BOSTON (TheStreet) -- Vertex Pharmaceuticals (VRTX) - Get Report is developing a new cystic-fibrosis drug VX-661 designed to be more effective than an existing drug lumacaftor and work better in future combination therapies for the most difficult-to-treat cystic-fibrosis patients.

On Monday, Vertex disclosed some new phase IIb study results that raise concerns VX-661 may not be as potent as previously hoped. The new VX-661 data in cystic-fibrosis patients aren't bad, per se, but just not as positive as investors had expected.

With Vertex shares trading near all-time highs going into Monday's announcement, any disappointment will undoubtedly weigh on the stock price. The stock was down 5.9% to $123.26 on Monday morning.

This phase IIb study enrolled 39 cystic-fibrosis patients homozygous for the F508del mutation. Twenty of the patients were treated with VX-661 50. They took a dose of 50 milligrams twice a day or 100 milligram once daily, plus Kalydeco, which is Vertex's currently approved cystic-fibrosis drug, while the remaining 20 patients received a placebo. Treatment lasted for 12 weeks, after which patients were assessed for safety, which was the primary goal, and for absolute change in forced expiratory volume, or FEV1, a measure of lung function (the key, secondary goal measuring efficacy).

At the 100 mg dose of VX-661 plus Kalydeco, patients reported a 3% improvement in lung function at 12 weeks, compared with a 1% improvement in lung function for patients treated with a placebo.

The 2% placebo-adjusted improvement in lung function at 12 weeks for VX-661 wasn't statistically significant and was on the low end of expectations. Coming into Monday's announcements, there were many analysts and investors wanting to see a minimum 4% placebo-adjusted improvement for VX-661, based on results from a previous study with a four-week treatment duration.

The efficacy of VX-661 also declined during the course of the phase IIb study. At four weeks, the placebo-adjusted improvement in lung function was 4.8% favoring VX-661.

Vertex spokesman Zach Barber said the primary goal of the phase IIb study was to generate enough safety data to support moving VX-661 into phase III studies required for eventual approval submissions. In this regard, the study was a success and Vertex has already started an large phase III program for VX-661 in cystic fibrosis, Barber said.

Barber also defended VX-661's efficacy, saying the phase IIb study was not designed to provide a "robust" evaluation of the drug's ability to improve lung function. Monday's VX-661 results both at four and 12 weeks are consistent with the previous, four-week study. "It's common to see fluctuations in (lung function) from week to week."

Vertex is developing a Kalydeco/VX-661 combination therapy to treat homozygous F508del patients (the same group of cystic-fibrosis patients to be treated with Kalydeco and lumacaftor.) More importantly, Vertex would like VX-661 to be a component of double- and triple-drug combination therapies that would treat an additional 20,000 or so cystic fibrosis patients with various heterozygous mutations of the F508del gene.

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.