EXPLAIN won’t give you any indication of how long a query will take.
At best you could use it to guess which of two queries might be faster, but unless one of them is obviously badly written then even that is going to be very hard.
You should also be aware that if you’re using sub-queries, even running EXPLAIN can be slow (almost as slow as the query itself in some cases).
As far as I’m aware, MySQL doesn’t provide any way to estimate the time a query will take to run. Could you log the time each query takes to run, then build an estimate based on the history of past similar queries?