Helianthamide is a potent inhibitor of human pancreatic α-amylase (HPA) ( KI = 0.01 nM) produced by the Caribbean sea anemone Stichodactyla helianthus. Helianthamide was previously shown to be structurally homologous to the β-defensins and represents a new structural class of protein inhibitors of α-amylase. To understand the source of this potent inhibition, we performed site-directed mutagenesis studies on helianthamide fusion proteins. A novel YIYH inhibitory motif that interacts with conserved active site residues was originally proposed as being central to inhibitory activity based on the X-ray crystal structure of the porcine pancreatic α-amylase-helianthamide complex. However, variants in which these polar residues were replaced, individually, with alanine or phenylalanine bound only 5-46-fold more weakly than wild-type helianthamide, suggesting modest contributions from these interactions. In contrast, individual replacement of helianthamide's six cysteine residues with alanine resulted in much larger decreases in potency (a ≤1.3 × 104 increase in KI compared to that of the wild type). In a complementary approach, a series of small peptides based on helianthamide's sequence were synthesized and tested. Of these 19 synthetic peptides, only two showed any appreciable affinity for HPA, with inhibition constants of 141 and 396 μM, significantly higher than that of intact helianthamide. These results suggest that helianthamide's potent HPA inhibition does not rely so much on the accumulation of individual polar contacts but rather its ability to form an extensive hydrophobic interface with the enzyme and occlude the active site cleft.