Three things you could try, sorted by estimated gain/change:

• Switch off AutoCommit and do a manual commit() every few lines or even only once after the loop. This should give you the biggest gain/change.
• It is not necessary to prepare(...) the statement handle within each iteration. But I guess this will not have a big impact.
• If program execution is still too slow, try to use the batch import tool of your DB. Create an import file first, then use the batch loader.