There are several ways.
Sometimes you know what the problem is in a specific disease, let’s say that a certain protein inside a cell is not working properly. Then you can design and make new molecules that might solve the problem.
Sometimes you just notice that a molecule has a strange effect, and you try to see if it could do something useful. It’s often the case for toxic molecules from plants or venomous animals. We’ve used them to make drugs against cancer or painkillers.
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