See https://youtrack.jetbrains.com/issue/DBE-5439 for a workaround. In general, one needs to rollback to 5.1.40 driver.
I connect to an Amazon Web Services MySQL RDS instance using SSL with the CA file provided at http://docs.aws.amazon.com/AmazonRDS/latest/UserGuide/UsingWithRDS.SSL.html (rds-downloads/rds-combined-ca-bundle.pem)
The other day I saw in my connection the option to update the MySQL driver, and since doing so I have been unable to connect using the SSL option. However, I can connect when not using SSL.
I have managed to get SSL to work again by switching from "MySQL Connector/J ver. 5.1.44" to "MySQL Connector/J ver. 5.1.40" found under Data Sources and Drivers > Drivers > MySQL > Driver Files.
So it seems there may be a problem with the MySQL Connector/J ver. 5.1.44 driver.