Starting with MySQL 5.7 we introduced the Query Rewrite Plugin. That tool is really useful for changing queries. Of course the best location to modify the query is the source code of the application, but this is not always possible. Either the application is not under your control or queries are generated from a framework like Hibernate and sometimes it is hard to change the query generation.
If you are interested in details about the Query Rewrite Plugin, I recommend this blogpost from the MySQL Engineering: http://mysqlserverteam.com/the-query-rewrite-plugins/
Recently I was asked how this works in replication environments. Which query goes into the binlog?

If you are using the Rewriter plugin that comes with MySQL 5.7, the answer is easy: This plugin only supports rewriting SELECT queries. SELECT queries don't get into the binlog …