Pharmaceutical companies can make no profit from herbs which humans have historically consumed. Instead, they create new molecules. They have a hard time creating molecules that affect only the system they want to affect, therefore there are inevitably side effects.

Quora: How much does medical science know about the human body and its functions

Nature, evolution, has done a better job at choosing which molecules are beneficial. All life is based on DNA, and molecules that are beneficial in one organism are likely to be beneficial for other organisms, which is why they consume each other for nutrients (not just for energy).

The odds that a pharmaceutical will have long term deleterious consequences are higher, if only because the molecule in question was not selected by nature for DNA based life forms. An allergic reaction can always be dangerous, but in the case of a pharmaceutical, the immune system can be challenged in a way in which evolution has no bearing.

“ Our lack of understanding of the global interactions between pharmaceuticals and the immune system confounds drug development, conceals potentially serious side effects of marketed compounds ” source

For any of the systems in the human body, reliable studies on long term effect from pharmaceuticals are lacking. Science is just beginning to understand the epigenome.

I believe the age of pharma will be an embarrassment to humanity, much like the former practices of bloodletting and labotomies.

“behavioral ethics research suggests that an especially large proportion of the population (in some studies more than 50%) may behave unethically, because their ability to objectively interpret the ethicality of their own behavior is highly limited.” source

For any pharmaceutical a doctor prescribes, it would be wise to perform an allergy test, just like you would to find out if you have a food allergy.
https://www.mayoclinic.org/diseases-conditions/drug-allergy/diagnosis-treatment/drc-20371839
https://www.sciencedirect.com/science/article/pii/S0300483X04007267
http://onlinelibrary.wiley.com/doi/10.1046/j.0105-4538.2001.00001.x-i8/full?wol1URL=/doi/10.1046/j.0105-4538.2001.00001.x-i8/full&regionCode=US-NY&identityKey=8d26dfc5-1c86-4200-8dc3-866ae0c45a33
http://onlinelibrary.wiley.com/doi/10.1111/all.12142/full
http://onlinelibrary.wiley.com/doi/10.1111/all.12350/full

Pharmaceutical drugs usually have a lot of unwanted side effects. So when your doctor suggests you take a certain drug, just tell them you'd like to first get an allergy test on that drug. There will likely be resistance and excuses towards not doing so, like trying to tell you that side effects are not allergies. While it is true that there can be effects not related to the immune system, toxicity can lead to an unnatural immune response.

You shouldn't be allergic to any drug you take, so what's the harm of a small test? Never mind that if you chew the pill in your mouth and let it sit for a minute, it leaves a burn on your gums. Your gums are made of cells just like the rest of your body. They test for food allergies by placing the food on your skin, so why shouldn't it be the same for a drug?

Maybe digestion chemically alters the molecule, but all too often, pharmaceuticals wreck havoc on the digestive system:
https://www.endo-world.com/resources/e-learning-patient-education/general-guides/harmful-effects-of-medicines-on-the-adult-digestive-system