Can there be any way to counteract the effects of long-term medication?

What Med & Issues: Medications are chemistry purified/extracted from nature, no other options exist. If the ratio of benefits to downsides for a given issue is not wide enough, called indication, the fda will not approve marketing/sales. However, meds chosen for wrong reasons can also be harmful; a common issue. Additionally we are open systems, meds don't last long. Please clarify concern & issues for better answer.