Drug delivery systems for reducing the quantity of residual antibiotics reaching the colon following oral or parenteral antibiotic therapy, and for delivering metallo-dependent enzymes, and methods of use thereof, are disclosed. The drug delivery systems include pectin beads that encapsulate the active agent (which can be a metallo-dependent enzyme). The pectin is crosslinked with zinc or other divalent cations, and the pectin beads are coated with Eudragit®-type polymers. The delivery of the active agent can be modulated to occur at various pre-selected sites of delivery within the intestinal tract. A stable metallo-dependent enzyme formulation can be delivered to the lower intestine or colon. The use of zinc cations to crosslink the pectin is particularly preferred when the metallo-dependent enzymes are zinc dependent, where other cationic used to gel the pectin beads might adversely affect the activity of such metallo-dependent enzymes.
