Cubist was founded in May 1992 by John K. Clarke, Paul R. Schimmel, Ph.D. and Barry M. 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 2011, the company acquired Adolor, maker of a drug for treatment of constipation.
The company expected sales of its drug Cubicin to grow to more than 1 billion dollars per year.
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 developed 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).
In 2011, its product pipeline focused on gram-negative bacterial infections,Clostridium difficile-associated diarrhea, and respiratory syncytial virus.