Fungal diseases are difficult to treat mainly because they are eukaryotic organisms just like us humans, and therefore have less differences for drugs to target without harming the human body as well. Most antibiotics target e.g. the peptidoglycan layer in the bacterial (a prokaryote) cell wall, which is a safe target since eukaryotic cells do not have equivalent structures. Similarly many differences in metabolic pathways between humans and prokaryotes is often targeted by antibiotics, but metabolism of fungi and humans is much more uniform, and hence it is difficult to exclusively target the fungi only.
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