Cubist Pharmaceuticals (NASDAQ:CBST) and Durata Therapeutics (NASDAQ:DRTX) both won this week with nods by the FDA's advisory panels on each company's antibacterial agents.

In two unanimous votes, the FDA panels agreed on the safety and efficacy of Cubist's tedizolid and Durata's dalbavancin. Both drugs would compete with Pfizer's (NYSE:PFE) Zyvox (linezolid).

Rivals or partners?
Both Cubist's Sivextro and Durata's Dalvance are targeted against serious bacterial skin infections caused by Gram-positive infections like MRSA (methicillin-resistant staphylococcus aureus). Vancomycin (generic) is now the first-line treatment for MRSA, but it's limited by side effects, toxicity, and is availability in IV form only.

While the two drugs target the same infections, from a macroscopic view, Durata can hardly be considered a true rival. With a vast misbalance in market cap, Durata is but a tiny blip compared to behemoth Cubist, which is already a leader in antibiotics with its blockbuster Cubicin.

Formed just five years ago, Durata is a relatively small biotech formed to buy Pfizer's antibiotic-focused subsidiary Vicuron Pharmaceuticals, an acquisition that resulted in dalbavancin changing hands. Pfizer originally paid $1.9 billion for Vicuron (and dalbavancin) in 2005.

Meanwhile, Cubist has been in full force for development and growth. It acquired Trius Therapeutics and Optimer Pharmaceuticals last summer for $1.6 billion, adding Sivextro to its portfolio in addition to Dificid, Optimer's infectious diarrhea treatment. The company plans to spend $400 million just this year in developing four new agents by 2020. Cubist also plans to file for approval this year an antibacterial agent against complicated urinary and abdominal infections.

Head to head, Durata will have a difficult time against Cubist. But the concurrent approval of their two antibiotics may speak to Durata's value as being a possible future acquisition for Cubist, a deal that analysts have speculated about in the past.

And the drugs themselves?
If both drugs are approved, Durata will severely lag in ability to market its drug compared to Cubist just based on infrastructure and funding, but comparing Dalvance to Sivextro yields a much narrower margin.

Sivextro wins on ease of dosing, offering a once daily pill or injection; meanwhile, Dalvance is given once a week for two weeks. As compared to Pfizer's Zyvox, Sivextro proved noninferiority and also enjoys the advantage of less frequent dosing, shorter course of treatment, and improved side effect profile. Dalvance also proved noninferiority to both vancomycin and vancomycin followed by linezolid, the main compound of Zyvox.

Dalvance specifically generated some concern regarding liver problems and dosing follow-up, but the advisory committees both requested that further safety studies be conducted after the drugs go to market. With both drugs meeting primary endpoints and raising only mild safety concerns, they're pretty comparable, although Dalvance may lag slightly due to the more complicated dosing schedule. Of course, this assumes that the FDA follows these committee recommendations, which is not guaranteed.

The final FDA decision is expected by June 20 for Sivextro and by May 26 for Dalvance.

Bottom line
Pfizer's Zyvox raked in $1.4 billion last year, and Sivextro and Dalvance are estimated to yield $219 million and $449 million by 2019, respectively. But Zyvox's loss of patent protection in 2015 will breed an array of cheap generic competitors, which will in turn also compete with the then newly approved Sivextro and Dalvance.

Cubist is, to my mind, unequivocally the larger, more stable, and safer company. Coupled with its proven success with antibiotics, its aggressive strategy of growth, and its stronger infrastructure for commercialization, Cubist will ultimately reign supreme on this particular fight.

No one expected otherwise, however. What is more notable here is that adding Dalvance to Durata's portfolio -- assuming approval -- would make it a much more attractive purchase, maybe even for Cubist. For the long term, I view Cubist as an excellent potential investment; however, in the short term, Durata is worth watching as it may be courted for purchase if Dalvance is approved.

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Amy Ho has no position in any stocks mentioned. The Motley Fool recommends Cubist Pharmaceuticals. The Motley Fool owns shares of Cubist Pharmaceuticals. Try any of our Foolish newsletter services free for 30 days. We Fools may not all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors. The Motley Fool has a disclosure policy.