The way both companies have been making deals lately, a partnership between Takeda Pharmaceutical and Alnylam (NASDAQ:ALNY) seemed almost inevitable.

In the last few months, Takeda has boosted its pipeline by partnering with Cell Genesys (NASDAQ:CEGE) and buying Millennium Pharmaceuticals. Alnylam, the leader in RNAi therapeutics -- a process to fight disease by turning off genes -- has licensed its technology to about 20 companies. It also recently set up a separate company, Regulus Therapeutics, with ISIS Pharmaceuticals (NASDAQ:ISIS) to develop microRNA therapeutics. Regulus just signed up GlaxoSmithKline (NYSE:GSK) as a partner last month.

The latest partnership for the habitual dealmakers looks like a pretty good deal for Alnylam. It gets $100 million in up-front payments, and in exchange, Takeda gets the "right of first negotiation" to sell Alnylam's RNAi drugs in Asia -- excluding its most advanced program to treat a virus that causes cold-like symptoms. Alnylam will get up to $171 million in development and commercial milestone payments, as well as royalties for each drug developed.

If that were the end of the partnership, I'd say it was a pretty balanced deal, but Alnylam is also getting $50 million in exchange for giving Takeda a non-exclusive license to develop RNAi drugs to treat cancer and metabolic diseases. As part of the deal, Alnylam has the option to co-develop and co-market four of Takeda's RNAi drugs in the U.S. Alnylam will have to pay half the development costs, but it doesn't have to make a decision about the drugs until after any phase 2 results are complete. Since the U.S. is such a large drug market, the deal could boost Alnylam's revenues down the road if any of Takeda's prospects pan out.

And maybe that's the rub. RNAi is still a new technology that hasn't been proven successful in a phase 3 trial yet, so it's hard to know which company will eventually benefit more from this partnership. In the meantime, Alnylam has another $150 million to pad its coffers, and Takeda has a call option on an unproven but promising set of drugs.