Isis may be the goddess of motherhood, but Isis Pharmaceuticals (Nasdaq: ISIS) is like a kid in a candy store as it rakes in cash from partnership deals.

Its latest payment -- $2 million from Bristol-Myers Squibb (NYSE: BMY) -- was triggered because Bristol has decided to begin developing an antisense drug that the companies have been working on for almost a year. Isis got $15 million when it signed the deal with Bristol last year. Yesterday's compensation is just the start of a long line of payments for milestones that Isis could receive if the drug is effective in the clinic.

The drug targets convertase subtilisin kexin 9 (PCSK9), a human proprotein that has been shown to increase LDL-cholesterol -- that's the bad kind. The antisense drug lowers the concentration of PCSK9 and thus LDL-cholesterol -- in the laboratory, at least. Bristol will be responsible for bringing it through the clinic and Isis will get royalty payments if it's approved.

The problem with most antisense drugs is that they're made up of nucleic acids which break down easily in acidic stomachs; therefore they need to be injected (or treat a disease on the outside of the body). This compound isn't going to be a top-selling cholesterol drug like Pfizer's (NYSE: PFE) Lipitor or Schering-Plough's (NYSE: SGP) and Merck's (NYSE: MRK) Vytorin, because patients prefer popping pills over injecting themselves. It's therefore likely that the drug will be used only by patients whose cholesterol levels can't be brought under control with oral medications.

Ironically, Bristol's new drug might be competing with another drug developed by Isis to treat those patients with extremely high cholesterol. The antisense drugmaker recently signed a marketing deal with Genzyme (Nasdaq: GENZ) to market its late-stage compound mipomersen.

Isis probably doesn't care which drug eventually wins, as long as both are approved by the FDA and it keeps getting handed lollypop milestone payments.

More antisense Foolishness:

Motley Fool Rule Breakers is always on the hunt for hot drug stocks and other cutting-edge picks. Click here to see all of our latest discoveries with a free 30-day trial subscription.

Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. Pfizer is a pick of both the Income Investor and Inside Value newsletters. The Fool has a disclosure policy.