Biotech and pharmaceutical stocks were down Friday, due largely to regulatory setbacks.

Pharmaceutical maker Medicines Co. ( MDCO) fell by $2.36, or 9.2%, to $23.21 after it announced that its application for a patent term extension on anticoagulant Angiomax was denied, according to a regulatory filing with the Securities and Exchange Commission. The company said it will seek a review of the decision and continue to pursue other actions.

Millennium Pharmaceuticals ( MLNM) on Thursday narrowed its net first-quarter loss to $6.8 million, or 2 cents a share, from $20.8 million, or 7 cents a share, in the year-ago quarter. Analysts polled by Thomson Financial expected the company to break even. JMP Securities downgraded the stock to underperform from market perform, and shares slipped 31 cents, or 2.7%, to $11.33.

Announcements burned other stocks, pushing indices lower. The Amex Biotechnology Index fell $3.90, or 0.5%, and the Nasdaq Biotechnology Index, which includes Medicines Co. and Millennium Pharmaceuticals, fell 4.93, or 0.6%.

Wyeth ( WYE) announced that CFO and Vice Chairman Kenneth Martin is leaving at the end of June to pursue personal interests. The company says it plans to name a new CFO in advance of his departure. Shares fell 52 cents, or 0.9%, to $55.48.

The Food and Drug Administration is questioning whether a survival benefit in patients with chronic obstructive pulmonary disease was enough to allow it to approve GlaxoSmithKline's ( GSK) a new indication of Advair, according to documents released on Friday ahead of a panel on Tuesday. Share price declined 45 cents, or 0.8%, to $57.97.

As expected, the FDA officially denied approval to Merck's ( MRK) Acroxia, a pain reliever similar to Vioxx. Merck has been trying to get the drug, currently available in 63 countries, approved since 2003. Shares fell 64 cents, or 1.2%, to $51.79.

Among stocks in positive territory, Penwest ( PPCO) was upgraded by Robert W. Baird to outperform from neutral Friday. Shares were up 30 cents, or 2.5%, to $12.31.

Applied Biosystems ( ABI) traded higher a day after reporting weak earnings that still beat expectations. It was up $1.29, or 4.4%, to $30.75.