scope of Section 101 are products of nature.
  2. There are two general arguments for excluding products of nature from patentable subject matter. First, is that products of nature are the “manifestations of laws of nature”. As the building blocks of science, to grant ownership to these fundamental products would do more harm than good to scientific innovation. Second, is the patent system’s purpose in encouraging inventorship. An inherent aspect of inventorship is interaction of human ingenuity with the natural world. Products of nature are excluded from patentability because they would grant ownership rights to the natural world without any element of human ingenuity. These product of nature patents would reward inventors for nature’s work.

Man has played no part in creating DNA. What required man’s ingenuity was isolating, purifying, and sequencing the DNA. These inventions deserve patent protection.

Other articles on this Open Access Journal on Patents, Patent Fights and Intellectual Property include:

Top Twenty Universities on a list of the top 100 worldwide universities that received the most U.S. utility patents in 2014

The Patents for CRISPR, the DNA editing technology as the Biggest Biotech Discovery of the Century

Innovators can exit with an idea: How to Monetizing Patents and ideas: launches Idea Lab

RNA related IP Patents Awards

Linus Pauling: On Lipoprotein(a) Patents and On Vitamin C

Recent Patents on Biomarkers

Litigation on the Way: Broad Institute Gets Patent on Revolutionary Gene-Editing Method






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Multi-Functional Anti-Inflammatory Drugs (MFAIDs): Small Molecule Invention of Dr. Saul Yedgar, HUJI and Yissum

Reporters: Larry H Bernstein and Aviva Lev-Ari, PhD, RN

Novel, non-steroidal, multifunctional approach to treating inflammatory/allergic diseases
Principal investigator and Inventor: Professor Saul YEDGAR

Professor Saul Yedgar

Walter & Greta Stiel Chair in Heart Studies

Department of Biochemistry

Hebrew University-Hadassah Medical School

Jerusalem, Israel 91120

Tel:   00972-2-643-9218 (office)

         00972-2-652-0159 (home)

Fax: 00972-2-675-7291



MFAID-Mechanism of Action-March-16


US Granted Venn Diagram

US Pending-Venn Diagram

The initiation of inflammatory/allergic processes involves two key activities:

1. Degradation of cell membrane lipids by the enzyme phospholipase A2 (PLA2), leading to a cascade of inflammatory lipid mediators (ILM), which includes two main families:

  • prostaglandins (PGs) and
  • leukotrienes (LTs),

produced via the COX and LOX pathways, respectively.
2. Degradation of the cell-surface protective layer composed of glycosaminoglycans (GAG) that protects cells and tissues from damaging agents, such as

  • free radicals,
  • endotoxins, and
  • enzymes that promote the formation of cancer metastasis.

A common and conventional approach to treating inflammatory processes has been the development of drugs that suppress the inflammatory lipid mediators (ILM) formation or action, focusing primarily on the PG-producing COX pathways (COX inhibitors), assumed to be the predominant ones.
3. However, deleterious ILM are produced also by the other pathways. Therefore, the selective COX inhibition, represented by NSAIDs, has not been successful, and related drugs (e.g., VIOXX from Merck) have been withdrawn from the market.
4. On these grounds, the approach of “inclusive pathway inhibition” has been proposed, aiming at containing theinflammatory lipid mediators (ILM) production by all pathways, by controlling the PLA2 activity.


5. At the same time, while the pharmaceutical industry has focused on the ILM production, the role of the cell-surface GAGs in inflammatory/allergic pathology has been ignored.

6. To address both needs (controlling ILM production and enriching the cell surface GAGs), Inventor  designed and synthesized a platform of novel and unique compounds composed of

  • PLA2-inhibiting lipid moieties conjugated to GAGs.

This structure enables the inhibiting lipid component to incorporate into the surface and anchor the conjugated GAG to the cell membrane.

These lipid-conjugates exert a dual protective effect:

  • the PLA2-inhibiting lipid moiety suppresses the ILM production, and
  • the membrane-anchored GAG enriches the cell surface protective layer.

This presents a platform of multi-functional anti-inflammatory drugs (MFAIDs) for the treatment of diseases associated with

  • lipid mediator production and/or
  • damage to cell surface.

The MFAIDs excellent safety been demonstrated in both

  • pre-clinical and
  • clinical data

generated with over 200 subjects that have been treated with MFAIDs in clinical trials.

Selected MFAIDs have been tested and found effective

  • in the suppression of inflammatory/allergic processes in different cell types (see List of Selected Publications below), as well as
  • in inhibiting the production and action of metastasis-promoting enzymes by human cancer cells.

Subsequently, the MFAIDS have been tested and found effective in treating diverse inflammatory conditions, in

  • animal models and
  • clinical studies

Clinical Trials (studies with patients and with human tissues):

a.  Contact dermatitis: Two clinical studies (presenting Phase I and Phase IIa/IIb, double blind) showed

excellent safety and efficacy in treating patients with contact dermatitis by topical application of MFAID.

b. Atopic Dermatitis (concluded on February 2015): Phase II clinical trial performed at Sheba Hospital in which patients with atopic dermatitis were treated with topical formulation (cream) of an MFAID (one dose).

Results showed no toxicity or adverse effects, but no significant efficacy

(should be retested using an appropriate formulation enabling a better penetration rate).

c. Airway Pathologies (see below)

Clinical Studies:

  • Allergic Rhinitis in allergic patients (in South Africa), treatment by intra-nasal (IN) administration (spraying) of MFAID solution (saline) – one dose (Slides 23-28 in the presentation).   Excellent safety (better than placebo)   Marked suppression of challenge-induced biochemical markers, IL-5, IL-13 TNF-α, MCP-1 and Exotoxin, as well as eosinophil level, in nasal lavage.

11% improvement of symptoms.

  • Chronic RhinoSinusitis (ex vivo), using Nasal polyps of patients suffering from Chronic RhinoSinusitis with polyps (CRSwP) (Slides 29-31 in the presentation).   Nasal polyps (cell dispersion) of patients suffering from CRSwP were stimulated with superantigen (SA = staphylococcus Aureus Enterotoxin).

Treatment with MFAID markedly suppressed

  • the SA-stimulated.
  • Production of IL-5, IL-13, IL-17 and to a lesser extent IFN-γ.
  • Gene expression (mNBA) of secretory PLA2s, gIB, gII (A, D &E), and gX


  • Broncho-Constriction

Prevention of OVA-induced broncho-constriction and airway resistance, as well as

  • infiltration of inflammatory cells (cellularity) in the lung (histology).
  • Suppression of the level of eicosanoids, including the broncho-constricting CysLts, PGD2 and TBX2, in BAL
    5-lipoxygenase (5-LO) protein expression in lung tissue.
  • Gene expression (mRNA) of PLA2s (including sPLA2gX)


1. A platform of molecules with potential to synthesize many APIs and formulations
2. Multi-factorial anti-inflammatory/allergic mechanisms:

  • Protecting cells from membrane phospholipid degradation, and
  • Enrichment of the protective layer of cell surface glycosaminoglycans (GAG)

3. The technology is protected by a very extensive patent portfolio
4. Human clinical trails

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