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Isis Sues Santaris for Infringing Patents Related to Gapmer Technology


By Doug Macron

Isis Pharmaceuticals has sued Santaris Pharma for allegedly infringing its intellectual property by providing antisense drugs and drug-discovery services to pharmaceutical partners.

Notably, Isis argues that Santaris' activities are not protected by a statutory patent exemption that permits companies to use patented technology in their drug-development efforts because the services it provides are commercial transactions “not ... related to the generation of data for submission” to the US Food and Drug Administration.

“A key element of our business is to make our patented technology available to researchers and drug developers who want to work in the antisense field,” Isis COO and CFO Lynne Parshall said in a statement. "The exemption from patent infringement for drug development was created to encourage rapid introduction of generic medicines. We allege Santaris' activities are not protected by this exemption and that case law affirms our position."

In an e-mail to Gene Silencing News, Santaris CEO Soren Tulstrup denied the allegations.

"The allegations in the complaint by Isis Pharmaceuticals are completely without merit,” he wrote, adding that the company will “vigorously defend its patent estate.”

In its suit, Isis claims that Santaris is infringing two of its US patents. 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 strand, 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.

Filed in a US District Court in California, Isis' suit charges that Santaris uses locked nucleic acid-containing gapmer antisense compounds in cell assays to 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 claims. “Santaris further sells and offers for sale in the United States the patented methods,” which is in direct competition with the services Isis offers.

At the same time, Isis alleges, Santaris “has attempted to compete directly with [it] 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 adds that Santaris has already sold to partner Enzon Pharmaceuticals antisense compounds that inhibit beta catenin, a move that it says violates the '500 patent. Further, it alleges that the '199 patent is infringed by Santaris' ongoing collaborations with Shire, Pfizer, and GlaxoSmithKline, under which the big pharmas are provided with Santaris-designed LNA-based drug candidates against specific targets.

Although the US Supreme Court ruled in 2005 that companies are free to use patented technology in the course of developing drugs, Isis said in its suit that this ruling does not apply to Santaris' activities.

The Supreme Court case, known as Merck KGaA v. Integra LifeSciences, centers around the statutory patent exemption 35 U.S.C. 271 (e)(1), that states in part that “it shall not be an act of infringement to make, use, offer to sell, or sell ... a patented invention … solely for uses reasonably related to the development and submission of information under a Federal law which regulates the manufacture, use, or sale of drugs or veterinary biological products.”

But Isis argues that 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, and therefore are not exempt from infringement by the safe harbor provision” of 35 U.S.C. 271 (e)(1).

“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,” Isis wrote in its complaint.

“Regardless of whether the pharmaceutical company customers later develop some of the resulting compounds and eventually advance a drug to a phase of development where the … exemption attaches, Santaris' commercial transactions are not themselves related to the generation of data for submission to the FDA,” it adds.

'Slightly Different View'

In addition to the Isis litigation, Santaris is currently defending itself in arbitration proceedings initiated in a Danish court by Exiqon, which has accused Santaris of violating a technology-use agreement between the companies (GSN 3/10/2011).

Santaris was established when Cureon, a company Exiqon founded to develop LNA-based therapeutics, merged with Panteco. Exiqon said earlier this year that under a licensing deal with Santaris, it holds all rights to the LNA technology outside of therapeutics, yet Santaris may be “commercializing products for the conduct of research.”

“We have a slightly different view of how we read [the companies' licensing] agreement and [arbitration] is the best way to figure out how we draw the line,” Exiqon CEO Lars Kongsbak told Gene Silencing News at the time. He added that the dispute specifically centers around the way Santaris is using raw materials, but didn't provide additional information.

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