A doctor can legally prescribe a medicine to treat an illness even if that medicine is not approved for that purpose. This is a so-called off-label use. While this practice is legal, drug companies are not allowed to "push" off-label uses to doctors.
Drug companies, obviously find this unfair. They argue, that if a drug works to treat an illness they should be able to promote it even before they have proceeded through the countless clinical trials needed in order to gain approval from the FDA. The basis of their argument - Free speech!
Allergan's complaint claims the FDA "has promulgated a series of overlapping and interlocking regulations that combine to render unlawful virtually all manufacturer communication, through any avenue, to any audience, about the lawful off-label use of a prescription drug." Furthermore, "the inability to share such important information proactively with the medical community violates the First Amendment and potentially diminishes the quality of patient care."
I think the First Amendment argument is a novel approach. The Courts, however, have often limited free speech if necessary for the greater good. One could argue that the FDA is already hopeless in combatting the power of drug companies, and this lawsuit is an attempt to cripple the FDA which serves an important and valid purpose for the general public.
A victory for Allergan clearly creates a slippery slope for drug manufacturers who will be able to enter a product into the market for one purpose and then promote it for countless others without the safeguards created by the FDA.