Neurotransmitters are often synthesized from amino acids. They have different functions in the body, often either inhibiting or exciting the neuron that it targets.

There are a bunch of different aspects to being awake. Caffeine works on adenosine, which has to do with wakefulness. But also things like adrenaline have a different aspect of wakefulness that amphetamines target. Modafinil targets orexin receptors I believe, which involve wakefulness as well as eating.