The effect of drugs depends upon the drug's pharmacodynamics and pharmacokinetics parameters. Some drugs produce response even after single dose, whereas others require multiple doses to achieve an observable response. In your case, you can check the pharmacological parameters of the drug under study, from where you can determine the approximate number of doses prior to performing RNA-seq. If your experimental drug has no prior pharmacological studies, then you may need to perform RNA-seq at multiple stages, i.e., after single dose, three doses, five/six doses, ten-twelve doses and so on. If your drug produces an observable phenotypical outcome, then you can collect samples for whole transcriptome analysis when the observable outcome has been achieved.

Good Luck!

As the prior answers suggest, repeated exposures and time-series analysis would likely tell you something, but since no one has the resources to test everything, your exposure selection should probably be hypothesis-driven. To put it another way, what is your alcohol exposure a model of,... binge drinking, tolerant drinking, alcoholism, withdrawal-induced excitotoxicity, etc? There are many exposure schedules that simply wouldn't impact the mechanisms you are interested in, while others will impact additional mechanisms you aren't interested in, so I would recommend starting with some hypothesis development. This is particularly important if you are attempting a drug rescue or exacerbation study, since you will need to conceptualize which of alcohol's many potential effects are going to be altered by the drug and its eventual translational relevance to human alcohol drinking.