By Chelsey Dulaney 

Drug maker Merck & Co. is facing criticism that it is overpaying for its planned $8.4 billion purchase of antibiotics specialist Cubist Pharmaceuticals Inc., in light of a court ruling issued hours after the deal was announced Monday that could dampen the sales potential for Cubist's top-selling drug.

Leerink Swann analyst Seamus Fernandez said the purchase price appeared to be about $2 billion to $3 billion too high, based on reduced sales expectations for the Cubist drug, the antibiotic Cubicin.

Merck shares fell 3.2% to $59.88 in recent trading Tuesday. Cubist shares fell 4.2% to $96.42, about 5% less than the $102-per-share that Merck has agreed to pay.

"This is a very tough start to a relatively sound strategic deal," Mr. Fernandez said in a research note.

An order issued Monday by U.S. Judge Gregory M. Sleet in federal court in Delaware invalidated claims in four patents covering Cubicin. If the ruling stands, rival Hospira Inc., which challenged the patents, could begin selling a generic version of Cubicin in mid-2016, when a remaining patent expires. That would be at least three years earlier than the now-invalidated patents were to expire in 2019 and 2020. Cubist said it would appeal the ruling, but some analysts believe it is unlikely to be overturned.

Cubicin generates annual sales of nearly $1 billion for Cubist, so the court ruling could end up wiping out a large chunk of potential sales due to low-cost generic competition from Hospira and others. Robert W. Baird & Co. analysts estimated Merck could lose out on more than $3 billion in potential revenue that would have helped justify the price tag Merck is paying.

Merck, Whitehouse Station, N.J., issued a statement Tuesday reiterating its belief in the value of the Cubist deal. Merck said the patent decision doesn't change its expectation that the deal will add more than $1 billion in revenue for 2015, and that it will add to earnings in 2016 and thereafter.

Before the court ruling, Merck Chief Executive Kenneth C. Frazier and other company officials had said they considered a range of possible outcomes of the Cubicin patent litigation before closing the deal, and were still comfortable with the acquisition. They touted other Cubist drugs that could support sales and profit growth in coming years, including an antibiotic, Zerbaxa, that could be approved by U.S. regulators this month. "This deal is not about one product, it's about a leadership position in the acute hospital setting," Adam H. Schechter, president of Merck's global human health unit, said in an interview Monday.

"We still feel the deal continues to bring strong economic value over the long-haul to the company," Merck spokesman Steve Cragle said Tuesday. "We're going to move forward with it."

Cubist, of Lexington, Mass., said late Monday the court ruling wouldn't affect its sale to Merck, and it expected the deal to close in early 2015.

Still, the $8.4 billion price tag and the patent ruling triggered skepticism. Bernstein analyst Tim Anderson said the deal would help flesh out Merck's portfolio of anti-infective drugs and bolster its presence in the market for products used in hospitals. "But the limited commercial life of Cubicin and the lack of a high-science, cutting edge [research and development] platform mutes our enthusiasm for the deal," Dr. Anderson wrote in a research note Monday, before the court ruling.

It may also be tough for Merck to back out. The purchase agreement specifically bars Merck from citing the outcome of the Hospira patent litigation as a so-called "material adverse effect" that could scuttle the deal.

One large Merck shareholder wasn't overly concerned about the price or timing of the deal. "Merck is going to be smart about how they proceed from here," said Tony Scherrer, director of research at Smead Capital Management in Seattle, which owns about 690,000 Merck shares. "We think Merck is looking at a deal like this in terms of what it can bring to the table over the next decade-plus, not just the next 18 months."

Cubist specializes in antibiotics, including those designed to treat complicated infections caused by bacteria that have developed resistance to older antibiotics. Cubicin, an intravenous antibiotic, was introduced in 2003 and is used primarily in hospital patients to treat skin and other infections. The company markets two other antibiotics, Dificid and Sivextro, and a drug to help bowel-surgery patients, Entereg.

The company's research pipeline includes Zerbaxa, a newer intravenous antibiotic designed to target a different set of infections including those of the urinary tract. Some analysts believe it has potential to generate sales of more than $1 billion a year if it is approved for sale, but it could face competition from other newer antibiotics including one that could be launched soon by Actavis PLC. Cubist also is developing treatments for clostridium difficile, a bug that causes diarrhea, and opioid-induced constipation.

Write to Peter Loftus at peter.loftus@wsj.com

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