This study identified echinoderm-derived metabolites that show strong binding affinity and inhibitory potential against aminoglycoside acetyltransferases (AACs), including AAC(3)-Ib, AAC(6′)-Im, AAC(3)-Iva, and Aminoglycoside 2′-N-acetyltransferase. These compounds demonstrate promising activity in disrupting the function of these enzymes, which are critical for bacterial resistance to aminoglycoside antibiotics.