First medical use. Second or further medical indications

If a new medical use is found for a compound which has not previously been used in any therapeutic or diagnostic context, then the EPO (and a few other countries) will allow a broad claim of the format:

EPO
Compound X for use as a medicament or for use in therapy 

Patent applications may also be based on new uses (e.g. repurposing) for previously-known medicines. For example, aspirin is well known for the treatment of headaches. If it was now found that it could be used to treat colon cancer, then a new patent application could be filed which claimed uses of aspirin to treat colon cancer.

Inventions based on the discovery of such new uses are claimed in different formats depending on the country where the patent application is filed. (The main reason for this is that most countries do not allow methods of treatments to be claimed directly, the most notable exception to this being the US.)

Examples of allowable formats include the following:

US
A method of treating colon cancer, comprising administering an effective amount of aspirin to a patient in need thereof

EPO
Aspirin for use in a method of treating colon cancer

Canada
Use of aspirin in the manufacture of a medicament for the treatment of colon cancer

Extending patent protection for drugs

Even if the medicament is already known for the treatment of a particular disease, it may still be possible to obtain patent protection in the following areas:

1. A specific treatment regimen (e.g. a weekly dose of 1mg drug/kg body weight).
2. A new mode of administration (e.g. intramuscularly).
3. Administration of the medicament to a defined group of patients (e.g. HIV+ patients).
4. A new formulation comprising the medicament (e.g. new buffers, preservatives)
5. A combination product comprising the medicament with another active agent.

However, justifying the non-obviousness of the above inventions can often be difficult; and in some cases proving infringement can also be a significant issue.