CHESHIRE, Conn. (TheStreet) -- Alexion Pharmaceuticals (ALXN - Get Report) shares fell 8% Wednesday over investor concerns about the planned $8.4 billion acquisition of Synageva BioPharma (GEVA). At that price, the deal carries one of the highest takeout premiums in Wall Street history, which a lot of people believe is too rich even if it does expand Alexion's pipeline of drugs to treat rare, inherited diseases.

But here's another theory to at least partially explain Alexion's Wednesday selloff: Company executives are worried about a third company and a competitive threat to its Soliris ultra-orphan blockbuster franchise. Investors see Alexion's willingness to write a huge check for Synageva as a tacit acknowledgment that Soliris' long-term future might be more at risk than the company lets on.

That third company is Alnylam Pharmaceuticals (ALNY), the maker of drugs based on gene silencing technology known as RNA interference. Alnylam is developing a drug which if successful would compete directly against Soliris as a treatment for rare, inherited blood disorders.

Soliris sales grew 44% to more than $2.2 billion last year. Buying Synageva and its orphan disease drugs in development will bolster Alexion's revenue and profits, but only if it can also maintain the blockbuster sales of its Soliris franchise.

Alnylam is not an imminent threat to Alexion. The company's drug, ALN-CC5, just entered the first stage of human clinical testing in healthy volunteers. But if ALN-CC5 passes this initial test, the drug will be advanced into studies enrolling patients with paroxysmal nocturnal hemoglobinuria (PNH), one of two rare blood disorders which Alexion relies on for the bulk of Soliris sales.

The first results from ALN-CC5 studies in healthy volunteers are expected this summer, with PNH patients enrolling before the end of the year, Alnylam says.

PNH and related diseases are caused by an over-activation of complement, a protein involved with the body's immune system. Soliris is a monoclonal antibody which targets and stops a specific type of complement known as complement component C5 from damaging blood cells. In order to have a therapeutic effect, large amounts of Soliris must be given to patients via an intravenous infusion every two weeks.

Alnylam's ALN-CC5 is an RNAi molecule designed to turn off the gene responsible for making disease-causing complement component C5. ALN-CC5 is administered by an injection just under the skin, and while dosing is still being worked out, Alnylam hopes the RNAi therapeutic can be given every two weeks or perhaps even once per month. Promising results from a primate study presented in 2013 demonstrated ALN-CC5 was capable of decreasing levels of complement component C5.

On a Wednesday conference call, Alexion executives said acquiring Synageva will strengthen the company's ability to develop and sell drugs targeting rare, inherited diseases. The executives also expressed confidence that peak sales of Synageva drugs, once approved, would more than justify the $8.4 billion cost of the acquisition. 

Alexion didn't mention Alnylam as a reason for buying Synageva and the subject wasn't raised by analysts on the conference call. That might change later this year depending on the profile of ALN-CC5 which emerges from the first, early studies.

Adam Feuerstein writes regularly for TheStreet. In keeping with company editorial policy, he doesn't own or short individual stocks, although he owns stock in TheStreet. He also doesn't invest in hedge funds or other private investment partnerships. Feuerstein appreciates your feedback; click here to send him an email.