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There was a time when the underperformance of Gilead Sciences' (GILD) - Get Gilead Sciences, Inc. Report stock price was viewed as an opportunity to buy shares of a historically great biotech company at a discount.

But Gilead's stock price continues to fall, trading today where it did two years ago. The value play looks more like a trap. Investors once okay with waiting patiently for a Gilead rebound are growing frustrated, even angry, at the company's lack of progress. (I wrote about the challenges to Gilead's M&A growth strategy in July.)

It's reaching the point now where Gilead CEO John Milligan (and before him, John Martin) is at risk of losing his perennial status as biotech's best, most trusted CEO.

"Investors have broadly lost confidence in management's ability to navigate the future competitive landscapes for its businesses and create value," wrote Piper Jaffray biotech analyst Josh Schimmer, in a research note on Gilead published this week.

That is not a sentence you'd see a sell-sider write about Gilead management a few years ago. It's a noteworthy change in sentiment.

At $78 per share, Gilead's stock price has retrenched to where it traded in April 2014. Over the past three months, Gilead is down 9%, while Amgen (AMGN) - Get Amgen Inc. Report is up 9%, Biogen (BIIB) - Get Biogen Inc. Report is up 8% and the Nasdaq Biotechnology Index is up 3%. Among large-cap biotechs, only Alexion Pharmaceuticals (ALXN) - Get Alexion Pharmaceuticals, Inc. Report is performing worse than Gilead.

Gilead continues to look cheap, trading at less than seven times next year's earnings estimate, but the same was said earlier this year when the stock broke below $100, then $90 and then $80 per share.

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"Investors are starting to become impatient, and that's what happens when a stock starts to lag and miss and guide down with murky visibility," said RBC Capital analyst Michael Yee, when I asked him to describe his recent conversations with investors about Gilead.

In July, Gilead lowered its forecast for net product sales in 2016 because of weakening demand and price uncertainties for its hepatitis C drugs Sovaldi and Harvoni. The number of prescriptions written for Gilead's hepatitis C drugs continued to fall in July and August, raising real concerns the company will report poor sales again in the third quarter, Yee said.

Gilead's HIV business remains strong, helped most recently by the launch of an improved version of its older drug, Viread, but even here, there is uncertainty about the future. GlaxoSmithKline (GSK) - Get GlaxoSmithKline Plc Report is testing a two-drug combination therapy which, if successful, could take a big bite from Gilead's dominant HIV market share.

The company's research pipeline, focused mostly on drugs targeting cancer and liver diseases like NASH, lacks the marquee assets to fuel the next leg of growth. Gilead management will disagree, but that's the consensus view from Wall Street. 

Investor confidence in Gilead's drug development efforts (outside of HIV and hepatitis C) is weak enough today that you're starting to hear rumblings about the need for a change in R&D leadership. There are some investors who believe Norbert Bischofberger, Gilead's longtime chief scientific officer, should be replaced.

Gilead has been so successful and grown so big that finding ways to keep growing is proving to be a significant challenge. That's a problem most biotech companies would kill to have. Nonetheless, Gilead executives need to find a solution quickly, whether that be internally or through acquisitions.

The stock feels like it's broken, not irreparably, but bad enough where a renewed sense of urgency to fix is needed.

Adam Feuerstein writes regularly for TheStreet. In keeping with company editorial policy, he doesn't own or short individual stocks, although he owns stock in TheStreet. He also doesn't invest in hedge funds or other private investment partnerships. Feuerstein appreciates your feedback; click here to send him an email.