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How are natural venoms and toxins (e.g. spider and snake venoms) used to make antidotes? In other words, what is in that venom that is part of a harmful substance but, when used correctly, can actually help us, and why can these molecules help or harm in different situations?

Also, why are we looking to natural toxins to produce new medicines instead of synthetic chemicals we could make or already have?

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You are probably thinking about antivenom using immune serum.

You give the venom to a host animal to induce an immune response, and then purify (to the extent possible) antibodies collected in serum from that animal, and then inject these to the patient to neutralize the venom. You don't use the venom directly.

Isolating components of venom could also allow for screening for molecules that will bind to them strongly and possibly block their action, though I'm not aware of specific antidotes that have been produced this way.

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