There are two functions happening usually: Binding and Activating, for an agonist.

For an antagonist, you'll have Binding and Blocking. Usually you'll have a greater binding affinity for antagonists that can knock an agonist off of the receptor.

I know you're mentioning messenger proteins, but a chemical example is how Naloxone will knock off morphine from a receptor due to its higher affinity. The naloxone then blocks morphine from activating the receptor.

When an agonist binds, it can change the channel's confirmation allowing influx, or efflux of ions. Depending, this can increase or decrease the chances of an action potential to occur.

Sometimes things get even more complicated. The chloride channel that Valium works on, the GABA receptor, has receptors for GABA and receptors for benzodiazepines (valium-type drugs).

One single channel, or one single neuron may not play a large role, BUT..., When hundreds and thousands and millions of receptors and neurons are affected, you see an overall effect in the subject.