Merck (NYSE: MRK) is stopping a clinical trial testing its HIV drug Isentress because the initial results of the study were underwhelming.

Which drug did Isentress lose to? Itself. Merck was trying to show that patients could take 800 mg of Isentress once a day instead of twice a day at 400 mg each. Unfortunately, only 83.2% of patients receiving the once-daily regimen achieved undetectable viral levels, compared to 88.9% of patients taking it twice a day.

The difference seems to be due to patients that started with high levels of virus: Only 74.3% in the once-daily group achieved viral suppression compared to 84.2% in the twice-daily group.

I doubt the Food and Drug Administration is going to accept the subset analysis and change the recommended dose to once-daily for patients with low viral loads. Merck will likely have to run an additional trial that only enrolls patients with a low viral load. Alternatively, it could run a trial where patients started at a dose of twice-daily and then switched to once-daily after viral loads were decreased.

The dosing regimen for HIV drugs is important because HIV patients are usually taking multiple medications, and missed doses can lead to the virus becoming resistant to the medication. Once-daily formulations have made drugs such as Gilead Sciences (Nasdaq: GILD) and Bristol-Myers Squibb's (NYSE: BMY) Atripla and GlaxoSmithKline's (NYSE: GSK) Epzicom popular.

Isentress is on its way to becoming a blockbuster despite its less-convenient dosing, because it's the only drug in a class called integrase inhibitors. But that's likely to change since one of the components of Gilead's quad pill is an integrase inhibitor, and GlaxoSmithKline and Pfizer's (NYSE: PFE) HIV joint venture is also developing an integrase inhibitor.

This was a trial pitting Merck against itself, but the loss extends farther than that. If Merck can't show that Isentress can be dosed once a day, it might lose patients after the second-generation integrase inhibitors make it to market.

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Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. The Fool has a disclosure policy.