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Driving DNA Interference (DNAi)

By Richard D. Gill

Sept. 13, 2007 | The past year has been an exciting one for nucleic acid drug development, with most of the attention justifiably on major news from the RNAi side of the equation. Craig Mello and Andy Fire shared the Nobel Prize for discovering how double-stranded RNA can switch off genes (See p. 10); Merck placed a $1-billion bet on RNAi in acquiring Sirna; and Alnylam, bolstered by a $331 million alliance with Hoffman-LaRoche, is striving to conquer the biggest and as yet unsolved, hurdle for nucleic acid drugs — the problem of in vivo delivery of therapeutic molecules — through promising lipid-based technologies. Clearly the rush is on, with hundreds of players in pursuit of early market success in the vast, promising territory of RNAi.

An equally promising and rapidly developing, but lesser known and virtually undiscovered territory in nucleic acid drugs, is DNA interference (DNAi). DNAi represents a novel approach to targeting specific disease genes, employing single strands of DNA targeted to treat non-transcribed regions of genomes involved in complex genetic diseases. DNAi constructs consist of single stranded 24-mer DNA oligos targeted to the 5’ prime promoter region of specific oncology genes, and which have to date been targeted toward the Bcl2 gene the myc gene in preclinical studies. This simple and elegant approach forms the basis of a highly promising and rapidly progressing new class of nucleic acid-based therapeutics.

Pros & Cons
The projected therapeutic effects of DNAi are markedly similar to those anticipated for RNAi and antisense — but without a number of also-anticipated drawbacks. For example, RNAi’s highly touted approach to binding oligonucleotides to messenger RNA (mRNA) transcripts, thereby combating the progress of disease or halting it entirely, comes with a few built-in problems.

RNAi therapies, by their nature, will probably require large doses, since disease genes are continuously transcribing mRNA molecules, which will have to be continuously destroyed by the RNAi therapies. A rough analogy for this process would be myriad tiny sponges absorbing every single drop of water from a firehose. Constant binding to every single molecule is an enormous task, which will necessitate a high volume of therapeutic — which in turn, may lead to high toxicity due to high dosage, not to mention the potential high cost of RNAi drugs.

DNAi takes a simpler and theoretically more effective approach. DNAi therapies need only target one to two copies of a disease gene in each cell to cut off their negative effects. In contrast to RNAi, DNAi would focus on “plugging the firehose” instead of laboriously wiping up each droplet of water. The benefits of this solution are readily apparent. DNAi drugs would likely need lower doses than RNAi therapies, possibly leading to lower toxicity, and ultimately, lower cost.

A further advantage of DNAi is that since it works at the DNA level, it can possibly be employed against diseases considered “untreatable” by small molecules. That capability alone goes far to validate DNAi-based drugs as a promising therapeutic avenue.

Both DNAi and RNAi, however, face the same problem that has prevented effective nucleic acid therapeutic development since its inception: how to deliver oligonucleotides into the nucleus safely and effectively. Fortunately, both camps are traveling in a similar, promising direction, using innovative liposome technologies. In many cases, they even use the same liposome technology vendors (such as Novosom, Tekmira, Protiva, Neopharm, and Octoplus), ensuring a commonality of delivery methods between the therapeutic approaches. In this crucial aspect, DNAi has kept pace with its RNAi cousins, and has in fact created current Good Manufacturing Practice-enabling delivery methods.

Inside the Lab
Also like RNAi, DNAi has demonstrated the ability to perform as a lab tool as well as a therapeutic, notably as a drug design engine. The basic premise for DNAi-enabled drug design is that technologies can potentially reduce lead identification time for drug candidates. Unlike approaches in small molecule drug design, DNAi technologies obviate the necessity to screen large chemical libraries to find effective compounds for proteins, as they can leverage publicly available information from the Human Genome Project to guide targeted therapy research.

Current progress has helped DNAi overcome previous obstacles to DNA-based therapies (issues with specificity and selectivity) and enabled DNAi drug candidates to anneal directly to disease genes in preclinical studies. (DNAi also differs from gene therapy approaches; while gene therapy seeks to restore the function of a faulty gene, DNAi seeks to turn off disease genes. For example, gene therapy would treat insufficient insulin production by adding the necessary gene. DNAi would interact with genomic DNA, leading to an apoptotic cascade, silencing genes.)

DNAi has demonstrated great promise as a parallel approach to the successful realization of nucleic acid therapeutics, and shown significant potential as it progresses alongside the highly trafficked RNAi road to drug development. Both technologies are making great strides toward the market. All things being equal, however, there is the definite possibility that DNAi’s compelling features — simpler approach, potential lower dose, toxicity and cost, and ease of transition to use in drug design — will lead to surprising successes for this new field.

Richard D. Gill, PhD, is president and CEO of ProNAi Therapeutics. Email:

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