It depends on their function or their interaction with you ~~intestinal~~ *gastrointestinal* system. Like you wouldn’t use a rapid acting insulin way before eating because you’d have a dramatic drop in blood sugar. Other medicines might irritate or damage part of you GI tract alone, so food might help you body cope. Other medicines might not get absorbed or digested properly if taken with food… and maybe even interact with the food and become less effective. Just a whole bunch of small reasons. I’m sure someone better versed in pharmacology will come along with better more detailed examples though.
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