Proteases are proteolytic enzymes that break down proteins into amino acids. This break down of proteins represents the first steps in catabolism. For bodybuilders it should seem counter intuitive to take a supplement that induces a catabolic state, but a relatively recent study tells a different story.
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In a study published in Medicine and Science in Sports and Exercise, scientists at Baylor University hypothesized that an oral protease supplement would decrease muscle damage and improve muscle function after a bout of heavy eccentric exercise. They postulated that improved post-exercise muscle function would be a result of reduced inflammation and the number of circulating macrophages and white blood cells (both indicators of heightened immune response).  In this double-blinded, randomized, placebo controlled study 29 subjects had baseline blood samples and muscle biopsies taken, underwent isokinetic muscle (leg) function testing, and a VO2 max test. For 21-days following, subjects either took a daily protease supplement or a placebo. After 21-days subjects returned to the lab where another blood sample was taken and then completed a 45-min downhill (eccentric) treadmill running protocol (at 60% of their VO2 max). Compared to the placebo group, those who received the protease supplement had greater overall force production and decreased serum cyclooxygenase 2, interlukin 6, and interlukin 12 levels after eccentric muscle damage. These observations indicate that prolonged protease supplementation significantly and beneficially alters the immune response and inflammation during exercise recovery.  

Reference:
Buford TW, Cooke MB, Redd LL, Hudson GM, Shelmadine BD, Willoughby DS.Protease Supplementation Improves Muscle Function after Eccentric Exercise. Med Sci Sports Exerc. 2009 Sep 2. [Epub ahead of print]