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In Countersuit, Santaris Aims to Invalidate Isis Gapmer Patents

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By Doug Macron

Santaris Pharma last week responded to a patent-infringement suit filed by Isis Pharmaceuticals, denying the allegations and asking the court hearing the case to invalidate the gapmer-related intellectual property at issue.

In its countersuit, Santaris asked for a court declaration that it does not infringe, directly or indirectly, two Isis patents, as well as a ruling that both pieces of IP are “invalid and unenforceable.

Santaris said the countersuit is "in response to repeated threats by Isis concerning numerous invalid and irrelevant patents, a pattern culminating in this lawsuit, through which Isis brazenly claims that its United States patents not only reach Santaris' activities in [its native] Denmark, but that its patents also cover work by Santaris that falls squarely within the protections” of a statutory patent exemption.

The legal tussle began in September when Isis sued Santaris for infringing two patents (GSN 9/29/2011). The first, No. 6,326,199, is entitled “Gapped 2' Modified Oligonucleotides” and claims oligos and macromolecules that have increased nuclease resistance, substituent groups for increasing binding affinity to complementary strands, and sub-sequences of 2'-deoxy-erythro-pentofuranosyl nucleotides that activate RNase H enzyme.

The second, No. 6,066,500, is entitled “Antisense Modulation of Beta Catenin Expression” and claims the use of antisense compounds “targeted to nucleic acids encoding beta catenin,” as well as methods of using these agents to treat diseases associated with the protein.

In its suit, Isis charges that Santaris uses the gapmer technology protected by the patents in certain of its locked nucleic acid molecules used in cell assays that help identify "potential gene targets and/or to screen the ability of synthesized oligonucleotides to inhibit the production of a specific protein.

“Thus, the Isis method patented in the '199 patent, which involves contracting a cell with a gapmer, is used by Santaris as a research tool to identify targets and/or to screen gapmer LNA antisense molecules for activity inhibiting a target,” Isis said in its suit. “Santaris further sells and offers for sale in the United States the patented methods,” which is in direct competition with the services Isis offers.

Furthermore, Isis said that Santaris is aiming to compete directly with Isis by “advancing and selling LNA gapmer compounds for a specific mRNA target for which Isis has already invested research time and money as a viable therapeutic target,” namely beta catenin.

Isis added that Santaris licensed beta catenin-inhibiting antisense agents to partner Enzon Pharmaceuticals, and has struck numerous deals under which it provides to partners such as GlaxoSmithKline and Pfizer LNA drug candidates that infringe the '199 patent.

Anticipating a possible objection by Santaris, Isis also said in its lawsuit that Santaris' activities do not fall under the statutory patent exemption 35 U.S.C. 271 (e)(1), which in part says that “it shall not be an act of infringement to make, use, offer to sell, or sell ... a patented invention” for uses related to the development and submission of a drug for market approval. The US Supreme Court upheld the exemption in 2005.

The “millions of dollars of revenue” generated by Santaris through the sale of the disputed antisense technology “are not reasonably related to the development and submission of information to the FDA for regulatory approval, Isis said. “Rather … the substantial sums received by Santaris, and the significant future payments contemplated by [its agreements with pharmaceutical partners], constitute commercial revenue that Santaris uses to fund and develop its business.”

Santaris countered in last week's response to Isis' suit that its allegedly infringing activities are covered by 35 U.S.C. 271 (e)(1), although it did not elaborate.

In addition to seeking a declaration that it has not infringed either the '199 or the '500 patents, and that both are invalid, Santaris asked the court for attorneys' fees.

Out of the Frying Pan...

Santaris' response to Isis comes just two months after the company settled a dispute with Exiqon over rights to market LNA amidites and oligos (GSN 10/13/2011).

In that dispute, Exiqon filed suit against Santaris after it became concerned over a “potential breach” of the companies' co-ownership arrangement for the LNA technology.

Both companies have rights to the LNA technology, but for different applications. Exiqon licensed it from its inventors in 1997 and created a subsidiary called Cureon to handle its development as a drug modality. Cureon later merged with Panteco and became Santaris, while Exiqon retained all rights to the LNA technology outside of therapeutics.

Exiqon said that Santaris appeared to be “commercializing products for the conduct of research” and initiated the court proceedings in a Danish court.

The matter was eventually settled by an arbiter, which ruled that Exiqon can sell the amidites and oligos to companies conducting research and development of pharmaceuticals in which LNAs are the active ingredient, and dismissed patent-infringement claims against Santaris.

Additionally, Santaris was awarded DKK2 million ($355,633) million in court fees.

Meantime, Santaris continues to fight microRNA drug startup Mirrx Therapeutics over the rights to a novel miRNA-silencing technology.

Mirrx has developed antisense molecules called Blockmirs that it claims can inhibit individual messenger RNA regulation by an miRNA. Last year, Santaris filed a lawsuit claiming that it owns the technology since Mirrx developed it using trade secrets (GSN 5/6/2010).

Most recently in that case, the European Patent Office rejected a request by Mirrx to continue prosecuting a patent application covering Blockmirs until the court has ruled on the lawsuit (GSN 7/21/2011).


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