Wait for the Shroobs to get a Poison Mushroom. The Boss will turn green. Then, start attacking him. Do not hit him if he is red.

Wait until one of the Shroob doctors gets a Poison Mushroom. Then, attack the one that has it. Use a Cannon Bros. item. It does 52 damage, and you can defeat the Boss very quickly. Attack him when green and hold back when he is red.