Similar to the original NES game, you must destroy the columns of Zebetites before reaching Mother Brain's chamber. Unlike the original, however, there are smaller Zebetites that you must kneel to destroy. After these smaller, morph-ball sized ones have been destroyed, use either a bomb-jump or Spring Ball to get through the gaps. A single Zebetite takes 10 Missiles or 5 Super Missiles to destroy.
Luckily, destroyed Zebetites do not respawn after leaving Mother Brain's room and coming back. Since they take numerous Missiles to destroy, it may be advantageous to backtrack to the Missile Recharge Station in a previous room in Tourian. It is also helpful to do this in low-% runs.