Anadys Pharmaceuticals Inc. said it developed for the first time a database that includes the annotation of the portion of the human genome that encodes for proteins that interact with RNA.
The database, called RiboBase, contains more than 1,000 nucleic acid-binding proteins.
“One of the things that’s becoming very hot is looking at RNA as a potential drug target,” said David Nelson, associate director of corporate development and strategy at San Diego-based Anadys. “The RNA world is really a rich source of drug targets.”
Scientists in pharmaceutical research have historically focused on protein targets, Nelson said, but by doing so have “ignored half of the playing field.” With Ribobase, a company can find small molecules or proteins that will bind to RNA and therefore have a therapeutic effect. For example, companies can discover either new proteins that bind to RNA, or, if the company has a known specific protein, the database would provide information about that protein, such as where it is expressed, he said.
Privately held Anadys is in discussions with several biotech and pharmaceutical companies with which it will consider partnering RiboBase, Nelson said. But it also will use RiboBase for its internal drug discovery efforts.
“We are exploring whether to offer it on a subscription basis, but that decision has not been made,” Nelson said, noting that the emphasis for Anadys is on collaborations and becoming “a partner of choice.”
Anadys’s focus is on developing small-molecule drugs as anti-infectives. In addition to using its drug discovery capabilities internally, Anadys works in development collaborations. Its partners include Aventis Pharma AG, of Frankfurt, Germany; Indianapolis-based Eli Lilly & Co.; and Pharmacia Corp., of Peapack, N.J.
And just last month, Anadys and Structural GenomiX Inc. announced a joint partnership to discover small- molecule drugs. (See BioWorld Today, Feb. 21, 2002.)
When building the database, Anadys started with about 200 proteins discovered in the company’s early years, and has since added information from academic labs and literature. Once common motifs were identified in the proteins, the human genome was searched using bioinformatics to see if other proteins in the genome would have those same motifs, Nelson said, and perhaps bind to RNA. Of the 1,000 proteins in the database, about 800 have been shown to bind to RNA, while the remaining 200 have been shown to bind to DNA, he said.
“What we will continue to find out is [whether] there are new motifs that will enable RNA binding,” he said. “In that sense, the work [for the database] will be ongoing.”
Among the drugs approved for the treatment of infectious diseases based on RNA and RNA-protein complexes are Neomycin, Zyvox and Zithromax, the company said.