Cubist Pharmaceuticals was a U.S. biopharmaceutical company with activities spanning from research and development to commercialization of pharmaceutical products. Its main products target pathogens like MRSA.

Cubist was one of the few firms that continued to research in antibiotics while larger pharmaceutical companies have abandoned such research. The company employs 638 people, with 370 in their headquarters in Lexington, MA. As of 2011, the company’s headquarters are under expansion and is expected to occupy 373,000 sq ft (34,700 m) in Lexington, MA. On 8 December 2014, Merck & Co. acquired Cubist for $102 per share in cash ($8.4 billion) as entree to the market for drugs that can combat superbugs.

Cubist was founded in May 1992 by John K. Clarke, Paul R. Schimmel, Ph.D. and Barry Bloom, Ph.D, all of whom were also directors. Cubist appeared on Fortune 2010’s List of fastest growing companies, and was named to the 2010 Deloitte Technology Fast 500. In 2006 it had the 19th highest sales among American based biotechnology companies.

In 2011, the company acquired Adolor, maker of a drug for treatment of constipation.

Cubist had an ambitious growth plan laid out for the 2012-2017 quinquennium. Under this plan, the company was expected to reach 2B dollars in sales and have 4 new drugs in late stage development by 2017. As a part of this plan, sales of its flagship drug Cubicin were expected to grow to more than 1B dollars per year.

In July 2013, Cubist Pharmaceuticals agreed to purchase Trius Therapeutics and Optimer Pharmaceuticals for around $1.6 billion.

In 2014, succeeding Michael Bonney as President, Robert J. Perez, was announced to take leadership on January 1, 2015. In January 2015 Cubist Pharmaceuticals became a wholly owned subsidiary of Merck & Co.

The company markets Cubicin (daptomycin) for injection, the first antibiotic in a class of anti-infectives called lipopeptides. In 2011, Cubist settled a patent litigation with Teva Pharmaceutical Industries regarding Cubicin. In April 2011 it reached a deal with Optimer Pharmaceuticals in which its class of bacterium fighting drugs will be co marketed with Optimer's Fidaxomicin/Dificid (for $15 million per year). Optimer chose Cubist because according to its CEO, "Cubist has a proven track record and well established relations with all stakeholders involved in the antibiotics space".

In 2011, its product pipeline focused on gram-negative bacterial infections, Clostridium difficile-associated diarrhea, and respiratory syncytial virus.

Tedizolid was approved by the US Food and Drug Administration on June 20, 2014.

Coordinates: 42°25′25.2″N 71°14′32.9″W / 42.423667°N 71.242472°W / 42.423667; -71.242472