An important area of Isis' basic research is to understand the molecular mechanisms of antisense. There are at least 12 known antisense mechanisms that can be exploited once an antisense drug binds to its target RNA. Isis has created proprietary chemical modifications to trigger many of these mechanisms for drug discovery. As its understanding of these mechanisms further improves, the Company expects to develop antisense drugs with enhanced performance and for broader therapeutic applications.

An antisense mechanism is defined as the process in which an antisense drug works after it binds (hybridizes) to a target RNA to form a duplex. The formation of this duplex, or two-stranded molecule, prevents the RNA from functioning normally and from producing a protein product.

Progress in Isis' mechanism of action research program is illustrated by the Company's accomplishments in understanding RNase H. The majority of late-stage antisense drugs in development bind to their target RNA and activate a cellular enzyme called RNase H. This enzyme destroys the target RNA, inhibiting production of a specific protein. Isis has cloned and characterized human RNase H and has effectively used that information to design its proprietary second-generation drugs. The Company expects to further improve its drugs, using its insights into the RNase H mechanism.

In addition to its RNase H expertise, Isis has made advancements in understanding and exploiting other antisense mechanisms.

RNA Interference (dsRNase, siRNA and RNAi)

Antisense drugs can be designed to bind to their target RNAs and recruit a different class of enzymes, called double-stranded RNases (dsRNase) that cleave the target RNA. There are many dsRNases in the cell, making this a potentially attractive mechanism. Isis' research led to one of the first scientific publications and key issued patents that address this mechanism. siRNAi and RNAi, for example, are dsRNase mechanisms that have received much attention in the drug discovery community.  Isis is making significant advances in understanding this mechanism through funding from partners including Lilly. Isis also has a strategic collaboration with a leader in RNAi therapeutics, Alnylam Pharmaceuticals, Inc. This alliance will utilize each company's intellectual property and expertise to expedite the development and commercialization of RNAi therapeutics.

Alternative Splicing

Alternative splicing has been shown to result in many diseases and accounts for most of the diversity in proteins. Alternative splicing is largely responsible for the functional complexity of the approximately 30,000-40,000 genes in the human genome; 40-60 percent of human genes have alternative splice forms.

Isis has pioneered the design of antisense drugs that can selectively direct alternative splicing to make one protein versus another. Today, Isis continues its drug discovery and development partnerships with Ercole Biotech, a company focused specifically on this mechanism. In the future, many diseases may be amenable to this approach.

The Role of Micro RNA

Researchers recently have discovered new families of natural antisense molecules made inside the cell called micro-RNAs; it is estimated there are hundreds of micro-RNA molecules in humans. These molecules appear to serve as master regulatory molecules for many biological processes. Isis scientists have been able to use micro-RNA in two ways. The first involves turning off, or inhibiting, genes in order to stop the production of a protein; an equivalent process to traditional antisense. The second involves turning on, or up regulating, genes so that specific proteins are made.

Isis has an internal research program to discover and identify the function of micro-RNAs, and design and optimize antisense inhibitors and small molecule modulators of therapeutically attractive micro-RNA targets, including discovering new micro-RNA drugs and antisense drugs to treat hepatitis C virus, cancer and metabolic disorders.