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There are a lot of different types of patents that can be filed with the intent of gaining protection for a drug invention. It is important to remember that the criteria for obtaining a patent is that something be novel (new), non-obvious, and useful.

For small molecule drugs, the composition of matter patent, the one that describes the drugs chemical structure is typically the key one. But one must show in this patent that the compound (or more likely family of compounds) does something and that the something is useful. Later patents might be obtained that find new ways to formulate the drug, make it, new indications, methods of use, new crystal forms, etc. But these must be non-obvious to anyone reading the initial patent, and may not infer much additional protection. Often, the 'prior art' that interferes with obtaining additional patent coverage is what is described in the initial patent.

Once a composition of matter patent expires (assuming the exclusivity window is closed), another company, like a generic firm, can make the compound. They only need to show it acts the same in the body as the original (and is no more impure). Some later patents, such as those that change formulation to affect adsorption profiles, may provide additional coverage, but many don't.

Bio-pharmaceuticals are often different animals (pun somewhat intended). Here the key patent is often a demonstration of usefulness but the preparation method is also seen as key as well since how the drug is made effectively defines what it is. With no clear generic path for biopharmaceuticals, exactly what is 'key' is open to more debate, and probably varies more case to case. Trade secrets play a larger role in biopharmaceuticals as well.

Hope that helps some.

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