If the products mentioned above have undergone a process of chemical transformation in such a way that its original substance and traits have been wholly changed, then it is considered halal (permissible), and thus, permissible for us to use. An example is that of alcohol turned into vinegar. The latter is halal while the former is not.  This is because the new substance is not considered alcohol; rather, it is reckoned as an altogether new substance. Originally, all things are considered pure and halal unless proven otherwise.

A medicine or protein of this kind is, therefore, is analogous to the relationship between alcohol and vinegar. Although the scientific root of vinegar is alcohol, alcohol itself is considered haram (prohibited), while vinegar is halal. The reason for this is that alcohol and vinegar are two glaringly different end products regardless of their roots.