In today's throwdown, we've got two drugmakers trying to establish technologies as the newest way to successfully develop drugs: Alnylam Pharmaceuticals (Nasdaq: ALNY) vs. Sangamo BioSciences (Nasdaq: SGMO).

But first, a little drug development 101
Most drugs work by inhibiting the function of a protein. Statins like Pfizer's Lipitor and AstraZeneca's Crestor, for instance, work by inhibiting a protein called HMG-CoA, which helps synthesize cholesterol. If you can't synthesize as much cholesterol, your cholesterol levels go down.

Finding targets to block is fairly easy; they're a dime a dozen. Figuring out how to block them is considerably harder. Drug companies have to find molecules that can bind and inactivate a specific protein, but don't target other proteins, which might cause side effects.

A second class of drugs, therapeutic antibodies, is less problematic on the targeting front since the job of antibodies is to seek out and bind tightly to proteins. By designing antibodies to human proteins -- rather than foreign invaders -- companies can inhibit proteins. The technology works well for surface proteins like VEGF, which Roche's Avastin targets. Targeting internal proteins is more problematic.

Next-generation tech
Rather than inhibit the protein, Alnylam and Sangamo are trying to directly affect the amount of protein in a cell, albeit through entirely different mechanisms.

Alnylam's RNAi technology acts on RNA molecules, the intermediaries between DNA and proteins. The RNAi drugs bind to RNA, causing the RNA molecule to be chopped up. Without the intermediary, proteins aren't formed.

Sangamo's zinc finger transcription factors work one step upstream of RNAi, inhibiting the process of making RNA. The zinc finger binds to the DNA next to the gene that's being turned off and inhibits the formation of RNA.

Both drug technologies can also be used to increase the amount of a protein. For RNAi, it's a matter of inhibiting an inhibitor of the protein that you want to regulate. For zinc finger transcription factors, the process is more straightforward; by using an activator instead of a repressor attached to the zinc finger, the drug can directly activate the expression of a gene.

Pipeline
Both companies have one phase 2 drug and numerous early stage compounds. Their lead drugs are most important because, if they pass the proof of concept phase, it'll be good evidence that their technology is viable.

Alnylam is going after an infectious disease, respiratory syncytial virus, to prove its case. The phase 2b trial for the drug, ALN-RSV01, should read out sometime next year.

Sangamo's lead drug candidate, SB-509, is designed to increase production of vascular endothelial growth factor–A, which is responsible for promoting growth of nerve and vascular cells. The drug is being tested in patients with diabetic neuropathy and should produce data by the end of this year.

Given the earlier readout, I think we've got to give this section to Sangamo.

Partnerships
In addition to bringing in some cash, licensing of the technology by other companies is an endorsement of the potential of the technology and shouldn't be overlooked.

RNAi has had a mixed bag of late. Roche recently abandoned its RNAi development and Novartis (NYSE: NVS) thanked Alnylam for its contribution to its pipeline, but didn't continue its partnership. Alnylam still has licensing deals with GlaxoSmithKline, Biogen Idec (Nasdaq: BIIB), and others. And ALN-RSV01 is partnered with Kyowa Hakko Kirin in Asia and Cubist Pharmaceuticals (Nasdaq: CBST) elsewhere.

Sangamo has quite a few partnerships but they aren't for human therapies. Sigma-Aldrich (Nasdaq: SIAL) sells reagents using the zinc finger technology for laboratory experiments. There's also a partnership with Dow Chemical (NYSE: DOW) using the technology in plants. Finally, the company has licensed its technology to Roche and Open Monoclonal Technology for protein pharmaceutical production and transgenic animals.

Given the endorsements in the clinic, where the big money is to be made, Alnylam takes this section.

Valuation
Sangamo is a little cheaper than Alnylam, but it really doesn't matter if you have a long-term perspective. Both companies are trading under $500 million. Either their technologies are going to work and they'll be multibillion-dollar companies – ten-baggers from here -- or they'll be worthless.

A clear draw in this category.

And the winner is ...
You'll get your vote below, but my suggestion is to invest in both. Developing a new technology is risky. It's better to have two shots on goal. Even if both technologies happen to work, they should be able to coexist since there are plenty of drug targets to go after. Please take our Motley Poll, then scroll down to the comments section to let your fellow Fools know why you voted the way you did.

Pfizer is a Motley Fool Inside Value recommendation. GlaxoSmithKline and Novartis AG are Motley Fool Global Gains picks. The Fool owns shares of GlaxoSmithKline. Try any of our Foolish newsletter services free for 30 days. We Fools may not all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors.

Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. The Fool has a disclosure policy.