Taking a medical breakthrough from concept through commercial success is like ascending a mountain that grows taller and more treacherous with every setback. It's taken Alnylam Pharmaceuticals, Inc. (NASDAQ:ALNY) 16 years to launch its first drug, so challenges have had plenty of time to take up positions along this company's path to a successful first launch.

Alnylam's new drug, Onpattro, is the first that uses RNA interference to silence troublesome genes. Here are three big hurdles its commercial launch is about to run into.

Businessman jumping a hurdle.

Image source: Getty Images.

1. The first time's the hardest

Alnylam regained rights to patisiran, now Onpattro, from Sanofi earlier this year. While this leaves Alnylam eligible to retain a larger portion of any profits the drug generates, the little biotech needs to build a sales and marketing team from scratch. 

Getting the Food and Drug Administration to approve a new drug is a tremendous achievement, but it doesn't guarantee commercial success. In fact, smaller biotechs that have tried launching drugs with blockbuster potential on their own have been huge disappointments in recent years. Shares of Puma Biotechnology, Acadia, and Tesaro have been cut in half, or worse since their first treatments earned FDA approvals. 

Having a big pharma partner to navigate the tricky minefield of pharmaceutical sales for the first time isn't always necessary. Highly motivated families affected by Duchenne muscular dystrophy have made Sarepta's Exondys 51 a commercial success despite controversial efficacy data. Onpattro is aimed at a small group of motivated patients with nerve damage caused by hereditary transthyretin-mediated (hATTR) amyloidosis that lack treatment options. With a bit of luck, these parallels to Sarepta's successful solo drug launch will give Alnylam's new marketing team a fighting chance. 

Onpattro packaging and a product vial

Image source: Alnylam Pharmaceuticals, Inc.

2. Sticker shock

Alnylam thinks there are just 3,000 Americans eligible for treatment with its new drug and the company intends to charge an eye-popping list price of $450,000 to each one for a year of treatment with Onpattro. Reaching most of these patients could make the drug a blockbuster, but convincing payers to hand over such lofty sums year after year will be a challenge.

Keeping Ph.D.s on the payroll while running clinical trials for years on end isn't cheap. Alnylam's operations started up in 2002 and the company's gone $2.38 billion in the hole in order to bring Onpattro, formerly patisiran, to patients who need it. That isn't the argument the company's been presenting insurers, though. Instead, Alnylam is offering value-based pricing agreements. 

Right now, Onpattro is the only treatment that can slow the progression of hATTR amyloidosis. Adults with this painful and debilitating disease can require a life of constant care at an enormous expense that makes the drug's price seem reasonable.

Alnylam's already signed up insurers that cover a combined 76% of U.S. medical lives to a complex money-back guarantee that allows for significant reimbursement if the drug doesn't help individual patients meet predetermined goals.

Value-based agreements for costly therapies aren't a new concept, but there aren't any big success stories, at least from a drug manufacturer's perspective. Investors will want to keep a close eye on quarterly reports for signs that Alnylam can buck the trend.

A female pharmacist writing on a clipboard while looking at medicines on shelves.

Image source: Getty Images.

3. Other options?

Value-based agreements fall apart as soon as viable treatment options enter the fray, and it looks like Pfizer (NYSE:PFE) has a potential contender. This spring, Pfizer presented data from a drug the FDA rejected years ago called tafamidis. Marketed as Vyndaqel in the EU, this is a simple, relatively inexpensive tablet that could become a major thorn in Alnylam's side if it eventually earns approval to treat the same patients as Onpattro.

Right now, Onpattro is an intravenous infusion specifically approved to treat people with nerve damage caused by hATTR amyloidosis, while tafamidis is approved outside of the U.S. for the treatment of heart damage due to the same root cause. Pfizer claims that tafamidis significantly reduced all-cause mortality for hATTR amyloidosis patients and promised to tell us just how significant the results were at an upcoming conference.

If the benefit Pfizer's drug provides isn't anything to get worked up about, insurers could have another option to use as leverage in negotiations. Partners Ionis Pharmaceuticals (NASDAQ:IONS) and Akcea Therapeutics (NASDAQ:AKCA) earned approval for inotersen in the European Union in July, and the FDA is expected to make a decision this October.

Other irons in the fire

I'm not optimistic about Alnylam's ability to make Onpattro into a blockbuster drug on its own, but that doesn't mean you should dump your shares of this promising biotech stock. The company has at least three rare-disease drugs in pivotal studies at the moment, and two more candidates will probably enter pivotal trials before the year's through. 

Onpattro's rollout might test your patience during the quarters ahead. Just remember that the company's worth hanging on to for years to come.

This article represents the opinion of the writer, who may disagree with the “official” recommendation position of a Motley Fool premium advisory service. We’re motley! Questioning an investing thesis -- even one of our own -- helps us all think critically about investing and make decisions that help us become smarter, happier, and richer.