Because the share price was at a relative high. They didn't do more than 3.5 because they beleive it has higher to go.
This is good money management. Even if they are 100% sure their drug will someday be approved and marketed, they still have to worry about financing. The credit crunch in 2008 wiped out the equity of many tiny botech companies who had to massively dilute to keep the pipeline alive. Trius wants to have control of their future. And even if they negotiate a sale to big pharma, they must first show they don't really need the big guy's money to obtain the best deal.