Papaya enzyme, also called papain, is a dietary supplement reputed to do a variety of things, from helping you lose weight to cleaning out your system. While papaya enzyme certainly has a function and some utility to humans, it's not a detoxifying agent, and can't "clean you out."
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The general public poorly understands enzymes, which results in a number of myths and misconceptions regarding their potential as dietary supplements. While your cells and systems rely upon enzymes to regulate and speed up the chemical reactions your body needs to run, you have to make these enzymes yourself -- nearly without exception, supplemental enzymes don't do you any good, though most won't hurt you.
Papain, or papaya enzyme, is a proteolytic. This means it breaks down protein, which is why it's such a common ingredient in marinades -- as a component of sauce, it helps to tenderize meat. One of the important properties of enzymes is that they're very reaction-specific, explain Drs. Reginald Garrett and Charles Grisham in their book "Biochemistry," meaning enzymes that digest protein can't digest non-proteins, or participate in any other chemical reactions.
"Cleaning Out Your System"
Different people mean different things when they talk about cleaning the system out, but regardless of what you're trying to accomplish with papaya enzyme, it can't detoxify you or help you get rid of things you don't want in your system. For instance, your very acidic stomach reacts with papain and destroys it, as enzymes are very acid-sensitive unless they're meant to work in an acidic environment, explain Drs. Mary Cambell and Shawn Farrell in their book "Biochemistry."
There's only one way in which you can clean out your system with papaya, and it's not a product of the papain enzyme. Like many fruits, papaya is full of fiber and water, both of which speed digestive function. If you eat too much papaya -- just as if you eat too many plums or prunes -- you'll experience a system "clean out" in the form of bowel movements, which may or may not be the effect you're after.