Java secured connection to remote MySQL server

I need a java console application (no GUI) that connects to a remote MySQL server (linux ubuntu 12.04), but more secure than directly to MySQL on 3306. Opening the mysql 3306 port directly to the public internet is not very secure as it cannot react to brute force attacks and other attacks and there are missing logs. Provide a more secure solution, involving (or not) java code, frameworks, and or (proxy) applications on the server. In your quote, please specify how you plan to solve the problem and if you have done this before.