Most investors would probably agree that Gilead Sciences Inc. (NASDAQ:GILD) had a pretty rotten year in 2016. Harvoni sales were down. Sovaldi sales were down. And, of course, Gilead's stock dropped more than 20%. The big biotech certainly made some bad decisions during the year, but there were some bright spots. Here are Gilead's best moves in 2016. 

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Huge stock buybacks

Gilead authorized a massive $15 billion stock repurchase program in 2015. The company followed up in a big way this year by authorizing another $12 billion in share buybacks. And it put its money where its mouth was, repurchasing $10 billion worth of shares in the first nine months of the year.

I think these huge buybacks were and are smart moves. The stock is dirt cheap and has been throughout most of 2016. Unless you think the biotech simply won't grow earnings for a long time to come, buying Gilead stock at current price levels should prove to be a good long-term investment. Obviously, Gilead's board and executive team strongly believe in the company's future prospects.

The reality is that shelling out $10 billion so far this year buying back shares didn't put too big of a dent in Gilead's cash position. Although momentum for the company's hepatitis C franchise has evaporated, Harvoni, Sovaldi, and now Epclusa continue to generate nice cash flow on top of Gilead's other products.   

Expansion of NASH portfolio

Although I would have loved for Gilead to make a game-changing acquisition this year, the company is taking its time. However, Gilead did make a relatively small transaction in 2016 that could be important: In April, it acquired Nimbus Therapeutics subsidiary Nimbus Apollo, Inc.

For $400 million up front (plus potential milestone payments later of up to $800 million), Gilead gained Nimbus' Acetyl-CoA Carboxylase (ACC) inhibitor program. This added another arrow to Gilead's quiver in its race to develop an effective treatment for nonalcoholic steatohepatitis (NASH).

Gilead already had an FXR agonist targeting NASH that it bought from Phenex Pharmaceuticals in early 2015. The biotech also has another potential NASH drug with ASK-1 inhibitor GS-4997. Given the failure of former NASH candidate simtuzumab, Gilead's strategy to spread its eggs across multiple baskets makes sense. 

Finalized filgotinib deal

Gilead also started off 2016 on a positive note by finalizing a deal with Galapagos (NASDAQ:GLPG) to license filgotinib. Gilead paid $300 million up front and bought nearly 15% of Galapagos for $425 million.

Filgotinib is a JAK1 inhibitor that is currently being evaluated in late-stage studies targeting three indications. A clinical study with filgotinib targeting treatment of Crohn's disease is scheduled to complete in late 2019. Another study targeting ulcerative colitis should wrap up around the same time. Perhaps the biggest opportunity for the drug is in treating rheumatoid arthritis. Gilead has three late-stage studies of filgotinib in progress for the indication, with the earliest completion expected in late 2018.

What's the potential for filgotinib? Analysts think the drug could reach peak annual sales of $2 billion to $3 billion if approved. The Galapagos deal could pay off for Gilead and open up a new therapeutic category for the big biotech.

Good things that didn't make the list

Gilead did have plenty of other good news during 2016. The company won U.S. and European regulatory approval for HIV medications Odefsey and Descovy.

On the hepatitis C front, Gilead received a thumbs-up from the U.S. Food and Drug Administration (FDA) for Epclusa in late June. A few days later, European regulators granted approval for the drug. (These approvals didn't make the list of the best moves by Gilead in 2016 because they really weren't actions taken by the biotech. Instead, these approvals were moves made by regulatory agencies in response to good moves by Gilead in preceding years.)

I suspect that continued buybacks will still be on the list of good moves by Gilead in 2017. We will probably also be able to add another acquisition or two (or more), likely in the oncology area. My final prediction is that the new year won't be as horrible as 2016 has been for Gilead's shareholders. A rebound in Gilead's stock price would definitely be the best move of all.

This article represents the opinion of the writer, who may disagree with the “official” recommendation position of a Motley Fool premium advisory service. We’re motley! Questioning an investing thesis -- even one of our own -- helps us all think critically about investing and make decisions that help us become smarter, happier, and richer.